SYMBOL INDEX (5812 symbols across 1083 files)

FILE: AnnotationLambda/AnnotationLambda.cs
  class AnnotationLambda (line 29) | public sealed class AnnotationLambda
    method Run (line 32) | public AnnotationResult Run(AnnotationConfig config, ILambdaContext co...
    method GetSuccessOutput (line 125) | private static AnnotationResult GetSuccessOutput(AnnotationResult result)
    method HandleException (line 132) | private static AnnotationResult HandleException(StringBuilder runLog, ...
    method GetTabixVirtualPosition (line 150) | internal static long GetTabixVirtualPosition(AnnotationRange annotatio...
    method GetAnnotationResources (line 159) | private static AnnotationResources GetAnnotationResources(AnnotationCo...

FILE: AnnotationLambda/S3Utilities.cs
  class S3Utilities (line 3) | public static class S3Utilities
    method GetKey (line 5) | public static string GetKey(string outputDir, string filename)

FILE: CacheUtils/CacheUtils.cs
  class CacheUtilsMain (line 16) | internal static class CacheUtilsMain
    method Main (line 18) | private static int Main(string[] args)

FILE: CacheUtils/Commands/CombineCacheDirectories/CombineCacheDirectoriesMain.cs
  class CombineCacheDirectoriesMain (line 25) | public static class CombineCacheDirectoriesMain
    method ProgramExecution (line 32) | private static ExitCodes ProgramExecution()
    method WriteTranscripts (line 89) | private static void WriteTranscripts(CacheHeader header,
    method WritePredictions (line 100) | private static void WritePredictions(string description, string filePath,
    method CombineTranscripts (line 114) | private static IntervalArray<ITranscript> CombineTranscripts(IntervalA...
    method GetNumCombinedTranscripts (line 131) | private static int GetNumCombinedTranscripts<T>(IntervalArray<T> inter...
    method CopyItems (line 140) | private static void CopyItems<T>(T[] src, T[] dest, ref int destIndex,...
    method GetUpdatedTranscript (line 147) | private static Interval<ITranscript> GetUpdatedTranscript(Interval<ITr...
    method CloneBaseHeader (line 160) | private static VariantAnnotation.IO.Caches.Header CloneBaseHeader(Vari...
    method CloneHeader (line 164) | private static PredictionHeader CloneHeader(PredictionHeader header) =>
    method CloneHeader (line 167) | private static CacheHeader CloneHeader(CacheHeader header) =>
    method CombinePredictions (line 170) | private static (Prediction[] Predictions, int Offset) CombinePredictio...
    method CombinePredictions (line 182) | private static Prediction[] CombinePredictions(string description, Pre...
    method LoadTranscriptCaches (line 199) | private static (TranscriptCacheData Cache, TranscriptCacheData Cache2)...
    method Run (line 218) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/CreateCache/CreateNirvanaDatabaseMain.cs
  class CreateNirvanaDatabaseMain (line 23) | public static class CreateNirvanaDatabaseMain
    method ProgramExecution (line 30) | private static ExitCodes ProgramExecution()
    method CreateGeneForest (line 88) | private static IIntervalForest<UgaGene> CreateGeneForest(IEnumerable<U...
    method MarkCanonicalTranscripts (line 111) | private static void MarkCanonicalTranscripts(MutableTranscript[] trans...
    method Run (line 122) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/Download/DownloadMain.cs
  class DownloadMain (line 5) | public static class DownloadMain
    method ProgramExecution (line 7) | private static ExitCodes ProgramExecution()
    method Run (line 13) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/Download/ExternalFiles.cs
  class ExternalFiles (line 16) | public static class ExternalFiles
    method Download (line 37) | public static void Download()
    method GetIdToGenbankEntryDict (line 66) | private static IEnumerable<GenbankEntry> GetIdToGenbankEntryDict(IEnum...
    method GetGenbankFiles (line 69) | private static List<GenbankFile> GetGenbankFiles(ICollection<RemoteFil...
    method GetElapsedDays (line 87) | public static double GetElapsedDays(DateTime creationTime) => DateTime...
    method GetNumGenbankFiles (line 89) | private static int GetNumGenbankFiles()
    method WriteDictionary (line 114) | private static void WriteDictionary(IEnumerable<GenbankEntry> entries)

FILE: CacheUtils/Commands/Download/GenbankFile.cs
  class GenbankFile (line 10) | public sealed class GenbankFile
    method GenbankFile (line 15) | public GenbankFile(int num)
    method Parse (line 21) | public void Parse()

FILE: CacheUtils/Commands/ExtractTranscripts/ExtractTranscriptsMain.cs
  class ExtractTranscriptsMain (line 21) | public static class ExtractTranscriptsMain
    method ProgramExecution (line 32) | private static ExitCodes ProgramExecution()
    method GetTranscriptStaging (line 59) | private static TranscriptCacheStaging GetTranscriptStaging(CacheHeader...
    method WriteCache (line 65) | private static void WriteCache(Stream stream, IStaging staging, string...
    method GetOutputStub (line 72) | private static string GetOutputStub(Chromosome chromosome, Source sour...
    method GetSource (line 75) | private static string GetSource(Source source) =>
    method GetPredictionStaging (line 78) | private static (PredictionCacheStaging Staging, Prediction[] Predictio...
    method GetPredictions (line 92) | private static Prediction[][] GetPredictions(ICollection<int> indexSet...
    method GetUniqueIndices (line 105) | private static HashSet<int> GetUniqueIndices(IEnumerable<ITranscript> ...
    method GetRegulatoryRegionIntervalArrays (line 117) | private static IntervalArray<IRegulatoryRegion>[] GetRegulatoryRegionI...
    method GetTranscripts (line 129) | private static List<ITranscript> GetTranscripts(DataBundle bundle, Chr...
    method Run (line 139) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/GFF/CreateGffMain.cs
  class CreateGffMain (line 18) | public static class CreateGffMain
    method ProgramExecution (line 25) | private static ExitCodes ProgramExecution()
    method Run (line 45) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/GFF/InternalGenes.cs
  class InternalGenes (line 8) | public static class InternalGenes
    method CreateDictionary (line 10) | public static Dictionary<IGene, int> CreateDictionary(IGene[] genes)

FILE: CacheUtils/Commands/Header/HeaderMain.cs
  class HeaderMain (line 12) | public static class HeaderMain
    method ProgramExecution (line 16) | private static ExitCodes ProgramExecution()
    method GetHeaderInformation (line 25) | private static (ushort Schema, ushort Data, ushort Vep) GetHeaderInfor...
    method Run (line 38) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/ParseVepCacheDirectory/ParseVepCacheDirectoryMain.cs
  class ParseVepCacheDirectoryMain (line 19) | public static class ParseVepCacheDirectoryMain
    method ProgramExecution (line 31) | private static ExitCodes ProgramExecution()
    method GetIdToGenbank (line 97) | private static Dictionary<string, GenbankEntry> GetIdToGenbank(GenomeA...
    method WriteRegulatoryRegions (line 113) | private static void WriteRegulatoryRegions(RegulatoryRegionWriter writ...
    method WriteTranscripts (line 118) | private static void WriteTranscripts(MutableTranscriptWriter writer, I...
    method WritePredictions (line 123) | private static void WritePredictions(PredictionWriter writer, IReadOnl...
    method GetSource (line 141) | public static Source GetSource(string source)
    method Run (line 149) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/Commands/ParseVepCacheDirectory/RegulatoryRegionMerger.cs
  class RegulatoryRegionMerger (line 10) | public static class RegulatoryRegionMerger
    method Merge (line 12) | public static IEnumerable<IRegulatoryRegion> Merge(IEnumerable<IRegula...
    method MergeRegulatoryRegion (line 37) | private static void MergeRegulatoryRegion(IRegulatoryRegion previous, ...

FILE: CacheUtils/Commands/ParseVepCacheDirectory/TranscriptFilter.cs
  class TranscriptFilter (line 14) | public static class TranscriptFilter
    method Log (line 18) | private static void Log(this TranscriptMergerLogger logger, string tra...
    method PickSpecificTranscript (line 21) | public static List<MutableTranscript> PickSpecificTranscript(
    method InvestigateInconsistentCdnaMaps (line 54) | public static List<MutableTranscript> InvestigateInconsistentCdnaMaps(...
    method DiffExonsAndCdnaMaps (line 79) | private static bool DiffExonsAndCdnaMaps(IReadOnlyList<MutableExon> ex...
    method ChooseEditedTranscripts (line 94) | public static List<MutableTranscript> ChooseEditedTranscripts(
    method RemoveFailedTranscripts (line 106) | public static List<MutableTranscript> RemoveFailedTranscripts(
    method RemoveTranscriptsWithLowestVersion (line 118) | public static List<MutableTranscript> RemoveTranscriptsWithLowestVersion(
    method Unique (line 133) | public static List<MutableTranscript> Unique(this IEnumerable<MutableT...
    method FixCodingRegionCdnaStart (line 140) | public static List<MutableTranscript> FixCodingRegionCdnaStart(this Li...
    method FixCodingRegionCdnaEnd (line 155) | public static List<MutableTranscript> FixCodingRegionCdnaEnd(this List...
    method FixGeneSymbolSource (line 170) | public static List<MutableTranscript> FixGeneSymbolSource(this List<Mu...
    method FixBioType (line 187) | public static List<MutableTranscript> FixBioType(this List<MutableTran...
    method GetDesiredBioType (line 221) | private static BioType GetDesiredBioType(ICollection<BioType> biotypes)
    method FixGeneId (line 238) | public static List<MutableTranscript> FixGeneId(this List<MutableTrans...
    method UnsupervisedFixGeneId (line 253) | public static List<MutableTranscript> UnsupervisedFixGeneId(this List<...
    method FixGeneSymbols (line 267) | public static List<MutableTranscript> FixGeneSymbols(this List<Mutable...
    method FixCanonical (line 286) | public static List<MutableTranscript> FixCanonical(this List<MutableTr...
    method FixHgncId (line 298) | public static List<MutableTranscript> FixHgncId(this List<MutableTrans...
    method FixGeneStart (line 313) | public static List<MutableTranscript> FixGeneStart(this List<MutableTr...
    method FixGeneEnd (line 329) | public static List<MutableTranscript> FixGeneEnd(this List<MutableTran...
    method UnsupervisedFixGeneSymbols (line 345) | private static List<MutableTranscript> UnsupervisedFixGeneSymbols(this...
    method GetClosest (line 356) | private static int GetClosest(IEnumerable<int> values, int targetValue)

FILE: CacheUtils/Commands/ParseVepCacheDirectory/TranscriptIdFilter.cs
  class TranscriptIdFilter (line 8) | public sealed class TranscriptIdFilter
    method TranscriptIdFilter (line 12) | public TranscriptIdFilter(Source source)
    method Pass (line 28) | public bool Pass(MutableTranscript transcript) => _whitelist.Any(prefi...

FILE: CacheUtils/Commands/ParseVepCacheDirectory/TranscriptMerger.cs
  class TranscriptMerger (line 10) | public static class TranscriptMerger
    method Merge (line 17) | public static List<MutableTranscript> Merge(TranscriptMergerLogger log...
    method Merge (line 25) | private static MutableTranscript Merge(TranscriptMergerLogger logger, ...

FILE: CacheUtils/Commands/ParseVepCacheDirectory/TranscriptMergerLogger.cs
  class TranscriptMergerLogger (line 6) | public sealed class TranscriptMergerLogger : IDisposable
    method TranscriptMergerLogger (line 10) | public TranscriptMergerLogger(Stream stream) => _writer = new StreamWr...
    method WriteLine (line 12) | public void WriteLine()         => _writer.WriteLine();
    method WriteLine (line 13) | public void WriteLine(string s) => _writer.WriteLine(s);
    method Write (line 14) | public void Write(string s)     => _writer.Write(s);
    method SetBold (line 16) | public void SetBold()    {
    method ResetColor (line 20) | public void ResetColor()
    method Dispose (line 25) | public void Dispose() => _writer.Dispose();

FILE: CacheUtils/Commands/ParseVepCacheDirectory/VepCacheParser.cs
  class VepCacheParser (line 16) | public sealed class VepCacheParser
    method VepCacheParser (line 21) | public VepCacheParser(Source source)
    method ParseDumpDirectory (line 27) | public (List<IRegulatoryRegion> RegulatoryRegions, List<MutableTranscr...
    method ParseRegulatoryFiles (line 35) | private static List<IRegulatoryRegion> ParseRegulatoryFiles(Chromosome...
    method ParseTranscriptFiles (line 49) | private List<MutableTranscript> ParseTranscriptFiles(Chromosome chromo...
    method ParseRegulatoryDumpFile (line 62) | private static void ParseRegulatoryDumpFile(Chromosome chromosome, str...
    method ParseTranscriptDumpFile (line 91) | private void ParseTranscriptDumpFile(Chromosome chromosome, string fil...
    method ParseRegulatoryRegions (line 114) | private static void ParseRegulatoryRegions(Chromosome chromosome, IImp...

FILE: CacheUtils/Commands/ParseVepCacheDirectory/VepRootDirectory.cs
  class VepRootDirectory (line 9) | public sealed class VepRootDirectory
    method VepRootDirectory (line 13) | public VepRootDirectory(Dictionary<string, Chromosome> refNameToChromo...
    method GetRefIndexToVepDir (line 18) | public Dictionary<ushort, string> GetRefIndexToVepDir(string dirPath)
    method GetSortedFiles (line 35) | public static IEnumerable<string> GetSortedFiles(IEnumerable<string> f...

FILE: CacheUtils/Commands/RegulatoryGFF/CreateRegulatoryGffMain.cs
  class CreateRegulatoryGffMain (line 15) | public static class CreateRegulatoryGffMain
    method ProgramExecution (line 21) | private static ExitCodes ProgramExecution()
    method Run (line 45) | public static ExitCodes Run(string command, string[] args)
    method WriteRegulatoryFeature (line 79) | private static void WriteRegulatoryFeature(TextWriter writer, IRegulat...
    method WriteGeneralAttributes (line 86) | private static void WriteGeneralAttributes(TextWriter writer, IRegulat...

FILE: CacheUtils/Commands/UniversalGeneArchive/FilePaths.cs
  class FilePaths (line 4) | public sealed class FilePaths
    class AssemblySpecificPaths (line 10) | public class AssemblySpecificPaths

FILE: CacheUtils/Commands/UniversalGeneArchive/UniversalGeneArchiveMain.cs
  class UniversalGeneArchiveMain (line 21) | public static class UniversalGeneArchiveMain
    method ProgramExecution (line 26) | private static ExitCodes ProgramExecution()
    method UniversalGeneArchiveCurrent (line 51) | private static bool UniversalGeneArchiveCurrent()
    method LoadDataStores (line 57) | private static (GeneInfoData GeneInfoData, AssemblyDataStore Assembly3...
    method CombineGenomeAssemblies (line 75) | private static UgaGene[] CombineGenomeAssemblies(Dictionary<ushort, Li...
    method UpdateGeneSymbols (line 85) | private static UgaGene[] UpdateGeneSymbols(this UgaGene[] genes, Dicti...
    method WriteGenes (line 93) | private static void WriteGenes(UgaGene[] genes)
    method GetFilePaths (line 106) | private static FilePaths GetFilePaths(string jsonPath)
    method UpdatePaths (line 125) | private static void UpdatePaths(FilePaths.AssemblySpecificPaths paths)
    method CheckPath (line 132) | private static void CheckPath(string filePath, string description)
    method CheckPaths (line 138) | private static void CheckPaths(FilePaths.AssemblySpecificPaths paths)
    method Run (line 145) | public static ExitCodes Run(string command, string[] args)

FILE: CacheUtils/DataDumperImport/DataStructures/GenomeSymbolSource.cs
  type GeneSymbolSource (line 3) | public enum GeneSymbolSource : byte

FILE: CacheUtils/DataDumperImport/DataStructures/Import/IImportNode.cs
  type IImportNode (line 3) | public interface IImportNode
  type IListMember (line 8) | public interface IListMember : IImportNode { }

FILE: CacheUtils/DataDumperImport/DataStructures/Import/ImportNodeExtensions.cs
  class ImportNodeExtensions (line 5) | public static class ImportNodeExtensions
    method GetInt32 (line 7) | public static int GetInt32(this IImportNode node)
    method GetBool (line 20) | public static bool GetBool(this IImportNode node)
    method GetString (line 26) | public static string GetString(this IImportNode node)
    method IsUndefined (line 38) | public static bool IsUndefined(this IImportNode node)

FILE: CacheUtils/DataDumperImport/DataStructures/Import/ListObjectKeyValueNode.cs
  class ListObjectKeyValueNode (line 5) | public sealed class ListObjectKeyValueNode : IImportNode
    method ListObjectKeyValueNode (line 10) | public ListObjectKeyValueNode(string key) => Key = key;
    method Add (line 11) | public void Add(IListMember node) => Values.Add(node);

FILE: CacheUtils/DataDumperImport/DataStructures/Import/ObjectKeyValueNode.cs
  class ObjectKeyValueNode (line 3) | public sealed class ObjectKeyValueNode : IImportNode
    method ObjectKeyValueNode (line 8) | public ObjectKeyValueNode(string key, ObjectValueNode value)

FILE: CacheUtils/DataDumperImport/DataStructures/Import/ObjectValueNode.cs
  class ObjectValueNode (line 5) | public sealed class ObjectValueNode : IListMember
    method ObjectValueNode (line 11) | internal ObjectValueNode(string type, List<IImportNode> values)

FILE: CacheUtils/DataDumperImport/DataStructures/Import/StringKeyValueNode.cs
  class StringKeyValueNode (line 3) | public sealed class StringKeyValueNode : IImportNode
    method StringKeyValueNode (line 8) | public StringKeyValueNode(string key, string value)

FILE: CacheUtils/DataDumperImport/DataStructures/Import/StringValueNode.cs
  class StringValueNode (line 3) | public sealed class StringValueNode : IListMember
    method StringValueNode (line 6) | public StringValueNode(string key) => Key = key;

FILE: CacheUtils/DataDumperImport/DataStructures/Mutable/MutableExon.cs
  class MutableExon (line 7) | public sealed class MutableExon : IEquatable<MutableExon>, IInterval
    method MutableExon (line 14) | public MutableExon(Chromosome chromosome, int start, int end, int phase)
    method Equals (line 22) | public bool Equals(MutableExon other)
    method GetHashCode (line 30) | public override int GetHashCode()

FILE: CacheUtils/DataDumperImport/DataStructures/Mutable/MutableGene.cs
  class MutableGene (line 8) | public sealed class MutableGene : IEquatable<MutableGene>, IFlatGene<Mut...
    method MutableGene (line 19) | public MutableGene(Chromosome chromosome, int start, int end, bool onR...
    method ToString (line 32) | public override string ToString()
    method Equals (line 38) | public bool Equals(MutableGene other)
    method GetHashCode (line 51) | public override int GetHashCode()
    method Clone (line 67) | public MutableGene Clone() => new MutableGene(Chromosome, Start, End, ...
    method ToUgaGene (line 70) | public UgaGene ToUgaGene(bool isGrch37)

FILE: CacheUtils/DataDumperImport/DataStructures/Mutable/MutableTranscript.cs
  class MutableTranscript (line 9) | public sealed class MutableTranscript : IEquatable<MutableTranscript>
    method MutableTranscript (line 52) | public MutableTranscript(Chromosome chromosome, int start, int end, st...
    method Equals (line 91) | public bool Equals(MutableTranscript other)
    method GetHashCode (line 105) | public override int GetHashCode()

FILE: CacheUtils/DataDumperImport/DataStructures/Mutable/MutableTranscriptRegion.cs
  class MutableTranscriptRegion (line 6) | public sealed class MutableTranscriptRegion : ITranscriptRegion
    method MutableTranscriptRegion (line 15) | public MutableTranscriptRegion(TranscriptRegionType type, ushort id, i...
    method Write (line 26) | public void Write(IExtendedBinaryWriter writer) => throw new System.No...

FILE: CacheUtils/DataDumperImport/FauxRegex/RegexDecisionTree.cs
  class RegexDecisionTree (line 7) | internal static class RegexDecisionTree
    method GetEntryType (line 9) | internal static (EntryType Type, string Key, string Value) GetEntryTyp...
    method GetEntryTypeNoArrow (line 19) | private static (EntryType Type, string Key, string Value) GetEntryType...
    method GetEntryTypeNoVar (line 25) | private static (EntryType Type, string Key, string Value) GetEntryType...
    method GetEntryTypeDataPos (line 42) | private static (EntryType Type, string Key, string Value) GetEntryType...
    method GetEntryTypeVar (line 48) | private static (EntryType Type, string Key, string Value) GetEntryType...
    method GetEntryTypeFatArrow (line 56) | private static (EntryType, string Key, string Value) GetEntryTypeFatAr...
    method GetEntryTypeStringKeyValue (line 78) | private static (EntryType, string Key, string Value) GetEntryTypeStrin...
    method GetKey (line 88) | private static string GetKey(string s, int secondQuotePos)
    method GetForwardString (line 94) | private static string GetForwardString(string s, int afterFirstQuote)
    method OnlyDigits (line 101) | internal static bool OnlyDigits(string s) => s.All(c => char.IsDigit(c...

FILE: CacheUtils/DataDumperImport/IO/DataDumperReader.cs
  class DataDumperReader (line 12) | public sealed class DataDumperReader : IDisposable
    method DataDumperReader (line 17) | public DataDumperReader(Stream stream) => _reader = FileUtilities.GetS...
    method GetNextLine (line 19) | private string GetNextLine() => _reader.ReadLine();
    method GetRootNode (line 21) | public ObjectKeyValueNode GetRootNode()
    method GetDigitKey (line 32) | private static StringValueNode GetDigitKey(string key) => new StringVa...
    method GetListObjectKeyValue (line 34) | private ListObjectKeyValueNode GetListObjectKeyValue(string key)
    method GetMultiLineKeyValue (line 62) | private StringKeyValueNode GetMultiLineKeyValue(string key, string value)
    method GetObjectValue (line 78) | private ObjectValueNode GetObjectValue()
    method Dispose (line 124) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/DataDumperImport/IO/EntryType.cs
  type EntryType (line 3) | internal enum EntryType

FILE: CacheUtils/DataDumperImport/Import/Attribute.cs
  class Attribute (line 13) | internal static class Attribute
    method Attribute (line 18) | static Attribute()
    method ParseList (line 34) | public static (IInterval[] MicroRnas, IRnaEdit[] RnaEdits, bool CdsSta...
    method GetInterval (line 76) | private static IInterval GetInterval(string s)
    method GetRnaEdit (line 87) | private static RnaEdit GetRnaEdit(string s)
    method ParseKeyValue (line 99) | private static (string Key, string Value) ParseKeyValue(ObjectValueNod...

FILE: CacheUtils/DataDumperImport/Import/ImportExon.cs
  class ImportExon (line 10) | internal static class ImportExon
    method ImportExon (line 14) | static ImportExon()
    method Parse (line 30) | public static MutableExon Parse(ObjectValueNode objectValue, Chromosom...
    method ParseList (line 71) | public static MutableExon[] ParseList(IImportNode importNode, Chromoso...

FILE: CacheUtils/DataDumperImport/Import/ImportGene.cs
  class ImportGene (line 8) | internal static class ImportGene
    method ImportGene (line 12) | static ImportGene()
    method Parse (line 23) | public static (int Start, int End, string Id, bool OnReverseStrand) Pa...

FILE: CacheUtils/DataDumperImport/Import/ImportIntron.cs
  class ImportIntron (line 8) | internal static class ImportIntron
    method ImportIntron (line 12) | static ImportIntron()
    method Parse (line 32) | private static IInterval Parse(ObjectValueNode objectValue)
    method ParseList (line 74) | public static IInterval[] ParseList(List<IListMember> members)

FILE: CacheUtils/DataDumperImport/Import/ImportKeys.cs
  class ImportKeys (line 3) | internal static class ImportKeys

FILE: CacheUtils/DataDumperImport/Import/ImportMapper.cs
  class ImportMapper (line 8) | internal static class ImportMapper
    method ImportMapper (line 12) | static ImportMapper()
    method Parse (line 30) | public static MutableTranscriptRegion[] Parse(ObjectValueNode objectVa...

FILE: CacheUtils/DataDumperImport/Import/ImportMapperPair.cs
  class ImportMapperPair (line 9) | internal static class ImportMapperPair
    method ImportMapperPair (line 13) | static ImportMapperPair()
    method Parse (line 26) | private static MutableTranscriptRegion Parse(ObjectValueNode objectValue)
    method GetCdnaMap (line 75) | private static MutableTranscriptRegion GetCdnaMap(int fromStart, int f...
    method ParseList (line 85) | public static MutableTranscriptRegion[] ParseList(List<IListMember> li...

FILE: CacheUtils/DataDumperImport/Import/ImportMapperUnit.cs
  class ImportMapperUnit (line 8) | internal static class ImportMapperUnit
    method ImportMapperUnit (line 12) | static ImportMapperUnit()
    method Parse (line 25) | public static (int Start, int End, MapperUnitType Type) Parse(ObjectVa...
  type MapperUnitType (line 59) | public enum MapperUnitType : byte

FILE: CacheUtils/DataDumperImport/Import/ImportPairGenomic.cs
  class ImportPairGenomic (line 8) | internal static class ImportPairGenomic
    method ImportPairGenomic (line 12) | static ImportPairGenomic()
    method Parse (line 23) | public static MutableTranscriptRegion[] Parse(ObjectValueNode objectVa...

FILE: CacheUtils/DataDumperImport/Import/ImportPrediction.cs
  class ImportPrediction (line 7) | internal static class ImportPrediction
    method ImportPrediction (line 11) | static ImportPrediction()
    method Parse (line 27) | public static string Parse(ObjectValueNode objectValue)

FILE: CacheUtils/DataDumperImport/Import/ImportProteinFunctionPredictions.cs
  class ImportProteinFunctionPredictions (line 8) | internal static class ImportProteinFunctionPredictions
    method ImportProteinFunctionPredictions (line 12) | static ImportProteinFunctionPredictions()
    method Parse (line 23) | public static (string SiftMatrix, string PolyphenMatrix) Parse(ObjectV...

FILE: CacheUtils/DataDumperImport/Import/ImportRegulatoryFeature.cs
  class ImportRegulatoryFeature (line 12) | public static class ImportRegulatoryFeature
    method ImportRegulatoryFeature (line 16) | static ImportRegulatoryFeature()
    method Parse (line 44) | public static IRegulatoryRegion Parse(ObjectValueNode objectValue, Chr...

FILE: CacheUtils/DataDumperImport/Import/ImportSeqEdits.cs
  class ImportSeqEdits (line 7) | internal static class ImportSeqEdits
    method ImportSeqEdits (line 11) | static ImportSeqEdits()
    method Parse (line 27) | public static int[] Parse(List<IListMember> members)

FILE: CacheUtils/DataDumperImport/Import/ImportTranscript.cs
  class ImportTranscript (line 18) | public static class ImportTranscript
    method ImportTranscript (line 22) | static ImportTranscript()
    method Parse (line 73) | public static MutableTranscript Parse(ObjectValueNode objectValue, Chr...
    method GetCodingRegionStart (line 240) | private static int GetCodingRegionStart(bool onReverseStrand, IInterva...
    method GetCodingRegionEnd (line 252) | private static int GetCodingRegionEnd(bool onReverseStrand, IInterval ...
    method GetTotalExonLength (line 264) | private static int GetTotalExonLength(IEnumerable<MutableExon> exons) ...

FILE: CacheUtils/DataDumperImport/Import/ImportTranscriptMapper.cs
  class ImportTranscriptMapper (line 8) | internal static class ImportTranscriptMapper
    method ImportTranscriptMapper (line 12) | static ImportTranscriptMapper()
    method Parse (line 26) | public static MutableTranscriptRegion[] Parse(ObjectValueNode objectVa...

FILE: CacheUtils/DataDumperImport/Import/ImportTranslation.cs
  class ImportTranslation (line 10) | internal static class ImportTranslation
    method ImportTranslation (line 14) | static ImportTranslation()
    method Parse (line 34) | public static (int Start, int End, string ProteinId, byte ProteinVersi...

FILE: CacheUtils/DataDumperImport/Import/ImportVariantEffectFeatureCache.cs
  class ImportVariantEffectFeatureCache (line 10) | internal static class ImportVariantEffectFeatureCache
    method ImportVariantEffectFeatureCache (line 14) | static ImportVariantEffectFeatureCache()
    method Parse (line 37) | public static (MutableTranscriptRegion[] CdnaMaps, IInterval[] Introns...

FILE: CacheUtils/DataDumperImport/Utilities/ImportUtilities.cs
  class ImportUtilities (line 9) | public static class ImportUtilities
    method GetPredictionData (line 11) | public static string GetPredictionData(this IImportNode node)
    method ParseObjectKeyValueNode (line 27) | public static T[] ParseObjectKeyValueNode<T>(this IImportNode node, Fu...
    method ParseListObjectKeyValueNode (line 43) | public static T[] ParseListObjectKeyValueNode<T>(this IImportNode node...

FILE: CacheUtils/DataDumperImport/Utilities/MutableTranscriptComparer.cs
  class MutableTranscriptComparer (line 9) | internal sealed class MutableTranscriptComparer : EqualityComparer<Mutab...
    method GeneEquals (line 11) | private static bool GeneEquals(MutableGene x, MutableGene y)
    method ExonEquals (line 23) | private static bool ExonEquals(MutableExon x, MutableExon y)
    method IntervalEquals (line 30) | private static bool IntervalEquals(IInterval x, IInterval y)
    method TranscriptRegionEquals (line 36) | private static bool TranscriptRegionEquals(ITranscriptRegion x, ITrans...
    method CodingRegionEquals (line 44) | private static bool CodingRegionEquals(ICodingRegion x, ICodingRegion y)
    method ArrayEquals (line 54) | private static bool ArrayEquals<T>(T[] x, T[] y, Func<T, T, bool> equals)
    method IntEquals (line 65) | private static bool IntEquals(int x, int y) => x == y;
    method Equals (line 67) | public override bool Equals(MutableTranscript x, MutableTranscript y)
    method GetHashCode (line 98) | public override int GetHashCode(MutableTranscript obj)

FILE: CacheUtils/DataDumperImport/Utilities/TranscriptUtilities.cs
  class TranscriptUtilities (line 10) | public static class TranscriptUtilities
    method TranscriptUtilities (line 17) | static TranscriptUtilities()
    method GetBiotype (line 26) | public static BioType GetBiotype(IImportNode node) => BioTypeHelper.Ge...
    method GetMapperUnitType (line 28) | public static MapperUnitType GetMapperUnitType(IImportNode node)
    method GetObjectValueNode (line 40) | public static ObjectValueNode GetObjectValueNode(this IImportNode node)
    method GetListMembers (line 46) | public static List<IListMember> GetListMembers(this IImportNode node)
    method GetStrand (line 52) | public static bool GetStrand(IImportNode node)
    method GetHgncId (line 65) | public static int GetHgncId(this IImportNode node)

FILE: CacheUtils/GFF/GeneralAttributes.cs
  class GeneralAttributes (line 3) | public sealed class GeneralAttributes : IGeneralAttributes
    method GeneralAttributes (line 13) | public GeneralAttributes(string geneId, string geneSymbol, string tran...

FILE: CacheUtils/GFF/GffCreator.cs
  class GffCreator (line 9) | public sealed class GffCreator
    method GffCreator (line 16) | public GffCreator(GffWriter writer, Dictionary<IGene, int> geneToInter...
    method Create (line 24) | public void Create(IEnumerable<IntervalArray<ITranscript>> transcriptI...
    method Write (line 35) | private void Write(ITranscript transcript)
    method WriteTranscript (line 51) | private void WriteTranscript(IInterval interval, IRequiredFields requi...
    method WriteGene (line 54) | private void WriteGene(IGene gene, IRequiredFields requiredFields, str...
    method WriteExon (line 63) | private void WriteExon(ITranscriptRegion exon, IRequiredFields require...
    method WriteUtr (line 71) | private void WriteUtr(IInterval codingRegion, ITranscriptRegion exon, ...
    method Write5PrimeUtr (line 79) | private void Write5PrimeUtr(IInterval codingRegion, ITranscriptRegion ...
    method Write3PrimeUtr (line 87) | private void Write3PrimeUtr(IInterval codingRegion, ITranscriptRegion ...
    method WriteCds (line 95) | private void WriteCds(IInterval codingRegion, ITranscriptRegion exon, ...
    method GetGene (line 102) | private static IGffGene GetGene(IGene gene, string id) => new GffGene(...
    method GetRequiredFields (line 105) | private static IRequiredFields GetRequiredFields(ITranscript transcript)
    method GetGeneralAttributes (line 111) | private IGeneralAttributes GetGeneralAttributes(ITranscript transcript)

FILE: CacheUtils/GFF/GffGene.cs
  class GffGene (line 3) | public sealed class GffGene : IGffGene
    method GffGene (line 12) | public GffGene(int start, int end, string id, string entrezGeneId, str...

FILE: CacheUtils/GFF/GffUtilities.cs
  class GffUtilities (line 11) | public static class GffUtilities
    method HasCds (line 13) | public static bool HasCds(IInterval codingRegion, IInterval exon)
    method GetCdsCoordinates (line 19) | public static IInterval GetCdsCoordinates(IInterval codingRegion, ITra...
    method HasUtr (line 30) | public static bool HasUtr(IInterval codingRegion, IInterval exon)
    method GetExons (line 36) | public static IEnumerable<ITranscriptRegion> GetExons(this ITranscript...
    method FilterNonExons (line 39) | private static ITranscriptRegion[] FilterNonExons(this IEnumerable<ITr...
    method Merge (line 42) | private static IEnumerable<ITranscriptRegion> Merge(this IReadOnlyColl...
    method MergeTranscriptRegions (line 57) | private static ITranscriptRegion MergeTranscriptRegions(ushort exonId,...

FILE: CacheUtils/GFF/GffWriter.cs
  class GffWriter (line 7) | public sealed class GffWriter : IDisposable
    method GffWriter (line 11) | public GffWriter(StreamWriter writer) => _writer = writer;
    method Dispose (line 13) | public void Dispose() => _writer.Dispose();
    method WriteRequiredFields (line 15) | private void WriteRequiredFields(IInterval interval, IRequiredFields f...
    method NotEmpty (line 21) | private static bool NotEmpty(string s) => !string.IsNullOrEmpty(s);
    method WriteGeneralAttributes (line 23) | private void WriteGeneralAttributes(IGeneralAttributes attribs)
    method WriteGene (line 35) | public void WriteGene(IGffGene gene, IRequiredFields requiredFields, i...
    method WriteInternalGeneId (line 45) | private void WriteInternalGeneId(int geneId) => _writer.WriteLine($"in...
    method WriteTranscript (line 47) | public void WriteTranscript(IInterval interval, IRequiredFields requir...
    method WriteExonicRegion (line 54) | public void WriteExonicRegion(IInterval interval, IRequiredFields requ...

FILE: CacheUtils/GFF/IGeneralAttributes.cs
  type IGeneralAttributes (line 3) | public interface IGeneralAttributes

FILE: CacheUtils/GFF/IGffGene.cs
  type IGffGene (line 5) | public interface IGffGene : IInterval

FILE: CacheUtils/GFF/IRequiredFields.cs
  type IRequiredFields (line 3) | public interface IRequiredFields

FILE: CacheUtils/GFF/RequiredFields.cs
  class RequiredFields (line 3) | public sealed class RequiredFields : IRequiredFields
    method RequiredFields (line 9) | public RequiredFields(string ucscName, string source, bool onReverseSt...

FILE: CacheUtils/Genbank/GenbankEntry.cs
  class GenbankEntry (line 5) | public sealed class GenbankEntry
    method GenbankEntry (line 16) | public GenbankEntry(string transcriptId, byte transcriptVersion, strin...

FILE: CacheUtils/Genbank/GenbankReader.cs
  class GenbankReader (line 10) | public sealed class GenbankReader : IDisposable
    method GenbankReader (line 31) | public GenbankReader(StreamReader reader) => _reader = reader;
    method GetGenbankEntry (line 33) | public GenbankEntry GetGenbankEntry()
    method ParseOrigin (line 50) | private void ParseOrigin()
    method GetNextLine (line 59) | private string GetNextLine()
    method ParseFeatures (line 66) | private FeatureData ParseFeatures()
    method ParseExonFeature (line 98) | private static void ParseExonFeature(bool isNewState, FeatureData feat...
    method ParseCdsFeature (line 103) | private static void ParseCdsFeature(bool isNewState, FeatureData featu...
    method ParseGeneFeature (line 109) | private static void ParseGeneFeature(string info, FeatureData featureD...
    method ParseHeader (line 115) | private (string TranscriptId, byte TranscriptVersion) ParseHeader()
    method ParseGeneSymbol (line 131) | private static string ParseGeneSymbol(string info) => info.Substring(G...
    method ParseGeneId (line 132) | private static string ParseGeneId(string info)     => info.Substring(G...
    method ParseProteinId (line 134) | private static void ParseProteinId(FeatureData featureData, string info)
    method GetInterval (line 140) | private static IInterval GetInterval(string info)
    method GetJoinInterval (line 152) | private static IInterval GetJoinInterval(string info)
    method GetFeatureState (line 160) | private static (FeaturesState State, bool IsNewState) GetFeatureState(...
    method HasLocus (line 170) | private bool HasLocus()
    method ParseVersion (line 176) | private static (string TranscriptId, byte TranscriptVersion) ParseVers...
    method Dispose (line 182) | public void Dispose() => _reader.Dispose();
    class FeatureData (line 184) | private sealed class FeatureData

FILE: CacheUtils/Genbank/GenbankState.cs
  type FeaturesState (line 3) | internal enum FeaturesState : byte

FILE: CacheUtils/Genes/Combiners/CombinerUtils.cs
  class CombinerUtils (line 7) | public static class CombinerUtils
    method Merge (line 9) | public static UgaGene Merge(UgaGene gene37, UgaGene gene38)
    method CombineField (line 18) | private static T CombineField<T>(T grch37, T grch38)
    method RemoveGenes (line 26) | internal static void RemoveGenes(IEnumerable<UgaGene> genes, ICollecti...
    method AddOrphans (line 31) | internal static void AddOrphans(ICollection<UgaGene> combinedGenes, IE...

FILE: CacheUtils/Genes/Combiners/HgncIdCombiner.cs
  class HgncIdCombiner (line 7) | public sealed class HgncIdCombiner : ICombiner
    method Combine (line 9) | public void Combine(List<UgaGene> combinedGenes, HashSet<UgaGene> rema...
    method GetGenesByHgncId (line 46) | private static List<UgaGene> GetGenesByHgncId(IReadOnlyDictionary<int,...
    method GetHgncIds (line 49) | private static IEnumerable<int> GetHgncIds(IEnumerable<UgaGene> remain...

FILE: CacheUtils/Genes/Combiners/ICombiner.cs
  type ICombiner (line 6) | public interface ICombiner
    method Combine (line 8) | void Combine(List<UgaGene> combinedGenes, HashSet<UgaGene> remainingGe...

FILE: CacheUtils/Genes/Combiners/PartitionCombiner.cs
  class PartitionCombiner (line 7) | public sealed class PartitionCombiner : ICombiner
    method Combine (line 9) | public void Combine(List<UgaGene> combinedGenes, HashSet<UgaGene> rema...
    method CombineSet (line 20) | private static void CombineSet(ICollection<UgaGene> combinedGenes, IEn...
    method GetGenesByKey (line 54) | private static List<UgaGene> GetGenesByKey(IReadOnlyDictionary<string,...
    method GetAllKeys (line 57) | private static IEnumerable<string> GetAllKeys(IEnumerable<string> keys...
    method GetKey (line 65) | private static string GetKey(UgaGene gene) =>
    method Partition (line 68) | private static (List<UgaGene> EnsemblOnly, List<UgaGene> Both, List<Ug...

FILE: CacheUtils/Genes/DataStores/AssemblyDataStore.cs
  class AssemblyDataStore (line 10) | public sealed class AssemblyDataStore
    method AssemblyDataStore (line 17) | private AssemblyDataStore(string description, EnsemblGtf ensemblGtf, R...
    method Create (line 25) | public static AssemblyDataStore Create(string description, FilePaths.A...
    method UpdateHgncIds (line 41) | public IUpdateHgncData UpdateHgncIds(Hgnc oldHgnc)

FILE: CacheUtils/Genes/DataStores/EnsemblGtf.cs
  class EnsemblGtf (line 11) | public sealed class EnsemblGtf
    method EnsemblGtf (line 16) | private EnsemblGtf(Dictionary<string, EnsemblGene> ensemblIdToGene, Di...
    method Create (line 22) | public static EnsemblGtf Create(string filePath, Dictionary<string, Ch...
    method LoadEnsemblGenes (line 30) | private static EnsemblGene[] LoadEnsemblGenes(StreamReader streamReader,

FILE: CacheUtils/Genes/DataStores/GeneInfoData.cs
  class GeneInfoData (line 9) | public sealed class GeneInfoData
    method GeneInfoData (line 13) | private GeneInfoData(Dictionary<string, string> entrezGeneIdToSymbol)
    method Create (line 18) | public static GeneInfoData Create(string filePath)
    method LoadGeneInfoGenes (line 25) | private static IEnumerable<GeneInfo> LoadGeneInfoGenes(string filePath)

FILE: CacheUtils/Genes/DataStores/GlobalCache.cs
  class GlobalCache (line 12) | public sealed class GlobalCache
    method GlobalCache (line 17) | private GlobalCache(Dictionary<ushort, List<MutableGene>> ensemblGenes...
    method Create (line 24) | public static GlobalCache Create(string refSeqCachePath, string ensemb...
    method FlattenGenes (line 33) | private static Dictionary<ushort, List<MutableGene>> FlattenGenes(IEnu...
    method LoadGenes (line 46) | private static IEnumerable<MutableGene> LoadGenes(Stream stream,
    method GetGeneKey (line 70) | private static string GetGeneKey(MutableGene gene) => gene.GeneId + '|...

FILE: CacheUtils/Genes/DataStores/Hgnc.cs
  class Hgnc (line 13) | public sealed class Hgnc
    method Hgnc (line 18) | private Hgnc(HgncGene[] hgncGenes, Dictionary<int, string> hgncIdToSym...
    method Create (line 24) | public static Hgnc Create(string filePath, Dictionary<string, Chromoso...
    method LoadHgncGenes (line 31) | private static HgncGene[] LoadHgncGenes(Stream stream, Dictionary<stri...
    method AddCoordinates (line 38) | public int AddCoordinates(EnsemblGtf ensemblGtf, RefSeqGff refSeqGff)
    method AddCoordinatesFromMultipleGenes (line 64) | private static void AddCoordinatesFromMultipleGenes(HgncGene hgncGene,...
    method AddCoordinatesFromGene (line 77) | private static void AddCoordinatesFromGene<T>(HgncGene hgncGene, IFlat...
    method GetGenes (line 83) | private static (List<RefSeqGene> RefSeqGenes, EnsemblGene EnsemblGene,...
    method Clone (line 93) | public Hgnc Clone()
    method GetEnsemblGene (line 100) | private static EnsemblGene GetEnsemblGene(string ensemblId, IReadOnlyD...
    method GetRefSeqGenes (line 108) | private static List<RefSeqGene> GetRefSeqGenes(string entrezGeneId, IR...
    method RemoveDuplicateEntries (line 114) | public (int NumEntrezGeneIdsRemoved, int NumEnsemblIdsRemoved) RemoveD...
    method RemoveDuplicatesByTranscriptSource (line 121) | private static int RemoveDuplicatesByTranscriptSource(IEnumerable<Hgnc...

FILE: CacheUtils/Genes/DataStores/IUpdateHgncData.cs
  type IUpdateHgncData (line 6) | public interface IUpdateHgncData

FILE: CacheUtils/Genes/DataStores/RefSeqGff.cs
  class RefSeqGff (line 12) | public sealed class RefSeqGff
    method RefSeqGff (line 17) | private RefSeqGff(Dictionary<string, List<RefSeqGene>> entrezGeneIdToG...
    method Create (line 23) | public static RefSeqGff Create(string gcfGffPath, string refGffPath, D...
    method LoadRefSeqGffGenes (line 38) | private static List<RefSeqGene> LoadRefSeqGffGenes(StreamReader gcfGff...
    method LoadRefSeqGff (line 48) | private static void LoadRefSeqGff(StreamReader streamReader, List<RefS...

FILE: CacheUtils/Genes/DataStores/UpdateHgncData.cs
  class UpdateHgncData (line 6) | public sealed class UpdateHgncData : IUpdateHgncData
    method UpdateHgncData (line 11) | public UpdateHgncData(Dictionary<ushort, List<MutableGene>> ensemblGen...

FILE: CacheUtils/Genes/DataStructures/EnsemblGene.cs
  class EnsemblGene (line 6) | public sealed class EnsemblGene : IFlatGene<EnsemblGene>
    method EnsemblGene (line 14) | public EnsemblGene(Chromosome chromosome, int start, int end, string g...
    method Clone (line 23) | public EnsemblGene Clone() => throw new NotImplementedException();

FILE: CacheUtils/Genes/DataStructures/GeneInfo.cs
  class GeneInfo (line 3) | public sealed class GeneInfo
    method GeneInfo (line 8) | public GeneInfo(string symbol, string entrezGeneId)

FILE: CacheUtils/Genes/DataStructures/HgncGene.cs
  class HgncGene (line 6) | public sealed class HgncGene : IChromosomeInterval
    method HgncGene (line 16) | public HgncGene(Chromosome chromosome, int start, int end, string symb...
    method Clone (line 28) | public HgncGene Clone() => new HgncGene(Chromosome, -1, -1, Symbol, En...

FILE: CacheUtils/Genes/DataStructures/IFlatGene.cs
  type IFlatGene (line 6) | public interface IFlatGene<out T>
    method Clone (line 11) | T Clone();

FILE: CacheUtils/Genes/DataStructures/RefSeqGene.cs
  class RefSeqGene (line 6) | public sealed class RefSeqGene : IFlatGene<RefSeqGene>
    method RefSeqGene (line 16) | public RefSeqGene(Chromosome chromosome, int start, int end, bool onRe...
    method Clone (line 28) | public RefSeqGene Clone() => new RefSeqGene(Chromosome, Start, End, On...

FILE: CacheUtils/Genes/DataStructures/UgaGene.cs
  class UgaGene (line 8) | public sealed class UgaGene
    method UgaGene (line 20) | public UgaGene(Chromosome chromosome, IInterval grch37, IInterval grch...
    method ToString (line 33) | public override string ToString()
    method GetInterval (line 41) | private static string GetInterval(IInterval interval) =>
    method ToGene (line 44) | public Gene ToGene(GenomeAssembly genomeAssembly)

FILE: CacheUtils/Genes/GeneFlattener.cs
  class GeneFlattener (line 8) | public static class GeneFlattener
    method FlattenGeneList (line 10) | public static List<T> FlattenGeneList<T>(this Dictionary<string, List<...
    method FlattenWithSameId (line 23) | internal static List<T> FlattenWithSameId<T>(List<T> genes) where T : ...

FILE: CacheUtils/Genes/GeneMerger.cs
  class GeneMerger (line 13) | public static class GeneMerger
    method MergeByHgnc (line 15) | public static Dictionary<ushort, List<UgaGene>> MergeByHgnc(this IUpda...
    method AddGenes (line 44) | private static void AddGenes(Dictionary<ushort, List<MutableGene>> sou...
    method GetMergedGenes (line 62) | private static (List<UgaGene> MergedGenes, int NumOrphanEntries, int N...
    method ConvertToUgaGenes (line 87) | private static List<UgaGene> ConvertToUgaGenes(IEnumerable<MutableGene...
    method GetMergedGene (line 101) | private static UgaGene GetMergedGene(MutableGene geneA, MutableGene ge...
    method GetMergedInterval (line 115) | private static IInterval GetMergedInterval(MutableGene geneA, MutableG...

FILE: CacheUtils/Genes/GeneSymbolUpdater.cs
  class GeneSymbolUpdater (line 10) | public sealed class GeneSymbolUpdater
    method GeneSymbolUpdater (line 22) | public GeneSymbolUpdater(Dictionary<int, string> hgncIdToSymbol,
    method Update (line 32) | public void Update(UgaGene[] mergedGenes)
    method UpdateGeneSymbol (line 42) | private void UpdateGeneSymbol(UgaGene gene)
    method UpdateBySymbolDict (line 75) | private static bool UpdateBySymbolDict<T>(UgaGene gene, Func<UgaGene, ...

FILE: CacheUtils/Genes/HgncIdConsolidator.cs
  class HgncIdConsolidator (line 9) | public static class HgncIdConsolidator
    method Consolidate (line 11) | public static int Consolidate(this Dictionary<ushort, List<MutableGene...
    method CreateAggregateGene (line 31) | private static void CreateAggregateGene(IReadOnlyList<MutableGene> genes)

FILE: CacheUtils/Genes/HgncIdUpdater.cs
  class HgncIdUpdater (line 9) | public static class HgncIdUpdater
    method Update (line 11) | public static Dictionary<ushort, List<MutableGene>> Update(this IEnume...
    method ReplaceHgncIds (line 19) | private static void ReplaceHgncIds(IEnumerable<MutableGene> genes, IRe...

FILE: CacheUtils/Genes/IO/EnsemblGtfReader.cs
  class EnsemblGtfReader (line 11) | public sealed class EnsemblGtfReader : IDisposable
    method EnsemblGtfReader (line 22) | public EnsemblGtfReader(StreamReader reader, Dictionary<string, Chromo...
    method GetGenes (line 29) | public EnsemblGene[] GetGenes()
    method AddGene (line 52) | private void AddGene(string[] cols, ICollection<EnsemblGene> genes)
    method GetGffFields (line 76) | private static (string EnsemblGeneId, string Name) GetGffFields(string...
    method Dispose (line 107) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/Genes/IO/GeneInfoReader.cs
  class GeneInfoReader (line 9) | public sealed class GeneInfoReader : IDisposable
    method GeneInfoReader (line 17) | public GeneInfoReader(StreamReader reader)
    method SetColumnIndices (line 24) | private void SetColumnIndices(string line)
    method Next (line 64) | private GeneInfo Next()
    method GetGenes (line 89) | public GeneInfo[] GetGenes()
    method Dispose (line 103) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/Genes/IO/HgncReader.cs
  class HgncReader (line 11) | public sealed class HgncReader : IDisposable
    method HgncReader (line 22) | public HgncReader(Stream stream, Dictionary<string, Chromosome> refNam...
    method Next (line 32) | private HgncGene Next()
    method GetGenes (line 58) | public HgncGene[] GetGenes()
    method GetChromosome (line 72) | private Chromosome GetChromosome(string cytogeneticBand)
    method GetArmPos (line 81) | private static int GetArmPos(string cytogeneticBand)
    method GetId (line 90) | private static string GetId(string s) => string.IsNullOrEmpty(s) ? nul...
    method Dispose (line 92) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/Genes/IO/RefSeqGffReader.cs
  class RefSeqGffReader (line 10) | public sealed class RefSeqGffReader : IDisposable
    method RefSeqGffReader (line 22) | public RefSeqGffReader(StreamReader reader, Dictionary<string, Chromos...
    method AddGenes (line 29) | public void AddGenes(List<RefSeqGene> refSeqGenes)
    method AddGene (line 46) | private void AddGene(string[] cols, ICollection<RefSeqGene> refSeqGenes)
    method GetChromosome (line 71) | internal static Chromosome GetChromosome(string referenceName, Diction...
    method GetGffFields (line 77) | private static (string Name, string EntrezGeneId, int HgncId)
    method GetIds (line 104) | private static (string EntrezGeneId, int HgncId) GetIds(IEnumerable<st...
    method Dispose (line 129) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/Genes/IO/UgaGeneReader.cs
  class UgaGeneReader (line 12) | public sealed class UgaGeneReader : IDisposable
    method UgaGeneReader (line 17) | public UgaGeneReader(Stream stream, Dictionary<string, Chromosome> ref...
    method Dispose (line 24) | public void Dispose() => _reader.Dispose();
    method GetGenes (line 26) | public UgaGene[] GetGenes()
    method GetNextGene (line 40) | private UgaGene GetNextGene()

FILE: CacheUtils/Genes/IO/UgaGeneWriter.cs
  class UgaGeneWriter (line 8) | public sealed class UgaGeneWriter : IDisposable
    method UgaGeneWriter (line 12) | public UgaGeneWriter(Stream stream, bool leaveOpen = false)
    method Dispose (line 17) | public void Dispose() => _writer.Dispose();
    method Write (line 19) | public void Write(UgaGene[] genes)

FILE: CacheUtils/Genes/UgaAssemblyCombiner.cs
  class UgaAssemblyCombiner (line 12) | public static class UgaAssemblyCombiner
    method Combine (line 16) | public static UgaGene[] Combine(Dictionary<ushort, List<UgaGene>> gene...
    method GetCombiners (line 35) | private static List<ICombiner> GetCombiners() =>
    method GetReferenceIndices (line 38) | private static IEnumerable<ushort> GetReferenceIndices(IEnumerable<ush...
    method CombineByReference (line 46) | private static IEnumerable<UgaGene> CombineByReference(IEnumerable<Uga...
    method GetRemainingGenes (line 62) | private static HashSet<UgaGene> GetRemainingGenes(IEnumerable<UgaGene>...
    method GetUgaGenesByRef (line 70) | private static IEnumerable<UgaGene> GetUgaGenesByRef(IReadOnlyDictiona...
    method MinCoordinate (line 73) | private static int MinCoordinate(UgaGene gene, Func<IInterval, int> co...

FILE: CacheUtils/Genes/Utilities/DictionaryUtilities.cs
  class DictionaryUtilities (line 7) | public static class DictionaryUtilities
    method GetSingleValueDict (line 9) | public static Dictionary<TK, T> GetSingleValueDict<T, TK>(this IEnumer...
    method GetMultiValueDict (line 22) | public static Dictionary<TK, List<T>> GetMultiValueDict<T, TK>(this IE...
    method GetKeyValueDict (line 35) | public static Dictionary<TK, TV> GetKeyValueDict<T, TK, TV>(this IEnum...
    method GetSet (line 48) | public static HashSet<TV> GetSet<T,TV>(this IEnumerable<T> elements, F...
    method CreateIndex (line 59) | public static Dictionary<T, int> CreateIndex<T>(this IEnumerable<T> el...

FILE: CacheUtils/Helpers/BioTypeHelper.cs
  class BioTypeHelper (line 7) | public static class BioTypeHelper
    method BioTypeHelper (line 11) | static BioTypeHelper()
    method GetBioType (line 83) | public static BioType GetBioType(string s)

FILE: CacheUtils/Helpers/GeneSymbolSourceHelper.cs
  class GeneSymbolSourceHelper (line 7) | public static class GeneSymbolSourceHelper
    method GeneSymbolSourceHelper (line 11) | static GeneSymbolSourceHelper()
    method GetGeneSymbolSource (line 27) | public static GeneSymbolSource GetGeneSymbolSource(string s)

FILE: CacheUtils/Helpers/RegulatoryRegionTypeHelper.cs
  class RegulatoryRegionTypeHelper (line 7) | public static class RegulatoryRegionTypeHelper
    method RegulatoryRegionTypeHelper (line 11) | static RegulatoryRegionTypeHelper()
    method GetRegulatoryRegionType (line 25) | public static RegulatoryRegionType GetRegulatoryRegionType(string s)

FILE: CacheUtils/Helpers/TranscriptCacheHelper.cs
  class TranscriptCacheHelper (line 10) | public static class TranscriptCacheHelper
    method GetCache (line 12) | public static TranscriptCacheData GetCache(string cachePath,

FILE: CacheUtils/IntermediateIO/CcdsReader.cs
  class CcdsReader (line 9) | public static class CcdsReader
    method GetCcdsIdToEnsemblId (line 14) | public static Dictionary<string, List<string>> GetCcdsIdToEnsemblId(st...

FILE: CacheUtils/IntermediateIO/GenbankReader.cs
  class GenbankReader (line 11) | internal sealed class GenbankReader : IDisposable
    method GenbankReader (line 15) | internal GenbankReader(Stream stream)
    method GetIdToGenbank (line 21) | public Dictionary<string, GenbankEntry> GetIdToGenbank()
    method GetNextEntry (line 35) | private GenbankEntry GetNextEntry()
    method ReadExons (line 47) | private IInterval[] ReadExons(int numExons)
    method ReadTranscriptInfo (line 70) | private static (string TranscriptId, byte TranscriptVersion, string Pr...
    method Dispose (line 91) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/IntermediateIO/GenbankWriter.cs
  class GenbankWriter (line 7) | internal sealed class GenbankWriter : IDisposable
    method GenbankWriter (line 11) | internal GenbankWriter(StreamWriter writer, IntermediateIoHeader header)
    method Write (line 18) | internal void Write(GenbankEntry entry)
    method Dispose (line 36) | public void Dispose() => _writer.Dispose();

FILE: CacheUtils/IntermediateIO/IntermediateIoCommon.cs
  class IntermediateIoCommon (line 5) | public static class IntermediateIoCommon
    type FileType (line 9) | public enum FileType : byte
    method ReadHeader (line 19) | public static IntermediateIoHeader ReadHeader(StreamReader reader, Fil...

FILE: CacheUtils/IntermediateIO/IntermediateIoHeader.cs
  class IntermediateIoHeader (line 8) | public sealed class IntermediateIoHeader
    method IntermediateIoHeader (line 16) | public IntermediateIoHeader(ushort vepVersion, long vepReleaseTicks, S...
    method Write (line 26) | internal void Write(StreamWriter writer, IntermediateIoCommon.FileType...
    method Read (line 32) | internal static (string Id, IntermediateIoCommon.FileType Type, Interm...

FILE: CacheUtils/IntermediateIO/LrgReader.cs
  class LrgReader (line 9) | public static class LrgReader
    method GetTranscriptIds (line 15) | public static HashSet<string> GetTranscriptIds(string lrgPath, Diction...
    method GetEnsemblTranscriptIds (line 43) | private static List<string> GetEnsemblTranscriptIds(string ccdsId,
    method Sanitize (line 51) | private static string Sanitize(string s) => s == "-" ? null : s;

FILE: CacheUtils/IntermediateIO/MutableTranscriptReader.cs
  class MutableTranscriptReader (line 17) | internal sealed class MutableTranscriptReader : IDisposable
    method MutableTranscriptReader (line 25) | internal MutableTranscriptReader(Stream stream, Dictionary<ushort, Chr...
    method GetTranscripts (line 32) | public MutableTranscript[] GetTranscripts()
    method GetNextTranscript (line 46) | private MutableTranscript GetNextTranscript()
    method AddMutableContents (line 74) | private void AddMutableContents(MutableTranscript mt)
    method ReadSelenocysteines (line 92) | private int[] ReadSelenocysteines()
    method ReadRnaEdits (line 106) | private IRnaEdit[] ReadRnaEdits()
    method ReadCdnaMaps (line 127) | private MutableTranscriptRegion[] ReadCdnaMaps()
    method ReadIntervals (line 149) | private IInterval[] ReadIntervals(string description)
    method ReadExons (line 169) | private MutableExon[] ReadExons(Chromosome chromosome)
    method ReadTranslation (line 190) | private (string Id, byte Version, ICodingRegion CodingRegion, string P...
    method ReadGene (line 209) | private MutableGene ReadGene(Chromosome chromosome)
    method ReadTranscriptInfo (line 224) | private (string Id, byte Version, Chromosome Chromosome, int Start, in...
    method GetColumns (line 254) | private string[] GetColumns(string keyword, string line = null)
    method Dispose (line 263) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/IntermediateIO/MutableTranscriptWriter.cs
  class MutableTranscriptWriter (line 10) | internal sealed class MutableTranscriptWriter : IDisposable
    method MutableTranscriptWriter (line 14) | internal MutableTranscriptWriter(StreamWriter writer, IntermediateIoHe...
    method Write (line 21) | internal void Write(MutableTranscript transcript)
    method WriteRnaEdits (line 34) | private void WriteRnaEdits(IReadOnlyCollection<IRnaEdit> rnaEdits)
    method WriteSelenocysteines (line 47) | private void WriteSelenocysteines(IReadOnlyCollection<int> positions)
    method WriteCdnaMaps (line 60) | private void WriteCdnaMaps(IReadOnlyCollection<ITranscriptRegion> cdna...
    method WriteIntervals (line 67) | private void WriteIntervals(IReadOnlyCollection<IInterval> intervals, ...
    method WriteExons (line 80) | private void WriteExons(IReadOnlyCollection<MutableExon> exons)
    method WriteTranslation (line 87) | private void WriteTranslation(ICodingRegion codingRegion, string prote...
    method WriteGene (line 90) | private static void WriteGene(TextWriter writer, MutableGene gene)
    method WriteTranscriptInfo (line 96) | private void WriteTranscriptInfo(MutableTranscript transcript)
    method BoolToChar (line 102) | private static char BoolToChar(bool b) => b ? 'Y' : 'N';
    method Dispose (line 104) | public void Dispose() => _writer.Dispose();

FILE: CacheUtils/IntermediateIO/PredictionReader.cs
  class PredictionReader (line 11) | public sealed class PredictionReader : IDisposable
    method PredictionReader (line 16) | public PredictionReader(Stream stream, Dictionary<ushort, Chromosome> ...
    method GetPredictionData (line 24) | public (string[] PredictionData, Dictionary<int, int> TranscriptToPred...
    method GetChromosomeHeader (line 42) | private (Chromosome Chromosome, int NumPredictions) GetChromosomeHeader()
    method GetNextPrediction (line 56) | private (List<int> TranscriptIndices, string PredictionData) GetNextPr...
    method GetTranscriptIndices (line 70) | private static List<int> GetTranscriptIndices(string s)
    method Dispose (line 78) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/IntermediateIO/PredictionWriter.cs
  class PredictionWriter (line 8) | internal sealed class PredictionWriter : IDisposable
    method PredictionWriter (line 12) | internal PredictionWriter(StreamWriter writer, IntermediateIoHeader he...
    method Write (line 20) | internal void Write(Chromosome chromosome, Dictionary<string, List<int...
    method WritePrediction (line 26) | private void WritePrediction(IEnumerable<int> transcriptIds, string pr...
    method Dispose (line 32) | public void Dispose() => _writer.Dispose();

FILE: CacheUtils/IntermediateIO/RegulatoryRegionReader.cs
  class RegulatoryRegionReader (line 14) | internal sealed class RegulatoryRegionReader : IDisposable
    method RegulatoryRegionReader (line 19) | internal RegulatoryRegionReader(Stream stream, Dictionary<ushort, Chro...
    method GetRegulatoryRegions (line 26) | public IRegulatoryRegion[] GetRegulatoryRegions()
    method GetNextRegulatoryRegion (line 40) | private IRegulatoryRegion GetNextRegulatoryRegion()
    method Dispose (line 56) | public void Dispose() => _reader.Dispose();

FILE: CacheUtils/IntermediateIO/RegulatoryRegionWriter.cs
  class RegulatoryRegionWriter (line 7) | internal sealed class RegulatoryRegionWriter : IDisposable
    method RegulatoryRegionWriter (line 11) | internal RegulatoryRegionWriter(StreamWriter writer, IntermediateIoHea...
    method Write (line 18) | internal void Write(IRegulatoryRegion region) => _writer.WriteLine(
    method Dispose (line 21) | public void Dispose() => _writer.Dispose();

FILE: CacheUtils/MiniCache/DataBundle.cs
  class DataBundle (line 15) | public sealed class DataBundle
    method DataBundle (line 30) | private DataBundle(CompressedSequenceReader sequenceReader, Prediction...
    method Load (line 42) | public void Load(Chromosome chromosome)
    method GetDataBundle (line 51) | public static DataBundle GetDataBundle(string referencePath, string ca...

FILE: CacheUtils/MiniCache/IStaging.cs
  type IStaging (line 5) | public interface IStaging
    method Write (line 7) | void Write(Stream stream);

FILE: CacheUtils/PredictionCache/PredictionCacheBuilder.cs
  class PredictionCacheBuilder (line 15) | public sealed class PredictionCacheBuilder
    method PredictionCacheBuilder (line 19) | public PredictionCacheBuilder(GenomeAssembly genomeAssembly) => _genom...
    method CreatePredictionCaches (line 21) | public (PredictionCacheStaging Sift, PredictionCacheStaging PolyPhen) ...
    method BuildCacheStaging (line 57) | private PredictionCacheStaging BuildCacheStaging(string description,
    method CreateHeader (line 72) | private PredictionHeader CreateHeader(int numReferenceSeqs, Prediction...
    method ConvertPredictions (line 78) | private static Prediction[][] ConvertPredictions(IReadOnlyList<Rounded...
    method ConvertReferencePredictions (line 92) | private static Prediction[] ConvertReferencePredictions(IReadOnlyList<...
    method CreateLut (line 106) | private static (Prediction.Entry[] Lut, Dictionary<RoundedEntry, byte>...
    method ProcessReference (line 140) | private static (RoundedEntryPrediction[] Sift, RoundedEntryPrediction[...
    method AssignPredictionIndices (line 153) | private static void AssignPredictionIndices(IReadOnlyList<MutableTrans...

FILE: CacheUtils/PredictionCache/PredictionCacheStaging.cs
  class PredictionCacheStaging (line 11) | public sealed class PredictionCacheStaging : IStaging
    method PredictionCacheStaging (line 16) | internal PredictionCacheStaging(PredictionHeader header, Prediction[][...
    method Write (line 22) | public void Write(Stream stream)

FILE: CacheUtils/PredictionCache/PredictionCacheWriter.cs
  class PredictionCacheWriter (line 10) | public sealed class PredictionCacheWriter : IDisposable
    method PredictionCacheWriter (line 17) | public PredictionCacheWriter(BlockStream blockStream, PredictionHeader...
    method Dispose (line 25) | public void Dispose()
    method Write (line 31) | internal void Write(Prediction.Entry[] lut, Prediction[][] predictions...
    method WritePredictions (line 39) | private void WritePredictions(IReadOnlyList<Prediction[]> predictionsP...
    method WriteLookupTable (line 60) | private static void WriteLookupTable(BinaryWriter writer, IReadOnlyCol...

FILE: CacheUtils/PredictionCache/PredictionExtensions.cs
  class PredictionExtensions (line 6) | public static class PredictionExtensions
    method GetRoundedEntryPredictions (line 8) | public static RoundedEntryPrediction[] GetRoundedEntryPredictions(this...
    method GetRoundedEntryPrediction (line 16) | private static RoundedEntryPrediction GetRoundedEntryPrediction(this s...

FILE: CacheUtils/PredictionCache/PredictionUtilities.cs
  class PredictionUtilities (line 11) | public static class PredictionUtilities
    method UpdateTranscripts (line 13) | internal static IntervalArray<ITranscript>[] UpdateTranscripts(IEnumer...
    method UpdatePredictions (line 32) | internal static ITranscript UpdatePredictions(this ITranscript t, int ...
    method GetNewIndex (line 40) | private static int GetNewIndex(IReadOnlyList<Prediction> oldPrediction...

FILE: CacheUtils/PredictionCache/RoundedEntry.cs
  type RoundedEntry (line 5) | public struct RoundedEntry : IEquatable<RoundedEntry>
    method RoundedEntry (line 10) | public RoundedEntry(ushort data)
    method Round (line 16) | private static ushort Round(ushort us) => (ushort)((ushort)Math.Round(...
    method Equals (line 18) | public bool Equals(RoundedEntry other) => Score == other.Score && Enum...
    method GetHashCode (line 20) | public override int GetHashCode()

FILE: CacheUtils/PredictionCache/RoundedEntryPrediction.cs
  class RoundedEntryPrediction (line 6) | public sealed class RoundedEntryPrediction
    method RoundedEntryPrediction (line 9) | public RoundedEntryPrediction(RoundedEntry[] entries) => Entries = ent...
    method Convert (line 11) | public Prediction Convert(Dictionary<RoundedEntry, byte> lutDict, Pred...

FILE: CacheUtils/TranscriptCache/CanonicalTranscriptMarker.cs
  class CanonicalTranscriptMarker (line 10) | public sealed class CanonicalTranscriptMarker
    method CanonicalTranscriptMarker (line 14) | public CanonicalTranscriptMarker(HashSet<string> lrgTranscriptIds)
    method MarkTranscripts (line 19) | public int MarkTranscripts(MutableTranscript[] transcripts)
    method GetTranscriptsByEntrezGeneId (line 26) | private SortedDictionary<int, HashSet<TranscriptMetadata>> GetTranscri...
    method GetCanonicalTranscriptsByGeneId (line 49) | private static SortedDictionary<int, string> GetCanonicalTranscriptsBy...
    method ConvertGeneIdToInt (line 68) | private static int ConvertGeneIdToInt(string geneId)
    method SetCanonicalFlags (line 76) | private static int SetCanonicalFlags(IReadOnlyDictionary<int, string> ...
    method GetSortedTrustedTranscripts (line 101) | private static List<TranscriptMetadata> GetSortedTrustedTranscripts(IE...
    class TranscriptMetadata (line 116) | public sealed class TranscriptMetadata : IEquatable<TranscriptMetadata>
      method TranscriptMetadata (line 124) | public TranscriptMetadata(string transcriptId, int accession, int tr...
      method Equals (line 133) | public bool Equals(TranscriptMetadata other)
      method GetHashCode (line 142) | public override int GetHashCode()

FILE: CacheUtils/TranscriptCache/Comparers/GeneComparer.cs
  class GeneComparer (line 6) | internal sealed class GeneComparer : EqualityComparer<IGene>
    method Equals (line 8) | public override bool Equals(IGene x, IGene y)
    method GetHashCode (line 20) | public override int GetHashCode(IGene obj)

FILE: CacheUtils/TranscriptCache/Comparers/IntervalComparer.cs
  class IntervalComparer (line 6) | internal sealed class IntervalComparer : EqualityComparer<IInterval>
    method Equals (line 8) | public override bool Equals(IInterval x, IInterval y) => x.Start == y....
    method GetHashCode (line 10) | public override int GetHashCode(IInterval obj)

FILE: CacheUtils/TranscriptCache/Comparers/RegulatoryRegionComparer.cs
  class RegulatoryRegionComparer (line 6) | internal sealed class RegulatoryRegionComparer : EqualityComparer<IRegul...
    method Equals (line 8) | public override bool Equals(IRegulatoryRegion x, IRegulatoryRegion y)
    method GetHashCode (line 17) | public override int GetHashCode(IRegulatoryRegion obj)

FILE: CacheUtils/TranscriptCache/Comparers/TranscriptRegionComparer.cs
  class TranscriptRegionComparer (line 6) | internal sealed class TranscriptRegionComparer : EqualityComparer<ITrans...
    method Equals (line 8) | public override bool Equals(ITranscriptRegion x, ITranscriptRegion y)
    method GetHashCode (line 15) | public override int GetHashCode(ITranscriptRegion obj)

FILE: CacheUtils/TranscriptCache/Comparers/UgaGeneComparer.cs
  class UgaGeneComparer (line 7) | public sealed class UgaGeneComparer : EqualityComparer<UgaGene>
    method Equals (line 9) | public override bool Equals(UgaGene x, UgaGene y)
    method Equals (line 23) | private static bool Equals(IInterval x, IInterval y)
    method GetHashCode (line 30) | private static int GetHashCode(IInterval x)
    method GetHashCode (line 36) | public override int GetHashCode(UgaGene obj)

FILE: CacheUtils/TranscriptCache/NSequence.cs
  class NSequence (line 6) | public sealed class NSequence : ISequence
    method Substring (line 9) | public string Substring(int offset, int length) => new string('N', len...

FILE: CacheUtils/TranscriptCache/SortExtensions.cs
  class SortExtensions (line 8) | public static class SortExtensions
    method Sort (line 10) | public static IOrderedEnumerable<T> Sort<T>(this IEnumerable<T> elemen...
    method SortInterval (line 13) | public static IOrderedEnumerable<T> SortInterval<T>(this IEnumerable<T...

FILE: CacheUtils/TranscriptCache/TranscriptCacheBuilder.cs
  class TranscriptCacheBuilder (line 15) | public sealed class TranscriptCacheBuilder
    method TranscriptCacheBuilder (line 22) | public TranscriptCacheBuilder(GenomeAssembly genomeAssembly, Source so...
    method CreateTranscriptCache (line 31) | public TranscriptCacheStaging CreateTranscriptCache(MutableTranscript[...
    method AssignUgaGenesToTranscripts (line 47) | private void AssignUgaGenesToTranscripts(IEnumerable<MutableTranscript...
    method PickGeneById (line 64) | private UgaGene PickGeneById(IReadOnlyList<UgaGene> genes, string geneId)

FILE: CacheUtils/TranscriptCache/TranscriptCacheStaging.cs
  class TranscriptCacheStaging (line 13) | public sealed class TranscriptCacheStaging : IStaging
    method TranscriptCacheStaging (line 17) | private TranscriptCacheStaging(TranscriptCacheData cacheData)
    method Write (line 22) | public void Write(Stream stream)
    method GetStaging (line 27) | public static TranscriptCacheStaging GetStaging(CacheHeader header,
    method GetUniqueData (line 39) | private static (IGene[] Genes, ITranscriptRegion[] TranscriptRegions, ...
    method AddIntervals (line 73) | private static void AddIntervals(ISet<IInterval> intervalSet, IInterva...
    method AddTranscriptRegions (line 79) | private static void AddTranscriptRegions(ISet<ITranscriptRegion> trans...
    method AddString (line 85) | private static void AddString(ISet<string> stringSet, string s)
    method GetUniqueStrings (line 91) | private static string[] GetUniqueStrings(ICollection<string> peptideSet)
    method GetUniqueIntervals (line 96) | private static IInterval[] GetUniqueIntervals(ICollection<IInterval> m...
    method GetUniqueTranscriptRegions (line 101) | private static ITranscriptRegion[] GetUniqueTranscriptRegions(ICollect...
    method GetUniqueGenes (line 106) | private static IGene[] GetUniqueGenes(ICollection<IGene> geneSet)

FILE: CacheUtils/TranscriptCache/TranscriptCacheUtilities.cs
  class TranscriptCacheUtilities (line 11) | public static class TranscriptCacheUtilities
    method GetTranscripts (line 13) | public static List<ITranscript> GetTranscripts(DataBundle bundle, Chro...
    method ToIntervalArrays (line 21) | public static IntervalArray<T>[] ToIntervalArrays<T>(this IEnumerable<...
    method ToIntervals (line 36) | private static Interval<T>[] ToIntervals<T>(this IEnumerable<T> items,...

FILE: CacheUtils/TranscriptCache/TranscriptCacheWriter.cs
  class TranscriptCacheWriter (line 18) | public sealed class TranscriptCacheWriter : IDisposable
    method TranscriptCacheWriter (line 25) | public TranscriptCacheWriter(Stream stream, CacheHeader header, bool l...
    method Dispose (line 33) | public void Dispose()
    method Write (line 42) | public void Write(TranscriptCacheData cacheData)
    method WriteIntervals (line 64) | private static void WriteIntervals<T>(IExtendedBinaryWriter writer, IR...
    method WriteItems (line 84) | internal static void WriteItems<T>(IExtendedBinaryWriter writer, IRead...
    method CreateIndex (line 102) | internal static Dictionary<T, int> CreateIndex<T>(IReadOnlyList<T> arr...

FILE: CacheUtils/TranscriptCache/TranscriptConversionExtensions.cs
  class TranscriptConversionExtensions (line 10) | public static class TranscriptConversionExtensions
    method ToTranscripts (line 12) | public static IEnumerable<ITranscript> ToTranscripts(this MutableTrans...
    method ToTranscript (line 19) | private static ITranscript ToTranscript(this MutableTranscript mt)
    method GetTranslation (line 34) | private static ITranslation GetTranslation(ICodingRegion oldCodingRegi...

FILE: CacheUtils/TranscriptCache/TranscriptRegionMerger.cs
  class TranscriptRegionMerger (line 11) | public static class TranscriptRegionMerger
    method GetTranscriptRegions (line 13) | public static ITranscriptRegion[] GetTranscriptRegions(IEnumerable<Mut...
    method AddCoords (line 34) | private static List<MutableTranscriptRegion> AddCoords(this List<Mutab...
    method GetExonCoords (line 48) | private static (int CdnaStart, int CdnaEnd) GetExonCoords(this IReadOn...
    method ToInterfaceArray (line 79) | private static ITranscriptRegion[] ToInterfaceArray(this IReadOnlyList...
    method CreateIntervals (line 91) | private static IdInterval[] CreateIntervals(IEnumerable<IInterval> int...
    method AddIds (line 108) | private static List<MutableTranscriptRegion> AddIds(this List<MutableT...
    method BinarySearch (line 130) | private static int BinarySearch(this IReadOnlyList<IdInterval> interva...
    method AddGaps (line 148) | private static List<MutableTranscriptRegion> AddGaps(this List<Mutable...
    method CalculateGapLength (line 166) | private static int CalculateGapLength(IInterval prevRegion, IInterval ...
    class IdInterval (line 168) | private sealed class IdInterval : IInterval, IComparable<IdInterval>
      method IdInterval (line 174) | public IdInterval(int start, int end, ushort id)
      method CompareTo (line 181) | public int CompareTo(IdInterval other)

FILE: CacheUtils/TranscriptCache/TranscriptRegionValidater.cs
  class TranscriptRegionValidater (line 11) | public static class TranscriptRegionValidater
    method Validate (line 13) | public static void Validate(string transcriptId, IEnumerable<MutableTr...
    method CheckGenomicCoordinateContiguity (line 32) | private static void CheckGenomicCoordinateContiguity(string transcript...
    method ValidateRegions (line 44) | private static void ValidateRegions(string transcriptId, IEnumerable<I...
    method DumpTranscriptRegions (line 58) | private static void DumpTranscriptRegions(IEnumerable<ITranscriptRegio...
    method DumpTranscriptRegion (line 64) | private static void DumpTranscriptRegion(ITranscriptRegion region) => ...
    method DumpCdnaMaps (line 66) | private static void DumpCdnaMaps(IEnumerable<MutableTranscriptRegion> ...
    method DumpCdnaMap (line 72) | private static void DumpCdnaMap(ITranscriptRegion cdnaMap) => Console....
    method DumpIntrons (line 74) | private static void DumpIntrons(IEnumerable<IInterval> introns)
    method DumpIntron (line 80) | private static void DumpIntron(IInterval intron) => Console.WriteLine(...
    method DumpExons (line 82) | private static void DumpExons(IEnumerable<MutableExon> exons)
    method DumpExon (line 88) | private static void DumpExon(IInterval exon) => Console.WriteLine($"{e...

FILE: CacheUtils/Utilities/AccessionUtilities.cs
  class AccessionUtilities (line 7) | internal static class AccessionUtilities
    method GetMaxVersion (line 9) | internal static (string Id, byte Version) GetMaxVersion(string origina...
    method GetAccessionNumber (line 15) | public static int GetAccessionNumber(string s)
    method GetRefSeqAccessionNumber (line 21) | private static int GetRefSeqAccessionNumber(string s)
    method GetEnsemblAccessionNumber (line 30) | private static int GetEnsemblAccessionNumber(string s)

FILE: CacheUtils/Utilities/HeaderUtilities.cs
  class HeaderUtilities (line 9) | public static class HeaderUtilities
    method GetHeader (line 11) | public static Header GetHeader(Source source, GenomeAssembly genomeAss...

FILE: CacheUtils/Utilities/RemoteFile.cs
  class RemoteFile (line 9) | public sealed class RemoteFile
    method RemoteFile (line 15) | static RemoteFile() => ServicePointManager.DefaultConnectionLimit = in...
    method RemoteFile (line 17) | public RemoteFile(string description, string url, bool addDate = true)
    method GetFilename (line 24) | internal static string GetFilename(string url, bool addDate)
    method Download (line 37) | public void Download()
    method SuccessfulDownload (line 48) | private bool SuccessfulDownload()

FILE: CacheUtils/Utilities/TaskExtensions.cs
  class TaskExtensions (line 10) | public static class TaskExtensions
    method Execute (line 12) | public static void Execute<T>(this IReadOnlyList<T> items, string desc...

FILE: Cloud/AmazonS3ClientWrapper.cs
  class AmazonS3ClientWrapper (line 8) | public sealed class AmazonS3ClientWrapper : IS3Client
    method AmazonS3ClientWrapper (line 12) | public AmazonS3ClientWrapper(AmazonS3Client s3Client) => _s3Client = s...
    method GetObjectAsync (line 14) | public Task<GetObjectResponse> GetObjectAsync(GetObjectRequest getRequ...
    method PutObjectAsync (line 16) | public Task<PutObjectResponse> PutObjectAsync(PutObjectRequest putRequ...

FILE: Cloud/Configuration.cs
  class Configuration (line 6) | public sealed class Configuration
    method Configuration (line 14) | public Configuration()

FILE: Cloud/LambdaUrlHelper.cs
  class LambdaUrlHelper (line 9) | public static class LambdaUrlHelper
    method GetBaseUrl (line 31) | public static string GetBaseUrl()
    method GetManifestBaseUrl (line 38) | public static string GetManifestBaseUrl() => GetBaseUrl() + Config.Man...
    method GetCacheFolder (line 40) | public static string GetCacheFolder() => GetBaseUrl()     + S3CacheFol...
    method GetUgaUrl (line 41) | public static string GetUgaUrl() => GetCacheFolder() + UgaFileName;
    method GetRefPrefix (line 42) | public static string GetRefPrefix() => GetBaseUrl()     + S3RefPrefix;
    method GetRefUrl (line 44) | public static string GetRefUrl(GenomeAssembly genomeAssembly) =>

FILE: Cloud/Messages/Annotation/AnnotationConfig.cs
  class AnnotationConfig (line 5) | public sealed class AnnotationConfig

FILE: Cloud/Messages/Annotation/AnnotationPosition.cs
  type AnnotationPosition (line 3) | public struct AnnotationPosition
    method AnnotationPosition (line 8) | public AnnotationPosition(string chromosome, int position)

FILE: Cloud/Messages/Annotation/AnnotationRange.cs
  class AnnotationRange (line 7) | public sealed class AnnotationRange
    method AnnotationRange (line 12) | public AnnotationRange(AnnotationPosition start, AnnotationPosition? end)
    method ToGenomicRange (line 18) | public GenomicRange ToGenomicRange(Dictionary<string, Chromosome> refN...

FILE: Cloud/Messages/Annotation/AnnotationResult.cs
  class AnnotationResult (line 6) | public sealed class AnnotationResult

FILE: Cloud/Messages/Custom/CustomConfig.cs
  class CustomConfig (line 5) | public sealed class CustomConfig

FILE: Cloud/Messages/Custom/CustomResult.cs
  class CustomResult (line 5) | public sealed class CustomResult

FILE: Cloud/Messages/FileList.cs
  class FileList (line 5) | public sealed class FileList

FILE: Cloud/Messages/Gene/GeneConfig.cs
  class GeneConfig (line 6) | public sealed class GeneConfig
    method Validate (line 14) | public void Validate()

FILE: Cloud/Messages/JwtFields.cs
  class JwtFields (line 3) | public class JwtFields

FILE: Cloud/Messages/Nirvana/NirvanaConfig.cs
  class NirvanaConfig (line 7) | public sealed class NirvanaConfig
    method CheckRequiredFieldsNotNull (line 24) | internal void CheckRequiredFieldsNotNull()
    method Validate (line 42) | public void Validate()

FILE: Cloud/Messages/Nirvana/NirvanaResult.cs
  class NirvanaResult (line 3) | public sealed class NirvanaResult

FILE: Cloud/Messages/S3Path.cs
  class S3Path (line 13) | public sealed class S3Path
    method Validate (line 22) | public void Validate(bool isDirectory)
    method CheckS3Region (line 33) | private void CheckS3Region()
    method ValidateCredentials (line 40) | private void ValidateCredentials(IS3Client s3Client, bool isDirectory)
    method ValidatePathFormat (line 84) | internal static void ValidatePathFormat(string path, bool isDirectory)
    method FormatPath (line 93) | public static string FormatPath(string path) => path.TrimStart('/');
    method GetS3Client (line 95) | public IS3Client GetS3Client(TimeSpan timeOut) => new AmazonS3ClientWr...

FILE: Cloud/Messages/SaUrls.cs
  class SaUrls (line 10) | public sealed class SaUrls
    method Validate (line 20) | public void Validate()
    method GetSaType (line 38) | internal CustomSaType GetSaType()
    method ToString (line 58) | public override string ToString()
  type CustomSaType (line 74) | public enum CustomSaType

FILE: Cloud/Messages/Single/SingleConfig.cs
  class SingleConfig (line 5) | public sealed class SingleConfig

FILE: Cloud/Messages/Single/SingleVariant.cs
  class SingleVariant (line 6) | public sealed class SingleVariant
    method Validate (line 23) | public void Validate()
    method GetVcfFields (line 44) | public string[] GetVcfFields()
    method GetStringFromNullableCollection (line 70) | private static string GetStringFromNullableCollection(string[] values,...

FILE: Cloud/Messages/StrValidation/ValidationConfig.cs
  class ValidationConfig (line 5) | public sealed class ValidationConfig
    method Validate (line 13) | public void Validate() => HttpUtilities.ValidateUrl(customStrUrl);

FILE: Cloud/Messages/StrValidation/ValidationResult.cs
  class ValidationResult (line 3) | public class ValidationResult

FILE: Cloud/Notifications/SNS.cs
  class SNS (line 6) | public static class SNS
    method SendMessage (line 8) | public static void SendMessage(string snsTopicArn, string snsMessage)
    method CreateMessage (line 24) | public static string CreateMessage(string message, string status, stri...

FILE: Cloud/RedactionUtilities.cs
  class RedactionUtilities (line 5) | public static class RedactionUtilities
    method Redact (line 13) | public static string Redact(this string s)
    method Mask (line 29) | private static char[] Mask(this char[] charArray, MatchCollection matc...

FILE: Cloud/Utilities/AwsExceptionUtilities.cs
  class AwsExceptionUtilities (line 8) | public static class AwsExceptionUtilities
    method TryConvertUserException (line 10) | public static Exception TryConvertUserException(Exception exception, S...

FILE: Cloud/Utilities/JsonUtilities.cs
  class JsonUtilities (line 7) | public static class JsonUtilities
    method Stringify (line 11) | public static string Stringify(object obj) => Encoding.UTF8.GetString(...
    method Serialize (line 13) | public static MemoryStream Serialize(object obj)
    method Deserialize (line 21) | public static T Deserialize<T>(MemoryStream memoryStream) => JsonSeria...

FILE: Cloud/Utilities/LambdaUtilities.cs
  class LambdaUtilities (line 8) | public static class LambdaUtilities
    method GarbageCollect (line 13) | public static void GarbageCollect()
    method GetEnvironmentVariable (line 19) | public static string GetEnvironmentVariable(string key)
    method DeleteTempOutput (line 26) | public static void DeleteTempOutput()
    method GetManifestUrl (line 33) | public static string GetManifestUrl(string version, GenomeAssembly gen...
    method GetCachePathPrefix (line 50) | public static string GetCachePathPrefix(GenomeAssembly genomeAssembly)

FILE: Cloud/Utilities/LogUtilities.cs
  class LogUtilities (line 10) | public static class LogUtilities
    method LogLambdaInfo (line 12) | public static void LogLambdaInfo(ILambdaContext context, string versio...
    method LogObject (line 15) | public static void LogObject<T>(string title, T config)
    method Log (line 32) | public static void Log(IEnumerable<string> environmentVariables)
    method UpdateLogger (line 47) | public static void UpdateLogger(ILambdaLogger logger, StringBuilder sb)

FILE: Cloud/Utilities/UploadUtilities.cs
  class UploadUtilities (line 10) | public static class UploadUtilities
    method DecryptUpload (line 12) | public static void DecryptUpload(this IS3Client s3Client, string bucke...
    method TryDecryptUpload (line 24) | internal static bool TryDecryptUpload(this IS3Client s3Client, string ...

FILE: CommandLine/Builders/ConsoleAppBuilder.cs
  class ConsoleAppBuilder (line 11) | public sealed class ConsoleAppBuilder : IConsoleAppBuilder
    method ConsoleAppBuilder (line 16) | public ConsoleAppBuilder(string[] args, OptionSet ops)
    method AddAdditionalOptions (line 28) | private void AddAdditionalOptions()
    method Parse (line 34) | public IConsoleAppValidator Parse()
    method UseVersionProvider (line 61) | public IConsoleAppBuilder UseVersionProvider(IVersionProvider versionP...
  class ConsoleAppValidator (line 68) | public sealed class ConsoleAppValidator : IConsoleAppValidator
    method ConsoleAppValidator (line 73) | public ConsoleAppValidator(IConsoleAppBuilderData data)
    method DisableOutput (line 79) | public IConsoleAppValidator DisableOutput(bool condition = true)
    method ShowBanner (line 85) | public IConsoleAppBanner ShowBanner(string authors)
    method SkipBanner (line 92) | public IConsoleAppBanner SkipBanner() => new ConsoleAppBanner(Data);
  class ConsoleAppBanner (line 95) | public sealed class ConsoleAppBanner : IConsoleAppBanner
    method ConsoleAppBanner (line 99) | public ConsoleAppBanner(IConsoleAppBuilderData data) => _data = data;
    method ShowHelpMenu (line 101) | public IConsoleAppHelpMenu ShowHelpMenu(string description, string com...
  class ConsoleAppHelpMenu (line 114) | public sealed class ConsoleAppHelpMenu : IConsoleAppHelpMenu
    method ConsoleAppHelpMenu (line 118) | public ConsoleAppHelpMenu(IConsoleAppBuilderData data) => _data = data;
    method ShowErrors (line 120) | public IConsoleAppErrors ShowErrors()
    method PrintErrors (line 133) | private void PrintErrors()
  class ConsoleAppErrors (line 146) | public sealed class ConsoleAppErrors : IConsoleAppErrors
    method ConsoleAppErrors (line 151) | public ConsoleAppErrors(IConsoleAppBuilderData data) => _data = data;
    method Execute (line 153) | public ExitCodes Execute(Func<ExitCodes> executeMethod)
    method ShowPerformanceData (line 173) | private void ShowPerformanceData(Benchmark benchmark)
  class ConsoleAppBuilderData (line 186) | public sealed class ConsoleAppBuilderData : IConsoleAppBuilderData
    method AddError (line 198) | public void AddError(string errorMessage, ExitCodes exitCode)

FILE: CommandLine/Builders/IConsoleAppBuilder.cs
  type IConsoleAppBuilder (line 12) | public interface IConsoleAppBuilder
    method UseVersionProvider (line 15) | IConsoleAppBuilder UseVersionProvider(IVersionProvider versionProvider);
    method Parse (line 16) | IConsoleAppValidator Parse();
  type IConsoleAppValidator (line 19) | public interface IConsoleAppValidator
    method DisableOutput (line 21) | IConsoleAppValidator DisableOutput(bool condition = true);
    method ShowBanner (line 22) | IConsoleAppBanner ShowBanner(string authors);
    method SkipBanner (line 23) | IConsoleAppBanner SkipBanner();
  type IConsoleAppBanner (line 28) | public interface IConsoleAppBanner
    method ShowHelpMenu (line 30) | IConsoleAppHelpMenu ShowHelpMenu(string description, string commandLin...
  type IConsoleAppHelpMenu (line 33) | public interface IConsoleAppHelpMenu
    method ShowErrors (line 35) | IConsoleAppErrors ShowErrors();
  type IConsoleAppErrors (line 38) | public interface IConsoleAppErrors
    method Execute (line 40) | ExitCodes Execute(Func<ExitCodes> executeMethod);
  type IConsoleAppBuilderData (line 43) | public interface IConsoleAppBuilderData
    method AddError (line 54) | void AddError(string errorMessage, ExitCodes exitCode);

FILE: CommandLine/Builders/ITopLevelAppBuilder.cs
  type ITopLevelAppBuilder (line 7) | public interface ITopLevelAppBuilder
    method Parse (line 10) | ITopLevelAppValidator Parse();
  type ITopLevelAppValidator (line 13) | public interface ITopLevelAppValidator
    method ShowBanner (line 15) | ITopLevelAppBanner ShowBanner(string authors);
  type ITopLevelAppBanner (line 19) | public interface ITopLevelAppBanner
    method ShowHelpMenu (line 21) | ITopLevelAppHelpMenu ShowHelpMenu(string description);
  type ITopLevelAppHelpMenu (line 24) | public interface ITopLevelAppHelpMenu
    method ShowErrors (line 26) | ITopLevelAppErrors ShowErrors();
  type ITopLevelAppErrors (line 29) | public interface ITopLevelAppErrors
    method Execute (line 31) | ExitCodes Execute();
  type ITopLevelAppBuilderData (line 34) | public interface ITopLevelAppBuilderData
    method AddError (line 47) | void AddError(string errorMessage, ExitCodes exitCode);

FILE: CommandLine/Builders/TopLevelAppBuilder.cs
  class TopLevelAppBuilder (line 9) | public sealed class TopLevelAppBuilder : ITopLevelAppBuilder
    method TopLevelAppBuilder (line 13) | public TopLevelAppBuilder(string[] args, Dictionary<string, TopLevelOp...
    method Parse (line 18) | public ITopLevelAppValidator Parse()
    method GetExecuteMethod (line 32) | private Func<string, string[], ExitCodes> GetExecuteMethod(string comm...
  class TopLevelAppValidator (line 44) | public sealed class TopLevelAppValidator : ITopLevelAppValidator
    method TopLevelAppValidator (line 48) | public TopLevelAppValidator(ITopLevelAppBuilderData data) => Data = data;
    method ShowBanner (line 50) | public ITopLevelAppBanner ShowBanner(string authors)
  class TopLevelAppBanner (line 57) | public sealed class TopLevelAppBanner : ITopLevelAppBanner
    method TopLevelAppBanner (line 61) | public TopLevelAppBanner(ITopLevelAppBuilderData data) => _data = data;
    method ShowHelpMenu (line 63) | public ITopLevelAppHelpMenu ShowHelpMenu(string description)
    method DisplayCommands (line 82) | private static void DisplayCommands(Dictionary<string, TopLevelOption>...
    method GetMaxCommandLen (line 104) | private static int GetMaxCommandLen(IEnumerable<string> ops)
  class TopLevelAppHelpMenu (line 110) | public sealed class TopLevelAppHelpMenu : ITopLevelAppHelpMenu
    method TopLevelAppHelpMenu (line 114) | public TopLevelAppHelpMenu(ITopLevelAppBuilderData data) => _data = data;
    method ShowErrors (line 116) | public ITopLevelAppErrors ShowErrors()
    method PrintErrors (line 128) | private void PrintErrors()
  class TopLevelAppErrors (line 141) | public sealed class TopLevelAppErrors : ITopLevelAppErrors
    method TopLevelAppErrors (line 146) | public TopLevelAppErrors(ITopLevelAppBuilderData data) => _data = data;
    method Execute (line 148) | public ExitCodes Execute()
  class TopLevelAppBuilderData (line 168) | public sealed class TopLevelAppBuilderData : ITopLevelAppBuilderData
    method TopLevelAppBuilderData (line 181) | public TopLevelAppBuilderData(string[] arguments, Dictionary<string, T...
    method AddError (line 188) | public void AddError(string errorMessage, ExitCodes exitCode)

FILE: CommandLine/Builders/TopLevelOption.cs
  class TopLevelOption (line 6) | public sealed class TopLevelOption
    method TopLevelOption (line 11) | public TopLevelOption(string description, Func<string, string[], ExitC...

FILE: CommandLine/Builders/ValidationExtensions.cs
  class ValidationExtensions (line 9) | public static class ValidationExtensions
    method CheckEachFilenameExists (line 11) | public static IConsoleAppValidator CheckEachFilenameExists(this IConso...
    method CheckInputFilenameExists (line 21) | public static IConsoleAppValidator CheckInputFilenameExists(this ICons...
    method CheckUrlExist (line 40) | private static bool CheckUrlExist(string url)
    method CheckOutputFilenameSuffix (line 54) | public static IConsoleAppValidator CheckOutputFilenameSuffix(this ICon...
    method CheckDirectoryExists (line 67) | public static IConsoleAppValidator CheckDirectoryExists(this IConsoleA...
    method HasRequiredParameter (line 86) | public static IConsoleAppValidator HasRequiredParameter<T>(this IConso...
    method HasRequiredDate (line 100) | public static IConsoleAppValidator HasRequiredDate(this IConsoleAppVal...

FILE: CommandLine/NDesk.Options/Options.cs
  class OptionValueCollection (line 47) | public sealed class OptionValueCollection
    method OptionValueCollection (line 52) | internal OptionValueCollection(OptionContext c)
    method Add (line 58) | public void Add(string item) { _values.Add(item); }
    method Clear (line 59) | public void Clear() { _values.Clear(); }
    method AssertValid (line 69) | private void AssertValid(int index)
  class OptionContext (line 91) | public sealed class OptionContext
    method OptionContext (line 93) | public OptionContext()
  type OptionValueType (line 107) | public enum OptionValueType
  class Option (line 114) | public abstract class Option
    method Option (line 116) | protected Option(string prototype, string description, int maxValueCount)
    method Parse (line 153) | protected static T Parse<T>(string value, OptionContext c)
    method ParsePrototype (line 174) | private OptionValueType ParsePrototype()
    method GetOptionValueType (line 216) | private static OptionValueType GetOptionValueType(char type) =>
    method AddSeparators (line 219) | private static void AddSeparators(string name, int end, ICollection<st...
    method Invoke (line 253) | public void Invoke(OptionContext c)
    method OnParseComplete (line 261) | protected abstract void OnParseComplete(OptionContext c);
  class OptionException (line 264) | public sealed class OptionException : Exception
    method OptionException (line 266) | public OptionException(string message)
    method OptionException (line 271) | public OptionException(string message, Exception innerException)
  class OptionSet (line 277) | public sealed class OptionSet : KeyedCollection<string, Option>
    method GetKeyForItem (line 279) | protected override string GetKeyForItem(Option item)
    method InsertItem (line 290) | protected override void InsertItem(int index, Option item)
    method AddImpl (line 296) | private void AddImpl(Option option)
    method Add (line 318) | public new void Add(Option option)
    class ActionOption (line 323) | private sealed class ActionOption : Option
      method ActionOption (line 327) | public ActionOption(string prototype, string description, int count,...
      method OnParseComplete (line 333) | protected override void OnParseComplete(OptionContext c)
      method ActionOption (line 352) | public ActionOption(string prototype, string description, Action<T> ...
      method OnParseComplete (line 358) | protected override void OnParseComplete(OptionContext c)
    method Add (line 339) | public void Add(string prototype, string description, Action<string> a...
    class ActionOption (line 348) | private sealed class ActionOption<T> : Option
      method ActionOption (line 327) | public ActionOption(string prototype, string description, int count,...
      method OnParseComplete (line 333) | protected override void OnParseComplete(OptionContext c)
      method ActionOption (line 352) | public ActionOption(string prototype, string description, Action<T> ...
      method OnParseComplete (line 358) | protected override void OnParseComplete(OptionContext c)
    method Add (line 364) | public void Add<T>(string prototype, string description, Action<T> act...
    method CreateOptionContext (line 369) | private static OptionContext CreateOptionContext()
    method Parse (line 374) | public List<string> Parse(IEnumerable<string> arguments)
    method Unprocessed (line 401) | private static void Unprocessed(ICollection<string> extra, Option def,...
    method GetOptionParts (line 416) | private bool GetOptionParts(string argument, out string flag, out stri...
    method Parse (line 438) | private bool Parse(string argument, OptionContext c)
    method ParseValue (line 469) | private static void ParseValue(string option, OptionContext c)
    method ParseBool (line 487) | private bool ParseBool(string option, string n, OptionContext c)
    method ParseBundledValue (line 503) | private bool ParseBundledValue(string f, string n, OptionContext c)
    method Invoke (line 539) | private static void Invoke(OptionContext c, string name, string value,...
    method WriteOptionDescriptions (line 549) | public void WriteOptionDescriptions(TextWriter o)
    method WriteOptionPrototype (line 577) | private static bool WriteOptionPrototype(TextWriter o, Option p, ref i...
    method GetNextOptionIndex (line 626) | private static int GetNextOptionIndex(IReadOnlyList<string> names, int i)
    method Write (line 635) | private static void Write(TextWriter o, ref int n, string s)
    method GetArgumentName (line 641) | private static string GetArgumentName(int index, int maxIndex, string ...
    method GetDescription (line 663) | private static string GetDescription(string description)
    method ParseDescription (line 678) | private static int ParseDescription(string description, int position, ...
    method GetLines (line 722) | private static IEnumerable<string> GetLines(string description)
    method IsEolChar (line 750) | private static bool IsEolChar(char c)
    method GetLineEnd (line 755) | private static int GetLineEnd(int start, int length, string description)

FILE: CommandLine/Utilities/Benchmark.cs
  class Benchmark (line 5) | public sealed class Benchmark
    method Benchmark (line 9) | public Benchmark() => Reset();
    method GetElapsedTime (line 11) | public TimeSpan GetElapsedTime()
    method ToHumanReadable (line 17) | public static string ToHumanReadable(TimeSpan span)
    method GetElapsedIterationsPerSecond (line 24) | public static double GetElapsedIterationsPerSecond(TimeSpan span, int ...
    method Reset (line 26) | public void Reset() => _startTime = DateTime.Now;

FILE: CommandLine/Utilities/CommandLineUtilities.cs
  class CommandLineUtilities (line 7) | public static class CommandLineUtilities
    method CommandLineUtilities (line 14) | static CommandLineUtilities()
    method GetCopyright (line 27) | private static string GetCopyright(Assembly entryAssembly)
    method GetVersion (line 33) | public static string GetVersion(Assembly entryAssembly)
    method GetInformationalVersion (line 39) | private static string GetInformationalVersion(Assembly entryAssembly)
    method GetTitle (line 45) | private static string GetTitle(Assembly entryAssembly)
    method GetAssemblyAttributes (line 51) | private static T GetAssemblyAttributes<T>(Assembly entryAssembly)
    method DisplayBanner (line 61) | public static void DisplayBanner(string author)

FILE: CommandLine/Utilities/Help.cs
  class Help (line 6) | public static class Help
    method Show (line 8) | public static void Show(OptionSet ops, string commonOptions, string de...

FILE: CommandLine/Utilities/MemoryUtilities.cs
  class MemoryUtilities (line 5) | public static class MemoryUtilities
    method GetPeakMemoryUsage (line 16) | public static long GetPeakMemoryUsage()
    method ToHumanReadable (line 24) | public static string ToHumanReadable(long numBytes)

FILE: CommandLine/Utilities/OutputHelper.cs
  class OutputHelper (line 6) | public static class OutputHelper
    method WriteLabel (line 8) | public static void WriteLabel(string label)
    method GetExecutableName (line 15) | public static string GetExecutableName()

FILE: CommandLine/VersionProviders/DefaultVersionProvider.cs
  class DefaultVersionProvider (line 5) | public sealed class DefaultVersionProvider : IVersionProvider

FILE: CommandLine/VersionProviders/IVersionProvider.cs
  type IVersionProvider (line 3) | public interface IVersionProvider

FILE: Compression/Algorithms/ICompressionAlgorithm.cs
  type ICompressionAlgorithm (line 3) | public interface ICompressionAlgorithm
    method Compress (line 5) | int Compress(byte[] source, int srcLength, byte[] destination, int des...
    method Decompress (line 6) | int Decompress(byte[] source, int srcLength, byte[] destination, int d...
    method GetDecompressedLength (line 7) | int GetDecompressedLength(byte[] source, int srcLength);
    method GetCompressedBufferBounds (line 8) | int GetCompressedBufferBounds(int srcLength);

FILE: Compression/Algorithms/Zlib.cs
  class Zlib (line 7) | public sealed class Zlib : ICompressionAlgorithm
    method Zlib (line 11) | public Zlib(int compressionLevel = 1)
    method Compress (line 17) | public int Compress(byte[] source, int srcLength, byte[] destination, ...
    method Decompress (line 27) | public int Decompress(byte[] source, int srcLength, byte[] destination...
    method GetDecompressedLength (line 37) | public int GetDecompressedLength(byte[] source, int srcLength)
    method GetCompressedBufferBounds (line 43) | public int GetCompressedBufferBounds(int srcLength) => (int)(srcLength...
    class SafeNativeMethods (line 45) | private static class SafeNativeMethods
      method bgzf_decompress (line 47) | [DllImport("BlockCompression", CallingConvention = CallingConvention...
      method bgzf_compress (line 50) | [DllImport("BlockCompression", CallingConvention = CallingConvention...

FILE: Compression/Algorithms/Zstandard.cs
  class Zstandard (line 7) | public sealed class Zstandard : ICompressionAlgorithm
    method Zstandard (line 11) | public Zstandard(int compressionLevel = 17)
    method Compress (line 17) | public int Compress(byte[] source, int srcLength, byte[] destination, ...
    method Decompress (line 27) | public int Decompress(byte[] source, int srcLength, byte[] destination...
    method GetDecompressedLength (line 37) | public int GetDecompressedLength(byte[] source, int srcLength) => (int...
    method GetCompressedBufferBounds (line 40) | public int GetCompressedBufferBounds(int srcLength) => srcLength + 32;
    class SafeNativeMethods (line 42) | private static class SafeNativeMethods
      method ZSTD_compress (line 44) | [DllImport("BlockCompression", CallingConvention = CallingConvention...
      method ZSTD_decompress (line 47) | [DllImport("BlockCompression", CallingConvention = CallingConvention...
      method ZSTD_getDecompressedSize (line 50) | [DllImport("BlockCompression", CallingConvention = CallingConvention...

FILE: Compression/DataStructures/Block.cs
  class Block (line 9) | public sealed class Block
    method Block (line 27) | public Block(ICompressionAlgorithm compressionAlgorithm, int size = De...
    method CopyTo (line 39) | public int CopyTo(byte[] array, int offset, int count)
    method CopyFrom (line 50) | public int CopyFrom(byte[] array, int offset, int count)
    method Write (line 61) | public void Write(Stream stream)
    method WriteEof (line 83) | public void WriteEof(Stream stream)
    method Read (line 90) | public int Read(Stream stream)
    method ReadCompressedBlock (line 106) | private int ReadCompressedBlock(Stream stream)
    method ReadUncompressedBlock (line 123) | private int ReadUncompressedBlock(Stream stream)

FILE: Compression/FileHandling/BgzBlockReader.cs
  class BgzBlockReader (line 7) | public sealed class BgzBlockReader:IDisposable
    method BgzBlockReader (line 15) | public BgzBlockReader(Stream stream, bool leaveStreamOpen = false)
    method ReadCompressedBlock (line 23) | public int ReadCompressedBlock(byte[] buffer)
    method Dispose (line 52) | public void Dispose()

FILE: Compression/FileHandling/BgzfBlock.cs
  class BgzfBlock (line 9) | public sealed class BgzfBlock
    method Read (line 16) | public string Read(Stream stream)

FILE: Compression/FileHandling/BgzipTextReader.cs
  class BgzipTextReader (line 8) | public sealed class BgzipTextReader : IDisposable
    method BgzipTextReader (line 15) | public BgzipTextReader(BlockGZipStream stream, bool leaveOpen = false)
    method ReadLine (line 35) | public string ReadLine() => _reader.ReadLine();
    method Dispose (line 37) | public void Dispose()

FILE: Compression/FileHandling/BgzipTextWriter.cs
  class BgzipTextWriter (line 8) | public sealed class BgzipTextWriter : StreamWriter, IDisposable
    method BgzipTextWriter (line 24) | public BgzipTextWriter(BlockGZipStream stream) : base(stream, Utf8With...
    method Flush (line 33) | public override void Flush()
    method WriteLine (line 42) | public override void WriteLine() => Write("\n");
    method WriteLine (line 44) | public override void WriteLine(string value) => Write(value + "\n");
    method Write (line 46) | public override void Write(string value)
    method Write (line 54) | public override void Write(StringBuilder sb)
    method WriteBytes (line 70) | private void WriteBytes(byte[] lineBytes, int length)
    method Dispose (line 100) | public new void Dispose()

FILE: Compression/FileHandling/BlockGZipStream.cs
  class BlockGZipStream (line 20) | public sealed class BlockGZipStream : Stream
    class BlockGZipFormatCommon (line 36) | public static class BlockGZipFormatCommon
    method Seek (line 59) | public override long Seek(long offset, SeekOrigin origin) => throw new...
    method SetLength (line 61) | public override void SetLength(long value) => throw new NotSupportedEx...
    method Flush (line 63) | public override void Flush() => _stream.Flush();
    method Dispose (line 65) | protected override void Dispose(bool disposing)
    method BlockGZipStream (line 95) | public BlockGZipStream(Stream stream, CompressionMode compressionMode,...
    method Flush (line 114) | private void Flush(int uncompressedSize)
    method HasValidHeader (line 123) | public static bool HasValidHeader(int numHeaderBytes, IReadOnlyList<by...
    method ReadBlock (line 135) | private void ReadBlock()
    method Read (line 178) | public override int Read(byte[] buffer, int offset, int count)
    method Write (line 216) | public override void Write(byte[] buffer, int offset, int count)
    method CloseBlock (line 237) | public void CloseBlock() => Flush(_blockOffset);
    method SeekVirtualFilePointer (line 239) | private void SeekVirtualFilePointer(ulong virtualPosition)
    method GetCompressedOffset (line 255) | private static long GetCompressedOffset(ulong virtualPosition)
    method GetUncompressedOffset (line 263) | private static int GetUncompressedOffset(ulong virtualPosition)

FILE: Compression/FileHandling/BlockHeader.cs
  class BlockHeader (line 6) | public sealed class BlockHeader
    method BlockHeader (line 18) | public BlockHeader() => _header = new byte[HeaderSize];
    method GetInt (line 20) | private int GetInt(int offset) => _header[offset] | _header[offset + 1...
    method Read (line 23) | public void Read(Stream stream)
    method SetInt (line 43) | private void SetInt(int value, int offset)
    method Write (line 51) | public void Write(Stream stream)

FILE: Compression/FileHandling/BlockStream.cs
  class BlockStream (line 11) | public sealed class BlockStream : Stream
    method Seek (line 30) | public override long Seek(long offset, SeekOrigin origin) => throw new...
    method SetLength (line 31) | public override void SetLength(long value)                => throw new...
    method Flush (line 39) | public override void Flush()
    method Dispose (line 44) | protected override void Dispose(bool disposing)
    method BlockStream (line 82) | public BlockStream(ICompressionAlgorithm compressionAlgorithm, Stream ...
    method WriteHeader (line 97) | public void WriteHeader(Action<BinaryWriter> headerWrite)
    method Read (line 103) | public override int Read(byte[] buffer, int offset, int count)
    method ValidateParameters (line 135) | private void ValidateParameters(byte[] array, int offset, int count)
    method Write (line 143) | public override void Write(byte[] buffer, int offset, int count)
    method GetBlockPosition (line 161) | public (long FileOffset, int InternalOffset) GetBlockPosition() => (_s...
    method SetBlockPosition (line 163) | public void SetBlockPosition(long fileOffset, int internalOffset = 0)

FILE: Compression/Utilities/BlockExtensions.cs
  class BlockExtensions (line 8) | public static class BlockExtensions
    method ReadCompressedByteArray (line 12) | public static byte[] ReadCompressedByteArray(this BinaryReader reader,...
    method WriteCompressedByteArray (line 27) | public static void WriteCompressedByteArray(this BinaryWriter writer, ...

FILE: Compression/Utilities/GZipUtilities.cs
  class GZipUtilities (line 11) | public static class GZipUtilities
    type CompressionAlgorithm (line 15) | private enum CompressionAlgorithm
    method GetAppropriateStreamReader (line 22) | public static StreamReader GetAppropriateStreamReader(string filePath)...
    method GetStreamWriter (line 23) | public static StreamWriter GetStreamWriter(string filePath) => new Str...
    method GetWriteStream (line 24) | private static Stream GetWriteStream(string filePath) => new BlockGZip...
    method GetAppropriateStream (line 26) | private static Stream GetAppropriateStream(Stream stream, CompressionA...
    method GetAppropriateStream (line 49) | public static Stream GetAppropriateStream(Stream stream)
    method GetAppropriateReadStream (line 58) | public static Stream GetAppropriateReadStream(string filePath)
    method GetHeader (line 72) | private static byte[] GetHeader(Stream stream)
    method IdentifyCompressionAlgorithm (line 95) | private static CompressionAlgorithm IdentifyCompressionAlgorithm(byte[...

FILE: Compression/Utilities/LibraryUtilities.cs
  class LibraryUtilities (line 8) | public static class LibraryUtilities
    method CheckLibrary (line 10) | public static void CheckLibrary()
    class SafeNativeMethods (line 26) | private static class SafeNativeMethods
      method get_library_id (line 28) | [DllImport("BlockCompression", CallingConvention = CallingConvention...

FILE: CustomAnnotationLambda/CustomAnnotationLambda.cs
  class CustomAnnotationLambda (line 22) | public sealed class CustomAnnotationLambda
    method Run (line 26) | public CustomResult Run(CustomConfig config, ILambdaContext context)
    method IsGeneAnnotationTsv (line 65) | private static bool IsGeneAnnotationTsv(string tsvUrl)
    method GetSuccessResult (line 78) | public static CustomResult GetSuccessResult(CustomConfig customSaConfi...
    method HandleException (line 97) | private static CustomResult HandleException(StringBuilder runLog, Cust...

FILE: CustomAnnotationLambda/CustomConfigExtensions.cs
  class CustomConfigExtensions (line 8) | public static class CustomConfigExtensions
    method CheckRequiredFieldsNotNull (line 10) | public static void CheckRequiredFieldsNotNull(this CustomConfig config)
    method CheckResourcesExist (line 25) | public static void CheckResourcesExist(this CustomConfig config)

FILE: CustomAnnotationLambda/GeneAnnotationCreator.cs
  class GeneAnnotationCreator (line 16) | public static class GeneAnnotationCreator
    method Create (line 19) | public static CustomResult Create(CustomConfig config, string inputFil...
    method GetGeneAnnotationsParserFromCustomTsvStream (line 95) | private static GeneAnnotationsParser GetGeneAnnotationsParserFromCusto...

FILE: CustomAnnotationLambda/VariantAnnotationCreator.cs
  class VariantAnnotationCreator (line 19) | public static class VariantAnnotationCreator
    method Create (line 21) | public static CustomResult Create(CustomConfig config, string inputFil...
    method GetVariantAnnotationsParserFromCustomTsvStream (line 139) | private static VariantAnnotationsParser GetVariantAnnotationsParserFro...

FILE: CustomStrValidationLambda/CustomStrValidationLambda.cs
  class CustomStrValidationLambda (line 21) | public class CustomStrValidationLambda
    method Run (line 23) | public ValidationResult Run(ValidationConfig config, ILambdaContext co...
    method TryLoadStrFile (line 53) | private static void TryLoadStrFile(Stream stream, GenomeAssembly genom...
    method HandleException (line 66) | private static ValidationResult HandleException(string id, Exception e...
    method GetSuccessOutput (line 83) | private static ValidationResult GetSuccessOutput(string id) =>

FILE: Downloader/AnnotationRepository.cs
  class AnnotationRepository (line 8) | public static class AnnotationRepository
    method DownloadMetadata (line 10) | public static void DownloadMetadata(IClient client, List<RemoteFile> f...
    method DownloadFiles (line 13) | public static void DownloadFiles(IClient client, List<RemoteFile> file...
    method Retry (line 16) | private static void Retry(RemoteFile file, Func<RemoteFile, bool> clie...

FILE: Downloader/Client.cs
  class Client (line 11) | public sealed class Client : IClient
    method Client (line 15) | public Client(string hostName)
    method DownloadLines (line 29) | public List<string> DownloadLines(string remotePath)
    method SetMetadata (line 53) | public bool SetMetadata(RemoteFile file)
    method DownloadFile (line 79) | public bool DownloadFile(RemoteFile file)

FILE: Downloader/Configuration.cs
  class Configuration (line 10) | public static class Configuration
    method Load (line 12) | public static (string HostName, string CacheDir, string ReferencesDir,...

FILE: Downloader/DownloaderMain.cs
  class DownloaderMain (line 16) | public static class DownloaderMain
    method ProgramExecution (line 23) | private static ExitCodes ProgramExecution()
    method Main (line 77) | public static int Main(string[] args)

FILE: Downloader/FileExtensions/CacheFileExtensions.cs
  class CacheFileExtensions (line 8) | public static class CacheFileExtensions
    method AddCacheFiles (line 10) | public static List<RemoteFile> AddCacheFiles(this List<RemoteFile> files,
    method AddCache (line 23) | private static void AddCache(this ICollection<RemoteFile> files, Genom...

FILE: Downloader/FileExtensions/ReferencesFileExtensions.cs
  class ReferencesFileExtensions (line 8) | public static class ReferencesFileExtensions
    method AddReferenceFiles (line 10) | public static List<RemoteFile> AddReferenceFiles(this List<RemoteFile>...
    method GetFilename (line 25) | public static string GetFilename(GenomeAssembly genomeAssembly) => $"H...

FILE: Downloader/FileExtensions/SupplementaryAnnotationFileExtensions.cs
  class SupplementaryAnnotationFileExtensions (line 7) | public static class SupplementaryAnnotationFileExtensions
    method SupplementaryAnnotationFileExtensions (line 11) | static SupplementaryAnnotationFileExtensions()
    method AddSupplementaryAnnotationFiles (line 19) | public static void AddSupplementaryAnnotationFiles(this List<RemoteFil...
    method AddDataSources (line 28) | private static void AddDataSources(this ICollection<RemoteFile> files,...
    method AddFile (line 38) | private static void AddFile(this ICollection<RemoteFile> files, Genome...

FILE: Downloader/IClient.cs
  type IClient (line 8) | public interface IClient
    method DownloadLines (line 10) | List<string> DownloadLines(string remotePath);
    method SetMetadata (line 11) | bool SetMetadata(RemoteFile file);
    method DownloadFile (line 12) | bool DownloadFile(RemoteFile file);

FILE: Downloader/Manifest.cs
  class Manifest (line 7) | public static class Manifest
    method GetRemotePaths (line 9) | public static Dictionary<GenomeAssembly, List<string>> GetRemotePaths(...
    method CreateGenomeAssemblyPaths (line 26) | internal static IEnumerable<(GenomeAssembly GenomeAssembly, string Man...

FILE: Downloader/OutputDirectory.cs
  class OutputDirectory (line 11) | public static class OutputDirectory
    method Create (line 13) | public static (string Cache, string Reference, string SupplementaryAnn...
    method CreateGenomeAssemblySubdirectories (line 28) | private static void CreateGenomeAssemblySubdirectories(string topLevel...
    method Cleanup (line 38) | public static void Cleanup(IEnumerable<RemoteFile> files, IEnumerable<...
    method GetReferenceFiles (line 58) | private static IEnumerable<string> GetReferenceFiles(string references...
    method GetExistingFiles (line 64) | private static IEnumerable<string> GetExistingFiles(IEnumerable<string...
    method RemoveOldFiles (line 82) | public static void RemoveOldFiles(IEnumerable<RemoteFile> files)
    method HasOlderFile (line 114) | private static bool HasOlderFile(in DateTimeOffset localOffset, DateTi...
    method HasDifferentFileSize (line 117) | private static bool HasDifferentFileSize(long localLength, long remote...
    method GetNumDownloadBytes (line 119) | public static long GetNumDownloadBytes(IEnumerable<RemoteFile> files)
    method RemoveSkippedFiles (line 126) | public static List<RemoteFile> RemoveSkippedFiles(List<RemoteFile> files)
    method CheckFiles (line 139) | public static void CheckFiles(IEnumerable<RemoteFile> files)
    method GetPaddedField (line 157) | private static string GetPaddedField(string s, int fieldLength)
    method PrintStatus (line 163) | private static void PrintStatus(RemoteFile file)

FILE: Downloader/RemoteFile.cs
  class RemoteFile (line 5) | public sealed class RemoteFile
    method RemoteFile (line 17) | public RemoteFile(string remotePath, string localPath, string descript...

FILE: Downloader/Utilities/ConsoleEmbellishments.cs
  class ConsoleEmbellishments (line 5) | public static class ConsoleEmbellishments
    method PrintWarning (line 7) | public static void PrintWarning(string s) => Highlight(s, ConsoleColor...
    method PrintError (line 9) | public static void PrintError(string s) => Highlight(s, ConsoleColor.R...
    method PrintSuccess (line 11) | public static void PrintSuccess(string s) => Highlight(s, ConsoleColor...
    method Highlight (line 13) | private static void Highlight(string s, ConsoleColor color)

FILE: Downloader/Utilities/DiskSpaceUtilities.cs
  class DiskSpaceUtilities (line 7) | public static class DiskSpaceUtilities
    method CheckAvailableDiskSpace (line 9) | public static void CheckAvailableDiskSpace(string outputDirectory, lon...
    method GetAbsolutePath (line 28) | private static string GetAbsolutePath(string directoryPath)
    method GetDriveWithLongestCommonPrefix (line 39) | private static DriveInfo GetDriveWithLongestCommonPrefix(string absolu...

FILE: Downloader/Utilities/GenomeAssemblyHelper.cs
  class GenomeAssemblyHelper (line 7) | public static class GenomeAssemblyHelper
    method GetGenomeAssemblies (line 9) | public static List<GenomeAssembly> GetGenomeAssemblies(string genomeAs...

FILE: Downloader/Utilities/ParallelUtilities.cs
  class ParallelUtilities (line 10) | public static class ParallelUtilities
    method ParallelExecute (line 14) | public static void ParallelExecute(this List<RemoteFile> files, Func<R...

FILE: Downloader/Utilities/SyncUtilities.cs
  class SyncUtilities (line 5) | public static class SyncUtilities
    method AsSync (line 7) | public static T AsSync<T>(this Task<T> task) => task.ConfigureAwait(fa...

FILE: ErrorHandling/ErrorCategory.cs
  type ErrorCategory (line 3) | public enum ErrorCategory

FILE: ErrorHandling/ExceptionUtilities.cs
  class ExceptionUtilities (line 7) | public static class ExceptionUtilities
    method MakeUserError (line 11) | public static Exception MakeUserError(this Exception e)
    method HasException (line 29) | public static bool HasException<T>(Exception e)
    method HasErrorMessage (line 35) | public static bool HasErrorMessage(this Exception e, string errorMessage)
    method GetInnermostException (line 41) | public static Exception GetInnermostException(Exception e)
    method ExceptionToErrorCategory (line 47) | public static ErrorCategory ExceptionToErrorCategory(Exception excepti...

FILE: ErrorHandling/Exceptions/CompressionException.cs
  class CompressionException (line 5) | public sealed class CompressionException : Exception
    method CompressionException (line 8) | public CompressionException(string message) : base(message) { }

FILE: ErrorHandling/Exceptions/DeploymentErrorException.cs
  class DeploymentErrorException (line 5) | public sealed class DeploymentErrorException : Exception
    method DeploymentErrorException (line 7) | public DeploymentErrorException(string message) : base(message) { }

FILE: ErrorHandling/Exceptions/FileNotSortedException.cs
  class FileNotSortedException (line 5) | public sealed class FileNotSortedException : Exception
    method FileNotSortedException (line 8) | public FileNotSortedException(string message) : base(message) { }

FILE: ErrorHandling/Exceptions/InvalidFileFormatException.cs
  class InvalidFileFormatException (line 5) | public sealed class InvalidFileFormatException : Exception
    method InvalidFileFormatException (line 8) | public InvalidFileFormatException(string message) : base(message) { }

FILE: ErrorHandling/Exceptions/MissingCompressionLibraryException.cs
  class MissingCompressionLibraryException (line 5) | public sealed class MissingCompressionLibraryException : Exception
    method MissingCompressionLibraryException (line 8) | public MissingCompressionLibraryException(string missingLibraryFilenam...
    method GetErrorMessage (line 13) | private static string GetErrorMessage(string missingLibraryFilename)

FILE: ErrorHandling/Exceptions/ProcessLockedFileException.cs
  class ProcessLockedFileException (line 5) | public sealed class ProcessLockedFileException : Exception
    method ProcessLockedFileException (line 8) | public ProcessLockedFileException(string message) : base(message) { }

FILE: ErrorHandling/Exceptions/UserErrorException.cs
  class UserErrorException (line 5) | public sealed class UserErrorException : Exception
    method UserErrorException (line 8) | public UserErrorException(string message) : base(message) { }

FILE: ErrorHandling/ExitCodeUtilities.cs
  class ExitCodeUtilities (line 8) | public static class ExitCodeUtilities
    method ExitCodeUtilities (line 15) | static ExitCodeUtilities()
    method GetExitCode (line 39) | internal static ExitCodes GetExitCode(Type exceptionType)
    method ShowException (line 49) | public static ExitCodes ShowException(Exception e)

FILE: ErrorHandling/ExitCodes.cs
  type ExitCodes (line 7) | public enum ExitCodes

FILE: GeneAnnotationLambda/GeneAnnotationLambda.cs
  class GeneAnnotationLambda (line 29) | public class GeneAnnotationLambda
    method Run (line 34) | public Stream Run(GeneConfig config, ILambdaContext context)
    method HandleException (line 64) | private static Stream HandleException(string id, string snsTopicArn, E...
    method GetGeneAnnotation (line 74) | public static string GetGeneAnnotation(GeneConfig input, string saMani...
    method GetHeader (line 100) | private static string GetHeader(IProvider geneAnnotationProvider)
    method GetNgaFileList (line 115) | public static IEnumerable<string> GetNgaFileList(string saManifestPath...

FILE: GeneAnnotationLambda/GeneResult.cs
  class LambdaResponse (line 10) | public static class LambdaResponse
    method Create (line 15) | public static Stream Create(string id, string status, string nirvanaJson)

FILE: Genome/Band.cs
  type Band (line 3) | public struct Band
    method Band (line 9) | public Band(int begin, int end, string name)
    method Compare (line 16) | public int Compare(int position)

FILE: Genome/Chromosome.cs
  class Chromosome (line 7) | public sealed class Chromosome : IComparable<Chromosome>
    method GetEmptyChromosome (line 20) | public static Chromosome GetEmptyChromosome(string name)
    method Chromosome (line 29) | public Chromosome(string ucscName, string ensemblName, string refSeqAc...
    method Write (line 46) | public void Write(ExtendedBinaryWriter writer)
    method Read (line 56) | public static Chromosome Read(ExtendedBinaryReader reader)
    method Equals (line 68) | public bool Equals(Chromosome other) => Index == other.Index && Length...
    method CompareTo (line 70) | public int CompareTo(Chromosome other) => Index == other.Index ? Lengt...
    method GetHashCode (line 72) | public override int GetHashCode()

FILE: Genome/ChromosomeInterval.cs
  class ChromosomeInterval (line 3) | public sealed class ChromosomeInterval : IChromosomeInterval
    method ChromosomeInterval (line 9) | public ChromosomeInterval(Chromosome chromosome, int start, int end)

FILE: Genome/ContigInfo.cs
  class ContigInfo (line 6) | public static class ContigInfo
    method GetChromLengthToAssembly (line 65) | private static Dictionary<string, Dictionary<int, GenomeAssembly>> Get...
    method GetGenomeAssembly (line 81) | public static GenomeAssembly GetGenomeAssembly(Chromosome chromosome, ...

FILE: Genome/CytogeneticBands.cs
  class CytogeneticBands (line 3) | public static class CytogeneticBands
    method Find (line 5) | public static string Find(this Band[] bands, Chromosome chromosome, in...
    method GetCytogeneticBand (line 23) | private static string GetCytogeneticBand(this Band[] bands, int pos)
    method BinarySearch (line 29) | private static int BinarySearch(Band[] array, int position)

FILE: Genome/GenomeAssembly.cs
  type GenomeAssembly (line 4) | public enum GenomeAssembly : byte

FILE: Genome/GenomeAssemblyHelper.cs
  class GenomeAssemblyHelper (line 6) | public static class GenomeAssemblyHelper
    method Convert (line 11) | public static GenomeAssembly Convert(string genomeAssembly)

FILE: Genome/GenomicPosition.cs
  type GenomicPosition (line 3) | public struct GenomicPosition
    method GenomicPosition (line 8) | public GenomicPosition(Chromosome chromosome, int position)

FILE: Genome/GenomicRange.cs
  class GenomicRange (line 3) | public sealed class GenomicRange
    method GenomicRange (line 8) | public GenomicRange(GenomicPosition start, GenomicPosition? end)

FILE: Genome/GenomicRangeChecker.cs
  class GenomicRangeChecker (line 3) | public sealed class GenomicRangeChecker
    method GenomicRangeChecker (line 8) | public GenomicRangeChecker(GenomicRange genomicRange)
    method OutOfRange (line 13) | public bool OutOfRange(Chromosome chromosome, int position)

FILE: Genome/IChromosomeInterval.cs
  type IChromosomeInterval (line 5) | public interface IChromosomeInterval : IInterval

FILE: Genome/ISequence.cs
  type ISequence (line 3) | public interface ISequence
    method Substring (line 7) | string Substring(int offset, int length);

FILE: Genome/ReferenceNameUtilities.cs
  class ReferenceNameUtilities (line 6) | public static class ReferenceNameUtilities
    method GetChromosome (line 8) | public static Chromosome GetChromosome(Dictionary<string, Chromosome> ...
    method GetChromosome (line 18) | public static Chromosome GetChromosome(Dictionary<ushort, Chromosome> ...
    method IsEmpty (line 28) | public static bool IsEmpty(this Chromosome chromosome) => chromosome.I...

FILE: Genome/SequenceUtilities.cs
  class SequenceUtilities (line 6) | public static class SequenceUtilities
    method SequenceUtilities (line 11) | static SequenceUtilities()
    method GetReverseComplement (line 30) | public static string GetReverseComplement(string bases)
    method HasNonCanonicalBase (line 49) | public static bool HasNonCanonicalBase(string bases) => !string.IsNull...

FILE: IO/BufferedBinaryReader.cs
  class BufferedBinaryReader (line 7) | public sealed class BufferedBinaryReader : IBufferedBinaryReader
    method BufferedBinaryReader (line 24) | public BufferedBinaryReader(Stream stream, bool leaveOpen = false, int...
    method FillBuffer (line 37) | private void FillBuffer()
    method ReadAsciiString (line 51) | public string ReadAsciiString()
    method ReadBoolean (line 57) | public bool ReadBoolean()
    method ReadByte (line 63) | public byte ReadByte()
    method ReadBytes (line 69) | public byte[] ReadBytes(int numBytes)
    method Read (line 78) | private void Read(byte[] buffer, int numBytes)
    method ReadOptInt32 (line 102) | public int ReadOptInt32()
    method ReadOptUInt16 (line 121) | public ushort ReadOptUInt16()
    method ReadUInt16 (line 140) | public unsafe ushort ReadUInt16()
    method ReadUInt32 (line 154) | public unsafe uint ReadUInt32()
    method Dispose (line 168) | public void Dispose()

FILE: IO/CacheConstants.cs
  class CacheConstants (line 4) | public static class CacheConstants
    method TranscriptPath (line 18) | public static string TranscriptPath(string prefix) => Combine(prefix, ...
    method SiftPath (line 19) | public static string SiftPath(string prefix)       => Combine(prefix, ...
    method PolyPhenPath (line 20) | public static string PolyPhenPath(string prefix)   => Combine(prefix, ...
    method BasesPath (line 21) | public static string BasesPath(string prefix)      => Combine(prefix, ...
    method Combine (line 23) | private static string Combine(string prefix, string suffix) => prefix ...

FILE: IO/ExtendedBinaryReader.cs
  class ExtendedBinaryReader (line 7) | public sealed class ExtendedBinaryReader : BinaryReader
    method ExtendedBinaryReader (line 9) | public ExtendedBinaryReader(Stream s) : this(s, new UTF8Encoding()) { }
    method ExtendedBinaryReader (line 11) | public ExtendedBinaryReader(Stream input, Encoding encoding, bool leav...
    method ReadOptUInt16 (line 18) | public ushort ReadOptUInt16()
    method ReadOptInt32 (line 38) | public int ReadOptInt32()
    method ReadOptInt64 (line 58) | public long ReadOptInt64()
    method ReadAsciiString (line 78) | public string ReadAsciiString()

FILE: IO/ExtendedBinaryWriter.cs
  class ExtendedBinaryWriter (line 6) | public sealed class ExtendedBinaryWriter : BinaryWriter, IExtendedBinary...
    method ExtendedBinaryWriter (line 8) | public ExtendedBinaryWriter(Stream output) : this(output, new UTF8Enco...
    method ExtendedBinaryWriter (line 10) | public ExtendedBinaryWriter(Stream output, Encoding encoding, bool lea...
    method WriteOpt (line 18) | public void WriteOpt(ushort value)
    method WriteOpt (line 34) | public void WriteOpt(int value)
    method WriteOpt (line 47) | public void WriteOpt(uint value)
    method WriteOpt (line 63) | public void WriteOpt(long value)
    method WriteOptAscii (line 79) | public void WriteOptAscii(string s)

FILE: IO/FilePathUtilities.cs
  class StringExtensions (line 5) | public static class StringExtensions
    method TrimStartToLast (line 7) | public static string TrimStartToLast(this string s, string value, bool...
    method TrimEndFromFirst (line 14) | public static string TrimEndFromFirst(this string s, string value, boo...
    method GetFileSuffix (line 21) | public static string GetFileSuffix(this string s, bool includeDot) => ...

FILE: IO/FileUtilities.cs
  class FileUtilities (line 6) | public static class FileUtilities
    method GetReadStream (line 10) | public static FileStream GetReadStream(string path)   => new FileStrea...
    method GetCreateStream (line 11) | public static FileStream GetCreateStream(string path) => new FileStrea...
    method GetStreamReader (line 13) | public static StreamReader GetStreamReader(Stream stream, bool leaveOp...
    method GetFileNamesInDir (line 16) | public static string[] GetFileNamesInDir(string directory, string patt...

FILE: IO/HttpUtilities.cs
  class HttpUtilities (line 12) | public static class HttpUtilities
    method GetLength (line 18) | public static long GetLength(string url)
    method TryGetResponse (line 27) | private static HttpWebResponse TryGetResponse(string url)
    method ValidateUrl (line 60) | public static void ValidateUrl(string url, bool isUserProvided = true)
    method IsWebProtocolErrorException (line 74) | public static bool IsWebProtocolErrorException(Exception exception)
    method ProcessHttpRequestWebProtocolErrorException (line 81) | public static Exception ProcessHttpRequestWebProtocolErrorException(Ex...
    method GetWebExceptionMessage (line 107) | private static (string Code, string Message) GetWebExceptionMessage(We...
    method IsUrl (line 118) | public static bool IsUrl(string path) => path.StartsWith("http", true,...

FILE: IO/IBufferedBinaryReader.cs
  type IBufferedBinaryReader (line 5) | public interface IBufferedBinaryReader : IDisposable
    method ReadAsciiString (line 7) | string ReadAsciiString();
    method ReadBoolean (line 8) | bool ReadBoolean();
    method ReadByte (line 9) | byte ReadByte();
    method ReadOptInt32 (line 10) | int ReadOptInt32();
    method ReadOptUInt16 (line 11) | ushort ReadOptUInt16();
    method ReadUInt32 (line 12) | uint ReadUInt32();

FILE: IO/IConnect.cs
  type IConnect (line 6) | public interface IConnect
    method Connect (line 8) | (HttpWebResponse Response, Stream Stream) Connect(long position);

FILE: IO/IExtendedBinaryWriter.cs
  type IExtendedBinaryWriter (line 3) | public interface IExtendedBinaryWriter
    method Write (line 5) | void Write(bool b);
    method Write (line 6) | void Write(byte b);
    method Write (line 7) | void Write(byte[] buffer);
    method Write (line 8) | void Write(ushort value);
    method Write (line 9) | void Write(uint value);
    method WriteOpt (line 10) | void WriteOpt(ushort value);
    method WriteOpt (line 11) | void WriteOpt(int value);
    method WriteOpt (line 12) | void WriteOpt(long value);
    method WriteOptAscii (line 13) | void WriteOptAscii(string s);

FILE: IO/IS3Client.cs
  type IS3Client (line 6) | public interface IS3Client
    method GetObjectAsync (line 8) | Task<GetObjectResponse> GetObjectAsync(GetObjectRequest getRequest);
    method PutObjectAsync (line 9) | Task<PutObjectResponse> PutObjectAsync(PutObjectRequest putRequest);

FILE: IO/ISerializable.cs
  type ISerializable (line 3) | public interface ISerializable
    method Write (line 5) | void Write(IExtendedBinaryWriter writer);

FILE: IO/LengthStream.cs
  class LengthStream (line 11) | public sealed class LengthStream : Stream
    method LengthStream (line 16) | public LengthStream(Stream stream, long length)
    method Read (line 22) | public override int Read(byte[] buffer, int offset, int count)
    method Flush (line 34) | public override void Flush()                                     => th...
    method Seek (line 35) | public override long Seek(long offset, SeekOrigin origin)        => th...
    method SetLength (line 36) | public override void SetLength(long value)                       => th...
    method Write (line 37) | public override void Write(byte[] buffer, int offset, int count) => th...

FILE: IO/Logger.cs
  class Logger (line 6) | public static class Logger
    method Logger (line 14) | static Logger()
    method SetBold (line 20) | public static void SetBold()    => Console.ForegroundColor = ConsoleCo...
    method ResetColor (line 21) | public static void ResetColor() => Console.ResetColor();
    method Silence (line 23) | public static void Silence()
    method Log (line 29) | public static void Log(Exception e)

FILE: IO/MD5Stream.cs
  class MD5Stream (line 7) | public sealed class MD5Stream : Stream
    method MD5Stream (line 15) | public MD5Stream(Stream stream) => _stream = stream;
    method Write (line 17) | public override void Write(byte[] buffer, int offset, int count)
    method GetFileMetadata (line 24) | public FileMetadata GetFileMetadata()
    method Flush (line 37) | public override void Flush() => _stream.Flush();
    method Read (line 39) | public override int Read(byte[] buffer, int offset, int count) => thro...
    method Seek (line 40) | public override long Seek(long offset, SeekOrigin origin)      => thro...
    method SetLength (line 41) | public override void SetLength(long value)                     => thro...
  class FileMetadata (line 48) | public sealed class FileMetadata
    method FileMetadata (line 53) | public FileMetadata(byte[] md5, long length)

FILE: IO/PersistentConnect.cs
  class PersistentConnect (line 7) | public sealed class PersistentConnect : IConnect
    method PersistentConnect (line 11) | public PersistentConnect(string url) => _url = url;
    method Connect (line 13) | public (HttpWebResponse Response, Stream Stream) Connect(long position)

FILE: IO/PersistentStream.cs
  class PersistentStream (line 9) | public sealed class PersistentStream : Stream
    method Flush (line 23) | public override void Flush()                                     => _s...
    method Seek (line 24) | public override long Seek(long offset, SeekOrigin origin)        => _s...
    method SetLength (line 25) | public override void SetLength(long value)                       => _s...
    method Write (line 26) | public override void Write(byte[] buffer, int offset, int count) => _s...
    method PersistentStream (line 39) | public PersistentStream(IConnect connect, long position)
    method ConnectWithRetries (line 46) | private void ConnectWithRetries(long position)
    method Disconnect (line 72) | private void Disconnect()
    method Read (line 77) | public override int Read(byte[] buffer, int offset, int count)
    method PersistentRead (line 95) | private int PersistentRead(byte[] buffer, int offset, int count)
    method Log (line 123) | private static void Log(string methodName, Exception e)
    method MethodName (line 129) | private static string MethodName([CallerMemberName] string caller = nu...
    method Dispose (line 131) | protected override void Dispose(bool disposing)

FILE: IO/PersistentStreamUtils.cs
  class PersistentStreamUtils (line 7) | public static class PersistentStreamUtils
    method GetReadStream (line 9) | public static Stream GetReadStream(string urlOrPath, long position = 0)
    method GetStreams (line 19) | public static List<Stream> GetStreams(List<string> locations)

FILE: IO/SpanBufferBinaryReader.cs
  class SpanBufferBinaryReader (line 8) | public static class SpanBufferBinaryReader
    method ReadOptUInt16 (line 13) | public static ushort ReadOptUInt16(ref ReadOnlySpan<byte> byteSpan)
    method ReadOptInt32 (line 36) | public static int ReadOptInt32(ref ReadOnlySpan<byte> byteSpan)
    method ReadOptUInt32 (line 59) | public static uint ReadOptUInt32(ref ReadOnlySpan<byte> byteSpan)
    method ReadOptInt64 (line 82) | public static long ReadOptInt64(ref ReadOnlySpan<byte> byteSpan)
    method ReadOptUInt64 (line 105) | public static ulong ReadOptUInt64(ref ReadOnlySpan<byte> byteSpan)
    method ReadUtf8String (line 128) | public static string ReadUtf8String(ref ReadOnlySpan<byte> byteSpan)
    method ReadAsciiString (line 139) | public static string ReadAsciiString(ref ReadOnlySpan<byte> byteSpan)
    method SkipString (line 150) | [MethodImpl(MethodImplOptions.AggressiveInlining)]
    method ReadByte (line 158) | [MethodImpl(MethodImplOptions.AggressiveInlining)]
    method ReadBytes (line 166) | [MethodImpl(MethodImplOptions.AggressiveInlining)]
    method ReadInt32 (line 174) | [MethodImpl(MethodImplOptions.AggressiveInlining)]
    method ReadUInt64 (line 182) | [MethodImpl(MethodImplOptions.AggressiveInlining)]
    method ReadUInt16 (line 190) | [MethodImpl(MethodImplOptions.AggressiveInlining)]

FILE: IO/UrlUtilities.cs
  class UrlUtilities (line 6) | public static class UrlUtilities
    method GetPath (line 10) | public static string GetPath(string url)     => new Uri(url).LocalPath...
    method GetFileName (line 11) | public static string GetFileName(string url) => Path.GetFileName(GetPa...
    method UrlCombine (line 13) | public static string UrlCombine(this string prefix, string suffix) =>

FILE: IO/v2/FileType.cs
  type FileType (line 3) | public enum FileType : ushort

FILE: IO/v2/Header.cs
  type Header (line 8) | public sealed record Header(FileType FileType, ushort FileFormatVersion)

FILE: Intervals/Extensions.cs
  class Extensions (line 3) | public static class Extensions
    method Overlaps (line 8) | public static bool Overlaps(this IInterval interval1, IInterval interv...
    method Overlaps (line 12) | public static bool Overlaps(this IInterval interval, int start, int en...
    method Contains (line 15) | public static bool Contains(this IInterval interval1, IInterval interv...
    method Intersects (line 18) | public static Interval Intersects(this IInterval interval1, IInterval ...

FILE: Intervals/IInterval.cs
  type IInterval (line 3) | public interface IInterval

FILE: Intervals/IIntervalForest.cs
  type IIntervalForest (line 3) | public interface IIntervalForest<out T>
    method OverlapsAny (line 5) | bool OverlapsAny(ushort refIndex, int begin, int end);
    method GetAllOverlappingValues (line 6) | T[] GetAllOverlappingValues(ushort refIndex, int begin, int end);

FILE: Intervals/IIntervalSearch.cs
  type IIntervalSearch (line 3) | public interface IIntervalSearch<out T>
    method GetAllOverlappingValues (line 5) | T[] GetAllOverlappingValues(int begin, int end);
  type Interval (line 8) | public struct Interval<T>
    method Interval (line 15) | public Interval(int begin, int end, T value)
    method CompareMax (line 26) | public int CompareMax(int position)
    method Overlaps (line 35) | public bool Overlaps(int intervalBegin, int intervalEnd)

FILE: Intervals/Interval.cs
  type Interval (line 3) | public struct Interval : IInterval
    method Interval (line 8) | public Interval(int start, int end)

FILE: Intervals/IntervalArray.cs
  class IntervalArray (line 5) | public sealed class IntervalArray<T> : IIntervalSearch<T>
    method IntervalArray (line 9) | public IntervalArray(Interval<T>[] array)
    method OverlapsAny (line 18) | public bool OverlapsAny(int begin, int end) => GetFirstIndexAny(begin,...
    method GetAllOverlappingValues (line 23) | public T[] GetAllOverlappingValues(int begin, int end)
    method GetAllOverlappingIntervals (line 29) | public Interval<T>[] GetAllOverlappingIntervals(int begin, int end)
    method AddOverlappingValues (line 47) | private T[] AddOverlappingValues(int firstIndex, int begin, int end)
    method GetFirstIndex (line 62) | private int GetFirstIndex(int intervalBegin, int intervalEnd)
    method GetFirstIndexAny (line 86) | private int GetFirstIndexAny(int intervalBegin, int intervalEnd)
    method SetMaxIntervals (line 108) | private void SetMaxIntervals()

FILE: Intervals/IntervalForest.cs
  class IntervalForest (line 3) | public sealed class IntervalForest<T> : IIntervalForest<T>
    method IntervalForest (line 8) | public IntervalForest(IntervalArray<T>[] intervalArrays)
    method OverlapsAny (line 17) | public bool OverlapsAny(ushort refIndex, int begin, int end)
    method GetAllOverlappingValues (line 28) | public T[] GetAllOverlappingValues(ushort refIndex, int begin, int end)
    method GetAllOverlappingIntervals (line 35) | public Interval<T>[] GetAllOverlappingIntervals(ushort refIndex, int b...

FILE: Intervals/NullIntervalSearch.cs
  class NullIntervalSearch (line 3) | public sealed class NullIntervalSearch<T> : IIntervalForest<T>, IInterva...
    method OverlapsAny (line 7) | public bool OverlapsAny(ushort refIndex, int begin, int end)
    method GetAllOverlappingValues (line 12) | public T[] GetAllOverlappingValues(ushort refIndex, int begin, int end)
    method GetAllOverlappingValues (line 21) | public T[] GetAllOverlappingValues(int begin, int end)

FILE: Intervals/OverlapType.cs
  type OverlapType (line 3) | public enum OverlapType
  type EndpointOverlapType (line 11) | public enum EndpointOverlapType

FILE: Intervals/Utilities.cs
  class Utilities (line 5) | public static class Utilities
    method Overlaps (line 7) | public static bool Overlaps(int firstStart, int firstEnd, int secondSt...
    method Contains (line 10) | public static bool Contains(int firstStart, int firstEnd, int secondSt...
    method GetOverlapType (line 14) | public static OverlapType GetOverlapType(int tStart, int tEnd, int vSt...
    method GetEndpointOverlapType (line 24) | public static EndpointOverlapType GetEndpointOverlapType(int tStart, i...
    method Intersects (line 34) | public static (int Start, int End) Intersects(int firstStart, int firs...

FILE: Jasix/DataStructures/JasixChrIndex.cs
  class JasixChrIndex (line 9) | public sealed class JasixChrIndex
    method JasixChrIndex (line 17) | public JasixChrIndex(string refName)
    method JasixChrIndex (line 25) | public JasixChrIndex(ExtendedBinaryReader reader) : this("")
    method ReadInterval (line 41) | private static Interval<long> ReadInterval(ExtendedBinaryReader reader)
    method Write (line 50) | public void Write(IExtendedBinaryWriter writer)
    method WriteInterval (line 71) | private static void WriteInterval(Interval<long> interval, IExtendedBi...
    method Add (line 78) | public void Add(int begin, int end, long filePosition)
    method Flush (line 100) | public void Flush()
    method FindFirstSmallVariant (line 109) | public long FindFirstSmallVariant(int start, int end)
    method FindFirstOverlappingNode (line 118) | private JasixNode FindFirstOverlappingNode(JasixNode searchNode)
    method FindLargeVariants (line 144) | public long[] FindLargeVariants(int begin, int end)

FILE: Jasix/DataStructures/JasixCommons.cs
  class JasixCommons (line 4) | public  static class JasixCommons

FILE: Jasix/DataStructures/JasixIndex.cs
  type FileRange (line 10) | public struct FileRange
    method FileRange (line 15) | public FileRange(long begin, long end = long.MaxValue)
  class JasixIndex (line 22) | public sealed class JasixIndex:IDisposable
    method JasixIndex (line 31) | public JasixIndex()
    method JasixIndex (line 39) | public JasixIndex(Stream stream) : this()
    method Write (line 76) | public void Write(Stream writeStream)
    method Flush (line 104) | public void Flush()
    method Add (line 112) | public void Add(string chr, int start, int end, long fileLoc, string c...
    method BeginSection (line 132) | public void BeginSection(string section, long fileLoc)
    method EndSection (line 140) | public void EndSection(string section, long fileLoc)
    method GetFirstVariantPosition (line 154) | public long GetFirstVariantPosition(string chr, int start, int end)
    method LargeVariantPositions (line 170) | public long[] LargeVariantPositions(string chr, int begin, int end)
    method GetChromosomeList (line 180) | public IEnumerable<string> GetChromosomeList()
    method ContainsChr (line 185) | public bool ContainsChr(string chr)
    method GetIndexChromName (line 190) | public string GetIndexChromName(string chromName)
    method GetSectionBegin (line 196) | public long GetSectionBegin(string section)
    method GetSectionEnd (line 200) | public long GetSectionEnd(string section)
    method Dispose (line 205) | public void Dispose()
    method GetSections (line 210) | public IEnumerable<string> GetSections() => _sectionRanges.Keys;

FILE: Jasix/DataStructures/JasixNode.cs
  class JasixNode (line 5) | public sealed class JasixNode : IComparable<JasixNode>
    method JasixNode (line 11) | public JasixNode(int start, int end, long location)
    method JasixNode (line 19) | public JasixNode(ExtendedBinaryReader reader)
    method Overlaps (line 27) | public bool Overlaps(JasixNode other)
    method CompareTo (line 32) | public int CompareTo(JasixNode other)
    method TryAdd (line 39) | public bool TryAdd(int start, int end)
    method Write (line 50) | public void Write(IExtendedBinaryWriter writer)

FILE: Jasix/DataStructures/JsonSchema.cs
  class JsonSchema (line 10) | public sealed class JsonSchema : IInterval

FILE: Jasix/DataStructures/Utilities.cs
  class Utilities (line 11) | public static class Utilities
    method ParseQuery (line 17) | public static (string Chromosome, int Start, int End) ParseQuery(strin...
    method PrintQuerySectionOpening (line 39) | public static void PrintQuerySectionOpening(string sectionName, Stream...
    method PrintQuerySectionClosing (line 44) | public static void PrintQuerySectionClosing(StreamWriter writer)
    method PrintJsonEntry (line 49) | public static void PrintJsonEntry(string entry, bool needComma, Stream...
    method IsLargeVariant (line 57) | public static bool IsLargeVariant(int start, int end)
    method GetJsonEntryEnd (line 62) | public static int GetJsonEntryEnd(JsonSchema jsonEntry)
    method IsNucleotideAllele (line 71) | public static bool IsNucleotideAllele(string altAllele)

FILE: Jasix/IndexCreator.cs
  class IndexCreator (line 14) | public sealed class IndexCreator : IDisposable
    method IndexCreator (line 22) | public IndexCreator(BlockGZipStream readStream, Stream writeStream)
    method IndexCreator (line 30) | public IndexCreator(string fileName)
    method CreateIndex (line 36) | public void CreateIndex()
    method IndexPositions (line 56) | private string IndexPositions(JasixIndex index)
    method IndexGenes (line 89) | private void IndexGenes(string lastLine, JasixIndex index)
    method IndexHeader (line 111) | private void IndexHeader(JasixIndex index)
    method CheckSorting (line 142) | private void CheckSorting(string chr, int pos, string previousChr, int...
    method GetChromPosition (line 155) | internal static (string chr, int position, int end) GetChromPosition(s...
    method Dispose (line 173) | public void Dispose()

FILE: Jasix/JasixMain.cs
  class JasixMain (line 15) | public static class JasixMain
    method Main (line 26) | public static int Main(string[] args)
    method ProgramExecution (line 84) | private static ExitCodes ProgramExecution()
    method ValidateIndexFile (line 135) | private static void ValidateIndexFile(string indexFileName)

FILE: Jasix/OnTheFlyIndexCreator.cs
  class OnTheFlyIndexCreator (line 10) | public sealed class OnTheFlyIndexCreator : IDisposable
    method OnTheFlyIndexCreator (line 18) | public OnTheFlyIndexCreator(Stream indexStream)
    method Add (line 24) | public void Add(IPosition position, long fileLocation)
    method BeginSection (line 49) | public void BeginSection(string sectionName, long fileLocation)
    method EndSection (line 54) | public void EndSection(string sectionName, long fileLocation)
    method Dispose (line 59) | public void Dispose()
    method Flush (line 65) | public void Flush()

FILE: Jasix/QueryProcessor.cs
  class QueryProcessor (line 13) | public sealed class QueryProcessor:IDisposable
    method Dispose (line 24) | public void Dispose()
    method QueryProcessor (line 32) | public QueryProcessor(StreamReader jsonReader, Stream indexStream, Str...
    method ListChromosomesAndSections (line 42) | public void ListChromosomesAndSections()
    method PrintHeaderOnly (line 55) | public void PrintHeaderOnly()
    method PrintSection (line 63) | public void PrintSection(string section)
    method ProcessQuery (line 75) | public int ProcessQuery(IEnumerable<string> queryStrings, bool printHe...
    method PrintAllVariantsFromQueryBegin (line 106) | private int PrintAllVariantsFromQueryBegin((string, int, int) query, b...
    method PrintLargeVariantsExtendingIntoQuery (line 118) | private int PrintLargeVariantsExtendingIntoQuery((string, int, int) qu...
    method ReadJsonLinesExtendingInto (line 130) | internal IEnumerable<string> ReadJsonLinesExtendingInto((string Chr, i...
    method RepositionReader (line 153) | private void RepositionReader(long location)
    method GetHeader (line 159) | public string GetHeader()
    method GetSectionLines (line 171) | public IEnumerable<string> GetSectionLines(string section)
    method ReadOverlappingJsonLines (line 187) | internal IEnumerable<string> ReadOverlappingJsonLines((string Chr, int...
    method ParseJsonEntry (line 217) | private static JsonSchema ParseJsonEntry(string line)

FILE: Jist/JistMain.cs
  class JistMain (line 9) | public class JistMain
    method Main (line 11) | public static int Main(string[] args)

FILE: Jist/JistUtilities.cs
  class JistUtilities (line 7) | public static class JistUtilities
    method GetCompressedBlock (line 9) | public static byte[] GetCompressedBlock(string s, int compressionLevel=1)

FILE: Jist/JsonStitcher.cs
  class JsonStitcher (line 13) | public sealed class JsonStitcher:IDisposable
    method JsonStitcher (line 21) | public JsonStitcher(Stream[] jsonStreams, Stream[] jasixStreams, Strea...
    method Stitch (line 38) | public int Stitch()
    method ReadGeneLines (line 70) | private int ReadGeneLines(Stream jsonStream)
    method WriteGeneBlocks (line 90) | private void WriteGeneBlocks(Stream stream)
    method WritePositionBlocks (line 114) | private int WritePositionBlocks(Stream jsonStream, Stream jasixStream,
    method Dispose (line 164) | public void Dispose()

FILE: MitoHeteroplasmy/MitoHeteroplasmyProvider.cs
  class MitoHeteroplasmyProvider (line 12) | public sealed class MitoHeteroplasmyProvider : IMitoHeteroplasmyProvider
    method MitoHeteroplasmyProvider (line 27) | public MitoHeteroplasmyProvider()
    method Add (line 33) | public void Add(int position, string altAllele, double[] vrfs, int[] a...
    method GetVrfPercentiles (line 39) | public double?[] GetVrfPercentiles(IVariant[] variants, double[] vrfs)
    method GetVrfPercentile (line 50) | private double? GetVrfPercentile(IVariant variant, double vrf)
    method EncodeMitoPositionAndAltAllele (line 64) | private static int EncodeMitoPositionAndAltAllele(int position, string...
    method ToRoundedVrf (line 66) | private static double ToRoundedVrf(double vrf) => Math.Round(vrf, 3, M...

FILE: MitoHeteroplasmy/MitoHeteroplasmyReader.cs
  class MitoHeteroplasmyReader (line 10) | public static class MitoHeteroplasmyReader
    method GetProvider (line 19) | public static MitoHeteroplasmyProvider GetProvider()

FILE: Nirvana/AnnotationFiles.cs
  class AnnotationFiles (line 11) | public sealed class AnnotationFiles
    method AddFiles (line 24) | public void AddFiles(string saDirectoryPath)
    method AddFiles (line 65) | public void AddFiles(SaUrls saUrls)
    method GetFiles (line 83) | private static IEnumerable<string> GetFiles(string directoryOrManifest...

FILE: Nirvana/AnnotationResources.cs
  class AnnotationResources (line 22) | public sealed class AnnotationResources : IAnnotationResources
    method AnnotationResources (line 45) | public AnnotationResources(string refSequencePath, string inputCachePr...
    method GetRepeatExpansionProvider (line 107) | private static IRepeatExpansionProvider GetRepeatExpansionProvider(Gen...
    method GetDataSourceVersions (line 114) | private static IEnumerable<IDataSourceVersion> GetDataSourceVersions(p...
    method SingleVariantPreLoad (line 123) | public void SingleVariantPreLoad(IPosition position)
    method GetVariantPositions (line 132) | public void GetVariantPositions(Stream vcfStream, GenomicRange genomic...
    method PreLoad (line 143) | public void PreLoad(Chromosome chromosome)
    method Dispose (line 151) | public void Dispose()

FILE: Nirvana/Nirvana.cs
  class Nirvana (line 19) | public static class Nirvana
    method ProgramExecution (line 35) | private static ExitCodes ProgramExecution()
    method GetAnnotationResources (line 55) | private static AnnotationResources GetAnnotationResources()
    method Main (line 73) | public static int Main(string[] args)

FILE: Nirvana/PreLoadUtilities.cs
  class PreLoadUtilities (line 11) | public static class PreLoadUtilities
    method GetPositions (line 13) | public static (Dictionary<Chromosome, List<int>> PositionsByChromosome...
    method IsRefMinor (line 59) | private static bool IsRefMinor(IRefMinorProvider refMinorProvider, Chr...
    method TryAddPosition (line 65) | public static void TryAddPosition(Dictionary<Chromosome, List<int>> ch...
    method SortPositionsAndGetCount (line 80) | private static int SortPositionsAndGetCount(Dictionary<Chromosome, Lis...

FILE: Nirvana/ProviderUtilities.cs
  class ProviderUtilities (line 18) | public static class ProviderUtilities
    method GetSequenceProvider (line 20) | public static ISequenceProvider GetSequenceProvider(string compressedR...
    method GetProteinConservationProvider (line 25) | public static ProteinConservationProvider GetProteinConservationProvid...
    method GetConservationProvider (line 30) | public static IAnnotationProvider GetConservationProvider(AnnotationFi...
    method GetDataAndIndexStreams (line 38) | private static (Stream, Stream) GetDataAndIndexStreams(string dataFile...
    method GetLcrProvider (line 55) | public static IAnnotationProvider GetLcrProvider(AnnotationFiles files...
    method GetRefMinorProvider (line 60) | public static IRefMinorProvider GetRefMinorProvider(AnnotationFiles fi...
    method GetGeneAnnotationProvider (line 68) | public static IGeneAnnotationProvider GetGeneAnnotationProvider(Annota...
    method GetNsaProvider (line 72) | public static IAnnotationProvider GetNsaProvider(AnnotationFiles files)
    method GetNsaReaders (line 84) | private static INsaReader[] GetNsaReaders(IReadOnlyCollection<(string ...
    method GetGsaProvider (line 95) | public static IAnnotationProvider GetGsaProvider(AnnotationFiles files)
    method GetNsiReaders (line 116) | private static INsiReader[] GetNsiReaders(IReadOnlyCollection<string> ...
    method GetGeneFusionReaders (line 123) | private static IGeneFusionSaReader[] GetGeneFusionReaders(IReadOnlyCol...
    method SortByJsonKey (line 132) | private static T[] SortByJsonKey<T>(this IEnumerable<T> entries) where...
    method GetTranscriptAnnotationProvider (line 135) | public static ITranscriptAnnotationProvider GetTranscriptAnnotationPro...

FILE: Nirvana/StreamAnnotation.cs
  class StreamAnnotation (line 26) | public static class StreamAnnotation
    method Annotate (line 28) | public static (int variantCount, ExitCodes exitCode) Annotate(Stream h...
    method ReturnPoolObjects (line 99) | private static void ReturnPoolObjects(IAnnotatedPosition annotatedPosi...
    method CheckGenomeAssembly (line 121) | private static void CheckGenomeAssembly(IAnnotationResources annotatio...
    method SetMitochondrialAnnotationBehavior (line 127) | private static void SetMitochondrialAnnotationBehavior(IAnnotationReso...
    method GetVcfReader (line 135) | private static VcfReader GetVcfReader(Stream headerStream, Stream vcfS...

FILE: NirvanaLambda/AnnotationJob.cs
  class AnnotationJob (line 14) | public sealed class AnnotationJob
    method AnnotationJob (line 27) | public AnnotationJob(ILambdaContext context, int jobIndex)
    method Invoke (line 33) | public AnnotationResultSummary Invoke(string functionArn, string funct...
    method InvokeAndRetryWhenThrottled (line 46) | private async Task<AnnotationResultSummary> InvokeAndRetryWhenThrottle...
    method GetResultSummaryFromSuccessInvocation (line 82) | internal static AnnotationResultSummary GetResultSummaryFromSuccessInv...
    method GetAnnotationResult (line 89) | private MemoryStream GetAnnotationResult(InvokeRequest invokeRequest)
    method CheckRemainingTime (line 109) | private void CheckRemainingTime()
    method CheckResponse (line 129) | internal void CheckResponse(InvokeResponse response)
    method GetResultSummaryFromFailedInvocation (line 144) | internal AnnotationResultSummary GetResultSummaryFromFailedInvocation(...

FILE: NirvanaLambda/AnnotationResultSummary.cs
  class AnnotationResultSummary (line 7) | public sealed class AnnotationResultSummary
    method Create (line 14) | public static AnnotationResultSummary Create(AnnotationResult annotati...

FILE: NirvanaLambda/NirvanaLambda.cs
  class NirvanaLambda (line 34) | public sealed class NirvanaLambda
    method Run (line 46) | public NirvanaResult Run(NirvanaConfig config, ILambdaContext context)
    method GetAnnotationRanges (line 84) | private static AnnotationRange[] GetAnnotationRanges(NirvanaConfig con...
    method HandleException (line 110) | private static NirvanaResult HandleException(StringBuilder runLog, Nir...
    method GetNirvanaFailResult (line 117) | private static NirvanaResult GetNirvanaFailResult(StringBuilder runLog...
    method GetFailedRunStatus (line 137) | internal static string GetFailedRunStatus(ErrorCategory errorCategory,...
    method GetNirvanaResult (line 155) | private static NirvanaResult GetNirvanaResult(AnnotationRange[] annota...
    method GetMostSevereErrorCategoryAndMessage (line 182) | private static (ErrorCategory?, string) GetMostSevereErrorCategoryAndM...
    method CallAnnotationLambdas (line 201) | private static Task<AnnotationResultSummary>[] CallAnnotationLambdas(N...
    method RunAnnotationJob (line 206) | private static Task<AnnotationResultSummary> RunAnnotationJob(NirvanaC...
    method DescribeAnnotationRegion (line 217) | private static string DescribeAnnotationRegion(AnnotationRange ar)
    method GetAnnotationConfig (line 224) | private static AnnotationConfig GetAnnotationConfig(NirvanaConfig conf...
    method GetIndexedPrefix (line 239) | internal static string GetIndexedPrefix(string inputVcfPath, int jobIn...
    method FirstCharToLower (line 242) | private static string FirstCharToLower(string input) => string.IsNullO...

FILE: NirvanaLambda/PartitionUtilities.cs
  class PartitionUtilities (line 17) | public static class PartitionUtilities
    method GetFileOffsets (line 19) | public static List<long> GetFileOffsets(string vcfUrl, int numPartitio...
    method GetBlockOffsets (line 26) | private static List<long> GetBlockOffsets(long[] sizeBasedOffsets, Tab...
    method FindEqualOrClosestSmallerOffsets (line 33) | internal static List<long> FindEqualOrClosestSmallerOffsets(long[] siz...
    method GetEqualSizeOffsets (line 54) | internal static long[] GetEqualSizeOffsets(long fileSize, int numParti...
    method GetAllLinearFileOffsets (line 65) | private static long[] GetAllLinearFileOffsets(Tabix.Index tabixIndex)
    method MergeConsecutiveEqualValues (line 72) | public static IEnumerable<T> MergeConsecutiveEqualValues<T>(IEnumerabl...
    method GenerateAnnotationRanges (line 86) | public static AnnotationRange[] GenerateAnnotationRanges(List<long> bl...
    method AdjustPartitionGenomicStarts (line 96) | private static AnnotationPosition[] AdjustPartitionGenomicStarts(IRead...
    method GetRanges (line 117) | private static AnnotationRange[] GetRanges(AnnotationPosition[] adjust...
    method GetFirstGenomicPosition (line 135) | private static AnnotationPosition GetFirstGenomicPosition(Stream vcfSt...
    method FindProperStartPosition (line 161) | private static AnnotationPosition FindProperStartPosition(AnnotationPo...

FILE: OptimizedCore/ExpandableArray.cs
  class ExpandableArray (line 5) | public static class ExpandableArray<T>
    method Get (line 7) | public static T[] Get(int size)
    method Resize (line 13) | public static T[] Resize(T[] array, int newSize)
    method Return (line 21) | public static void Return(T[] array)

FILE: OptimizedCore/NullSequenceEqual.cs
  class NullSequenceEqual (line 3) | public static class NullSequenceEqual
    method ArrayEqual (line 5) | public static bool ArrayEqual<T>(this T[] first, T[] second)

FILE: OptimizedCore/StringBuilderPool.cs
  class StringBuilderPool (line 6) | public static class StringBuilderPool
    method Get (line 10) | public static StringBuilder Get()
    method GetStringAndReturn (line 17) | public static string GetStringAndReturn(StringBuilder sb)
    method Return (line 24) | public static void Return(StringBuilder sb)

FILE: OptimizedCore/StringExtensions.cs
  class StringExtensions (line 5) | public static class StringExtensions
    method OptimizedSplit (line 7) | public static unsafe string[] OptimizedSplit(this string s, char delim...
    method OptimizedKeyValue (line 43) | public static (string Key, string Value) OptimizedKeyValue(this string s)
    method OptimizedParseInt32 (line 52) | public static unsafe (int Number, bool FoundError) OptimizedParseInt32...
    method OptimizedStartsWith (line 98) | public static bool OptimizedStartsWith(this string s, char ch) => s.Le...
    method OptimizedEndsWith (line 100) | public static bool OptimizedEndsWith(this string s, char ch) => s.Leng...

FILE: ReferenceSequence/Commands/CreateReferenceMain.cs
  class CreateReferenceMain (line 18) | public static class CreateReferenceMain
    method ProgramExecution (line 28) | private static ExitCodes ProgramExecution()
    method GetGenomeLength (line 75) | private static long GetGenomeLength(IEnumerable<FastaSequence> fastaSe...
    method CreateReferenceSequences (line 78) | private static List<Creation.ReferenceSequence> CreateReferenceSequenc...
    method CheckChrYPadding (line 94) | private static void CheckChrYPadding(IEnumerable<FastaSequence> fastaS...
    method GetFastaSequences (line 108) | private static List<FastaSequence> GetFastaSequences(string fastaPrefi...
    method CheckReferenceIndexContiguity (line 126) | private static void CheckReferenceIndexContiguity(IEnumerable<Chromoso...
    method CreateReferenceSequenceFile (line 144) | private static void CreateReferenceSequenceFile(GenomeAssembly genomeA...
    method CountNs (line 154) | private static int CountNs(string s)
    method Run (line 161) | public static ExitCodes Run(string command, string[] args)

FILE: ReferenceSequence/Commands/CreateSubstringMain.cs
  class CreateSubstringMain (line 18) | public static class CreateSubstringMain
    method ProgramExecution (line 30) | private static ExitCodes ProgramExecution()
    method GetCytogeneticBands (line 63) | private static List<Band> GetCytogeneticBands(ushort refIndex, int num...
    method CreateReferenceSequenceFile (line 74) | private static void CreateReferenceSequenceFile(GenomeAssembly genomeA...
    method CreateReferenceSequence (line 83) | private static Creation.ReferenceSequence CreateReferenceSequence(Fast...
    method GetFastaSequence (line 90) | private static FastaSequence GetFastaSequence(string fastaPath, Dictio...
    method Run (line 107) | public static ExitCodes Run(string command, string[] args)

FILE: ReferenceSequence/Commands/CreateTestSeqMain.cs
  class CreateTestSeqMain (line 16) | public static class CreateTestSeqMain
    method ProgramExecution (line 20) | private static ExitCodes ProgramExecution()
    method CreateReferenceSequenceFile (line 41) | private static void CreateReferenceSequenceFile(GenomeAssembly genomeA...
    method CreateReferenceSequence (line 50) | private static Creation.ReferenceSequence CreateReferenceSequence(Fast...
    method Run (line 56) | public static ExitCodes Run(string command, string[] args)

FILE: ReferenceSequence/Common/IndexEntry.cs
  class IndexEntry (line 3) | internal sealed class IndexEntry
    method IndexEntry (line 10) | internal IndexEntry(ushort refIndex, long fileOffset)

FILE: ReferenceSequence/Common/MaskedEntry.cs
  class MaskedEntry (line 3) | internal sealed class MaskedEntry
    method MaskedEntry (line 8) | internal MaskedEntry(int begin, int end)

FILE: ReferenceSequence/Common/Sequence.cs
  class Sequence (line 7) | public sealed class Sequence : ISequence
    method Sequence (line 22) | public Sequence()
    method GetBaseIndexAndShift (line 29) | private static (int BaseIndex, int Shift) GetBaseIndexAndShift(int ref...
    method GetNumBufferBytes (line 37) | internal static int GetNumBufferBytes(int numBases) =>
    method EnableNSequence (line 40) | public void EnableNSequence() => _useNSequence = true;
    method Set (line 42) | internal void Set(int length, int sequenceOffset, byte[] twoBitBuffer,
    method Substring (line 53) | public string Substring(int offset, int length)
    method MaskBases (line 116) | private int MaskBases(int offset, int length, int baseIndex, MaskedEnt...

FILE: ReferenceSequence/Compression/TwoBitCompressor.cs
  class TwoBitCompressor (line 6) | internal static class TwoBitCompressor
    method TwoBitCompressor (line 11) | static TwoBitCompressor()
    method GetNumBufferBytes (line 23) | private static int GetNumBufferBytes(int numBases) => (int)(numBases /...
    method Compress (line 25) | public static (byte[] Buffer, MaskedEntry[] MaskedEntries) Compress(st...

FILE: ReferenceSequence/Creation/FastaSequence.cs
  class FastaSequence (line 5) | internal sealed class FastaSequence
    method FastaSequence (line 10) | internal FastaSequence(Chromosome chromosome, string bases)

FILE: ReferenceSequence/Creation/ReferenceBuffer.cs
  class ReferenceBuffer (line 3) | public sealed class ReferenceBuffer
    method ReferenceBuffer (line 9) | public ReferenceBuffer(ushort refIndex, byte[] buffer, int bufferSize)

FILE: ReferenceSequence/Creation/ReferenceDictionaryUtils.cs
  class ReferenceDictionaryUtils (line 7) | internal static class ReferenceDictionaryUtils
    method GetRefNameToChromosome (line 9) | internal static Dictionary<string, Chromosome> GetRefNameToChromosome(...

FILE: ReferenceSequence/Creation/ReferenceSequence.cs
  class ReferenceSequence (line 9) | internal sealed class ReferenceSequence
    method ReferenceSequence (line 17) | internal ReferenceSequence(byte[] buffer, MaskedEntry[] maskedEntries,...
    method GetReferenceBuffer (line 27) | internal ReferenceBuffer GetReferenceBuffer(ushort refIndex)
    method WriteMetadata (line 50) | private void WriteMetadata(IExtendedBinaryWriter writer)
    method WriteCytogeneticBands (line 56) | private void WriteCytogeneticBands(IExtendedBinaryWriter writer)
    method WriteMaskedEntries (line 68) | private void WriteMaskedEntries(IExtendedBinaryWriter writer)
    method WriteBuffer (line 79) | private void WriteBuffer(IExtendedBinaryWriter writer)

FILE: ReferenceSequence/IO/AssemblyReader.cs
  class AssemblyReader (line 9) | public static class AssemblyReader
    method GetChromosomes (line 17) | public static List<Chromosome> GetChromosomes(Stream stream, Dictionar...
    method Sanitize (line 46) | private static string Sanitize(this string s) => s == "na" ? null : s;
    method GetRefIndex (line 48) | private static ushort GetRefIndex(Dictionary<string, Chromosome> refNa...

FILE: ReferenceSequence/IO/CytogeneticBandsReader.cs
  class CytogeneticBandsReader (line 7) | public static class CytogeneticBandsReader
    method GetCytogeneticBands (line 9) | public static List<Band>[] GetCytogeneticBands(Stream stream, int numR...

FILE: ReferenceSequence/IO/FastaReader.cs
  class FastaReader (line 11) | internal static class FastaReader
    method AddReferenceSequences (line 21) | internal static void AddReferenceSequences(Stream stream, Dictionary<s...
    method GetBases (line 45) | private static string GetBases(StringBuilder sb, StreamReader reader, ...
    method GetChromosome (line 66) | private static Chromosome GetChromosome(Dictionary<string, Chromosome>...
    method GetName (line 78) | private static string GetName(string s)

FILE: ReferenceSequence/IO/ReferenceNamesReader.cs
  class ReferenceNamesReader (line 9) | public static class ReferenceNamesReader
    method GetReferenceNames (line 15) | public static List<Chromosome> GetReferenceNames(Stream stream)

FILE: ReferenceSequence/IO/ReferenceSequenceReader.cs
  class CompressedSequenceReader (line 12) | public sealed class CompressedSequenceReader : IDisposable
    method CompressedSequenceReader (line 31) | public CompressedSequenceReader(Stream stream)
    method Dispose (line 42) | public void Dispose()
    method CheckHeaderVersion (line 48) | private void CheckHeaderVersion()
    method GetCompressedSequence (line 59) | public void GetCompressedSequence(Chromosome chromosome)
    method GetMetadata (line 87) | private static (int SequenceOffset, int NumBases) GetMetadata(Extended...
    method GetCytogeneticBands (line 94) | private static Band[] GetCytogeneticBands(ExtendedBinaryReader reader)
    method GetMaskedEntries (line 111) | private static IntervalArray<MaskedEntry> GetMaskedEntries(ExtendedBin...
    method GetTwoBitBuffer (line 127) | private static byte[] GetTwoBitBuffer(ExtendedBinaryReader reader)
    method LoadHeader (line 133) | private void LoadHeader()
    method AddChromosomes (line 140) | private void AddChromosomes()
    method LoadIndex (line 149) | private IndexEntry[] LoadIndex()
    method AddReferenceName (line 174) | private void AddReferenceName(Chromosome chromosome)

FILE: ReferenceSequence/IO/ReferenceSequenceWriter.cs
  class ReferenceSequenceWriter (line 11) | internal sealed class ReferenceSequenceWriter : IDisposable
    method ReferenceSequenceWriter (line 16) | internal ReferenceSequenceWriter(Stream stream, IReadOnlyCollection<Ch...
    method Dispose (line 23) | public void Dispose() => _writer.Dispose();
    method WriteHeader (line 25) | private void WriteHeader(GenomeAssembly genomeAssembly, byte patchLeve...
    method Write (line 36) | internal void Write(List<Creation.ReferenceSequence> referenceSequences)
    method CreateIndex (line 58) | private static IndexEntry[] CreateIndex(IReadOnlyCollection<ReferenceB...
    method WriteIndex (line 74) | private void WriteIndex(IReadOnlyCollection<IndexEntry> indexEntries)
    method WriteReferenceBuffers (line 86) | private void WriteReferenceBuffers(IEnumerable<ReferenceBuffer> refere...

FILE: ReferenceSequence/ReferenceSequenceCommon.cs
  class ReferenceSequenceCommon (line 3) | public static class ReferenceSequenceCommon

FILE: ReferenceSequence/ReferenceUtilsMain.cs
  class ReferenceUtilsMain (line 8) | internal static class ReferenceUtilsMain
    method Main (line 10) | private static int Main(string[] args)

FILE: ReferenceSequence/Utilities/SequenceHelper.cs
  class SequenceHelper (line 8) | public static class SequenceHelper
    method GetDictionaries (line 10) | public static (Dictionary<ushort, Chromosome> refIndexToChromosome, Di...

FILE: RepeatExpansions/IO/RepeatExpansionReader.cs
  class RepeatExpansionReader (line 13) | public static class RepeatExpansionReader
    method Load (line 26) | public static IIntervalForest<RepeatExpansionPhenotype> Load(Stream st...
    method GetPhenotype (line 69) | private static (ushort RefIndex, Interval<RepeatExpansionPhenotype> In...
    method GetInterval (line 95) | private static Interval GetInterval(string s)
    method CheckHeader (line 104) | private static void CheckHeader(TextReader reader, GenomeAssembly desi...

FILE: RepeatExpansions/IRepeatExpansionProvider.cs
  type IRepeatExpansionProvider (line 5) | public interface IRepeatExpansionProvider
    method Annotate (line 7) | void Annotate(IAnnotatedPosition annotatedPosition);

FILE: RepeatExpansions/Matcher.cs
  class Matcher (line 8) | public sealed class Matcher
    method Matcher (line 12) | public Matcher(IIntervalForest<RepeatExpansionPhenotype> phenotypeFore...
    method GetMatchingAnnotations (line 14) | public ISupplementaryAnnotation GetMatchingAnnotations(RepeatExpansion...
    method ExactMatch (line 34) | private static bool ExactMatch(IInterval variant, IInterval variantPhe...

FILE: RepeatExpansions/PercentileUtilities.cs
  class PercentileUtilities (line 7) | public static class PercentileUtilities
    method ComputePercentiles (line 9) | public static double[] ComputePercentiles(int valueCount, IReadOnlyLis...
    method GetPercentile (line 26) | public static double GetPercentile<T>(T inputValue, T[] referenceValue...

FILE: RepeatExpansions/RepeatExpansionPhenotype.cs
  class RepeatExpansionPhenotype (line 8) | public sealed class RepeatExpansionPhenotype
    method RepeatExpansionPhenotype (line 22) | public RepeatExpansionPhenotype(ChromosomeInterval chromosomeInterval,...
    method GetAnnotation (line 34) | public string GetAnnotation(int repeatNumber)
    method GetJson (line 42) | private string GetJson(double percentile, IEnumerable<string> classifi...
    method GetClassifications (line 53) | private IEnumerable<string> GetClassifications(int repeatNumber)

FILE: RepeatExpansions/RepeatExpansionProvider.cs
  class RepeatExpansionProvider (line 13) | public sealed class RepeatExpansionProvider : IRepeatExpansionProvider
    method RepeatExpansionProvider (line 17) | public RepeatExpansionProvider(GenomeAssembly genomeAssembly, Dictiona...
    method GetTsvStream (line 27) | private static Stream GetTsvStream(GenomeAssembly genomeAssembly, stri...
    method Annotate (line 40) | public void Annotate(IAnnotatedPosition annotatedPosition)

FILE: RepeatExpansions/RepeatExpansionSupplementaryAnnotation.cs
  class RepeatExpansionSupplementaryAnnotation (line 7) | public sealed class RepeatExpansionSupplementaryAnnotation : ISupplement...
    method RepeatExpansionSupplementaryAnnotation (line 12) | public RepeatExpansionSupplementaryAnnotation(List<string> jsonEntries...
    method SerializeJson (line 14) | public void SerializeJson(StringBuilder sb) => sb.Append($"[{string.Jo...

FILE: SAUtils/AAConservation/AaConservationMain.cs
  class AaConservationMain (line 14) | public static class AaConservationMain
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 64) | private static ExitCodes ProgramExecution()

FILE: SAUtils/AAConservation/AaConservationUtilities.cs
  class AaConservationUtilities (line 9) | public static class AaConservationUtilities
    method GetTranscriptData (line 11) | public static TranscriptCacheData GetTranscriptData(Dictionary<ushort,...

FILE: SAUtils/AAConservation/ProteinConservationParser.cs
  class ProteinConservationParser (line 10) | public sealed class ProteinConservationParser:IDisposable
    method ProteinConservationParser (line 24) | public ProteinConservationParser(Stream stream)
    method GetItems (line 29) | public IEnumerable<ProteinConservationItem> GetItems()
    method ParseHeader (line 55) | private void ParseHeader(string line)
    method Dispose (line 65) | public void Dispose()=>_stream?.Dispose();

FILE: SAUtils/AAConservation/ProteinConservationWriter.cs
  class ProteinConservationWriter (line 13) | public sealed class ProteinConservationWriter:IDisposable
    method ProteinConservationWriter (line 25) | public ProteinConservationWriter(Stream stream, Stream groupStream, Tr...
    method Write (line 33) | public void Write(IEnumerable<ProteinConservationItem> items)
    method WriteTranscriptGroups (line 80) | private void WriteTranscriptGroups(Dictionary<string, List<string>> tr...
    method CheckProteinSetOverlap (line 102) | private static void CheckProteinSetOverlap(Dictionary<string, byte[]> ...
    method GetProteinWithUniqueScores (line 113) | private static Dictionary<string, byte[]> GetProteinWithUniqueScores(I...
    method Dispose (line 142) | public void Dispose()=>_writer?.Dispose();

FILE: SAUtils/ClinGen/DosageMapRegionItem.cs
  class DosageMapRegionItem (line 8) | public sealed class DosageMapRegionItem : ISuppIntervalItem
    method DosageMapRegionItem (line 16) | public DosageMapRegionItem(Chromosome chromosome, int start, int end, ...
    method GetJsonString (line 25) | public string GetJsonString()

FILE: SAUtils/ClinGen/DosageMapRegionParser.cs
  class DosageMapRegionParser (line 13) | public sealed class DosageMapRegionParser : IDisposable
    method DosageMapRegionParser (line 27) | public DosageMapRegionParser(Stream stream, Dictionary<string, Chromos...
    method Dispose (line 33) | public void Dispose()
    method GetItems (line 38) | public IEnumerable<DosageMapRegionItem> GetItems()
    method GetDosageMapRegionItem (line 61) | private DosageMapRegionItem GetDosageMapRegionItem(string line, Dictio...
    method ParseHeaderLine (line 79) | private void ParseHeaderLine(string line)
    method GetColumnIndices (line 84) | private void GetColumnIndices(string line)
    method ParseGenomeLocation (line 96) | private static (string chromName, int Start, int End) ParseGenomeLocat...
    method ReportStatistics (line 112) | private void ReportStatistics(IEnumerable<DosageMapRegionItem> items)

FILE: SAUtils/ClinGen/DosageMapRegions.cs
  class DosageMapRegions (line 16) | public static class DosageMapRegions
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/ClinGen/DosageSensitivity.cs
  class DosageSensitivity (line 13) | public static class DosageSensitivity
    method Run (line 18) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 49) | private static ExitCodes ProgramExecution()

FILE: SAUtils/ClinGen/DosageSensitivityItem.cs
  class DosageSensitivityItem (line 8) | public sealed class DosageSensitivityItem : ISuppGeneItem
    method DosageSensitivityItem (line 14) | public DosageSensitivityItem(string geneSymbol, int hiScore, int tsScore)
    method GetJsonString (line 26) | public string GetJsonString()

FILE: SAUtils/ClinGen/DosageSensitivityParser.cs
  class DosageSensitivityParser (line 12) | public sealed class DosageSensitivityParser:IDisposable
    method DosageSensitivityParser (line 26) | public DosageSensitivityParser(Stream stream)
    method Dispose (line 30) | public void Dispose()
    method GetItems (line 35) | public Dictionary<string, List<ISuppGeneItem>> GetItems()
    method GetGeneAndScores (line 72) | private ISuppGeneItem GetGeneAndScores(string line)
    method MissingIndices (line 83) | private bool MissingIndices()
    method ParseHeaderLine (line 91) | private void ParseHeaderLine(string line)
    method GetColumnIndices (line 96) | private void GetColumnIndices(string line)
    method ReportStatistics (line 106) | private void ReportStatistics(Dictionary<string, List<ISuppGeneItem>> ...

FILE: SAUtils/ClinGen/GeneDiseaseValidity.cs
  class GeneDiseaseValidity (line 16) | public static class GeneDiseaseValidity
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 59) | private static ExitCodes ProgramExecution()
    method GetHgncIdToGeneSymbols (line 82) | private static Dictionary<int, string> GetHgncIdToGeneSymbols()

FILE: SAUtils/ClinGen/GeneDiseaseValidityItem.cs
  class GeneDiseaseValidityItem (line 9) | public sealed class GeneDiseaseValidityItem: ISuppGeneItem
    method GeneDiseaseValidityItem (line 19) | public GeneDiseaseValidityItem(string geneSymbol, string diseaseId, st...
    method GetJsonString (line 29) | public string GetJsonString()
    method CompareDate (line 44) | public int CompareDate(GeneDiseaseValidityItem other)

FILE: SAUtils/ClinGen/GeneDiseaseValidityParser.cs
  class GeneDiseaseValidityParser (line 11) | public sealed class GeneDiseaseValidityParser: IDisposable
    method GeneDiseaseValidityParser (line 29) | public GeneDiseaseValidityParser(Stream stream, Dictionary<int, string...
    method Dispose (line 34) | public void Dispose()
    method GetItems (line 39) | public Dictionary<string, List<ISuppGeneItem>> GetItems()
    method GetLatestAnnotations (line 85) | private static Dictionary<string, List<ISuppGeneItem>> GetLatestAnnota...
    method AddLatest (line 102) | private static void AddLatest(Dictionary<string, GeneDiseaseValidityIt...
    method GetAnnotationItem (line 112) | private GeneDiseaseValidityItem GetAnnotationItem(string line)
    method ReportStatistics (line 136) | private void ReportStatistics(Dictionary<string, List<ISuppGeneItem>> ...
    method MissingIndices (line 162) | private bool MissingIndices()
    method ParseHeaderLine (line 171) | private void ParseHeaderLine(string line)

FILE: SAUtils/ClinGen/ScoreToDescription.cs
  class Data (line 5) | public static class Data

FILE: SAUtils/CosmicGeneFusions/Cache/ReferenceLoader.cs
  class ReferenceLoader (line 8) | public static class ReferenceLoader
    method GetRefIndexToChromosome (line 10) | public static Dictionary<ushort, Chromosome> GetRefIndexToChromosome(s...

FILE: SAUtils/CosmicGeneFusions/Cache/TranscriptCache.cs
  class TranscriptCache (line 12) | public sealed class TranscriptCache
    method TranscriptCache (line 16) | public TranscriptCache(Dictionary<string, ITranscript> idToTranscript)...
    method Create (line 18) | public static TranscriptCache Create(Stream stream, Dictionary<ushort,...
    method GetTranscriptIdToTranscript (line 26) | internal static Dictionary<string, ITranscript> GetTranscriptIdToTrans...
    method GetGene (line 50) | public (string GeneId, string GeneSymbol) GetGene(string transcriptId)
    method HandleMissingTranscripts (line 62) | internal static (string GeneId, string GeneSymbol) HandleMissingTransc...

FILE: SAUtils/CosmicGeneFusions/Conversion/CosmicConverter.cs
  class CosmicConverter (line 8) | public static class CosmicConverter
    method Convert (line 10) | public static Dictionary<ulong, string[]> Convert(Dictionary<int, Hash...
    method ToJsonArray (line 32) | internal static Dictionary<ulong, string[]> ToJsonArray(this Dictionar...
    method GetCosmicGeneFusion (line 40) | internal static (ulong FusionKey, string Json) GetCosmicGeneFusion(int...
    method AggregateRawCosmicGeneFusions (line 58) | internal static (int[] PubMedIds, int NumSamples, string HgvsNotation)...

FILE: SAUtils/CosmicGeneFusions/Conversion/CosmicGeneFusion.cs
  type CosmicGeneFusion (line 8) | public sealed record CosmicGeneFusion(string id, int numSamples, string[...
  type CosmicCount (line 18) | public sealed record CosmicCount(string name, int numSamples);

FILE: SAUtils/CosmicGeneFusions/Conversion/HgvsRnaFixer.cs
  class HgvsRnaFixer (line 6) | public static class HgvsRnaFixer
    method Fix (line 9) | public static string Fix(string hgvsNotation)

FILE: SAUtils/CosmicGeneFusions/Conversion/HgvsRnaParser.cs
  class HgvsRnaParser (line 10) | public static class HgvsRnaParser
    method GetTranscripts (line 14) | public static (string[] GeneSymbols, ulong FusionKey) GetTranscripts(s...
    method Parse (line 26) | public static (string TranscriptId5, string TranscriptId3) Parse(strin...

FILE: SAUtils/CosmicGeneFusions/Conversion/Histology.cs
  class Histology (line 8) | public static class Histology
    method GetCounts (line 11) | public static CosmicCount[] GetCounts(HashSet<RawCosmicGeneFusion> fus...
    method GetMostSpecificValue (line 34) | private static string GetMostSpecificValue(string primary, string subt...

FILE: SAUtils/CosmicGeneFusions/Conversion/RawCosmicGeneFusion.cs
  type RawCosmicGeneFusion (line 3) | public sealed record RawCosmicGeneFusion(int SampleId, int FusionId, str...

FILE: SAUtils/CosmicGeneFusions/Conversion/Site.cs
  class Site (line 8) | public static class Site
    method GetCounts (line 11) | public static CosmicCount[] GetCounts(HashSet<RawCosmicGeneFusion> fus...
    method CombineLevels (line 32) | private static string CombineLevels(string primary, string subtype1) =>

FILE: SAUtils/CosmicGeneFusions/CreateCosmicGeneFusions.cs
  class CreateCosmicGeneFusions (line 18) | public static class CreateCosmicGeneFusions
    method ProgramExecution (line 27) | private static ExitCodes ProgramExecution()
    method WriteGeneFusions (line 57) | private static void WriteGeneFusions(string outputDirectory, Dictionar...
    method CreateDataSourceVersion (line 66) | internal static DataSourceVersion CreateDataSourceVersion(string versi...
    method Run (line 72) | public static ExitCodes Run(string command, string[] commandArgs)

FILE: SAUtils/CosmicGeneFusions/IO/CosmicGeneFusionParser.cs
  class CosmicGeneFusionParser (line 7) | public static class CosmicGeneFusionParser
    method Parse (line 11) | public static Dictionary<int, HashSet<RawCosmicGeneFusion>> Parse(Stre...
    method GroupByFusionId (line 49) | private static Dictionary<int, HashSet<RawCosmicGeneFusion>> GroupByFu...
    method RemoveUnderlines (line 67) | internal static string RemoveUnderlines(string s) => s.Replace('_', ' ');

FILE: SAUtils/CosmicGeneFusions/IO/GeneFusionJsonWriter.cs
  class GeneFusionJsonWriter (line 13) | public sealed class GeneFusionJsonWriter : IDisposable
    method GeneFusionJsonWriter (line 17) | public GeneFusionJsonWriter(Stream stream, string jsonKey, IDataSource...
    method WriteHeader (line 25) | private void WriteHeader()
    method Write (line 31) | public void Write(Dictionary<ulong, string[]> geneKeyToJson)
    method Dispose (line 50) | public void Dispose() => _writer.Dispose();

FILE: SAUtils/CosmicGeneFusions/Utilities/CosmicCountUtilities.cs
  class CosmicCountUtilities (line 6) | public static class CosmicCountUtilities
    method GetCosmicCounts (line 8) | public static CosmicCount[] GetCosmicCounts(this Dictionary<string, in...

FILE: SAUtils/CreateClinvarDb/ClinVarMain.cs
  class ClinVarMain (line 14) | public static class ClinVarMain
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 62) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateClinvarDb/ClinVarStats.cs
  class ClinVarStats (line 15) | public class ClinVarStats
    method GetClinvarSaItemsStats (line 25) | public void GetClinvarSaItemsStats(List<IClinVarSaItem> items)
    method ToString (line 54) | public override string ToString()

FILE: SAUtils/CreateCosmicDb/Main.cs
  class Main (line 13) | public static class Main
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 64) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateDbsnpDb/Main.cs
  class Main (line 15) | public static class Main
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateDecipherDb/Main.cs
  class Main (line 16) | public static class Main
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 60) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateGlobalAllelesDb/Main.cs
  class Main (line 14) | public static class Main
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateGmeDb/Main.cs
  class Main (line 14) | public static class Main
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateOneKgDb/Main.cs
  class Main (line 14) | public static class Main
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/CreateTopMedDb/Main.cs
  class Main (line 14) | public static class Main
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/Custom/AllowedValues.cs
  class AllowedValues (line 7) | public static class AllowedValues
    method ValidatePredictionValue (line 26) | public static void ValidatePredictionValue(string value, string line)
    method ValidateFilterValue (line 32) | public static void ValidateFilterValue(string value, string line) => C...
    method ValidateIdentifierValue (line 34) | public static void ValidateIdentifierValue(string value, string line) ...
    method ValidateDescriptionValue (line 36) | public static void ValidateDescriptionValue(string value, string line)...
    method ValidateScoreValue (line 38) | public static void ValidateScoreValue(string value, string line)
    method IsEmptyValue (line 51) | public static bool IsEmptyValue(string value) => EmptyValues.Contains(...
    method CheckValueLength (line 53) | private static void CheckValueLength(string value, string line, int ma...

FILE: SAUtils/Custom/CaUtilities.cs
  class CaUtilities (line 16) | public static class CaUtilities
    method GetNsaWriter (line 18) | public static NsaWriter GetNsaWriter(Stream nsaStream, Stream indexStr...
    method GetNsiWriter (line 38) | public static NsiWriter GetNsiWriter(Stream nsiStream, DataSourceVersi...
    method GetNgaWriter (line 40) | public static NgaWriter GetNgaWriter(Stream ngaStream, GeneAnnotations...
    method WriteSmallVariants (line 47) | public static (string JsonTag, int NsaItemsCount, SaJsonSchema Interva...
    method GetInputFileName (line 57) | public static string GetInputFileName(string inputFilePath)

FILE: SAUtils/Custom/CustomGene.cs
  class CustomGene (line 9) | public sealed class CustomGene : ISuppGeneItem
    method CustomGene (line 17) | public CustomGene(string geneSymbol, List<string[]> values, SaJsonSche...
    method GetJsonString (line 25) | public string GetJsonString()

FILE: SAUtils/Custom/GeneAnnotationsParser.cs
  class GeneAnnotationsParser (line 16) | public sealed class GeneAnnotationsParser : IDisposable
    method GeneAnnotationsParser (line 41) | internal GeneAnnotationsParser(StreamReader reader, Dictionary<string,...
    method Create (line 48) | public static GeneAnnotationsParser Create(StreamReader reader, Dictio...
    method ParseHeaderLines (line 59) | internal void ParseHeaderLines()
    method InitiateSchema (line 91) | private void InitiateSchema()
    method CheckTagsAndSetJsonKeys (line 96) | private void CheckTagsAndSetJsonKeys()
    method AddHeaderAnnotation (line 111) | private void AddHeaderAnnotation()
    method GetItems (line 121) | public Dictionary<string, List<ISuppGeneItem>> GetItems(bool skipGeneI...
    method AddItem (line 145) | private void AddItem(string line, Dictionary<string, List<ISuppGeneIte...
    method GetUnknownGenes (line 179) | public IReadOnlyList<string> GetUnknownGenes() => _unknownGenes.OrderB...
    method Dispose (line 180) | public void Dispose() => _reader?.Dispose();

FILE: SAUtils/Custom/GeneMain.cs
  class GeneMain (line 13) | public static class GeneMain
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 61) | private static ExitCodes ProgramExecution()
    method GetOutputPrefix (line 85) | private static string GetOutputPrefix(string inputFilePath)
    method GetInputFileName (line 93) | private static string GetInputFileName(string inputFilePath)

FILE: SAUtils/Custom/ParserUtilities.cs
  class ParserUtilities (line 10) | public static class ParserUtilities
    method ParseMatchVariantsBy (line 12) | public static (bool MatchByAllele, bool IsArray, SaJsonValueType Prima...
    method ParseTags (line 50) | public static string[] ParseTags(string line, string prefix, int numRe...
    method ParseCategories (line 62) | public static CustomAnnotationCategories[] ParseCategories(string line...
    method ParseDescriptions (line 117) | public static string[] ParseDescriptions(string line, int numRequiredC...
    method ParseTypes (line 133) | public static SaJsonValueType[] ParseTypes(string line, int numRequire...
    method CheckPrefix (line 162) | internal static void CheckPrefix(string line, string prefix)
    method CheckJsonTagConflict (line 168) | public static bool CheckJsonTagConflict(string value)

FILE: SAUtils/Custom/VariantAnnotationsParser.cs
  class VariantAnnotationsParser (line 19) | public sealed class VariantAnnotationsParser : IDisposable
    method VariantAnnotationsParser (line 61) | internal VariantAnnotationsParser(StreamReader streamReader, ISequence...
    method Create (line 68) | public static VariantAnnotationsParser Create(StreamReader streamReade...
    method ParseHeaderLines (line 80) | internal void ParseHeaderLines()
    method CheckRequiredFields (line 124) | private void CheckRequiredFields(bool hasMatchByLine)
    method CheckTagsAndSetJsonKeys (line 137) | private void CheckTagsAndSetJsonKeys()
    method CheckPosAndRefColumns (line 152) | internal void CheckPosAndRefColumns()
    method CheckAltAndEndColumns (line 158) | internal void CheckAltAndEndColumns()
    method GetItems (line 187) | public IEnumerable<CustomItem> GetItems()
    method InitiateSchema (line 206) | private void InitiateSchema()
    method AddPredefinedTypeAnnotation (line 212) | private void AddPredefinedTypeAnnotation()
    method AddHeaderAnnotation (line 221) | private void AddHeaderAnnotation()
    method ExtractItems (line 232) | internal CustomItem ExtractItems(string line)
    method IsSymbolicAllele (line 286) | private bool IsSymbolicAllele(string altAllele)
    method IsInterval (line 291) | private bool IsInterval(string[] splits) => _endColumnIndex != -1 && !...
    method CheckAnnotationSorted (line 293) | private void CheckAnnotationSorted(Chromosome chrom, int position, str...
    method GetCustomIntervals (line 307) | public List<CustomInterval> GetCustomIntervals() => _intervals.Count >...
    method IsValidAltAllele (line 309) | internal static bool IsValidAltAllele(string sequence)
    method Dispose (line 322) | public void Dispose()

FILE: SAUtils/Custom/VariantMain.cs
  class VariantMain (line 16) | public static class VariantMain
    method Run (line 23) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 64) | private static ExitCodes ProgramExecution()
    method GetOutputPrefix (line 111) | private static string GetOutputPrefix(string inputFilePath)

FILE: SAUtils/Dann/Create.cs
  class Create (line 16) | public static class Create
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 59) | private static ExitCodes ProgramExecution()

FILE: SAUtils/DataStructures/AlleleFrequencyItem.cs
  class AlleleFrequencyItem (line 7) | public sealed class AlleleFrequencyItem:ISupplementaryDataItem
    method AlleleFrequencyItem (line 16) | public AlleleFrequencyItem(Chromosome chromosome, int position, string...
    method GetJsonString (line 26) | public string GetJsonString()

FILE: SAUtils/DataStructures/AncestralAlleleItem.cs
  class AncestralAlleleItem (line 6) | public sealed class AncestralAlleleItem: ISupplementaryDataItem
    method AncestralAlleleItem (line 15) | public AncestralAlleleItem(Chromosome chromosome, int position, string...
    method GetJsonString (line 25) | public string GetJsonString()

FILE: SAUtils/DataStructures/ClinGenItem.cs
  type ClinicalInterpretation (line 10) | public enum ClinicalInterpretation
  class ClinGenItem (line 22) | public sealed class ClinGenItem:ISuppIntervalItem
    method ClinGenItem (line 41) | public ClinGenItem(string id, Chromosome chromosome, int start, int en...
    method GetJsonString (line 59) | public string GetJsonString()
    method GetClinicalDescription (line 81) | private static string GetClinicalDescription(ClinicalInterpretation cl...

FILE: SAUtils/DataStructures/ClinVarItem.cs
  class ClinVarItem (line 12) | public sealed class ClinVarItem : IClinVarSaItem
    method ClinVarItem (line 38) | public ClinVarItem(Chromosome chromosome,
    method GetJsonString (line 80) | public string GetJsonString()
    method GetValues (line 85) | private List<string[]> GetValues()
    method CompareTo (line 108) | public int CompareTo(IClinVarSaItem other)

FILE: SAUtils/DataStructures/ComputingUtilities.cs
  class ComputingUtilities (line 6) | public static class ComputingUtilities
    method ComputeFrequency (line 8) | public static string ComputeFrequency(int? alleleNumber, int? alleleCo...
    method GetCoverage (line 15) | public static int GetCoverage(double depth, double allAlleleNumber)

FILE: SAUtils/DataStructures/ConservationItem.cs
  class PhylopItem (line 6) | public sealed class PhylopItem
    method PhylopItem (line 12) | public PhylopItem(Chromosome chromosome, int position, double score)

FILE: SAUtils/DataStructures/CosmicItem.cs
  class CosmicItem (line 11) | public sealed class CosmicItem : ISupplementaryDataItem
    method CosmicItem (line 24) | public CosmicItem(
    class CosmicStudy (line 44) | public sealed class CosmicStudy : IEquatable<CosmicStudy>
      method CosmicStudy (line 54) | public CosmicStudy(string studyId, IEnumerable<string> histologies, ...
      method Equals (line 61) | public bool Equals(CosmicStudy other)
      method GetHashCode (line 69) | public override int GetHashCode()
    method GetJsonString (line 77) | public string GetJsonString()
    method GetTissueCounts (line 95) | internal Dictionary<string,int> GetTissueCounts()
    method GetCancerTypeCounts (line 116) | internal Dictionary<string,int> GetCancerTypeCounts()
    method GetJsonStringFromDict (line 136) | private static string GetJsonStringFromDict(string dataType, Dictionar...

FILE: SAUtils/DataStructures/CounterDictionary.cs
  class CounterDictionary (line 8) | public sealed class CounterDictionary<TKey> : Dictionary<TKey, uint>, IJ...
    method Add (line 12) | public void Add(TKey key)
    method SerializeJson (line 25) | public void SerializeJson(StringBuilder sb)

FILE: SAUtils/DataStructures/CustomInterval.cs
  class CustomInterval (line 10) | public sealed class CustomInterval : ISuppIntervalItem
    method CustomInterval (line 24) | public CustomInterval(Chromosome chromosome, int start, int end, List<...
    method GetJsonString (line 35) | public string GetJsonString()

FILE: SAUtils/DataStructures/CustomItem.cs
  class CustomItem (line 10) | public sealed class CustomItem : ISupplementaryDataItem
    method CustomItem (line 20) | public CustomItem(Chromosome chromosome, int start, string refAllele, ...
    method GetJsonString (line 31) | public string GetJsonString()

FILE: SAUtils/DataStructures/DbSnpItem.cs
  class DbSnpItem (line 6) | public sealed class DbSnpItem: ISupplementaryDataItem
    method DbSnpItem (line 16) | public DbSnpItem(Chromosome chromosome,
    method GetJsonString (line 32) | public string GetJsonString()

FILE: SAUtils/DataStructures/DecipherItem.cs
  class DecipherItem (line 8) | public sealed class DecipherItem : ISuppIntervalItem
    method DecipherItem (line 20) | public DecipherItem(Chromosome chrom, int start, int end,
    method GetJsonString (line 33) | public string GetJsonString()

FILE: SAUtils/DataStructures/DgvItem.cs
  class DgvItem (line 9) | public sealed class DgvItem : ISuppIntervalItem
    method DgvItem (line 28) | public DgvItem(string id, Chromosome chromosome, int start, int end, i...
    method GetJsonString (line 45) | public string GetJsonString()
    method Equals (line 64) | public override bool Equals(object obj)
    method GetHashCode (line 82) | public override int GetHashCode()

FILE: SAUtils/DataStructures/GlobalMinorItem.cs
  class GlobalMinorItem (line 8) | public sealed class GlobalMinorItem:ISupplementaryDataItem
    method GlobalMinorItem (line 18) | public GlobalMinorItem(Chromosome chromosome, int position, string all...
    method GetJsonString (line 26) | public string GetJsonString()

FILE: SAUtils/DataStructures/GmeItem.cs
  class GmeItem (line 8) | public sealed class GmeItem : ISupplementaryDataItem
    method GmeItem (line 22) | public GmeItem(Chromosome chrom, int position, string refAllele, strin...
    method GetJsonString (line 35) | public string GetJsonString()

FILE: SAUtils/DataStructures/GnomadItem.cs
  type GnomadDataType (line 10) | public enum GnomadDataType : byte
  class GnomadItem (line 17) | public sealed class GnomadItem : ISupplementaryDataItem
    method GnomadItem (line 76) | public GnomadItem(Chromosome chromosome,
    method RemoveAlleleNumberZero (line 154) | private void RemoveAlleleNumberZero()
    method GetJsonString (line 256) | public string GetJsonString()
    method CompareTo (line 329) | public static int CompareTo(GnomadItem item, GnomadItem other)

FILE: SAUtils/DataStructures/GnomadSvItem.cs
  type GnomadSvItem (line 10) | public sealed record GnomadSvItem(Chromosome Chromosome, string InputLin...

FILE: SAUtils/DataStructures/KeyCounts.cs
  class KeyCounts (line 8) | public class KeyCounts: IJsonSerializer
    method KeyCounts (line 12) | public KeyCounts(IEnumerable<string> keys)
    method Increment (line 21) | public void Increment(string key)
    method SerializeJson (line 26) | public void SerializeJson(StringBuilder sb)

FILE: SAUtils/DataStructures/MinHeap.cs
  class MinHeap (line 6) | public sealed class MinHeap<T>
    method MinHeap (line 12) | public MinHeap(Func<T,T, int> comparerFunc)
    method Add (line 18) | public void Add(T item)
    method Heapify (line 24) | private void Heapify()
    method ExtractMin (line 38) | public T ExtractMin()
    method SwapItems (line 63) | private static void SwapItems(List<T> list, int i, int j)
    method GetMin (line 70) | public T GetMin()
    method Count (line 75) | public int Count()
    method ToString (line 80) | public override string ToString()

FILE: SAUtils/DataStructures/OmimItem.cs
  class OmimItem (line 13) | public sealed class OmimItem : ISuppGeneItem
    method OmimItem (line 22) | public OmimItem(string geneSymbol, string geneName, string description...
    method GetJsonString (line 32) | public string GetJsonString()
    class Phenotype (line 54) | public sealed class Phenotype : IJsonSerializer
      method Phenotype (line 64) | public Phenotype(int mimNumber, string phenotype, string description...
      method SerializeJson (line 76) | public void SerializeJson(StringBuilder sb)
    type Mapping (line 101) | public enum Mapping : byte
    type Comment (line 113) | public enum Comment : byte

FILE: SAUtils/DataStructures/OneKGenItem.cs
  class OneKGenItem (line 8) | public sealed class OneKGenItem : ISupplementaryDataItem
    method OneKGenItem (line 31) | public OneKGenItem(Chromosome chromosome,
    method GetJsonString (line 72) | public string GetJsonString()

FILE: SAUtils/DataStructures/OnekGenSvItem.cs
  class OnekGenSvItem (line 9) | public sealed class OnekGenSvItem: ISuppIntervalItem
    method OnekGenSvItem (line 25) | public OnekGenSvItem(Chromosome chromosome, int start, int end, Varian...
    method GetJsonString (line 45) | public string GetJsonString()

FILE: SAUtils/DataStructures/RefMinorItem.cs
  class RefMinorItem (line 8) | public sealed class RefMinorItem:ISupplementaryDataItem
    method RefMinorItem (line 16) | public RefMinorItem(Chromosome chromosome, int position, string global...
    method GetJsonString (line 23) | public string GetJsonString()

FILE: SAUtils/DataStructures/SuppDataUtilities.cs
  class SuppDataUtilities (line 11) | public static class SuppDataUtilities
    method CompareTo (line 13) | public static int CompareTo(ISupplementaryDataItem item, ISupplementar...
    method Trim (line 19) | public static void Trim(this ISupplementaryDataItem saItem)
    method BinarySearch (line 31) | public static int BinarySearch<T>(List<T> items, int value) where T:IC...
    method DeDuplicatePrimateAiItems (line 48) | public static List<ISupplementaryDataItem> DeDuplicatePrimateAiItems(L...
    method RemoveConflictingAlleles (line 70) | public static List<ISupplementaryDataItem> RemoveConflictingAlleles(Li...
    method GetPositionalAnnotation (line 101) | public static ISupplementaryDataItem GetPositionalAnnotation(List<ISup...
    method GetConsensus (line 117) | private static ISupplementaryDataItem GetConsensus(List<ISupplementary...
    method GetGlobalMinor (line 135) | private static ISupplementaryDataItem GetGlobalMinor(List<ISupplementa...
    method GetMostFrequentAllele (line 165) | public static string GetMostFrequentAllele(Dictionary<string, double> ...

FILE: SAUtils/DataStructures/TopMedItem.cs
  class TopMedItem (line 8) | public sealed class TopMedItem : ISupplementaryDataItem
    method TopMedItem (line 22) | public TopMedItem(Chromosome chrom, int position, string refAllele, st...
    method GetJsonString (line 35) | public string GetJsonString()

FILE: SAUtils/DbSnpRemapper/ChromMapper.cs
  class ChromMapper (line 14) | internal sealed class ChromMapper
    method ChromMapper (line 26) | public ChromMapper(StreamReader srcReader, StreamReader destReader, St...
    method Map (line 39) | public Dictionary<string, StreamWriter> Map()
    method ProcessNextChromSource (line 73) | private string ProcessNextChromSource(string line)
    method GetNextChromDestinations (line 122) | private string GetNextChromDestinations(string line)
    method WriteRemappedEntry (line 163) | private void WriteRemappedEntry(string chrom, int pos, string refAllel...

FILE: SAUtils/DbSnpRemapper/DbSnpRemapperMain.cs
  class DbSnpRemapperMain (line 13) | public static class DbSnpRemapperMain
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 63) | private static ExitCodes ProgramExecution()

FILE: SAUtils/DbSnpRemapper/GenomicLocation.cs
  type GenomicLocation (line 3) | public struct GenomicLocation
    method GenomicLocation (line 8) | public GenomicLocation(string chrom, int pos)

FILE: SAUtils/DbSnpRemapper/LeftoverMapper.cs
  class LeftoverMapper (line 14) | public sealed class LeftoverMapper
    method LeftoverMapper (line 21) | public LeftoverMapper(StreamReader leftoverReader, StreamReader destRe...
    method Map (line 30) | public int Map()
    method WriteMappedLeftovers (line 94) | private void WriteMappedLeftovers(Dictionary<(long, string), List<Geno...
    method AppendToChromFile (line 113) | private void AppendToChromFile(List<GenomicLocation> leftoverLocations...

FILE: SAUtils/DbSnpRemapper/Utilities.cs
  class Utilities (line 6) | public static class Utilities
    method GetRsids (line 8) | public static long[] GetRsids(string idField)

FILE: SAUtils/DegenerateBaseUtilities.cs
  class DegenerateBaseUtilities (line 5) | public static class DegenerateBaseUtilities
    method GetAllPossibleSequences (line 21) | public static List<string> GetAllPossibleSequences(string sequenceWith...
    method GetSequences (line 28) | private static void GetSequences(string inputSequence, ICollection<str...
    method MapBase (line 40) | private static List<char> MapBase(char inputBase) => DegenerateBaseNot...

FILE: SAUtils/ExtractCosmicSvs/CosmicCnvItem.cs
  class CosmicCnvItem (line 11) | public sealed class CosmicCnvItem
    method CosmicCnvItem (line 23) | public CosmicCnvItem(int cnvId, Chromosome chromosome, int start, int ...
    method GetJsonString (line 39) | public string GetJsonString()
    method GetJsonStrings (line 56) | private static IEnumerable<string> GetJsonStrings(Dictionary<string, i...
    method Merge (line 64) | public void Merge(CosmicCnvItem other)
    method MergeCounts (line 80) | private static void MergeCounts(Dictionary<string, int> countDict1, Di...

FILE: SAUtils/ExtractCosmicSvs/CosmicCnvReader.cs
  class CosmicCnvReader (line 11) | public sealed class CosmicCnvReader:IDisposable
    method CosmicCnvReader (line 36) | public CosmicCnvReader(Stream cnvStream, Dictionary<string, Chromosome...
    method GetEntries (line 43) | public IEnumerable<CosmicCnvItem> GetEntries()
    method GetColumnIndices (line 82) | internal void GetColumnIndices(string headerLine)
    method ExtractCosmicCnv (line 161) | private CosmicCnvItem ExtractCosmicCnv(string line)
    method GetChromStartStop (line 207) | private static (string, int, int) GetChromStartStop(string chromPos)
    method TryAddValue (line 216) | private static void TryAddValue(Dictionary<string, int> cancerTypes, s...
    method Dispose (line 222) | public void Dispose() => _reader?.Dispose();

FILE: SAUtils/ExtractCosmicSvs/CosmicSvReader.cs
  class CosmicSvReader (line 9) | public sealed class CosmicSvReader:IDisposable
    method CosmicSvReader (line 18) | public CosmicSvReader(Stream cnvStream, Stream breakendStream, DataSou...
    method Dispose (line 52) | public void Dispose()

FILE: SAUtils/ExtractCosmicSvs/ExtractCosmicSvsMain.cs
  class ExtractCosmicSvsMain (line 11) | public static class ExtractCosmicSvsMain
    method Run (line 18) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 60) | private static ExitCodes ProgramExecution()

FILE: SAUtils/ExtractMiniSa/ExtractMiniSaMain.cs
  class ExtractMiniSaMain (line 8) | internal static class ExtractMiniSaMain
    method ProgramExecution (line 26) | private static ExitCodes ProgramExecution()
    method Run (line 36) | public static ExitCodes Run(string command,string[] commandArgs)

FILE: SAUtils/ExtractMiniSa/MiniSaExtractor.cs
  class MiniSaExtractor (line 7) | public sealed class MiniSaExtractor
    method MiniSaExtractor (line 18) | public MiniSaExtractor(string compressedRefFile, string saPath, int be...
    method GetMiniSaPath (line 33) | private static string GetMiniSaPath(string referenceName, int begin, i...
    method Extract (line 72) | public int Extract()
    method GetGlobaleMajorAlleleAndRefMinors (line 100) | private List<(int,string)> GetGlobaleMajorAlleleAndRefMinors(IEnumerab...

FILE: SAUtils/ExtractMiniXml/ExtractMiniXmlMain.cs
  class ExtractMiniXmlMain (line 10) | public static class ExtractMiniXmlMain
    method ProgramExecution (line 16) | private static ExitCodes ProgramExecution()
    method GetAccessions (line 34) | private static List<string> GetAccessions(string accString)
    method Run (line 51) | public static ExitCodes Run(string command, string[] commandArgs)

FILE: SAUtils/ExtractMiniXml/RcvXmlExtractor.cs
  class RcvXmlExtractor (line 10) | public sealed class RcvXmlExtractor
    method RcvXmlExtractor (line 20) | public RcvXmlExtractor(string inputXmlFile, List<string>  rcvIds, stri...
    method Extract (line 27) | public void Extract()
    method DetectRcv (line 59) | private static string DetectRcv(List<string> rcvs, string rcvContents)
    method WriteToFile (line 73) | private static void WriteToFile(string fileName, string targetedContent)

FILE: SAUtils/ExtractMiniXml/VcvXmlExtractor.cs
  class VcvXmlExtractor (line 10) | public sealed class VcvXmlExtractor
    method VcvXmlExtractor (line 23) | public VcvXmlExtractor(string inputXmlFile, List<string> vcvIds, strin...
    method Extract (line 30) | public void Extract()
    method WriteToFile (line 62) | private static void WriteToFile(string fileName, string targetedContent)
    method DetectVcv (line 73) | private static string DetectVcv(List<string> vcvs, string rcvContents)

FILE: SAUtils/FusionCatcher/CollectionType.cs
  type CollectionType (line 3) | public enum CollectionType : byte

FILE: SAUtils/FusionCatcher/CreateFusionCatcher.cs
  class CreateFusionCatcher (line 21) | public static class CreateFusionCatcher
    method ProgramExecution (line 29) | private static ExitCodes ProgramExecution()
    method GetReferences (line 131) | private static Dictionary<ushort, Chromosome> GetReferences(string ref...
    method AddGenes (line 140) | private static void AddGenes(string cachePath, Dictionary<ushort, Chro...
    method WriteGeneFusions (line 162) | private static void WriteGeneFusions(string outputDirectory, uint[] on...
    method CreateDataSourceVersion (line 173) | private static DataSourceVersion CreateDataSourceVersion(string filePath)
    method GetStream (line 189) | private static Stream GetStream(string filename) => GZipUtilities.GetA...
    method Run (line 191) | public static ExitCodes Run(string command, string[] commandArgs)

FILE: SAUtils/FusionCatcher/FusionCatcherDataSource.cs
  class FusionCatcherDataSource (line 9) | public static class FusionCatcherDataSource
    method Parse (line 11) | public static void Parse(Stream stream, GeneFusionSource source, Colle...

FILE: SAUtils/FusionCatcher/FusionCatcherOncogenes.cs
  class FusionCatcherOncogenes (line 8) | public static class FusionCatcherOncogenes
    method Parse (line 10) | public static void Parse(Stream stream, string description, HashSet<ui...

FILE: SAUtils/FusionCatcher/GeneFusionSourceBuilder.cs
  class GeneFusionSourceBuilder (line 6) | public sealed class GeneFusionSourceBuilder
    method Create (line 14) | public GeneFusionSourceCollection Create()

FILE: SAUtils/FusionCatcher/GeneFusionSourceWriter.cs
  class GeneFusionSourceWriter (line 13) | public sealed class GeneFusionSourceWriter : IDisposable
    method GeneFusionSourceWriter (line 17) | public GeneFusionSourceWriter(Stream stream, string jsonKey, IDataSour...
    method WriteHeader (line 25) | private void WriteHeader()
    method Write (line 31) | public void Write(uint[] oncogeneKeys, GeneFusionSourceCollection[] in...
    method Dispose (line 50) | public void Dispose() => _writer.Dispose();

FILE: SAUtils/FusionCatcher/IndexBuilder.cs
  class IndexBuilder (line 9) | public static class IndexBuilder
    method Convert (line 11) | public static (GeneFusionSourceCollection[] Index, GeneFusionIndexEntr...
    method BuildIndexEntries (line 23) | private static GeneFusionIndexEntry[] BuildIndexEntries(Dictionary<ulo...
    method BuildIndex (line 40) | private static (GeneFusionSourceCollection[] Index, Dictionary<GeneFus...
    method GetSourceCollection (line 72) | private static Dictionary<ulong, GeneFusionSourceCollection> GetSource...
    class BuilderMetadata (line 86) | private sealed class BuilderMetadata

FILE: SAUtils/GERP/GerpMain.cs
  class GerpMain (line 16) | public class GerpMain
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 60) | private static ExitCodes ProgramExecution()

FILE: SAUtils/GeneIdentifiers/GeneSymbolUpdater.cs
  class GeneSymbolUpdater (line 11) | public sealed class GeneSymbolUpdater
    method GeneSymbolUpdater (line 26) | public GeneSymbolUpdater(Dictionary<string, string> entrezGeneIdToSymb...
    method UpdateGeneSymbol (line 34) | public string UpdateGeneSymbol(string oldGeneSymbol, string ensemblGen...
    method ResolveGeneSymbolConflict (line 77) | private static string ResolveGeneSymbolConflict(string oldGeneSymbol, ...
    method AddSymbol (line 94) | private static void AddSymbol(Dictionary<string, int> symbolCounts, st...
    method GetSymbol (line 100) | private static string GetSymbol(string geneId, IReadOnlyDictionary<str...
    method DisplayStatistics (line 106) | public void DisplayStatistics()

FILE: SAUtils/GeneIdentifiers/GeneUtilities.cs
  class GeneUtilities (line 11) | public static class GeneUtilities
    method GetGeneSymbolFromId (line 13) | public static string GetGeneSymbolFromId(string geneId, Dictionary<str...
    method ParseUniversalGeneArchive (line 22) | public static (Dictionary<string, string> EntrezGeneIdToSymbol, Dictio...
    method GetGeneIdToSymbol (line 42) | private static Dictionary<string, string> GetGeneIdToSymbol(this IEnum...

FILE: SAUtils/GenericScore/GenericScoreParser/GenericScoreItem.cs
  class GenericScoreItem (line 7) | public sealed class GenericScoreItem : ISupplementaryDataItem
    method GenericScoreItem (line 16) | public GenericScoreItem(Chromosome chromosome, int position, string re...
    method GetJsonString (line 25) | [Obsolete]

FILE: SAUtils/GenericScore/GenericScoreParser/GenericScoreParser.cs
  class GenericScoreParser (line 11) | public sealed class GenericScoreParser : IDisposable
    method GenericScoreParser (line 21) | public GenericScoreParser(
    method GetItems (line 39) | public IEnumerable<GenericScoreItem> GetItems()
    method GetItemsAtOnePosition (line 83) | private IEnumerable<GenericScoreItem> GetItemsAtOnePosition(Chromosome...
    method MaxRepresentativeScores (line 95) | public static void MaxRepresentativeScores(string altAllele, double sc...
    method NonConflictingScore (line 101) | public static void NonConflictingScore(string altAllele, double score,...
    method MinRepresentativeScores (line 109) | public static void MinRepresentativeScores(string altAllele, double sc...
    method Dispose (line 115) | public void Dispose()

FILE: SAUtils/GenericScore/GenericScoreParser/SaItemValidator.cs
  class SaItemValidator (line 7) | public sealed class SaItemValidator
    method SaItemValidator (line 19) | public SaItemValidator(bool? strictSnvCheck, bool? strictReferenceCheck)
    method Validate (line 25) | public bool Validate(GenericScoreItem saItem, ISequenceProvider refPro...
    method CheckReference (line 30) | private bool CheckReference(GenericScoreItem saItem, ISequenceProvider...
    method CheckParRegion (line 49) | private bool CheckParRegion(GenericScoreItem saItem, ISequenceProvider...
    method CheckSnv (line 56) | private bool CheckSnv(GenericScoreItem saItem)

FILE: SAUtils/GenericScore/ParserSettings.cs
  class ParserSettings (line 6) | public sealed class ParserSettings
    method ParserSettings (line 14) | public ParserSettings(
  class ColumnIndex (line 26) | public sealed class ColumnIndex
    method ColumnIndex (line 35) | public ColumnIndex(

FILE: SAUtils/GenericScore/ScoreFileWriter.cs
  class ScoreFileWriter (line 16) | public sealed class ScoreFileWriter : IDisposable
    method ScoreFileWriter (line 28) | public ScoreFileWriter(
    method WriteHeader (line 72) | private void WriteHeader()
    method Write (line 79) | public void Write(IEnumerable<GenericScoreItem> saItems)
    method AddEncodedScoreToNucleotideArray (line 166) | private void AddEncodedScoreToNucleotideArray(byte[] nucleotideArray, ...
    method AddNewChromosome (line 180) | private (ushort chromosomeIndex, int chromosomeStartingPosition) AddNe...
    method WriteBlankBlocks (line 189) | private void WriteBlankBlocks(ushort chromosomeIndex, int blankBlockCo...
    method WriteToDiskAndUpdateIndex (line 203) | private void WriteToDiskAndUpdateIndex(ushort chromosomeIndex)
    method AddBlockToIndex (line 210) | private void AddBlockToIndex(ushort chromosomeIndex, long fileStarting...
    method PositionToBlockLocation (line 215) | private (uint blockNumber, uint localBlockIndex) PositionToBlockLocati...
    method Dispose (line 222) | public void Dispose()

FILE: SAUtils/GenericScore/WriterSettings.cs
  class WriterSettings (line 8) | public sealed class WriterSettings
    method WriterSettings (line 22) | public WriterSettings(

FILE: SAUtils/GnomadGeneScores/GnomadGeneItem.cs
  class GnomadGeneItem (line 8) | public sealed class GnomadGeneItem : ISuppGeneItem, IComparable<GnomadGe...
    method GnomadGeneItem (line 19) | public GnomadGeneItem(string gene, double? pLi, double? pRec, double? ...
    method GetJsonString (line 31) | public string GetJsonString()
    method CompareTo (line 49) | public int CompareTo(GnomadGeneItem other)

FILE: SAUtils/GnomadGeneScores/GnomadGeneParser.cs
  class GnomadGeneParser (line 9) | public sealed class GnomadGeneParser : IDisposable
    method GnomadGeneParser (line 32) | public GnomadGeneParser(StreamReader reader, Dictionary<string, string...
    method Dispose (line 38) | public void Dispose()
    method GetItems (line 43) | public Dictionary<string, List<ISuppGeneItem>> GetItems()
    method GetGeneAndScores (line 76) | private ISuppGeneItem GetGeneAndScores(string line)
    method GetScore (line 96) | private static double? GetScore(string score)
    method GetColumnIndices (line 102) | private bool GetColumnIndices(string line)

FILE: SAUtils/GnomadGeneScores/GnomadGenesMain.cs
  class GnomadGenesMain (line 16) | public static class GnomadGenesMain
    method Run (line 23) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 68) | private static ExitCodes ProgramExecution()
    method LoadGenesFromCache (line 92) | private static Dictionary<string, string> LoadGenesFromCache(Reference...

FILE: SAUtils/InputFileParsers/AncestralAlleleReader.cs
  class AncestralAlleleReader (line 14) | public sealed class AncestralAlleleReader:IDisposable
    method AncestralAlleleReader (line 22) | public AncestralAlleleReader(StreamReader streamReader, ISequenceProvi...
    method Clear (line 29) | private void Clear()
    method GetItems (line 34) | public IEnumerable<AncestralAlleleItem> GetItems()
    method ExtractItems (line 56) | private List<AncestralAlleleItem> ExtractItems(string vcfLine)
    method ParseInfoField (line 90) | private void ParseInfoField(string infoFields)
    method GetAncestralAllele (line 105) | private static string GetAncestralAllele(string value)
    method IsNucleotide (line 113) | private static bool IsNucleotide(char c)
    method Dispose (line 119) | public void Dispose()

FILE: SAUtils/InputFileParsers/ClinGen/ClinGenReader.cs
  class ClinGenReader (line 11) | public sealed class ClinGenReader : IDisposable
    method ClinGenReader (line 20) | public ClinGenReader(StreamReader reader, Dictionary<string, Chromosom...
    method GetItems (line 26) | public IEnumerable<ClinGenItem> GetItems()
    method GetVariantType (line 58) | private static VariantType GetVariantType(string variantTypeDescription)
    method GetClinInterpretation (line 73) | private static ClinicalInterpretation GetClinInterpretation(string s)
    method IsClinGenHeader (line 92) | private static bool IsClinGenHeader(string line)
    method Dispose (line 97) | public void Dispose()

FILE: SAUtils/InputFileParsers/ClinVar/ClinVarCommon.cs
  class ClinVarCommon (line 6) | public static class ClinVarCommon
    method NormalizeAllele (line 8) | public static string NormalizeAllele(string allele)
    type ReviewStatus (line 38) | public enum ReviewStatus
    method GetSignificances (line 86) | public static string[] GetSignificances(string description, string exp...

FILE: SAUtils/InputFileParsers/ClinVar/ClinVarParser.cs
  class ClinVarParser (line 19) | public sealed class ClinVarParser :IDisposable
    method ClearClinvarFields (line 77) | private void ClearClinvarFields()
    method ClinVarParser (line 95) | public ClinVarParser(Stream rcvStream, Stream vcvStream, ISequenceProv...
    method GetItems (line 105) | public IEnumerable<ISupplementaryDataItem> GetItems()
    method ReportStatistics (line 146) | private void ReportStatistics(List<IClinVarSaItem> items)
    method GetRcvItems (line 161) | public List<ClinVarItem> GetRcvItems()
    method GetVariationRecords (line 198) | private List<VcvItem> GetVariationRecords()
    method GetValidItems (line 207) | private List<ClinVarItem> GetValidItems(List<ClinVarItem> clinVarItems)
    method ExtractClinVarItems (line 261) | private List<ClinVarItem> ExtractClinVarItems(XElement xElement)
    method GetOmimIds (line 307) | private HashSet<string> GetOmimIds(ClinvarVariant variant)
    method ParseAssertions (line 319) | private void ParseAssertions(XElement xElement)
    method IsInvalidVariant (line 331) | private bool IsInvalidVariant(ClinvarVariant variant)
    method ValidateRefAllele (line 351) | private bool ValidateRefAllele(ClinVarItem clinvarVariant)
    method GetReferenceAllele (line 362) | private static string GetReferenceAllele(ClinVarItem variant, ISequenc...
    method GetAltAllele (line 367) | private static string GetAltAllele(ClinVarItem variant, ISequence comp...
    method ParseDate (line 372) | internal static long ParseDate(string s)
    method ParseRefClinVarAssertion (line 389) | private void ParseRefClinVarAssertion(XElement xElement)
    method ParseClinvarAssertion (line 406) | private void ParseClinvarAssertion(XElement xElement)
    method ParseObservedIn (line 418) | private void ParseObservedIn(XElement xElement)
    method ParseTraitSet (line 432) | private void ParseTraitSet(XElement xElement)
    method ParseTrait (line 442) | private void ParseTrait(XElement xElement)
    method ParsePnenotype (line 454) | private void ParsePnenotype(XElement xElement)
    method ParsePhenotypeElementValue (line 463) | private void ParsePhenotypeElementValue(XElement xElement)
    method ParseXref (line 481) | private void ParseXref(XElement xElement)
    method TrimOmimId (line 509) | private static string TrimOmimId(string id)
    method ParseCitation (line 517) | private void ParseCitation(XElement xElement)
    method ParseGenotypeSet (line 541) | private void ParseGenotypeSet(XElement xElement)
    method ParseMeasureSet (line 551) | private void ParseMeasureSet(XElement xElement)
    method ParseMeasure (line 564) | private void ParseMeasure(XElement xElement, string variantId)
    method UpdateVariantType (line 606) | private static void UpdateVariantType(ClinvarVariant variant)
    method AddIupacVariants (line 637) | private void AddIupacVariants(ClinvarVariant variant, List<ClinvarVari...
    method GetClinvarVariant (line 657) | private static ClinvarVariant GetClinvarVariant(XElement xElement, Gen...
    method AdjustVariant (line 692) | private static void AdjustVariant(ref int start, ref string referenceA...
    method GetClinicalSignificance (line 704) | private void GetClinicalSignificance(XElement xElement)
    method ValidateSignificance (line 717) | private void ValidateSignificance(string[] significances)
    method Dispose (line 729) | public void Dispose()

FILE: SAUtils/InputFileParsers/ClinVar/ClinVarSchema.cs
  class ClinVarSchema (line 9) | public static class ClinVarSchema
    method Get (line 48) | public static SaJsonSchema Get()

FILE: SAUtils/InputFileParsers/ClinVar/ClinVarVariationReader.cs
  class ClinVarVariationReader (line 10) | public sealed class ClinVarVariationReader : IDisposable
    method ClinVarVariationReader (line 30) | public ClinVarVariationReader(Stream readStream)
    method GetItems (line 35) | public IEnumerable<VcvItem> GetItems()
    method ExtractVariantRecord (line 55) | private static VcvItem ExtractVariantRecord(XElement xElement)
    method GetSignificances (line 95) | private static List<string> GetSignificances(XElement interpretations)
    method Dispose (line 120) | public void Dispose()

FILE: SAUtils/InputFileParsers/ClinVar/ClinvarVariant.cs
  class ClinvarVariant (line 6) | public sealed class ClinvarVariant
    method ClinvarVariant (line 17) | public ClinvarVariant(Chromosome chr, int start, int stop, string vari...

FILE: SAUtils/InputFileParsers/ClinVar/IClinVarSaItem.cs
  type IClinVarSaItem (line 7) | public interface IClinVarSaItem: ISupplementaryDataItem, IComparable<ICl...

FILE: SAUtils/InputFileParsers/ClinVar/VariantAligner.cs
  class VariantAligner (line 8) | public sealed class VariantAligner
    method VariantAligner (line 16) | public VariantAligner(ISequence compressedSequence)
    method LeftAlign (line 25) | public (int RefPosition, string RefAllele, string AltAllele) LeftAlign...
    method GetUpstreamSeq (line 68) | private string GetUpstreamSeq(int position, int length, bool isCircula...

FILE: SAUtils/InputFileParsers/ClinVar/VcvItem.cs
  class VcvItem (line 8) | public sealed class VcvItem : IComparable<int>, IComparable<VcvItem>
    method VcvItem (line 17) | public VcvItem(string accession, string version, long updatedDateTicks...
    method GetJsonString (line 29) | public string GetJsonString()
    method CompareTo (line 42) | public int CompareTo(int vcvId)
    method CompareTo (line 47) | public int CompareTo(VcvItem other)

FILE: SAUtils/InputFileParsers/ClinVar/VcvSaItem.cs
  class VcvSaItem (line 10) | public sealed class VcvSaItem: IClinVarSaItem, IEquatable<VcvSaItem>
    method VcvSaItem (line 24) | public VcvSaItem(Chromosome chromosome, int position, string refAllele...
    method GetJsonString (line 38) | public string GetJsonString()
    method CompareTo (line 55) | public int CompareTo(IClinVarSaItem other)
    method Equals (line 63) | public bool Equals(VcvSaItem other)
    method GetHashCode (line 69) | public override int GetHashCode()

FILE: SAUtils/InputFileParsers/Cosmic/MergedCosmicReader.cs
  class MergedCosmicReader (line 15) | public sealed class MergedCosmicReader
    method MergedCosmicReader (line 33) | public MergedCosmicReader(string vcfFile, string tsvFile, ISequencePro...
    method GetItems (line 42) | public IEnumerable<CosmicItem> GetItems()
    method AddCosmicStudy (line 77) | private void AddCosmicStudy(string line)
    method GetHistologies (line 94) | private List<string> GetHistologies(string[] columns)
    method GetSites (line 103) | private List<string> GetSites(string[] columns)
    method TryAddValue (line 113) | private static void TryAddValue(string value, ISet<string> sites)
    method IsHeaderLine (line 119) | private static bool IsHeaderLine(string line) => line.Contains(StudyId...
    method GetColumnIndexes (line 121) | private void GetColumnIndexes(string headerLine)
    method ExtractCosmicItems (line 161) | internal List<CosmicItem> ExtractCosmicItems(string vcfLine)
    method Clear (line 198) | private void Clear()
    method ParseInfoField (line 204) | private void ParseInfoField(string infoFields)
    method SetInfoField (line 220) | private void SetInfoField(string vcfId, string value)

FILE: SAUtils/InputFileParsers/DGV/DgvReader.cs
  class DgvReader (line 11) | public sealed class DgvReader: IDisposable
    method DgvReader (line 21) | public DgvReader(StreamReader reader, Dictionary<string, Chromosome> r...
    method ExtractDgvItem (line 30) | public static DgvItem ExtractDgvItem(string line, Dictionary<string, C...
    method GetItems (line 57) | public IEnumerable<DgvItem> GetItems()
    method IsDgvHeader (line 76) | private static bool IsDgvHeader(string line)
    method Dispose (line 81) | public void Dispose()

FILE: SAUtils/InputFileParsers/DataSourceVersionReader.cs
  class DataSourceVersionReader (line 13) | public sealed class DataSourceVersionReader : IDisposable
    method Dispose (line 21) | public void Dispose()
    method DataSourceVersionReader (line 29) | public DataSourceVersionReader(Stream fileStream)
    method GetSourceVersion (line 34) | public static DataSourceVersion GetSourceVersion(string versionFileName)
    method GetSourceVersion (line 47) | private static DataSourceVersion GetSourceVersion(Stream versionFileSt...
    method GetVersion (line 56) | public DataSourceVersion GetVersion()

FILE: SAUtils/InputFileParsers/DbSnp/DbSnpReader.cs
  class DbSnpReader (line 13) | public sealed class DbSnpReader : IDisposable
    method DbSnpReader (line 19) | public DbSnpReader(Stream stream, ISequenceProvider sequenceProvider)
    method GetItems (line 25) | public IEnumerable<DbSnpItem> GetItems()
    method ExtractItem (line 52) | public IEnumerable<DbSnpItem> ExtractItem(string vcfLine)
    method Dispose (line 76) | public void Dispose()

FILE: SAUtils/InputFileParsers/DbSnp/GlobalMinorReader.cs
  class GlobalMinorReader (line 13) | public sealed class GlobalMinorReader
    method GlobalMinorReader (line 19) | public GlobalMinorReader(Stream stream, Dictionary<string, Chromosome>...
    method GetItems (line 25) | public IEnumerable<AlleleFrequencyItem> GetItems()
    method ExtractItem (line 52) | private List<AlleleFrequencyItem> ExtractItem(string vcfline)
    method GetAlleleFrequencies (line 79) | private static Dictionary<string, double> GetAlleleFrequencies(string ...
    method GetFrequency (line 113) | private static double GetFrequency(string alleleFrequency)

FILE: SAUtils/InputFileParsers/Decipher/DecipherParser.cs
  class DecipherParser (line 10) | public sealed class DecipherParser : IDisposable
    method DecipherParser (line 30) | public DecipherParser(StreamReader reader, IDictionary<string, Chromos...
    method GetItems (line 36) | public IEnumerable<DecipherItem> GetItems()
    method Dispose (line 67) | public void Dispose()

FILE: SAUtils/InputFileParsers/Gme/GmeParser.cs
  class GmeParser (line 13) | public sealed class GmeParser : IDisposable
    method GmeParser (line 23) | public GmeParser(StreamReader streamReader, ISequenceProvider sequence...
    method Clear (line 30) | private void Clear()
    method GetItems (line 37) | public IEnumerable<GmeItem> GetItems()
    method Dispose (line 75) | public  void    Dispose() => _reader?.Dispose();

FILE: SAUtils/InputFileParsers/OneKGen/OneKGenReader.cs
  class OneKGenReader (line 15) | public sealed class OneKGenReader :IDisposable
    method OneKGenReader (line 38) | public OneKGenReader(Stream stream, ISequenceProvider sequenceProvider)
    method Clear (line 45) | private void Clear()
    method GetItems (line 66) | public IEnumerable<OneKGenItem> GetItems()
    method ExtractItems (line 88) | internal IEnumerable<OneKGenItem> ExtractItems(string vcfLine)
    method GetAlleleCount (line 140) | private static int? GetAlleleCount(int[] alleleCounts, int i)
    method ParseInfoField (line 147) | private void ParseInfoField(string infoFields, bool hasSymbolicAllele)
    method SetInfoField (line 161) | private  void SetInfoField(string vcfAfId, string value, bool hasSymbo...
    method GetAncestralAllele (line 223) | private static string GetAncestralAllele(string value)
    method IsNucleotide (line 231) | private static bool IsNucleotide(char c)
    method Dispose (line 237) | public void Dispose()

FILE: SAUtils/InputFileParsers/OneKGen/RefMinorReader.cs
  class RefMinorReader (line 14) | public sealed class RefMinorReader:IDisposable
    method RefMinorReader (line 23) | public RefMinorReader(StreamReader reader, ISequenceProvider sequenceP...
    method Clear (line 30) | private void Clear()
    method GetItems (line 36) | public IEnumerable<AlleleFrequencyItem> GetItems()
    method ExtractItems (line 58) | private List<AlleleFrequencyItem> ExtractItems(string vcfLine)
    method GetAlleleCount (line 96) | private static int? GetAlleleCount(int[] alleleCounts, int i)
    method ParseInfoField (line 104) | private void ParseInfoField(string infoFields)
    method Dispose (line 126) | public void Dispose()

FILE: SAUtils/InputFileParsers/OneKGen/oneKGenSvReader.cs
  class OneKGenSvReader (line 12) | public sealed class OneKGenSvReader:IDisposable
    method OneKGenSvReader (line 36) | public OneKGenSvReader(StreamReader reader, Dictionary<string, Chromos...
    method GetItems (line 42) | public IEnumerable<OnekGenSvItem> GetItems()
    method Clear (line 58) | private void Clear()
    method ExtractOneKGenSvItem (line 71) | private OnekGenSvItem ExtractOneKGenSvItem(string line)
    method RemoveMissingValues (line 94) | private static string RemoveMissingValues(string idField)
    method ParseInfoField (line 100) | private void ParseInfoField(string infoFields)
    method SetInfoField (line 114) | private void SetInfoField(string vcfAfId, string value)
    method Dispose (line 148) | public void Dispose()

FILE: SAUtils/InputFileParsers/SequenceExtensions.cs
  class SequenceExtensions (line 5) | public static class SequenceExtensions
    method Validate (line 7) | public static bool Validate( this ISequence referenceSequence, int sta...

FILE: SAUtils/InputFileParsers/TOPMed/TopMedReader.cs
  class TopMedReader (line 13) | public sealed class TopMedReader : IDisposable
    method TopMedReader (line 23) | public TopMedReader(StreamReader streamReader, ISequenceProvider seque...
    method Clear (line 30) | private void Clear()
    method GetItems (line 37) | public IEnumerable<TopMedItem> GetItems()
    method ExtractItems (line 53) | private TopMedItem ExtractItems(string vcfLine)
    method ParseInfoField (line 91) | private void ParseInfoField(string infoFields)
    method SetInfoField (line 105) | private void SetInfoField(string vcfId, string value)
    method Dispose (line 122) | public void Dispose() => _reader?.Dispose();

FILE: SAUtils/MakeAaDb/Main.cs
  class Main (line 13) | public static class Main
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/MakeClinGenDb/Main.cs
  class Main (line 16) | public static class Main
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 59) | private static ExitCodes ProgramExecution()

FILE: SAUtils/MitoHeteroplasmy/MitoHeteroplasmyDb.cs
  class MitoHeteroplasmyDb (line 10) | public static class MitoHeteroplasmyDb
    method Run (line 17) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 48) | private static ExitCodes ProgramExecution()

FILE: SAUtils/MitoHeteroplasmy/MitoHeteroplasmyParser.cs
  class MitoHeteroplasmyParser (line 11) | public sealed class MitoHeteroplasmyParser : IDisposable
    method MitoHeteroplasmyParser (line 15) | public MitoHeteroplasmyParser(Stream stream)
    method Dispose (line 20) | public void Dispose()
    method GetOutputLines (line 25) | public IEnumerable<string> GetOutputLines()
    method ExtractItems (line 43) | private static IEnumerable<string> ExtractItems(string line)
    method MergeAndSortByVrf (line 60) | private static (string formattedVrfs, string alleleDepths) MergeAndSor...
    method GetAlleleStats (line 83) | private static IEnumerable<(string, string, AlleleStats)> GetAlleleSta...
    method DeserializeStats (line 102) | public static PositionStats DeserializeStats(string s)
    method IsNucleotide (line 115) | private static bool IsNucleotide(char c)

FILE: SAUtils/MitoHeteroplasmy/StatClasses.cs
  class PositionStats (line 19) | public sealed class PositionStats
  class AlleleStats (line 39) | public class AlleleStats

FILE: SAUtils/MitoMap/CircularGenomeModel.cs
  class CircularGenomeModel (line 6) | public sealed class CircularGenomeModel
    method CircularGenomeModel (line 11) | public CircularGenomeModel(ISequence compressedSequence)
    method PseudoToCircular (line 18) | private (int, int) PseudoToCircular((int, int) interval) =>  (GetCircu...
    method GetCircularPosition (line 20) | private int GetCircularPosition(int posi) => (posi - 1) % _genomeLengt...
    method SplitInterval (line 23) | private List<(int, int)> SplitInterval((int, int) interval)
    method ExtractIntervalSequence (line 37) | public string ExtractIntervalSequence((int, int) interval)

FILE: SAUtils/MitoMap/MitoMapDatabaseUtilities.cs
  class MitoMapDatabaseUtilities (line 9) | internal static class MitoMapDatabaseUtilities
    method Create (line 12) | public static MitoMapInputDb Create(string mitoMapDatabase)
    method ProcessReferenceInfo (line 46) | private static void ProcessReferenceInfo(string line, Dictionary<strin...
    method TryGetTable (line 53) | private static MitoMapTable TryGetTable(string line)
  type MitoMapTable (line 59) | public enum MitoMapTable

FILE: SAUtils/MitoMap/MitoMapInputDb.cs
  type MitoMapInputDb (line 5) | public struct MitoMapInputDb
    method MitoMapInputDb (line 9) | public MitoMapInputDb(Dictionary<string, string> internalReferenceIdTo...

FILE: SAUtils/MitoMap/MitoMapItem.cs
  class MitoMapDataTypes (line 13) | public static class MitoMapDataTypes
  class MitoDLoop (line 23) | public static class MitoDLoop
  class MitomapParsingParameters (line 30) | public static class MitomapParsingParameters
  class MitoMapItem (line 35) | public sealed class MitoMapItem : ISupplementaryDataItem
    method MitoMapItem (line 51) | public MitoMapItem(Chromosome chromosome, int posi, string refAllele, ...
    method TryAddPaddingBase (line 74) | private static (int, string, string) TryAddPaddingBase(string refAllel...
    method AddPaddingBase (line 82) | private static (int, string, string) AddPaddingBase(string allele, boo...
    method IsEmptyOrDash (line 88) | private static bool IsEmptyOrDash(string allele) => string.IsNullOrEmp...
    method GetJsonString (line 90) | public string GetJsonString()
    method AggregatedMutationsSamePosition (line 113) | public static Dictionary<(string, string), MitoMapItem> AggregatedMuta...
    method Merge (line 131) | private static MitoMapItem Merge(MitoMapItem mitoMapItem1, MitoMapItem...
    method MergeCollections (line 154) | private static IEnumerable<string> MergeCollections(ICollection<string...
    method HasConflictValue (line 166) | private static bool HasConflictValue<T>(T originalValue, T newValue)
    method IsNullOrEmpty (line 174) | private static bool IsNullOrEmpty<T>(T value)

FILE: SAUtils/MitoMap/MitoMapSvItem.cs
  class MitoMapSvItem (line 9) | public sealed class MitoMapSvItem : ISuppIntervalItem
    method MitoMapSvItem (line 16) | public MitoMapSvItem(Chromosome chromosome, int start, int end, Varian...
    method GetJsonString (line 24) | public string GetJsonString()

FILE: SAUtils/MitoMap/MitoMapSvReader.cs
  class MitoMapSvReader (line 16) | public sealed class MitoMapSvReader
    method MitoMapSvReader (line 30) | public MitoMapSvReader(FileInfo mitoMapFileInfo, ISequenceProvider seq...
    method GetDataType (line 39) | private string GetDataType()
    method GetMitoMapSvItems (line 47) | private IEnumerable<MitoMapSvItem> GetMitoMapSvItems()
    method ParseLine (line 72) | internal List<MitoMapSvItem> ParseLine(string line)
    method ExtractSvItemFromDeletionsSingle (line 81) | private List<MitoMapSvItem> ExtractSvItemFromDeletionsSingle(List<stri...
    method ExtractSvItemFromSimpleInsertions (line 100) | private List<MitoMapSvItem> ExtractSvItemFromSimpleInsertions(IReadOnl...
    method GetSortedItems (line 122) | public static IEnumerable<MitoMapSvItem> GetSortedItems(IEnumerable<Mi...

FILE: SAUtils/MitoMap/MitoMapVariantReader.cs
  class MitoMapVariantReader (line 17) | public sealed class MitoMapVariantReader
    method MitoMapVariantReader (line 55) | public MitoMapVariantReader(FileInfo mitoMapFileInfo, MitoMapInputDb m...
    method GetDataType (line 65) | private string GetDataType()
    method GetMitoMapItems (line 72) | private IEnumerable<MitoMapItem> GetMitoMapItems()
    method ParseLine (line 100) | internal static List<MitoMapItem> ParseLine(string line, string dataTy...
    method ExtractVariantItemFromDeletionsSingle (line 121) | private static List<MitoMapItem> ExtractVariantItemFromDeletionsSingle...
    method ExtractVariantItemFromInsertionsSimple (line 142) | private static List<MitoMapItem> ExtractVariantItemFromInsertionsSimpl...
    method ExtractVariantItem (line 174) | private static List<MitoMapItem> ExtractVariantItem(List<string> info,...
    method GetStatus (line 224) | private static string GetStatus(List<string> info, int[] fields)
    method GetNumFullLengthSequences (line 230) | internal static int GetNumFullLengthSequences(string field, string dat...
    method GetPlasmy (line 260) | private static bool? GetPlasmy(List<string> info, int fields)
    method GetAltAlleles (line 267) | internal static IEnumerable<string> GetAltAlleles(string rawAltAllele)...
    method DescribedAsDuplicatedRecord (line 270) | private static bool DescribedAsDuplicatedRecord(string mitomapDiseaseS...
    method GetDiseaseInfo (line 280) | private static string GetDiseaseInfo(List<string> info, int fieldIndex)
    method GetFunctionalInfo (line 290) | private static (string, string) GetFunctionalInfo(List<string> info, i...
    method GetClinicalSignificance (line 301) | private static string GetClinicalSignificance(string significanceString)
    method GetRefAltAlleles (line 312) | private static (string RefAllele, string RawAltAllele, int? ExtractedP...
    method Evaluate_8042delAT (line 343) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_C_C_2_8 (line 362) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_A_C_or_CC (line 382) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_3902_3908invACCTTGC (line 393) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_C9537insC (line 407) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_8042del2 (line 420) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_16021_16022del (line 431) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method Evaluate_C123T (line 443) | private static (bool Success, string RefAllele, string RawAltAllele, i...
    method GetRefAllelesFromReference (line 454) | private static string GetRefAllelesFromReference(ISequenceProvider seq...
    method ReverseSequence (line 457) | private static string ReverseSequence(string sequence)
    method GetMergeAndSortedItems (line 471) | public static IEnumerable<MitoMapItem> GetMergeAndSortedItems(IEnumera...
    method GetLeftAlignedVariant (line 479) | private static (int RefPosition, string RefAllele, string AltAllele) G...

FILE: SAUtils/MitoMap/ParsingUtilities.cs
  class ParsingUtilities (line 8) | public static class ParsingUtilities
    method GetPubMedIds (line 11) | public static List<string> GetPubMedIds(string field, MitoMapInputDb m...
    method ExtractInternalIds (line 30) | public static string[] ExtractInternalIds(string field)

FILE: SAUtils/MitoMap/SmallVarDb.cs
  class SmallVarDb (line 14) | public static class SmallVarDb
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 62) | private static ExitCodes ProgramExecution()

FILE: SAUtils/MitoMap/StructVarDb.cs
  class StructVarDb (line 17) | public static class StructVarDb
    method Run (line 23) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/NgaWriter.cs
  class NgaWriter (line 14) | public sealed class NgaWriter : IDisposable
    method NgaWriter (line 18) | public NgaWriter(Stream stream, ISerializable version, string jsonKey,...
    method WriteHeader (line 27) | private static void WriteHeader(Stream stream, ISerializable version, ...
    method Dispose (line 40) | public void Dispose() => _writer.Dispose();
    method Write (line 42) | public int Write(Dictionary<string, List<ISuppGeneItem>> geneToEntries)

FILE: SAUtils/NsaConcatenator/ConcatUtilities.cs
  class ConcatUtilities (line 13) | public static class ConcatUtilities
    method GetIndexFields (line 15) | private static (IDataSourceVersion version, string jsonKey, bool match...
    method GetNsaReader (line 39) | private static NsaReader GetNsaReader(ushort chromIndex, List<NsaReade...
    method ConcatenateNsaFiles (line 56) | public static void ConcatenateNsaFiles(IEnumerable<string> filePaths, ...
    method GetChromIndices (line 86) | private static IEnumerable<ushort> GetChromIndices(List<NsaReader> nsa...

FILE: SAUtils/NsaConcatenator/NsaConcatenator.cs
  class NsaConcatenator (line 10) | public static class NsaConcatenator
    method Run (line 15) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 45) | private static ExitCodes ProgramExecution()

FILE: SAUtils/NsaIndexUpdater/UpdateIndex.cs
  class UpdateIndex (line 10) | public static class UpdateIndex
    method Run (line 15) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 52) | private static ExitCodes ProgramExecution()

FILE: SAUtils/NsaWriter.cs
  class NsaWriter (line 19) | public sealed class NsaWriter : IDisposable
    method NsaWriter (line 41) | public NsaWriter(Stream nsaStream, Stream indexStream, IDataSourceVers...
    method Write (line 62) | internal void Write(ushort chromIndex, NsaReader nsaReader)
    method Write (line 82) | public int Write(IEnumerable<ISupplementaryDataItem> saItems)
    method WriteUptoPosition (line 152) | private void WriteUptoPosition(MinHeap<ISupplementaryDataItem> itemsHe...
    method WritePosition (line 177) | private void WritePosition(List<ISupplementaryDataItem> items)
    method Flush (line 211) | private void Flush(ushort chromIndex)
    method Dispose (line 222) | public void Dispose()

FILE: SAUtils/Omim/Downloader.cs
  class Downloader (line 10) | public static class Downloader
    method Run (line 18) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 54) | private static ExitCodes ProgramExecution()

FILE: SAUtils/Omim/EntryApiResponse/EntryResponse.cs
  class EntryRoot (line 4) | public sealed class EntryRoot
  class RootItem (line 10) | public class RootItem
  class Entry (line 16) | public class Entry
  class EntryItem (line 21) | public class EntryItem
  class TextSection (line 30) | public class TextSection
  class TextSectionItem (line 35) | public class TextSectionItem

FILE: SAUtils/Omim/EntryApiResponse/GeneMap.cs
  class GeneMap (line 5) | public class GeneMap
  class PhenotypeMap (line 12) | public class PhenotypeMap
  class PhenotypeMapItem (line 17) | public class PhenotypeMapItem

FILE: SAUtils/Omim/Main.cs
  class Main (line 15) | public static class Main
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 59) | private static ExitCodes ProgramExecution()

FILE: SAUtils/Omim/OmimParser.cs
  class OmimParser (line 15) | public sealed class OmimParser
    method OmimParser (line 25) | public OmimParser(string mimToGeneSymbolFile, string omimJsonFile, SaJ...
    method GetVersion (line 32) | public DataSourceVersion GetVersion() => DataSourceVersionReader.GetSo...
    method GetItems (line 34) | public IEnumerable<OmimItem> GetItems()
    method GetPhenotypeDescriptions (line 47) | private static Dictionary<int, string> GetPhenotypeDescriptions(EntryR...
    method GetMimNumberToGeneSymbol (line 66) | private Dictionary<int, string> GetMimNumberToGeneSymbol()
    method GetEntryRootObject (line 85) | private EntryRoot GetEntryRootObject()
    method GetOmimItems (line 97) | private IEnumerable<OmimItem> GetOmimItems(EntryRoot entryRoot, Dictio...

FILE: SAUtils/Omim/OmimPhenotypeSchema.cs
  class OmimPhenotypeSchema (line 7) | public static class OmimPhenotypeSchema
    method Get (line 20) | public static SaJsonSchema Get()

FILE: SAUtils/Omim/OmimQuery.cs
  class OmimQuery (line 13) | public sealed class OmimQuery : IDisposable
    method OmimQuery (line 33) | public OmimQuery(string apiKey, string outputDirectory)
    method GetMimTitlesUrl (line 45) | private static string GetMimTitlesUrl(string apiKey) => $"{OmimDownloa...
    method GetMimsToDownload (line 47) | private List<string> GetMimsToDownload()
    method GenerateMimToGeneSymbolFile (line 67) | public void GenerateMimToGeneSymbolFile(GeneSymbolUpdater geneSymbolUp...
    method GenerateJsonResponse (line 92) | public void GenerateJsonResponse()
    method SetPrefixAndGetEntriesString (line 124) | private string SetPrefixAndGetEntriesString(string responseContent)
    method GetMimNumbersString (line 140) | private static string GetMimNumbersString(List<string> allMimNumbers, ...
    method GetApiQueryUrl (line 155) | private static string GetApiQueryUrl(string baseAddress, string handle...
    method Dispose (line 176) | public void Dispose()

FILE: SAUtils/Omim/OmimSchema.cs
  class OmimSchema (line 8) | public static class OmimSchema
    method Get (line 19) | public static SaJsonSchema Get()

FILE: SAUtils/Omim/OmimStatistics.cs
  class OmimStatistics (line 8) | public class OmimStatistics
    method Add (line 15) | public void Add(OmimItem omimItem)
    method ToString (line 30) | public override string ToString()

FILE: SAUtils/Omim/OmimUtilities.cs
  class OmimUtilities (line 13) | public static class OmimUtilities
    method GetPhenotype (line 15) | public static OmimItem.Phenotype GetPhenotype(PhenotypeMap phenotypeMap,
    method ExtractInheritances (line 26) | private static HashSet<string> ExtractInheritances(string inheritance)
    method ExtractPhenotypeAndComments (line 40) | internal static (string Phenotype, OmimItem.Comment[] Comments) Extrac...
    method GetComment (line 52) | private static OmimItem.Comment GetComment(char symbol)
    method GetGeneToOmimEntriesAndSchema (line 64) | public static Dictionary<string, List<ISuppGeneItem>> GetGeneToOmimEnt...
    method RemoveLinks (line 88) | public static string RemoveLinks(this string text) => text == null
    method RemoveFormatControl (line 95) | public static string RemoveFormatControl(this string text) => text == ...
    method ExtractAndProcessItemDescription (line 98) | public static string ExtractAndProcessItemDescription(EntryItem item)

FILE: SAUtils/Omim/OmimVersion.cs
  class OmimVersion (line 6) | public static class OmimVersion
    method WriteToFile (line 12) | public static void WriteToFile(string outputPrefix, string outputDirec...

FILE: SAUtils/OneKGenSvDb/Create.cs
  class Create (line 16) | public static class Create
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/OneKGenSvDb/VcfToBed.cs
  class VcfToBed (line 14) | public static class VcfToBed
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 49) | private static ExitCodes ProgramExecution()
    method GetSvEndString (line 77) | private static string GetSvEndString(string infoFields)

FILE: SAUtils/ParseUtils/SAParseUtilities.cs
  class SaParseUtilities (line 5) | public static class SaParseUtilities
    method GetSequenceAlterationType (line 7) | public static VariantType GetSequenceAlterationType(string dgvType, st...
    method GetSequenceAlteration (line 70) | public static VariantType GetSequenceAlteration(string svType)
    method Add (line 108) | public static int? Add(int? x, int? y)

FILE: SAUtils/ParseUtils/SplitLine.cs
  class SplitLine (line 6) | public sealed class SplitLine
    method SplitLine (line 10) | public SplitLine(in string inputLine, in char delimiter)
    method GetString (line 15) | public string GetString(in int index)
    method ParseInteger (line 20) | public int? ParseInteger(in int index)
    method ParseDouble (line 25) | public double? ParseDouble(in int index)
    method ParseInteger (line 30) | public static int? ParseInteger(string valueString)
    method ParseDouble (line 42) | public static double? ParseDouble(string valueString)

FILE: SAUtils/ParseUtils/TsvIndices.cs
  type TsvIndices (line 3) | public struct TsvIndices
    method TsvIndices (line 48) | public TsvIndices()

FILE: SAUtils/PhyloP/Main.cs
  class Main (line 13) | public static class Main
    method Run (line 19) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/PhyloP/NpdWriter.cs
  class NpdWriter (line 14) | public sealed class NpdWriter:IDisposable
    method NpdWriter (line 31) | public NpdWriter(Stream dbStream, Stream indexStream, DataSourceVersio...
    method Write (line 50) | public void Write(IEnumerable<PhylopItem> items)
    method WriteCompressed (line 96) | private void WriteCompressed(int lastPosition)
    method Dispose (line 109) | public void Dispose()

FILE: SAUtils/PhyloP/PhylopParser.cs
  class PhylopParser (line 11) | public sealed class PhylopParser : IDisposable
    method PhylopParser (line 17) | public PhylopParser(Stream stream, GenomeAssembly assembly, Dictionary...
    method GetItems (line 24) | public IEnumerable<PhylopItem> GetItems()
    method StartNewInterval (line 56) | private (Chromosome chrom, int position, int step) StartNewInterval(st...
    method Dispose (line 70) | public void Dispose()

FILE: SAUtils/PrimateAi/PrimateAiDb.cs
  class PrimateAiDb (line 15) | public static class PrimateAiDb
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 67) | private static ExitCodes ProgramExecution()

FILE: SAUtils/PrimateAi/PrimateAiItem.cs
  class PrimateAiItem (line 8) | public sealed class PrimateAiItem : ISupplementaryDataItem
    method PrimateAiItem (line 16) | public PrimateAiItem(Chromosome chromosome, int position, string refAl...
    method GetJsonString (line 26) | public string GetJsonString()

FILE: SAUtils/PrimateAi/PrimateAiParser.cs
  class PrimateAiParser (line 10) | public sealed class PrimateAiParser : IDisposable
    method PrimateAiParser (line 17) | public PrimateAiParser(Stream stream, ISequenceProvider referenceProvi...
    method GetItems (line 26) | public IEnumerable<PrimateAiItem> GetItems()
    method ExtractItem (line 52) | private PrimateAiItem ExtractItem(string line)
    method Dispose (line 79) | public void Dispose()

FILE: SAUtils/PrimateAi/PrimateAiUtilities.cs
  class PrimateAiUtilities (line 7) | public static class PrimateAiUtilities
    method GetIdToSymbols (line 9) | public static (Dictionary<string, string> entrezToHgnc, Dictionary<str...

FILE: SAUtils/ProcessSpliceNetTsv/PredictionFilter.cs
  class PredictionFilter (line 9) | public static class PredictionFilter
    method Filter (line 22) | public static void Filter(string intputTsv, string gffFile1, string gf...
    method AnyScorePassTheCutoff (line 50) | private static bool AnyScorePassTheCutoff(string[] columns, int[] scor...
    method GetIntronFlankingRegions (line 59) | private static IntervalForest<byte> GetIntronFlankingRegions(string gf...
    method GetIntervals (line 74) | private static IEnumerable<Interval<byte>> GetIntervals(IEnumerable<in...
    method GetIntronFlankingRegionStarts (line 76) | private static HashSet<int>[] GetIntronFlankingRegionStarts(string gff...
    method ProcessBufferedBoundaries (line 123) | private static void ProcessBufferedBoundaries(List<Interval> exonBound...
    method GetChrIndex (line 134) | private static ushort GetChrIndex(string chrName)

FILE: SAUtils/ProcessSpliceNetTsv/SpliceNetPredictionFilterMain.cs
  class SpliceNetPredictionFilterMain (line 7) | public static class SpliceNetPredictionFilterMain
    method Run (line 14) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 56) | private static ExitCodes ProgramExecution()

FILE: SAUtils/RefMinorDb/Main.cs
  class Main (line 14) | public static class Main
    method Run (line 20) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/RefMinorDb/RefMinorDbWriter.cs
  class RefMinorDbWriter (line 15) | public sealed class RefMinorDbWriter:IDisposable
    method RefMinorDbWriter (line 23) | public RefMinorDbWriter(ExtendedBinaryWriter writer, ExtendedBinaryWri...
    method Write (line 32) | public void Write(IEnumerable<ISupplementaryDataItem> saItems)
    method WriteUptoPosition (line 75) | private void WriteUptoPosition(MinHeap<ISupplementaryDataItem> itemsHe...
    method WritePosition (line 94) | private void WritePosition(List<ISupplementaryDataItem> saItems)
    method GetRefMinorItem (line 106) | private static ISupplementaryDataItem GetRefMinorItem(List<ISupplement...
    method IsSnv (line 129) | private static bool IsSnv(string allele)
    method Dispose (line 138) | public void Dispose()

FILE: SAUtils/RegionUtilities.cs
  class RegionUtilities (line 8) | public static class RegionUtilities
    method OverlapsParRegion (line 17) | public static bool OverlapsParRegion(ISupplementaryDataItem variant, G...

FILE: SAUtils/Revel/Create.cs
  class Create (line 15) | public static class Create
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/SAUtils.cs
  class SaUtils (line 25) | public static class SaUtils
    method Main (line 27) | public static int Main(string[] args)

FILE: SAUtils/SaUtilsCommon.cs
  class SaUtilsCommon (line 5) | public static class SaUtilsCommon
    method IsNumberNullOrZero (line 7) | public static bool IsNumberNullOrZero(int? item)
    method ReverseSaReducedAllele (line 19) | public static string ReverseSaReducedAllele(string saAltAllele, string...
    method HasFailedFilters (line 39) | public static bool HasFailedFilters(string filters)

FILE: SAUtils/Schema/SaJsonKeyAnnotation.cs
  class SaJsonKeyAnnotation (line 5) | public sealed class SaJsonKeyAnnotation
    method SaJsonKeyAnnotation (line 10) | private SaJsonKeyAnnotation() { }
    method CreateFromProperties (line 12) | public static SaJsonKeyAnnotation CreateFromProperties(SaJsonValueType...
    method CreateFromSubSchema (line 17) | public static SaJsonKeyAnnotation CreateFromSubSchema(SaJsonSchema sch...

FILE: SAUtils/Schema/SaJsonKeyProperties.cs
  class SaJsonKeyProperties (line 5) | public sealed class SaJsonKeyProperties
    method SaJsonKeyProperties (line 11) | public SaJsonKeyProperties(SaJsonValueType valueType, CustomAnnotation...

FILE: SAUtils/Schema/SaJsonSchema.cs
  class SaJsonSchema (line 12) | public sealed class SaJsonSchema
    method SaJsonSchema (line 28) | internal SaJsonSchema(StringBuilder sb)
    method Create (line 34) | public static SaJsonSchema Create(StringBuilder sb, string jsonTag, Sa...
    method SetNonSaKeys (line 52) | public void SetNonSaKeys(string[] nonSaKeys)
    method AddAnnotation (line 57) | private void AddAnnotation(SaJsonKeyAnnotation annotation)
    method AddAnnotationProperties (line 70) | private void AddAnnotationProperties(SaJsonKeyAnnotation annotation)
    method AddValueTypes (line 85) | private void AddValueTypes(SaJsonValueType jsonValueType)
    method AddJsonDataType (line 94) | private void AddJsonDataType(JsonDataType jsonType)
    method AddSchemaVersion (line 101) | private void AddSchemaVersion() => _jsonObject.AddStringValue("$schema...
    method GetJsonType (line 103) | private SaJsonValueType GetJsonType(string key) => _keyAnnotation[key]...
    method GetCategory (line 104) | private CustomAnnotationCategories GetCategory(string key) => _keyAnno...
    method AddAnnotation (line 106) | public void AddAnnotation(string key, SaJsonKeyAnnotation annotation)
    method ToString (line 112) | public override string ToString()
    method FinalizeSchema (line 118) | private void FinalizeSchema()
    method OutputRequiredKeys (line 140) | private void OutputRequiredKeys(IReadOnlyCollection<string> requiredKeys)
    method DisallowExtraProperites (line 145) | private void DisallowExtraProperites()
    method GetJsonStringGenerationAction (line 150) | private Action<JsonObject, List<string[]>> GetJsonStringGenerationActi...
    method CountKeyIfAdded (line 205) | public void CountKeyIfAdded(bool keyAdded, string key)
    method GetJsonString (line 210) | public string GetJsonString(List<string[]> values)
    method OutputKeyAnnotation (line 225) | internal void OutputKeyAnnotation(string key)
    method CheckAndGetBoolFromString (line 235) | internal static bool CheckAndGetBoolFromString(string value)
    method CheckAndGetNullableDoubleFromString (line 250) | internal static double? CheckAndGetNullableDoubleFromString(string value)
    method GetSubSchema (line 260) | public SaJsonSchema GetSubSchema(string key)

FILE: SAUtils/Schema/SaJsonValueType.cs
  class SaJsonValueType (line 7) | public sealed class SaJsonValueType : IEquatable<SaJsonValueType>
    method SaJsonValueType (line 19) | private SaJsonValueType(params JsonDataType[] dataTypes)
    method Create (line 24) | private static SaJsonValueType Create(params JsonDataType[] dataTypes)
    method JsonTypeEquals (line 32) | private bool JsonTypeEquals(params JsonDataType[] dataTypes) => JsonDa...
    method Equals (line 36) | public bool Equals(SaJsonValueType other)
    method GetHashCode (line 42) | public override int GetHashCode()

FILE: SAUtils/SpliceAi/SpliceAiDb.cs
  class SpliceAiDb (line 17) | public static class SpliceAiDb
    method Run (line 24) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 77) | private static ExitCodes ProgramExecution()

FILE: SAUtils/SpliceAi/SpliceAiItem.cs
  class SpliceAiItem (line 8) | public sealed class SpliceAiItem:ISupplementaryDataItem
    method SpliceAiItem (line 28) | public SpliceAiItem(Chromosome chromosome, int position, string refAll...
    method GetJsonString (line 50) | public string GetJsonString()

FILE: SAUtils/SpliceAi/SpliceAiParser.cs
  class SpliceAiParser (line 14) | public sealed class SpliceAiParser:IDisposable
    method SpliceAiParser (line 35) | public SpliceAiParser(Stream stream, ISequenceProvider sequenceProvide...
    method GetItems (line 44) | public IEnumerable<SpliceAiItem> GetItems()
    method GetFieldIndices (line 99) | private void GetFieldIndices(string line) {
    method ExtractItem (line 123) | private SpliceAiItem ExtractItem(string vcfLine)
    method UpdateGeneSymbol (line 156) | private void UpdateGeneSymbol(SpliceAiItem item)
    method HasSignificantScore (line 165) | private bool HasSignificantScore()
    method ParseInfoField (line 174) | private void ParseInfoField(string infoFields)
    method Clear (line 192) | private void Clear()
    method Dispose (line 207) | public void Dispose()

FILE: SAUtils/SpliceAi/SpliceUtilities.cs
  class SpliceUtilities (line 12) | public static class SpliceUtilities
    method GetSpliceIntervals (line 15) | public static Dictionary<ushort, IntervalArray<byte>> GetSpliceInterva...
    method GetEnstToGeneSymbols (line 56) | public static Dictionary<string, string> GetEnstToGeneSymbols(ISequenc...
    method GetSpliceAiGeneSymbols (line 79) | public static Dictionary<string, string> GetSpliceAiGeneSymbols(Stream...
    method GetSymbolMapping (line 95) | public static Dictionary<string, string> GetSymbolMapping(Dictionary<s...

FILE: SAUtils/gnomAD/GnomadSnvMain.cs
  class GnomadSnvMain (line 18) | public sealed class GnomadSnvMain
    method Run (line 26) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 72) | private static ExitCodes ProgramExecution()
    method CreateNsa (line 108) | private static void CreateNsa(string[] exomeFiles, string genomeFile, ...
    method GetExomeReader (line 125) | private static StreamReader GetExomeReader(string[] exomeFileNames, st...
    method GetChromName (line 140) | private static string GetChromName(string filePath)
    method GetVersion (line 153) | private static DataSourceVersion GetVersion()
    method GetVcfFiles (line 173) | private static string[] GetVcfFiles(string directory)

FILE: SAUtils/gnomAD/GnomadSnvReader.cs
  class GnomadSnvReader (line 14) | public sealed class GnomadSnvReader
    method GnomadSnvReader (line 66) | public GnomadSnvReader(StreamReader genomeReader, StreamReader exomeRe...
    method Clear (line 73) | private void Clear()
    method GetCombinedItems (line 124) | public IEnumerable<GnomadItem> GetCombinedItems()
    method GetMinItems (line 187) | private static (Dictionary<(string refAllele, string altAllele), Gnoma...
    method GetRemainingItems (line 221) | private IEnumerable<GnomadItem> GetRemainingItems(IEnumerator<GnomadIt...
    method GetItems (line 237) | private IEnumerable<GnomadItem> GetItems(StreamReader reader, GnomadDa...
    method ExtractItems (line 267) | private List<GnomadItem> ExtractItems(string line, GnomadDataType type)
    method GetCount (line 320) | private static int? GetCount(int[] counts, int i)
    method ParseInfoField (line 333) | private void ParseInfoField(string infoFields)
    method SetInfoField (line 351) | private void SetInfoField(string vcfId, string value)

FILE: SAUtils/gnomAD/GnomadSvBedParser.cs
  class GnomadSvBedParser (line 10) | public sealed class GnomadSvBedParser : GnomadSvParser
    method GnomadSvBedParser (line 12) | public GnomadSvBedParser(
    method ParseLine (line 68) | protected override GnomadSvItem ParseLine(string inputLine)
    method SvTypeMapper (line 148) | private static VariantType SvTypeMapper(string svType)

FILE: SAUtils/gnomAD/GnomadSvMain.cs
  class GnomadSvMain (line 16) | public static class GnomadSvMain
    method Run (line 22) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 58) | private static ExitCodes ProgramExecution()

FILE: SAUtils/gnomAD/GnomadSvParser.cs
  class GnomadSvParser (line 11) | public abstract class GnomadSvParser : IDisposable
    method GnomadSvParser (line 20) | protected GnomadSvParser(
    method GetItems (line 29) | public IEnumerable<GnomadSvItem> GetItems()
    method ParseLine (line 46) | protected abstract GnomadSvItem ParseLine(string inputLine);
    method Dispose (line 48) | public void Dispose()

FILE: SAUtils/gnomAD/GnomadSvTsvParser.cs
  class GnomadSvTsvParser (line 12) | public sealed class GnomadSvTsvParser : GnomadSvParser
    method GnomadSvTsvParser (line 14) | public GnomadSvTsvParser(
    method ParseLine (line 34) | protected override GnomadSvItem ParseLine(string inputLine)
    method ParseValues (line 99) | private static Dictionary<string, T> ParseValues<T>(string subString, ...
    method SvTypeMapper (line 121) | private static VariantType SvTypeMapper(string svType)

FILE: SAUtils/gnomAD/GnomadUtilities.cs
  class GnomadUtilities (line 10) | public static class GnomadUtilities
    method GetMergedItems (line 12) | public static Dictionary<(string refAllele, string altAllele), GnomadI...
    method GetNormalizedItem (line 36) | public static GnomadItem GetNormalizedItem(GnomadItem item, ISequenceP...
    method MergeItems (line 92) | private static GnomadItem MergeItems(GnomadItem item1, GnomadItem item2)

FILE: SAUtils/gnomAD/LcrInterval.cs
  class LcrInterval (line 6) | public class LcrInterval:ISuppIntervalItem
    method GetJsonString (line 11) | public string GetJsonString() => string.Empty;
    method LcrInterval (line 13) | public LcrInterval(Chromosome chromosome, int start, int end)

FILE: SAUtils/gnomAD/LcrRegionParser.cs
  class LcrRegionParser (line 10) | public sealed class LcrRegionParser:IDisposable
    method LcrRegionParser (line 17) | public LcrRegionParser(StreamReader reader, ISequenceProvider refProvi...
    method Dispose (line 23) | public void Dispose() => _reader?.Dispose();
    method GetItems (line 24) | public IEnumerable<ISuppIntervalItem> GetItems()
    method GetLcrRegion (line 54) | private ISuppIntervalItem GetLcrRegion(string line)
    method IsNRegion (line 67) | private bool IsNRegion(Chromosome chrom, int start, int end)
    method ParsePosition (line 85) | private (string ChromName, int Start, int End) ParsePosition(string line)

FILE: SAUtils/gnomAD/LcrRegionsMain.cs
  class LcrRegionsMain (line 15) | public class LcrRegionsMain
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 57) | private static ExitCodes ProgramExecution()

FILE: SAUtils/makeDgvDb/Main.cs
  class Main (line 16) | public static class Main
    method Run (line 21) | public static ExitCodes Run(string command, string[] commandArgs)
    method ProgramExecution (line 59) | private static ExitCodes ProgramExecution()

FILE: Sandbox/AminoAcidAligner/AlignmentBuilder.cs
  class AlignmentBuilder (line 9) | public class AlignmentBuilder
    method AlignmentBuilder (line 15) | public AlignmentBuilder(string id)
    method Add (line 21) | public void Add(string transcriptId, string species, string sequence)
    method ToString (line 35) | public override string ToString()
    method CheckAlignments (line 48) | private bool CheckAlignments()
    method GetScoresLine (line 68) | public string GetScoresLine()

FILE: Sandbox/AminoAcidAligner/ExonToTranscript.cs
  class ExonToTranscript (line 8) | public static class ExonToTranscript
    method Main (line 10) | public static void Main(string[] args)
    method CreateTranscriptAlignments (line 42) | private static int CreateTranscriptAlignments(StreamReader reader, Str...
    method GetNextSequence (line 74) | private static (string name, string sequence) GetNextSequence(StreamRe...

FILE: Sandbox/AminoAcidAligner/Utilities.cs
  class Utilities (line 8) | public static class Utilities
    method ParseSequenceName (line 10) | public static (string TranscriptId, string Species, string Chromosome)...
    method GroupTranscripts (line 34) | public static List<HashSet<string>> GroupTranscripts(string fileName)
    method GetEquivalentIds (line 64) | public static Dictionary<string, HashSet<string>> GetEquivalentIds(Lis...

FILE: Sandbox/GenerateMustGenotypeVcf/ConfigurationSettings.cs
  class ConfigurationSettings (line 3) | public static class ConfigurationSettings

FILE: Sandbox/GenerateMustGenotypeVcf/GenerateMustGenotypeVcfsMain.cs
  class GenerateMustGenotypeVcfsMain (line 8) | sealed class GenerateMustGenotypeVcfsMain : AbstractCommandLineHandler
    method Main (line 10) | public static int Main(string[] args)
    method GenerateMustGenotypeVcfsMain (line 49) | public GenerateMustGenotypeVcfsMain(string programDescription, OptionS...
    method ValidateCommandLine (line 53) | protected override void ValidateCommandLine()
    method ProgramExecution (line 61) | protected override void ProgramExecution()

FILE: Sandbox/GenerateMustGenotypeVcf/MustGenotypeExtractor.cs
  class MustGenotypeExtractor (line 16) | public sealed class MustGenotypeExtractor:IDisposable
    method MustGenotypeExtractor (line 230) | public MustGenotypeExtractor(string compressedSeqPath, string oneKGeno...
    method Dispose (line 253) | public void Dispose()
    method Dispose (line 261) | private void Dispose(bool disposing)
    method Close (line 278) | private void Close()
    method ExtractEntries (line 287) | public void ExtractEntries()
    method ExtractFromCosmic (line 304) | private void ExtractFromCosmic()
    method ProcessHeaderLine (line 357) | private void ProcessHeaderLine(StreamWriter writer, string line)
    method WriteContigLines (line 378) | private void WriteContigLines(StreamWriter writer)
    method IsRequiredHeaderLine (line 393) | private static bool IsRequiredHeaderLine(string line)
    method IsLargeVariants (line 399) | private static bool IsLargeVariants(string refAllele, string altAlleles)
    method HasMinCount (line 414) | private static bool HasMinCount(string info)
    method ExtractFromClinVar (line 428) | private void ExtractFromClinVar()
    method ValidateReference (line 473) | private bool ValidateReference(string chromosome, int pos, string refA...
    method ExtractFromOneKg (line 481) | private void ExtractFromOneKg()
    method GetChrName (line 533) | private string GetChrName(string chromosome)
    method IsSnv (line 543) | private static bool IsSnv(string refAllele, string altAlleles)
    method IsSnv (line 550) | private static bool IsSnv(string allele)
    method IsRefMinorPosition (line 561) | private static bool IsRefMinorPosition(string info)

FILE: Sandbox/Piano/ConfigurationSettings.cs
  class ConfigurationSettings (line 3) | public static class ConfigurationSettings

FILE: Sandbox/Piano/Piano.cs
  class Piano (line 22) | sealed class Piano
    method ProgramExecution (line 33) | private  ExitCodes ProgramExecution()
    method UpdatePerformanceMetrics (line 84) | private int UpdatePerformanceMetrics(int previousChromIndex, Chromosom...
    method WriteAnnotatedPostion (line 96) | private static void WriteAnnotatedPostion(IAnnotatedPosition annotated...
    method Main (line 133) | static int Main(string[] args)

FILE: Sandbox/Piano/PianoAnnotatedTranscript.cs
  class PianoAnnotatedTranscript (line 12) | public class PianoAnnotatedTranscript:IAnnotatedTranscript
    method SerializeJson (line 14) | public void SerializeJson(StringBuilder sb)
    method PianoAnnotatedTranscript (line 35) | public PianoAnnotatedTranscript(ITranscript transcript, string referen...
    method ToString (line 47) | public override string ToString()
    method GetAlleleString (line 64) | private static string GetAlleleString(string a, string b)
    method CombineIdAndVersion (line 69) | private static string CombineIdAndVersion(ICompactId id, byte version)...
    method GetNullablePositionRange (line 71) | private static string GetNullablePositionRange(NullableInterval interval)

FILE: Sandbox/Piano/PianoAnnotationProvider.cs
  class PianoAnnotationProvider (line 14) | public class PianoAnnotationProvider:IAnnotationProvider
    method PianoAnnotationProvider (line 24) | public PianoAnnotationProvider(string pathPrefix, ISequenceProvider se...
    method InitiateCache (line 35) | private static TranscriptCache InitiateCache(Stream stream,
    method Annotate (line 43) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method LoadPredictionCaches (line 53) | private void LoadPredictionCaches(ushort refIndex)
    method ClearCache (line 64) | private void ClearCache()
    method AddTranscripts (line 70) | private void AddTranscripts(IAnnotatedPosition annotatedPosition)

FILE: Sandbox/Piano/PianoAnnotationUtils.cs
  class PianoAnnotationUtils (line 11) | public static class PianoAnnotationUtils
    method GetAnnotatedTranscripts (line 16) | public static void GetAnnotatedTranscripts(IVariant variant, ITranscri...
    method GetAnnotatedTranscript (line 33) | private static IAnnotatedTranscript GetAnnotatedTranscript(IVariant va...

FILE: Sandbox/Piano/PianoAnnotator.cs
  class PianoAnnotator (line 15) | public class PianoAnnotator:IAnnotator
    method PianoAnnotator (line 23) | public PianoAnnotator(IAnnotationProvider taProvider, ISequenceProvide...
    method GetGenomeAssembly (line 32) | private GenomeAssembly GetGenomeAssembly()
    method Annotate (line 48) | public IAnnotatedPosition Annotate(IPosition position)
    method GetAnnotatedVariants (line 66) | private static IAnnotatedVariant[] GetAnnotatedVariants(IVariant[] var...
    method GetAnnotatedGenes (line 76) | public IList<IAnnotatedGene> GetAnnotatedGenes()
    method EnableMitochondrialAnnotation (line 81) | public void EnableMitochondrialAnnotation()

FILE: Sandbox/Piano/PianoTranscriptAnnotator.cs
  class PianoTranscriptAnnotator (line 13) | public static class PianoTranscriptAnnotator
    method GetAnnotatedTranscript (line 16) | public static IAnnotatedTranscript GetAnnotatedTranscript(ITranscript ...
    method GetFlankingPeptides (line 57) | private static string GetFlankingPeptides(string peptideSeq, int prote...
    method GetCodonsAndAminoAcids (line 75) | private static Tuple<string, string, string, string> GetCodonsAndAmino...
    method AssignCodonsAndAminoAcids (line 94) | private static void AssignCodonsAndAminoAcids(string transcriptRefAlle...
    method GetConsequences (line 105) | private static List<ConsequenceTag> GetConsequences(ITranscript transc...
    method GetVariantEffect (line 115) | private static VariantEffect GetVariantEffect(ITranscript transcript, ...
    method AssignExtended (line 127) | private static void AssignExtended(string transcriptReferenceAllele, s...

FILE: Sandbox/Piano/ProviderUtilities.cs
  class ProviderUtilities (line 10) | public static class ProviderUtilities
    method GetSequenceProvider (line 12) | public static ISequenceProvider GetSequenceProvider(string compressedR...
    method GetTranscriptAnnotationProvider (line 17) | public static IAnnotationProvider GetTranscriptAnnotationProvider(stri...
    method GetAnnotator (line 22) | public static IAnnotator GetAnnotator(IAnnotationProvider taProvider, ...

FILE: Sandbox/UnitTests/Piano/PianoAnnotatedTranscriptTests.cs
  class PianoAnnotatedTranscriptTests (line 12) | public class PianoAnnotatedTranscriptTests
    method Empty_upstreamAminoAcids_return_dot (line 14) | [Fact]
    method refSeq_gene_return_entrezId (line 37) | [Fact]

FILE: Sandbox/UnitTests/Piano/PianoTests.cs
  class PianoTests (line 14) | public class PianoTests
    method GetMockedTranscriptOnForwardStrand (line 18) | private static ITranscript GetMockedTranscriptOnForwardStrand()
    method MissenseVariant (line 65) | [Fact]
    method missense_variant_in_TSS_returns (line 79) | [Fact]
    method synounymous_mutation_returns_no_change (line 92) | [Fact]
    method Frameshift_mutation_returns_no_downStreamAminoAcids (line 105) | [Fact]

FILE: Sandbox/UnitTests/Piano/SimpleSequence.cs
  class SimpleSequence (line 5) | public sealed class SimpleSequence : ISequence
    method SimpleSequence (line 11) | public SimpleSequence(string s, int zeroBasedStartOffset = 0)
    method Substring (line 17) | public string Substring(int offset, int length)

FILE: Sandbox/UnitTests/Utilities/ResourceUtilities.cs
  class ResourceUtilities (line 6) | public static class ResourceUtilities
    method GetResourceStream (line 13) | public static Stream GetResourceStream(string resourcePath, bool check...

FILE: Sandbox/UnitTests/Utilities/Resources.cs
  class Resources (line 6) | public static class Resources
    method TopPath (line 9) | public static string TopPath(string path) => Path.Combine(Top, path);
    method Resources (line 11) | static Resources()
    method GetParentDirectory (line 17) | private static string GetParentDirectory(string directory, int numLevels)

FILE: SingleAnnotationLambda/CacheConfiguration.cs
  class CacheConfiguration (line 6) | public sealed class CacheConfiguration : IEquatable<CacheConfiguration>
    method CacheConfiguration (line 12) | public CacheConfiguration(GenomeAssembly genomeAssembly, string supple...
    method Equals (line 19) | public bool Equals(CacheConfiguration other)
    method GetHashCode (line 28) | public override int GetHashCode()
    method ToString (line 39) | public override string ToString()

FILE: SingleAnnotationLambda/CacheUtilities.cs
  class CacheUtilities (line 7) | public static class CacheUtilities
    method IsVepVersionSupported (line 13) | public static bool IsVepVersionSupported(int vepVersion) =>
    method GetSupportedVersions (line 16) | public static string GetSupportedVersions() => string.Join(", ", Suppo...
    method UrlCombine (line 18) | private static string UrlCombine(string baseUrl, string relativeUrl) =...
    method GetCachePathPrefix (line 20) | public static string GetCachePathPrefix(int vepVersion, GenomeAssembly...

FILE: SingleAnnotationLambda/ExceptionHandler.cs
  class ExceptionHandler (line 10) | public static class ExceptionHandler
    method GetStream (line 12) | public static Stream GetStream(string id, string snsTopicArn, Exceptio...
    method GetMessage (line 28) | private static string GetMessage(ErrorCategory errorCategory, string e...
    method FirstCharToLower (line 34) | private static string FirstCharToLower(string input) => string.IsNullO...

FILE: SingleAnnotationLambda/SingleAnnotationLambda.cs
  class SingleAnnotationLambda (line 30) | public class SingleAnnotationLambda
    method Run (line 37) | public Stream Run(SingleConfig config, ILambdaContext context)
    method GetAndCacheAnnotationResources (line 77) | private AnnotationResources GetAndCacheAnnotationResources(SingleConfi...
    method GetAnnotationResources (line 109) | private static AnnotationResources GetAnnotationResources(SingleConfig...
    method GetPositionAnnotation (line 129) | private static string GetPositionAnnotation(IPosition position, IAnnot...
    method WriteAnnotatedPosition (line 150) | private static void WriteAnnotatedPosition(IAnnotatedPosition annotate...

FILE: SingleAnnotationLambda/SingleConfigExtensions.cs
  class SingleConfigExtensions (line 15) | public static class SingleConfigExtensions
    method Validate (line 17) | public static void Validate(this SingleConfig config)
    method ValidateSupplementaryAnnotations (line 27) | private static void ValidateSupplementaryAnnotations(this SingleConfig...
    method ValidateVepVersion (line 34) | private static void ValidateVepVersion(this SingleConfig config)
    method GetPositionAndSampleNames (line 41) | public static (IPosition, string[]) GetPositionAndSampleNames(this Sin...
    method ToPosition (line 44) | private static IPosition ToPosition(string[] vcfFields, ISequenceProvi...

FILE: SingleAnnotationLambda/SingleResult.cs
  class SingleResult (line 10) | public static class SingleResult
    method Create (line 15) | public static Stream Create(string id, string status, string nirvanaJson)

FILE: SingleAnnotationLambda/SupplementaryAnnotationUtilities.cs
  class SupplementaryAnnotationUtilities (line 5) | public static class SupplementaryAnnotationUtilities
    method IsValueSupported (line 9) | public static bool IsValueSupported(string supplementaryAnnotations)
    method GetSupportedValues (line 15) | public static string GetSupportedValues() => string.Join(", ", Support...

FILE: Tabix/BgzfBlockVcfReader.cs
  class BgzfBlockVcfReader (line 8) | public static class BgzfBlockVcfReader
    method FindVariantsInBlocks (line 10) | public static bool FindVariantsInBlocks(Stream stream, long beginOffse...
    method HasVcfPositionsOnInterval (line 24) | internal static bool HasVcfPositionsOnInterval(string s, Chromosome ch...

FILE: Tabix/BinUtilities.cs
  class BinUtilities (line 5) | internal static class BinUtilities
    method FirstBin (line 7) | internal static int FirstBin(int bin) => ((1 << ((bin << 1) + bin)) - ...
    method ParentBin (line 8) | internal static int ParentBin(int bin) => (bin - 1) >> 3;
    method BottomBin (line 10) | internal static int BottomBin(int bin)
    method ConvertPositionToBin (line 20) | internal static int ConvertPositionToBin(int begin) => 4681 + (begin >...
    method OverlappingBinsWithVariants (line 22) | internal static IEnumerable<int> OverlappingBinsWithVariants(int begin...

FILE: Tabix/Constants.cs
  class Constants (line 3) | internal static class Constants

FILE: Tabix/Index.cs
  class Index (line 5) | public sealed class Index
    method Index (line 21) | public Index(int format, int sequenceNameIndex, int beginIndex, int en...

FILE: Tabix/Interval.cs
  type Interval (line 3) | public struct Interval
    method Interval (line 8) | public Interval(ulong begin, ulong end)

FILE: Tabix/Reader.cs
  class Reader (line 10) | public static class Reader
    method Read (line 13) | public static Index Read(BinaryReader reader, Dictionary<string, Chrom...
    method GetTabixIndex (line 46) | public static Index GetTabixIndex(Stream tabixStream, Dictionary<strin...
    method GetReferenceSequenceNames (line 54) | private static string[] GetReferenceSequenceNames(byte[] concatenatedB...
    method GetNullIndexes (line 70) | private static IEnumerable<int> GetNullIndexes(IReadOnlyList<byte> byt...
    method ReadReferenceSequence (line 78) | private static ReferenceIndex ReadReferenceSequence(BinaryReader reade...
    method ReadBin (line 103) | private static (int Id, Interval[] Chunks) ReadBin(BinaryReader reader)
    method ReadChunk (line 114) | private static Interval ReadChunk(BinaryReader reader)

FILE: Tabix/ReferenceIndex.cs
  class ReferenceIndex (line 6) | public sealed class ReferenceIndex
    method ReferenceIndex (line 14) | public ReferenceIndex(Chromosome chromosome, Dictionary<int, Interval[...

FILE: Tabix/Search.cs
  class Search (line 9) | public sealed class Search
    method Search (line 14) | public Search(Index index, Stream vcfStream)
    method HasVariants (line 21) | public bool HasVariants(string chromosomeName, int begin, int end)
    method HasVariantsInBin (line 40) | private bool HasVariantsInBin(Chromosome chromosome, int begin, int en...

FILE: Tabix/SearchUtilities.cs
  class SearchUtilities (line 3) | public static class SearchUtilities
    method GetOffset (line 6) | public static long GetOffset(this Index index, string chromosomeName, ...
    method AdjustBegin (line 31) | internal static int AdjustBegin(int begin)
    method FirstNonZeroValue (line 40) | internal static long FirstNonZeroValue(this ulong[] offsets)
    method GetTabixReferenceSequence (line 51) | internal static ReferenceIndex GetTabixReferenceSequence(this Index in...
    method GetMinOverlapOffset (line 59) | internal static long GetMinOverlapOffset(Interval[] chunks, ulong minO...
    method GetMinOffset (line 75) | internal static ulong GetMinOffset(ReferenceIndex refSeq, int begin)
    method GetMaxOffset (line 95) | internal static ulong GetMaxOffset(ReferenceIndex refSeq, int end)
    method GetMinMaxVirtualFileOffset (line 110) | internal static (long MinOffset, long MaxOffset) GetMinMaxVirtualFileO...

FILE: Tabix/VirtualPosition.cs
  class VirtualPosition (line 3) | public static class VirtualPosition
    method From (line 5) | public static (long FileOffset, int BlockOffset) From(long virtualPosi...
    method To (line 14) | public static long To(long fileOffset, int blockOffset) => (fileOffset...

FILE: UnitTests/AnnotationLambda/AnnotationLambdaTests.cs
  class AnnotationLambdaTests (line 11) | public sealed class AnnotationLambdaTests
    method GetTabixVirtualPosition_AsExpected (line 13) | [Fact]
    method GetTabixVirtualPosition_ReturnZeroWhenNoRangeSpecified (line 34) | [Fact]

FILE: UnitTests/AnnotationLambda/S3UtilitiesTests.cs
  class S3UtilitiesTests (line 6) | public sealed class S3UtilitiesTests
    method GetKey_Theory (line 8) | [Theory]

FILE: UnitTests/CacheUtils/DataDumperImport/DataStructures/Import/ImportNodeExtensionsTests.cs
  class ImportNodeExtensionsTests (line 7) | public sealed class ImportNodeExtensionsTests
    method GetInt32_Nominal (line 9) | [Fact]
    method GetInt32_ReturnMinusOne_WhenNull (line 17) | [Fact]
    method GetInt32_ThrowException_When_NotNumber (line 25) | [Fact]
    method GetString_ThrowException_When_NotCorrectType (line 37) | [Fact]
    method GetString_ReturnNull_IfEmptyOrMinus (line 49) | [Fact]
    method GetBool_ReturnTrue (line 61) | [Fact]
    method GetBool_ReturnFalse (line 69) | [Fact]
    method IsUndefined_ReturnTrue (line 77) | [Fact]
    method IsUndefined_ReturnFalse (line 85) | [Fact]
    method IsUndefined_ReturnFalse_IncorrectType (line 93) | [Fact]

FILE: UnitTests/CacheUtils/DataDumperImport/FauxRegex/RegexDecisionTreeTests.cs
  class RegexDecisionTreeTests (line 8) | public sealed class RegexDecisionTreeTests
    method GetEntryType_RootObjectKeyValue (line 10) | [Fact]
    method GetEntryType_ListObjectKeyValue (line 19) | [Fact]
    method GetEntryType_OpenBraces (line 28) | [Fact]
    method GetEntryType_StringKeyValue (line 37) | [Fact]
    method GetEntryType_DigitKeyValue (line 46) | [Fact]
    method GetEntryType_EndBracesWithDataType (line 55) | [Fact]
    method GetEntryType_EndBraces (line 64) | [Fact]
    method GetEntryType_ObjectKeyValue (line 73) | [Fact]
    method GetEntryType_UndefKeyValue (line 82) | [Fact]
    method GetEntryType_EmptyListKeyValue (line 91) | [Fact]
    method GetEntryType_EmptyValueKeyValue (line 100) | [Fact]
    method GetEntryType_ReferenceStringKeyValue (line 109) | [Fact]
    method GetEntryType_DigitKey (line 118) | [Fact]
    method GetEntryType_ThrowsNotImplementedException (line 127) | [Theory]
    method OnlyDigits (line 140) | [Theory]

FILE: UnitTests/CacheUtils/DataDumperImport/FileHandling/DataDumperReaderTests.cs
  class DataDumperReaderTests (line 9) | public sealed class DataDumperReaderTests
    method GetRootNode_EndToEnd (line 11) | [Fact]
    method GetRootNode_ObjectValue_UnhandledEntryType_ThrowsException (line 98) | [Fact]
    method GetRootNode_ListObjectKeyValue_UnhandledEntryType_ThrowsException (line 120) | [Fact]
    method GetRootNode_EmptyStream_ThrowsException (line 142) | [Fact]
    method GetRootNode_NoRootObject_ThrowsException (line 154) | [Fact]

FILE: UnitTests/CacheUtils/DataDumperImport/Import/ImportRegulatoryFeatureTests.cs
  class ImportRegulatoryFeatureTests (line 12) | public sealed class ImportRegulatoryFeatureTests
    method ImportRegulatoryFeatureTests (line 16) | public ImportRegulatoryFeatureTests()
    method GetDataDumperOutput (line 24) | private static string GetDataDumperOutput()
    method GetObjectValueNode (line 139) | private static ObjectValueNode GetObjectValueNode(string dataDumperOut...
    method Parse_Nominal (line 170) | [Fact]

FILE: UnitTests/CacheUtils/DataDumperImport/Import/ImportTranscriptTests.cs
  class ImportTranscriptTests (line 14) | public sealed class ImportTranscriptTests
    method ImportTranscriptTests (line 18) | public ImportTranscriptTests()
    method GetDataDumperOutput (line 26) | private static string GetDataDumperOutput()
    method GetObjectValueNode (line 602) | private static ObjectValueNode GetObjectValueNode(string dataDumperOut...
    method Parse_Nominal (line 630) | [Fact]

FILE: UnitTests/CacheUtils/Genes/Combiners/CombinerUtilsTests.cs
  class CombinerUtilsTests (line 10) | public sealed class CombinerUtilsTests
    method Merge_DifferentCombinations (line 12) | [Fact]
    method Merge_ThrowException_IfValuesDifferent (line 24) | [Fact]

FILE: UnitTests/CacheUtils/Genes/Combiners/HgncIdCombinerTests.cs
  class HgncIdCombinerTests (line 10) | public sealed class HgncIdCombinerTests
    method Combine_CombineWhenAllIdsMatch (line 14) | [Fact]
    method Combine_DoNotCombine_MixedStrands (line 33) | [Fact]
    method Combine_MIR6859_CombineWhenMissingGeneId (line 48) | [Fact]

FILE: UnitTests/CacheUtils/Genes/Combiners/PartitionCombinerTests.cs
  class PartitionCombinerTests (line 10) | public sealed class PartitionCombinerTests
    method Combine_MergeIfSameIds_EntrezGeneOnly (line 14) | [Fact]
    method Combine_MergeIfSameIds_EnsemblOnly (line 33) | [Fact]
    method Combine_DoNotCombine_MixedIds (line 52) | [Fact]

FILE: UnitTests/CacheUtils/Genes/GeneFlattenerTests.cs
  class GeneFlattenerTests (line 9) | public sealed class GeneFlattenerTests
    method Flatten_AllGenesShouldBeCombined (line 11) | [Fact]
    method Flatten_ReturnSameGene_WhenListHasOneEntry (line 30) | [Fact]
    method Flatten_ReturnNull_WhenInputNull (line 45) | [Fact]
    method Flatten_NoGenesShouldBeCombined (line 52) | [Fact]

FILE: UnitTests/CacheUtils/Genes/Utilities/DictionaryUtilitiesTests.cs
  class DictionaryUtilitiesTests (line 9) | public sealed class DictionaryUtilitiesTests
    method GetSingleValueDict_OneKey_OneValue (line 11) | [Fact]
    method GetSingleValueDict_ThrowException_IfMultipleValuesShareKey (line 24) | [Fact]
    method GetMultiValueDict_OneKey_WithTwoValues (line 38) | [Fact]
    method GetKeyValueDict_OneKey_OneValue (line 55) | [Fact]
    method CreateIndex_ThreeValues (line 71) | [Fact]

FILE: UnitTests/CacheUtils/IO/Caches/TranscriptCacheWriterTests.cs
  class TranscriptCacheWriterTests (line 7) | public sealed class TranscriptCacheWriterTests
    method CreateIndex_PopulatedDictionary (line 9) | [Fact]
    method CreateIndex_EmptyDictionary_WhenInputNull (line 18) | [Fact]

FILE: UnitTests/CacheUtils/TranscriptCache/TranscriptRegionMergerTests.cs
  class TranscriptRegionMergerTests (line 12) | public sealed class TranscriptRegionMergerTests
    method GetTranscriptRegions_OneExon (line 16) | [Fact]
    method GetTranscriptRegions_WithGap_Forward (line 39) | [Fact]
    method GetTranscriptRegions_WithGap_Reverse (line 109) | [Fact]
    method GetTranscriptRegions_Reverse (line 154) | [Fact]
    method GetTranscriptRegions_TwoExonsNoGap_Forward (line 186) | [Fact]

FILE: UnitTests/CacheUtils/Utilities/AccessionUtilitiesTests.cs
  class AccessionUtilitiesTests (line 7) | public sealed class AccessionUtilitiesTests
    method GetMaxVersion_Dupl (line 9) | [Fact]
    method GetMaxVersion_IdVersionMax (line 19) | [Fact]
    method GetMaxVersion_SuppliedVersionMax (line 29) | [Fact]
    method GetAccessionNumber_ReturnNumber_RefSeq (line 39) | [Fact]
    method GetAccessionNumber_ReturnNumber_Ensembl (line 47) | [Fact]
    method GetAccessionNumber_ReturnMinusOne (line 55) | [Fact]
    method GetAccessionNumber_ThrowException_IfUnderlineMissingRefSeq (line 63) | [Fact]

FILE: UnitTests/CacheUtils/Utilities/RemoteFileTests.cs
  class RemoteFileTests (line 8) | public sealed class RemoteFileTests
    method GetFilename_WithoutUrlPrefix (line 10) | [Fact]
    method GetFilename_WithoutDate (line 18) | [Fact]
    method GetFilename_WithUrlPrefix (line 26) | [Fact]

FILE: UnitTests/Cloud/ConsistencyTests.cs
  class ConsistencyTests (line 7) | public sealed class ConsistencyTests
    method Consistency_with_SAUtils (line 9) | [Fact]

FILE: UnitTests/Cloud/JsonUtilitiesTests.cs
  class JsonUtilitiesTests (line 9) | public sealed class JsonUtilitiesTests
    method Serialize_AsExpected (line 12) | [Fact]
    method Stringify_AsExpected (line 29) | [Fact]
  class ObjectExample (line 44) | public sealed class ObjectExample

FILE: UnitTests/Cloud/LambdaUrlHelperTests.cs
  class LambdaUrlHelperTests (line 12) | public sealed class LambdaUrlHelperTests
    method GetDataUrlBase_AsExpected (line 14) | [Fact]
    method GetS3RefLocation_AsExpected (line 22) | [Fact]
    method GetS3_SaManifest_Location_AsExpected (line 29) | [Fact]
    method GetS3_SaManifest_Location_from_config (line 37) | [Fact]

FILE: UnitTests/Cloud/RedactionUtilitiesTests.cs
  class RedactionUtilitiesTests (line 6) | public sealed class RedactionUtilitiesTests
    method Redact_PresignedUrl (line 8) | [Fact]
    method Redact_AwsSignatureVersion4 (line 18) | [Fact]

FILE: UnitTests/Cloud/S3PathTests.cs
  class S3PathTests (line 7) | public sealed class S3PathTests
    method ValidatePathFormat_AsExpected (line 9) | [Theory]
    method FormatPath_AsExpected (line 17) | [Fact]

FILE: UnitTests/Cloud/SaUrlsTests.cs
  class SaUrlsTests (line 7) | public sealed class SaUrlsTests
    method SetSaType_InvalidValues_ThrowException (line 9) | [Theory]
    method SetSaType_AsExpected (line 23) | [Theory]

FILE: UnitTests/Cloud/UploadUtilitiesTests.cs
  class UploadUtilitiesTests (line 14) | public sealed class UploadUtilitiesTests
    method GetS3ClientMock (line 20) | private static Mock<IS3Client> GetS3ClientMock()
    method GetS3ClientMockAlwaysFail (line 27) | private static Mock<IS3Client> GetS3ClientMockAlwaysFail()
    method GetS3ClientMockCanWorkAfterRetries (line 34) | private static Mock<IS3Client> GetS3ClientMockCanWorkAfterRetries()
    method TryDecryptUpload_AsExpected (line 46) | [Fact]
    method TryDecryptUpload_FileNotFound (line 54) | [Fact]
    method DecryptUpload_OnlyPutOnceWhenSuccess (line 62) | [Fact]
    method DecryptUpload_SuccessWithRetries (line 71) | [Fact]
    method DecryptUpload_TimeOutWhenFail (line 80) | [Fact]

FILE: UnitTests/CommandLine/Builders/ConsoleAppBuilderDataTests.cs
  class ConsoleAppBuilderDataTests (line 8) | public sealed class ConsoleAppBuilderDataTests
    method VersionProvider_Set (line 10) | [Fact]
  class ConsoleAppValidatorTests (line 23) | public sealed class ConsoleAppValidatorTests
    method ShowBanner_EnabledOutput (line 25) | [Fact]

FILE: UnitTests/CommandLine/Builders/ConsoleAppBuilderTests.cs
  class ConsoleAppBuilderTests (line 8) | public sealed class ConsoleAppBuilderTests
    method Parse_UnsupportedOption (line 10) | [Fact]
    method Parse_Version (line 23) | [Fact]
    method Parse_HelpMenu (line 43) | [Fact]
    method Parse_ShowOutput (line 63) | [Fact]

FILE: UnitTests/CommandLine/Builders/TopLevelAppBuilderTests.cs
  class TopLevelAppBuilderTests (line 8) | public sealed class TopLevelAppBuilderTests
    method TopLevelAppBuilderTests (line 12) | public TopLevelAppBuilderTests()
    method EmptyMethod (line 20) | private static ExitCodes EmptyMethod(string command, string[] args) =>...
    method Parse_UnsupportedOption (line 22) | [Fact]
    method Parse_ShowHelpMenu (line 37) | [Fact]
    method Parse_Nominal (line 52) | [Fact]

FILE: UnitTests/CommandLine/Builders/ValidationExtensionsTests.cs
  class ValidationExtensionsTests (line 11) | public sealed class ValidationExtensionsTests
    method Execute (line 13) | private static ExitCodes Execute(IConsoleAppValidator validator)
    method CheckInputFilenameExists_FileExists_SuccessExitCode (line 23) | [Fact]
    method CheckInputFilenameExists_MissingFiles_FileNotFoundExitCode (line 38) | [Fact]
    method CheckInputFilenameExists_MissingArguments_MissingCommandLineExitCode (line 52) | [Fact]
    method CheckInputFilenameExists_EmptyPath_MissingCommandLineExitCode (line 64) | [Fact]
    method CheckInputFilenameExists_IgnoredPath_SuccessExitCode (line 76) | [Fact]
    method CheckDirectoryExists_MissingDirectory_PathNotFoundExitCode (line 88) | [Fact]
    method CheckDirectoryExists_EmptyPath_MissingCommandLineOptionExitCode (line 100) | [Fact]
    method CheckEachFilenameExists_MissingFile_MissingCommandLineOptionExitCode (line 112) | [Fact]
    method HasRequiredParameter_Exists_SuccessExitCode (line 125) | [Fact]
    method HasRequiredDate_Exists_SuccessExitCode (line 141) | [Fact]
    method HasRequiredDate_Exists_BadFormat (line 157) | [Fact]
    method HasRequiredDate_DoesNotExist_MissingCommandLineExitCode (line 170) | [Fact]
    method CheckOutputFilenameSuffix_True (line 184) | [Fact]
    method CheckOutputFilenameSuffix_False (line 197) | [Fact]
    method HasRequiredParameter_DoesNotExist_MissingCommandLineExitCode (line 210) | [Fact]
    method HasRequiredParameter_MissingArguments_MissingCommandLineExitCode (line 230) | [Fact]

FILE: UnitTests/CommandLine/NDesk.Options/OptionContextTests.cs
  class OptionContextTests (line 7) | public sealed class OptionContextTests
    method OptionContextTests (line 11) | public OptionContextTests()
    method Should_ThrowException_When_ContextIsEmpty (line 19) | [Fact]
    method Should_ThrowException_When_IndexGreaterThanLength (line 31) | [Fact]
    method Should_ThrowException_When_RequiredValueMissing (line 43) | [Fact]

FILE: UnitTests/CommandLine/NDesk.Options/OptionSetTests.cs
  class OptionSetTests (line 10) | public sealed class OptionSetTests
    method OptionSetTests (line 15) | public OptionSetTests()
    method BundledValues (line 26) | [Fact]
    method RequiredValues (line 59) | [Fact]
    method OptionalValues (line 83) | [Fact]
    method BooleanValues (line 120) | [Fact]
    method CombinationPlatter (line 139) | [Fact]
    method Should_ThrowException_When_MissingRequiredValue (line 182) | [Fact]
    method ShouldNot_ThrowException_When_ProvidingMoreOptionsThanExpected (line 191) | [Fact]
    method ShouldNot_ThrowException_When_ProvidingUnregisteredNamedOption (line 203) | [Fact]
    method Should_ThrowException_When_ArgumentNull (line 215) | [Fact]
    method Should_ThrowException_With_InvalidType (line 224) | [Fact]
    method Should_ThrowException_When_BundlingWithOptionRequiringValue (line 233) | [Fact]
    method WriteOptionDescriptions (line 242) | [Fact]
    method OptionBundling (line 304) | [Fact]
    method HaltProcessing (line 327) | [Fact]
    class ContextCheckerOption (line 342) | private sealed class ContextCheckerOption : Option
      method ContextCheckerOption (line 348) | public ContextCheckerOption(string p, string d, string eName, string...
      method OnParseComplete (line 356) | protected override void OnParseComplete(OptionContext c)
    method OptionContext (line 367) | [Fact]
    method DefaultHandler (line 381) | [Fact]
    method MixedDefaultHandler (line 398) | [Fact]
    method DefaultHandlerRuns (line 416) | [Fact]
    class Foo (line 450) | private class Foo
      method Foo (line 454) | private Foo(string s) { _s = s; }
      method ToString (line 455) | public override string ToString() { return _s; }

FILE: UnitTests/CommandLine/NDesk.Options/OptionsTests.cs
  class OptionsTests (line 8) | public sealed class OptionsTests
    method Should_ThrowException_When_PrototypeNull (line 10) | [Fact]
    method Should_ThrowException_When_PrototypeEmpty (line 20) | [Fact]
    method Should_ThrowException_When_OptionNameEmpty (line 30) | [Fact]
    method Should_ThrowException_When_OptionTypesConflict (line 40) | [Fact]
    method Should_ThrowException_When_DefaultHandlerRequiresValue (line 50) | [Fact]
    method Should_ThrowException_When_DefaultHandlerRequiresValues (line 60) | [Fact]
    method Should_Not_ThrowException (line 76) | [Fact]
    method Should_ThrowException_When_MaxValueCountOutOfRange (line 93) | [Fact]
    method Should_ThrowException_When_MaxValueCountZero_And_RequiredType (line 103) | [Fact]
    method Should_ThrowException_With_IllFormedSeparator (line 113) | [Fact]
    method Should_ThrowException_When_CannotProvideSeparatorsWhenTakingOneValue (line 147) | [Fact]
    class DefaultOption (line 169) | private sealed class DefaultOption : Option
      method DefaultOption (line 171) | public DefaultOption(string prototypes, string description)
      method DefaultOption (line 175) | public DefaultOption(string prototypes, string description, int c)
      method OnParseComplete (line 179) | protected override void OnParseComplete(OptionContext c)

FILE: UnitTests/CommandLine/Utilities/BenchmarkTests.cs
  class BenchmarkTests (line 7) | public sealed class BenchmarkTests
    method ToHumanReadable_Days (line 9) | [Fact]
    method ToHumanReadable_LessThanOneDay (line 18) | [Fact]
    method Benchmark_EndToEnd (line 27) | [Fact]

FILE: UnitTests/CommandLine/Utilities/MemoryUtilitiesTests.cs
  class MemoryUtilitiesTests (line 6) | public sealed class MemoryUtilitiesTests
    method ToHumanReadable_Convert_Bytes (line 8) | [Fact]
    method ToHumanReadable_Convert_KiloBytes (line 15) | [Fact]
    method ToHumanReadable_Convert_MegaBytes (line 22) | [Fact]
    method ToHumanReadable_Convert_GigaBytes (line 29) | [Fact]

FILE: UnitTests/CommandLine/VersionProviders/DefaultVersionProviderTests.cs
  class DefaultVersionProviderTests (line 6) | public sealed class DefaultVersionProviderTests
    method GetProgramVersion (line 8) | [Fact]

FILE: UnitTests/Compression/CompressionAlgorithmTests.cs
  class CompressionAlgorithmTests (line 8) | public sealed class CompressionAlgorithmTests
    method CompressionAlgorithmTests (line 13) | public CompressionAlgorithmTests()
    method RoundTrip (line 18) | [Theory]
    method GetCompressionAlgorithm (line 57) | private static ICompressionAlgorithm GetCompressionAlgorithm(Compressi...
  type CompressionAlgorithms (line 71) | public enum CompressionAlgorithms

FILE: UnitTests/Compression/DataStructures/BlockTests.cs
  class BlockTests (line 12) | public sealed class BlockTests
    method BlockTests (line 18) | static BlockTests()
    method GetBlockStream (line 26) | private static MemoryStream GetBlockStream(ICompressionAlgorithm compr...
    method QuickLzBlock (line 38) | [Fact]
    method BlockZeroLengthCopy (line 56) | [Fact]
    method BlockWrongSize (line 66) | [Fact]
    method BlockTruncation (line 95) | [Fact]
    method UncompressedBlockTruncation (line 112) | [Fact]

FILE: UnitTests/Compression/FileHandling/BgzipTextWriterTests.cs
  class BgzipTextWriterTests (line 9) | public sealed class BgzipTextWriterTests
    method BgzipTextWriter_EndToEnd (line 11) | [Fact]

FILE: UnitTests/Compression/FileHandling/BlockGZipStreamTests.cs
  class BlockGZipStreamTests (line 13) | public sealed class BlockGZipStreamTests
    method BlockGZipStreamTests (line 21) | public BlockGZipStreamTests()
    method FileIO (line 27) | [Fact]
    method InvalidHeader (line 74) | [Fact]
    method NullStream (line 112) | [Fact]
    method NotImplementedMethods (line 123) | [Fact]
    method StreamIO (line 145) | [Fact]
    method StreamTypeMismatch (line 193) | [Fact]
    method VariableDataLength (line 221) | [Theory]
    method EndOfFile (line 265) | [Fact]
    method ReadBlockCorrupted (line 297) | [Fact]
    method DoubleDispose (line 339) | [Fact]
    method GrabBytes (line 350) | private static byte[] GrabBytes(Stream s)

FILE: UnitTests/Compression/FileHandling/BlockHeaderTests.cs
  class BlockHeaderTests (line 8) | public sealed class BlockHeaderTests
    method ReadAndWrite (line 10) | [Fact]
    method SizeMismatch (line 38) | [Fact]
    method WrongHeaderId (line 54) | [Fact]

FILE: UnitTests/Compression/FileHandling/BlockStreamTests.cs
  class BlockStreamTests (line 20) | public sealed class BlockStreamTests
    method BlockStream_EndToEnd (line 30) | [Fact]
    method GetRandomString (line 47) | private static string GetRandomString(int length)
    method GetRandomBytes (line 53) | public static byte[] GetRandomBytes(int numBytes)
    method ReadFromBlockStream (line 61) | private static void ReadFromBlockStream(ICompressionAlgorithm compress...
    method CheckString (line 87) | private static void CheckString(ExtendedBinaryReader reader, string ex...
    method WriteBlockStream (line 95) | private static void WriteBlockStream(ICompressionAlgorithm compression...
    method CheckReadException (line 118) | private static void CheckReadException(Stream writer)
    method CheckWriteException (line 131) | private static void CheckWriteException(Stream reader)
    method NullStream (line 144) | [Fact]
    method NotImplementedMethods (line 155) | [Fact]
    method StreamTypeMismatch (line 179) | [Fact]
    method CanReadWriteSeek (line 207) | [Fact]
    method ValidateParameters (line 221) | [Fact]
    method EndOfFile (line 239) | [Fact]
    method DoubleDispose (line 268) | [Fact]
  class DemoHeader (line 280) | public sealed class DemoHeader : Header
    method DemoHeader (line 284) | public DemoHeader(string identifier, ushort schemaVersion, ushort data...
    method Write (line 291) | public new void Write(BinaryWriter writer)
    method Read (line 297) | public static DemoHeader Read(Stream stream)
  class DemoCustomHeader (line 314) | public sealed class DemoCustomHeader
    method DemoCustomHeader (line 319) | public DemoCustomHeader(long fileOffset, int internalOffset)
    method Write (line 325) | public void Write(BinaryWriter writer)
    method Read (line 331) | public static DemoCustomHeader Read(BinaryReader reader)

FILE: UnitTests/Compression/Utilities/GZipUtilitiesTests.cs
  class GZipUtilitiesTests (line 10) | public sealed class GZipUtilitiesTests
    method GetAppropriateReadStream_Handle_TextFile (line 14) | [Fact]
    method GetAppropriateReadStream_Handle_GZipFile (line 33) | [Fact]
    method GetAppropriateReadStream_Handle_BlockGZipFile (line 52) | [Fact]

FILE: UnitTests/Compression/Utilities/LibraryUtilitiesTests.cs
  class LibraryUtilitiesTests (line 6) | public sealed class LibraryUtilitiesTests
    method CheckLibrary_ValidLibrary_NoExceptionThrown (line 8) | [Fact]

FILE: UnitTests/CustomAnnotationLambda/CustomAnnotationConfigTests.cs
  class CustomAnnotationConfigTests (line 9) | public sealed class CustomAnnotationConfigTests
    method CheckFieldsNotNull_AsExpected (line 11) | [Fact]
    method GetConfig (line 61) | private static CustomConfig GetConfig() => new CustomConfig

FILE: UnitTests/Downloader/AnnotationRepositoryTests.cs
  class AnnotationRepositoryTests (line 10) | public class AnnotationRepositoryTests
    method DownloadFiles_Nominal (line 12) | [Fact]

FILE: UnitTests/Downloader/ConfigurationTests.cs
  class ConfigurationTests (line 7) | public sealed class ConfigurationTests
    method Load_ExpectedResults (line 9) | [Fact]
    method Load_OverrideHostName (line 22) | [Fact]
    method Load_OverrideManifest (line 29) | [Fact]

FILE: UnitTests/Downloader/FileExtensions/CacheFileExtensionsTests.cs
  class CacheFileExtensionsTests (line 11) | public sealed class CacheFileExtensionsTests
    method AddCacheFiles_Nominal (line 13) | [Fact]

FILE: UnitTests/Downloader/FileExtensions/ReferencesFileExtensionTests.cs
  class ReferencesFileExtensionsTests (line 11) | public sealed class ReferencesFileExtensionsTests
    method AddReferenceFiles_Nominal (line 13) | [Fact]

FILE: UnitTests/Downloader/FileExtensions/SupplementaryAnnotationFileExtensionsTests.cs
  class SupplementaryAnnotationFileExtensionsTests (line 10) | public sealed class SupplementaryAnnotationFileExtensionsTests
    method AddSupplementaryAnnotationFiles_Nominal (line 12) | [Fact]

FILE: UnitTests/Downloader/GenomeAssemblyHelperTests.cs
  class GenomeAssemblyHelperTests (line 9) | public sealed class GenomeAssemblyHelperTests
    method GetGenomeAssemblies_GRCh37 (line 11) | [Fact]
    method GetGenomeAssemblies_GRCh38 (line 19) | [Fact]
    method GetGenomeAssemblies_Both (line 27) | [Fact]
    method GetGenomeAssemblies_Unknown (line 36) | [Fact]

FILE: UnitTests/Downloader/ManifestTests.cs
  class ManifestTests (line 9) | public sealed class ManifestTests
    method CreateGenomeAssemblyPaths_GRCh37 (line 14) | [Fact]
    method CreateGenomeAssemblyPaths_GRCh38 (line 24) | [Fact]
    method CreateGenomeAssemblyPaths_Both (line 34) | [Fact]
    method CreateGenomeAssemblyPaths_Unknown (line 42) | [Fact]

FILE: UnitTests/Downloader/RemoteFileComparer.cs
  class RemoteFileComparer (line 6) | internal sealed class RemoteFileComparer : EqualityComparer<RemoteFile>
    method Equals (line 8) | public override bool Equals(RemoteFile x, RemoteFile y)
    method GetHashCode (line 15) | public override int GetHashCode(RemoteFile obj)

FILE: UnitTests/EndToEndTests.cs
  class EndToEndTests (line 11) | public sealed class EndToEndTests
    method EndToEndTests (line 15) | public EndToEndTests() => _cacheFilePrefix = Resources.EndToEnd37("chr...
    method Annotation_RefMinor_not_annotated_when_no_SA (line 17) | [Fact]
    method Annotate_with_SA (line 27) | [Obsolete("We need to extract the SA files to enable these again.")]
    method Annotate_NonInformativeAllele_MinimalAnnotation_NoSa_AsExpected (line 49) | [Theory]

FILE: UnitTests/ErrorHandling/ExceptionUtilitiesTests.cs
  class ExceptionUtilitiesTests (line 10) | public sealed class ExceptionUtilitiesTests
    method HasException_AsExpected (line 16) | [Fact]
    method GetInnermostException_AsExpected (line 24) | [Fact]
  class MockHttpWebResponse (line 33) | public sealed class MockHttpWebResponse : WebResponse
    method MockHttpWebResponse (line 38) | public MockHttpWebResponse(Stream stream, HttpStatusCode statusCode)
    method GetResponseStream (line 44) | public override Stream GetResponseStream() => _stream;

FILE: UnitTests/ErrorHandling/Exceptions/ExceptionsTests.cs
  class ExceptionsTests (line 10) | public sealed class ExceptionsTests
    class ExceptionGenerator (line 12) | private sealed class ExceptionGenerator : IEnumerable<object[]>
      method GetEnumerator (line 24) | public IEnumerator<object[]> GetEnumerator() => _data.GetEnumerator();
      method GetEnumerator (line 25) | IEnumerator IEnumerable.GetEnumerator() => GetEnumerator();
    method Check_ExceptionToExitCode_Mapping (line 28) | [Theory]

FILE: UnitTests/ErrorHandling/ExitCodeUtilitiesTests.cs
  class ExitCodeUtilitiesTests (line 9) | public sealed class ExitCodeUtilitiesTests
    method ShowException_CompressionException_CheckExitCode (line 11) | [Fact]
    method ShowException_UnknownException_ExitCode_ShouldBeOne (line 20) | [Fact]
    method ShowException_AggregateException_ExitCode_ShouldBeOne (line 28) | [Fact]

FILE: UnitTests/GeneAnnotationLambda/GeneAnnotationLambdaTests.cs
  class GeneAnnotationLambdaTests (line 10) | public sealed class GeneAnnotationLambdaTests
    method GetNgaFiles_AsExpected (line 16) | [Fact]
    method GetGeneAnnotation_AsExpected (line 32) | [Fact]

FILE: UnitTests/GeneAnnotationLambda/GeneConfigTests.cs
  class GeneConfigTests (line 7) | public sealed class GeneConfigTests
    method Validate_NoId_ThrowException (line 9) | [Fact]
    method Validate_NoGeneSymbols_ThrowException (line 16) | [Fact]
    method Validate_EmptyGeneSymbols_ThrowException (line 23) | [Fact]

FILE: UnitTests/Genome/ChromosomeIntervalTests.cs
  class ChromosomeIntervalTests (line 7) | public sealed class ChromosomeIntervalTests
    method ChromosomeInterval_Setup (line 9) | [Fact]

FILE: UnitTests/Genome/CytogeneticBandTests.cs
  class CytogeneticBandTests (line 7) | public sealed class CytogeneticBandTests
    method GetCytogeneticBand_Range (line 14) | [Theory]
    method GetCytogeneticBand_UnknownReference_ReturnNull (line 28) | [Fact]
    method GetCytogeneticBand_UnknownReferenceIndex_ReturnNull (line 35) | [Fact]

FILE: UnitTests/Genome/EmptyChromosomeTests.cs
  class EmptyChromosomeTests (line 7) | public sealed class EmptyChromosomeTests
    method Equals_True (line 12) | [Fact]
    method Equals_False (line 18) | [Fact]
    method GetHashCode_True (line 25) | [Fact]
    method GetHashCode_False (line 31) | [Fact]

FILE: UnitTests/Genome/GenomeAssemblyHelperTests.cs
  class GenomeAssemblyHelperTests (line 7) | public sealed class GenomeAssemblyHelperTests
    method Convert_GenomeAssemblyExists (line 9) | [Theory]
    method Convert_GenomeAssemblyDoesNotExist (line 21) | [Fact]

FILE: UnitTests/Genome/ReferenceNameUtilitiesTests.cs
  class ReferenceNameUtilitiesTests (line 8) | public sealed class ReferenceNameUtilitiesTests
    method GetChromosome_RefIndex_Exists (line 10) | [Fact]
    method GetChromosome_RefIndex_DoesNotExist (line 17) | [Fact]
    method GetChromosome_RefName_Exists (line 26) | [Fact]
    method GetChromosome_RefName_DoesNotExist (line 33) | [Fact]
    method GetChromosome_RefName_NullName (line 43) | [Fact]

FILE: UnitTests/Genome/SequenceUtilitiesTests.cs
  class SequenceUtilitiesTests (line 6) | public sealed class SequenceUtilitiesTests
    method GetReverseComplement (line 8) | [Theory]
    method HasNonCanonicalBase (line 17) | [Theory]

FILE: UnitTests/IO/BufferedBinaryReaderTests.cs
  class BufferedBinaryReaderTests (line 9) | public sealed class BufferedBinaryReaderTests
    method ReadBoolean (line 11) | [Fact]
    method ReadByte (line 19) | [Fact]
    method ReadBytes (line 27) | [Fact]
    method ReadUInt16 (line 35) | [Fact]
    method ReadUInt32 (line 43) | [Fact]
    method ReadAsciiString (line 51) | [Fact]
    method ReadOptUInt16_HandleExtremeIntegers (line 59) | [Theory]
    method ReadOptInt32_HandleExtremeIntegers (line 69) | [Theory]
    method GetObservedValue (line 79) | private static T GetObservedValue<T>(Action<ExtendedBinaryWriter> writ...

FILE: UnitTests/IO/ExtendedBinaryReaderTests.cs
  class ExtendedBinaryReaderTests (line 9) | public sealed class ExtendedBinaryReaderTests
    method ReadOptInt32_HandleSmallIntegers (line 11) | [Theory]
    method ReadOptInt32_HandleExtremeIntegers (line 21) | [Theory]
    method ReadOptInt32_ThrowException_WithCorruptData (line 30) | [Fact]
    method ReadOptUInt16_HandleExtremeIntegers (line 53) | [Theory]
    method ReadOptInt64_HandleSmallIntegers (line 62) | [Theory]
    method ReadOptInt64_HandleExtremeIntegers (line 72) | [Theory]
    method ReadOptInt64_ThrowException_WithCorruptData (line 81) | [Fact]
    method ReadAsciiString_NullString (line 105) | [Fact]
    method BufferedBinaryReader_EndToEnd_DoNotLeaveOpen (line 112) | [Fact]
    method GetObservedValue (line 135) | private static T GetObservedValue<T>(Action<ExtendedBinaryWriter> writ...

FILE: UnitTests/IO/FilePathUtilitiesTests.cs
  class FilePathUtilitiesTests (line 6) | public sealed class FilePathUtilitiesTests
    method GetFileSuffix_AsExpected (line 8) | [InlineData("C:\\Input files\\input.test.mp3", ".mp3", true)]

FILE: UnitTests/IO/FileUtilitiesTests.cs
  class FileUtilitiesTests (line 8) | public sealed class FileUtilitiesTests
    method GetReadStream_GetCreateStream_Loopback (line 10) | [Fact]

FILE: UnitTests/IO/HttpUtilitiesTests.cs
  class HttpUtilitiesTests (line 12) | public sealed class HttpUtilitiesTests
    method IsWebProtocolErrorException_AsExpected (line 14) | [Fact]
    method ProcessHttpRequestForbiddenException_AsExpected (line 24) | [Theory]
    method ValidateUrl_invalid_user_provided (line 42) | [Fact]
    method ValidateUrl_invalid_deployment (line 50) | [Fact]
    method ValidateUrl_valid (line 58) | [Fact]

FILE: UnitTests/IO/LengthStreamTests.cs
  class LengthStreamTests (line 9) | public sealed class LengthStreamTests
    method Length_AsExpected (line 11) | [Fact]
    method StreamTests_AsExpected (line 36) | [Fact]
    method StreamTests_Throws_NotSupportedException (line 62) | [Fact]
    method ThrowsNotSupportedException (line 78) | private static void ThrowsNotSupportedException<T>(LengthStream length...
    method ThrowsNotSupportedException (line 87) | private static void ThrowsNotSupportedException(LengthStream lengthStr...

FILE: UnitTests/IO/MD5StreamTests.cs
  class MD5StreamTests (line 10) | public sealed class MD5StreamTests
    method GetFileMetadata_AsExpected (line 12) | [Fact]
    method StreamTests_AsExpected (line 38) | [Fact]
    method StreamTests_Throws_NotSupportedException (line 58) | [Fact]
    method ThrowsNotSupportedException (line 73) | private static void ThrowsNotSupportedException<T>(MD5Stream md5Stream...
    method ThrowsNotSupportedException (line 82) | private static void ThrowsNotSupportedException(MD5Stream lengthStream...
    method StringToByteArray (line 91) | private static byte[] StringToByteArray(string hex)

FILE: UnitTests/IO/PersistentStreamTests.cs
  class PersistentStreamTests (line 9) | public sealed class PersistentStreamTests
    method GetMockStream (line 11) | private static Stream GetMockStream()
    method GetWebRequest_connect_on_third (line 25) | private static IConnect GetWebRequest_connect_on_third()
    method GetWebRequest_flaky_stream (line 38) | private static IConnect GetWebRequest_flaky_stream()
    method GetWebRequest_connect_on_seventh (line 49) | private static IConnect GetWebRequest_connect_on_seventh()
    method TestFlakyConnection (line 66) | [Fact]
    method FailToConnect (line 74) | [Fact]
    method ReadFlakyStream (line 80) | [Fact]

FILE: UnitTests/IO/UrlUtilitiesTests.cs
  class UrlUtilitiesTests (line 6) | public sealed class UrlUtilitiesTests
    method Combine_Nominal (line 8) | [Theory]
    method GetFileName_Nominal (line 19) | [Fact]

FILE: UnitTests/Intervals/IntervalArrayTests.cs
  class IntervalArrayTests (line 8) | public sealed class IntervalArrayTests
    method IntervalArrayTests (line 12) | public IntervalArrayTests()
    method OverlapsAny (line 25) | [Theory]
    method GetAllOverlappingValues (line 35) | [Theory]

FILE: UnitTests/Intervals/IntervalExtensionsTests.cs
  class IntervalExtensionsTests (line 6) | public sealed class IntervalExtensionsTests
    method Overlaps_TwoIntervalsWithFlankingLength (line 8) | [Theory]
    method Overlaps_IntervalAndCoordinates (line 20) | [Theory]
    method Contains_TwoIntervals (line 30) | [Fact]
    method Intersects_TwoIntervals (line 39) | [Theory]

FILE: UnitTests/Intervals/IntervalForestTests.cs
  class IntervalForestTests (line 8) | public sealed class IntervalForestTests
    method IntervalForestTests (line 12) | public IntervalForestTests()
    method GetIntervalArrayRefIndex0 (line 21) | private static IntervalArray<string> GetIntervalArrayRefIndex0()
    method GetIntervalArrayRefIndex1 (line 31) | private static IntervalArray<string> GetIntervalArrayRefIndex1()
    method GetIntervalArrayRefIndex2 (line 40) | private static IntervalArray<string> GetIntervalArrayRefIndex2()
    method OverlapsAny (line 49) | [Theory]
    method GetAllOverlappingValues (line 59) | [Theory]
    method GetIntervalArray (line 70) | private static IntervalArray<string> GetIntervalArray(List<Interval<st...

FILE: UnitTests/Intervals/IntervalOperationsTests.cs
  class IntervalOperationsTests (line 6) | public sealed class IntervalOperationsTests
    method Overlaps (line 8) | [Theory]
    method Contains (line 21) | [Theory]
    method Intersects (line 34) | [Theory]

FILE: UnitTests/Intervals/NullIntervalSearchTests.cs
  class NullIntervalSearchTests (line 6) | public sealed class NullIntervalSearchTests
    method OverlapsAny_IIntervalForest (line 8) | [Fact]
    method GetAllOverlappingValues_IIntervalForest (line 15) | [Fact]
    method GetAllOverlappingValues_IIntervalSearch (line 22) | [Fact]

FILE: UnitTests/Intervals/OverlapTypeTests.cs
  class OverlapTypeTests (line 6) | public sealed class OverlapTypeTests
    method GetOverlapType (line 9) | [Theory]

FILE: UnitTests/Jasix/IndexTests.cs
  class IndexTests (line 13) | public sealed class IndexTests
    method Query_succeedes_when_it_overlaps_tail_of_previous_bin (line 15) | [Fact]
    method Add_fill_node_and_start_another (line 36) | [Fact]
    method GetFirstVariantPosition_multi_chrom_index (line 61) | [Fact]
    method FindLargeVaritants_method_does_not_return_small_variants (line 82) | [Fact]
    method Write_and_read_back (line 104) | [Fact]
    method BgzipTestReader_basic (line 145) | [Fact]
    method IndexCreation_multChromosome (line 162) | [Fact]
    method Begin_end_section_and_readback (line 188) | [Fact]
    method GetChromosomeList (line 202) | [Fact]
    method GetHeaderOnly (line 226) | [Fact]
    method GetGeneSection (line 251) | [Fact]

FILE: UnitTests/Jasix/JasixFunctionalityTests.cs
  class JasixFunctionalityTests (line 6) | public sealed class JasixFunctionalityTests
    method ParsingDeletionJsonLine (line 8) | [Fact]
    method ParsingSnvJsonLine (line 20) | [Fact]
    method ParsingJsonInsertionLine (line 32) | [Fact]
    method ParseJsonStructuralVariant (line 44) | [Fact]
    method ParseJsonBreakEnd (line 56) | [Fact]

FILE: UnitTests/Jasix/JasixQueryProcessingTests.cs
  class JasixQueryProcessingTests (line 15) | public sealed class JasixQueryProcessingTests
    method Combination_of_large_and_small_variants (line 17) | [Fact]
    method Quiring_large_variants_overlapping_range_but_starting_before (line 42) | [Fact]
    method First_variant_position_when_the_first_variant_is_large (line 67) | [Fact]
    method TestQuerySingle (line 87) | [Fact]
    method TestQueryMultiple (line 104) | [Fact]
    method TestQueryMultipleWithSkippingMiddleOne (line 119) | [Fact]
    method TestQueryChr1 (line 133) | [Fact]
    method Query_onthefly_Ensembl_and_Ucsc (line 148) | [Fact]
    method Query_with_header (line 164) | [Fact]
    method Report_overlapping_small_and_extending_large_variants (line 184) | [Fact]
    method Report_overlapping_small_and_extending_multiple_large_variants (line 204) | [Fact]
    method Report_overlapping_small_and_large_variants_starting_at_same_location (line 224) | [Fact]

FILE: UnitTests/Jasix/OtfIndexCreatorTests.cs
  class OtfIndexCreatorTests (line 11) | public sealed class OtfIndexCreatorTests
    method Add_one_chrom (line 13) | [Fact]

FILE: UnitTests/Jist/JiSTtests.cs
  class JiSTtests (line 20) | public sealed class JiSTtests
    method GetJsonStreams (line 26) | private static (Stream jsonStream, Stream jasixStream) GetJsonStreams(...
    method All_jsons_with_genes (line 67) | [Fact]
    method Some_with_genes (line 119) | [Fact]
    method All_jsons_without_genes (line 172) | [Fact]
    method GetNirvanaJsonStream (line 226) | private static (Stream jsonStream, Stream jasixStream) GetNirvanaJsonS...
    method EndToEndStitching (line 264) | [Fact]
    method GetNirvanaJsonStreamWithoutGenes (line 316) | private static (Stream jsonStream, Stream jasixStream) GetNirvanaJsonS...
    method StitchingWithoutGenes (line 345) | [Fact]

FILE: UnitTests/MitoHeteroplasmy/MitoHeteroplasmyProviderTests.cs
  class MitoHeteroplasmyProviderTests (line 9) | public sealed class MitoHeteroplasmyProviderTests
    method GetProvider (line 12) | private static MitoHeteroplasmyProvider GetProvider()
    method GetVrfPercentiles_AsExpected (line 22) | [Fact]
    method GetVrfPercentiles_NullIfNoValue (line 52) | [Fact]
    method GetVrfPercentiles_ProperRounding (line 74) | [Fact]
    method GetVrfPercentiles_zero (line 96) | [Fact]
    method GetVrfPercentiles_100 (line 118) | [Fact]
    method CapVrf (line 140) | [Fact]

FILE: UnitTests/MockedData/Genes.cs
  class Genes (line 8) | public static class Genes

FILE: UnitTests/MockedData/TranscriptRegions.cs
  class TranscriptRegions (line 7) | public static class TranscriptRegions

FILE: UnitTests/MockedData/Transcripts.cs
  class Transcripts (line 9) | public static class Transcripts

FILE: UnitTests/MockedData/Translations.cs
  class Translations (line 8) | public static class Translations

FILE: UnitTests/Nirvana/AnnotationFilesTests.cs
  class AnnotationFilesTests (line 10) | public sealed class AnnotationFilesTests
    method GetFiles_FromDirectory_AsExpected (line 12) | [Fact]
    method GetFiles_FromDirectoryNoSa_NoFileAdded (line 48) | [Fact]

FILE: UnitTests/Nirvana/PreLoadUtilitiesTests.cs
  class PreLoadUtilitiesTests (line 11) | public sealed class PreLoadUtilitiesTests
    method GetVcfStream (line 13) | private static Stream GetVcfStream()
    method GetAllPositions (line 33) | [Fact]
    method GetPositions_inRange (line 45) | [Fact]
    method GetRefMinorVcfStream (line 56) | private static Stream GetRefMinorVcfStream()
    method GetAllPositions_skip_refs (line 80) | [Fact]

FILE: UnitTests/Nirvana/ProviderUtilitiesTests.cs
  class ProviderUtilitiesTests (line 6) | public sealed class ProviderUtilitiesTests
    method GetNsaProvider_NoSaFile_ReturnNull (line 8) | [Fact]

FILE: UnitTests/NirvanaLambda/AnnotationJobTests.cs
  class AnnotationJobTests (line 12) | public sealed class AnnotationJobTests
    method GetResultSummaryFromSuccessInvocation_AsExpected (line 14) | [Fact]
    method GetResultSummaryFromSuccessInvocation_PassFailedStatus_FromAnnotationJob (line 27) | [Fact]
    method CheckResponse_AsExpected (line 40) | [Fact]
    method GetResultSummaryFromFailedInvocation_AsExpected (line 47) | [Fact]

FILE: UnitTests/NirvanaLambda/NirvanaConfigTests.cs
  class NirvanaConfigTests (line 8) | public sealed class NirvanaConfigTests
    method CheckFieldsNotNull_AsExpected (line 10) | [Fact]
    method GetConfig (line 40) | private static NirvanaConfig GetConfig() => new NirvanaConfig

FILE: UnitTests/NirvanaLambda/NirvanaLambdaTests.cs
  class NirvanaLambdaTests (line 7) | public sealed class NirvanaLambdaTests
    method GetIndexedPrefix_AsExpected (line 9) | [Theory]
    method GetFailedRunStatus_AsExpected (line 22) | [Theory]

FILE: UnitTests/NirvanaLambda/PartitionUtilitiesTests.cs
  class PartitionUtilitiesTests (line 7) | public sealed class PartitionUtilitiesTests
    method FindEqualOrClosestSmallerOffsets_AsExpected (line 9) | [Fact]
    method MergeConsecutiveEqualValues_AsExpected (line 21) | [Fact]
    method GetEqualSizeOffsets_AsExpected (line 31) | [Fact]

FILE: UnitTests/OptimizedCore/StringBuilderCacheTests.cs
  class StringBuilderCacheTests (line 6) | public sealed class StringBuilderCacheTests
    method Acquire_UseAndRelease (line 8) | [Fact]

FILE: UnitTests/OptimizedCore/StringExtensionsTests.cs
  class StringExtensionsTests (line 6) | public sealed class StringExtensionsTests
    method OptimizedSplit (line 8) | [Theory]
    method OptimizedParseInt32 (line 19) | [Theory]
    method OptimizedStartsWith (line 38) | [Theory]
    method OptimizedKeyValue (line 48) | [Theory]
    method OptimizedEndsWith (line 61) | [Theory]

FILE: UnitTests/RepeatExpansions/MatcherTests.cs
  class MatcherTests (line 11) | public sealed class MatcherTests
    method MatcherTests (line 15) | public MatcherTests()
    method GetMatchingAnnotations_Overlap_ReturnEntry (line 36) | [Fact]
    method GetMatchingAnnotations_NoOverlap_ReturnNull (line 49) | [Fact]

FILE: UnitTests/RepeatExpansions/PercentileUtilitiesTests.cs
  class PercentileUtilitiesTests (line 6) | public sealed class PercentileUtilitiesTests
    method ComputePercentiles_Nominal (line 11) | [Fact]
    method GetPercentile_RepeatNumberInRange_PositiveIndex (line 26) | [Fact]
    method GetPercentile_RepeatNumberOutOfRange_NegativeIndex (line 33) | [Fact]

FILE: UnitTests/RepeatExpansions/RepeatExpansionProviderTests.cs
  class RepeatExpansionProviderTests (line 15) | public sealed class RepeatExpansionProviderTests
    method RepeatExpansionProviderTests (line 22) | public RepeatExpansionProviderTests()
    method Annotate_NotRepeatExpansion_NullPhenotypes (line 28) | [Fact]
    method Annotate_RepeatExpansion_NotExactMatch_NullPhenotypes (line 46) | [Fact]
    method Annotate_RepeatExpansion_no_refRepeatCount (line 62) | [Fact]
    method Annotate_RepeatExpansion_ExactMatch_OnePhenotype (line 78) | [Fact]
    method GetAnnotatedPosition (line 104) | private static IAnnotatedPosition GetAnnotatedPosition(IVariant variant)

FILE: UnitTests/SAUtils/AnnotationItems/CosmicCnvItemTests.cs
  class CosmicCnvItemTests (line 10) | public sealed class CosmicCnvItemTests
    method Merge_add_new_items (line 12) | [Fact]
    method GetJsonString (line 43) | [Fact]
    method GetJsonString_unspecified_copy_number (line 61) | [Fact]
    method Merge_same_histology_site (line 80) | [Fact]
    method Merge_avoid_double_counting (line 111) | [Fact]
    method Merge_check_adjust_counts (line 141) | [Fact]
    method Merge_throws_exception_if_cnvs_differ (line 171) | [Fact]

FILE: UnitTests/SAUtils/ClinGen/GeneDiseaseValidityTests.cs
  class GeneDiseaseValidityTests (line 8) | public sealed class GeneDiseaseValidityTests
    method GetGeneValidityStream (line 10) | private static Stream GetGeneValidityStream()
    method GetIdToSymbols (line 36) | private static Dictionary<int, string> GetIdToSymbols()
    method ParserTest (line 46) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/Cache/TranscriptCacheTests.cs
  class TranscriptCacheTests (line 12) | public sealed class TranscriptCacheTests
    method HandleMissingTranscripts_ExpectedResults (line 14) | [Theory]
    method HandleMissingTranscripts_UnknownTranscriptId_ThrowException (line 28) | [Fact]
    method GetTranscriptIdToTranscript (line 34) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/Conversion/CosmicConverterTests.cs
  class CosmicConverterTests (line 11) | public sealed class CosmicConverterTests
    method Convert_ExpectedResults (line 13) | [Fact]
    method GetFusionIdToEntries (line 37) | private static Dictionary<int, HashSet<RawCosmicGeneFusion>> GetFusion...
    method ToJsonArray_ExpectedResults (line 58) | [Fact]
    method GetCosmicGeneFusion_NullHgvs_ReturnNull (line 75) | [Fact]
    method AggregateRawCosmicGeneFusions_ExpectedResults (line 92) | [Fact]
    method AggregateRawCosmicGeneFusions_MultipleHgvsStrings_ThrowException (line 115) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/Conversion/HgvsRnaFixerTests.cs
  class HgvsRnaFixerTests (line 6) | public sealed class HgvsRnaFixerTests
    method CorrectHgvsNotationUsingRegex_ExpectedResults (line 8) | [Theory]

FILE: UnitTests/SAUtils/CosmicGeneFusions/Conversion/HgvsRnaParserTests.cs
  class HgvsRnaParserTests (line 11) | public sealed class HgvsRnaParserTests
    method Parse_ExpectedResults (line 13) | [Theory]
    method Parse_UnexpectedTranscriptCount_ThrowException (line 31) | [Theory]
    method GetTranscripts_ExpectedResults (line 39) | [Fact]
    method GetTranscriptCache (line 55) | public static (TranscriptCache TranscriptCache, ITranscript Transcript...

FILE: UnitTests/SAUtils/CosmicGeneFusions/Conversion/HistologyTests.cs
  class HistologyTests (line 8) | public sealed class HistologyTests
    method GetCounts_ExpectedResults (line 18) | [Fact]
    method GetCounts_WrongSampleCount_ThrowException (line 39) | [Theory]

FILE: UnitTests/SAUtils/CosmicGeneFusions/Conversion/SiteTests.cs
  class SiteTests (line 8) | public sealed class SiteTests
    method GetCounts_ExpectedResults (line 18) | [Fact]
    method GetCounts_TotalSampleCountTooHigh_ThrowException (line 39) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/CreateCosmicGeneFusionsTests.cs
  class CreateCosmicGeneFusionsTests (line 8) | public sealed class CreateCosmicGeneFusionsTests
    method CreateDataSourceVersion_ExpectedResults (line 10) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/IO/CosmicGeneFusionParserTests.cs
  class CosmicGeneFusionParserTests (line 11) | public sealed class CosmicGeneFusionParserTests
    method Parse_ExpectedResults (line 13) | [Fact]
    method Parse_IncorrectColumnCount_ThrowException (line 59) | [Fact]
    method GetCosmicTestData (line 74) | private static StreamReader GetCosmicTestData(Stream stream, List<stri...
    method RemoveUnderlines_ExpectedResults (line 86) | [Fact]

FILE: UnitTests/SAUtils/CosmicGeneFusions/IO/GeneFusionJsonWriterTests.cs
  class GeneFusionJsonWriterTests (line 12) | public sealed class GeneFusionJsonWriterTests
    method GeneFusionJsonWriter_ExpectedResults (line 14) | [Fact]
    method GetKeyToJson (line 46) | private static Dictionary<ulong, string[]> GetKeyToJson()

FILE: UnitTests/SAUtils/CustomAnnotations/AllowedValuesTests.cs
  class AllowedValuesTests (line 7) | public sealed class AllowedValuesTests
    method IsEmptyValue_AsExpected (line 9) | [Fact]
    method ValidatePredictionValue_Pass (line 17) | [Fact]
    method ValidatePredictionValue_ThrowException (line 27) | [Fact]

FILE: UnitTests/SAUtils/CustomAnnotations/GeneAnnotationParserTests.cs
  class GeneAnnotationParserTests (line 11) | public sealed class GeneAnnotationParserTests
    method GetReadStream (line 26) | private static StreamReader GetReadStream(string text)
    method ParseHeaderLines_AsExpected (line 40) | [Fact]
    method ParseHeaderLines_version_and_Description (line 79) | [Fact]
    method ParseHeaderLines_InconsistentFields (line 99) | [Fact]
    method GetItems_UnrecognizedGeneId_ThrowException (line 114) | [Fact]
    method GetItems_SameGene_MultipleEntries_ThrowException (line 131) | [Fact]
    method GetItems_EmptyAnnotation_ThrowException (line 148) | [Fact]
    method GetItems_AsExpected (line 166) | [Fact]

FILE: UnitTests/SAUtils/CustomAnnotations/ParserUtilitiesTests.cs
  class ParserUtilitiesTests (line 9) | public sealed class ParserUtilitiesTests
    method CheckPrefix_InvalidPrefix_ThrowException (line 13) | [Fact]
    method ParseTags_LessThanRequiredColumns_ThrowException (line 19) | [Fact]
    method ParseTypes_ValidType_Pass (line 25) | [Theory]
    method ParseTypes_InvalidType_ThrowException (line 35) | [Theory]
    method ParseCategories_InvalidValue_ThrowException (line 45) | [Fact]

FILE: UnitTests/SAUtils/CustomAnnotations/VariantAnnotationsParserTests.cs
  class VariantAnnotationsParserTests (line 16) | public sealed class VariantAnnotationsParserTests
    method GetReadStream (line 22) | private static StreamReader GetReadStream(string text)
    method CheckPosAndRefColumns_InvalidPosOrRef_ThrowException (line 37) | [Fact]
    method CheckAltAndEndColumns_NoAltAndEnd_ThrowException (line 48) | [Fact]
    method ParseHeaderLines_AsExpected (line 56) | [Fact]
    method ParseHeaderLines_matchBy_sv (line 104) | [Fact]
    method ParseHeaderLines_InconsistentFields (line 123) | [Fact]
    method GetItems (line 139) | [Fact]
    method GetIntervals_noALT (line 161) | [Fact]
    method GetIntervals_start (line 182) | [Fact]
    method GetItems_OnlyAlleleFrequencyTreatedAsDouble_OtherNumbersPrintAsIs (line 205) | [Fact]
    method GetItems_invalid_scores (line 229) | [Fact]
    method GetItems_missing_scores (line 249) | [Fact]
    method GetItems_ExtractCustomFilters (line 272) | [Fact]
    method GetItems_missing_filter (line 296) | [Fact]
    method GetItems_ExtractCustomFilters_failsOnLargeText (line 321) | [Fact]
    method GetItems_UnsortedData_ThrowException (line 340) | [Fact]
    method GetIntervals (line 360) | [Fact]
    method IsValidNucleotideSequence_IsValidSequence_Pass (line 386) | [Fact]
    method ExtractItems_TrimmedAndLeftShifted (line 394) | [Fact]
    method Extract_symbolic_alleles (line 414) | [Fact]
    method ParseTitle_Conflict_JsonTag (line 436) | [Fact]
    method ParseTitle_IncorrectFormat (line 451) | [Fact]
    method ParseGenomeAssembly_UnsupportedAssembly_ThrowException (line 465) | [Fact]
    method ParseGenomeAssembly_IncorrectFormat_ThrowException (line 479) | [Fact]
    method ParseHeader_version_and_description (line 494) | [Fact]
    method GetMockedSequenceProvider (line 514) | private static ISequenceProvider GetMockedSequenceProvider()
    method GetMockedSequence (line 523) | private static ISequence GetMockedSequence()

FILE: UnitTests/SAUtils/Dann/DannParserTests.cs
  class DannParserTests (line 10) | public sealed class DannParserTests
    method GetStream (line 12) | private static Stream GetStream()
    method DannReader_GetItems_AsExpected (line 34) | [Fact]

FILE: UnitTests/SAUtils/DataStructures/CounterDictionaryTests.cs
  class CounterDictionaryTests (line 8) | public sealed class CounterDictionaryTests
    method TestCounterDictionary (line 10) | [Fact]

FILE: UnitTests/SAUtils/DbVar/DosageMapRegionParserTests.cs
  class DosageMapRegionParserTests (line 9) | public sealed class DosageMapRegionParserTests
    method GetStream (line 11) | private static Stream GetStream()
    method StandardParsing (line 32) | [Fact]

FILE: UnitTests/SAUtils/DbVar/DosageSensitivityParserTests.cs
  class DosageSensitivityParserTests (line 7) | public sealed class DosageSensitivityParserTests
    method GetStream (line 9) | private static Stream GetStream()
    method StandardParsing (line 31) | [Fact]

FILE: UnitTests/SAUtils/FusionCatcher/FusionCatcherDataSourceTests.cs
  class FusionCatcherDataSourceTests (line 11) | public sealed class FusionCatcherDataSourceTests
    method Parse_ExpectedResults (line 13) | [Fact]
    method Parse_IncorrectFileFormat_ThrowException (line 55) | [Fact]
    method Parse_MultipleCollections_ExpectedResults (line 75) | [Fact]
    method AddData (line 106) | private static void AddData(MemoryStream ms)

FILE: UnitTests/SAUtils/FusionCatcher/GeneFusionSourceWriterTests.cs
  class GeneFusionSourceWriterTests (line 13) | public sealed class GeneFusionSourceWriterTests
    method GeneFusionSourceWriter_ExpectedResults (line 15) | [Fact]
    method GetKeyToGeneFusion (line 60) | internal static (uint[] OncogeneKeys, GeneFusionSourceCollection[] Ind...

FILE: UnitTests/SAUtils/FusionCatcher/IndexBuilderTests.cs
  class IndexBuilderTests (line 9) | public sealed class IndexBuilderTests
    method Convert_ExpectedResults (line 11) | [Fact]
    method GetGeneKeyToSourceBuilder (line 39) | private static Dictionary<ulong, GeneFusionSourceBuilder> GetGeneKeyTo...

FILE: UnitTests/SAUtils/GERP/GerpParserTests.cs
  class GerpParserTests (line 10) | public sealed class GerpParserTests
    method GetGerpWigStream (line 12) | private static Stream GetGerpWigStream()
    method GetGerpTsvStream (line 35) | private static Stream GetGerpTsvStream()
    method ReadWigItems (line 59) | [Fact]
    method ReadTsvItems (line 78) | [Fact]
    method TestScientificNotationScore (line 97) | [Fact]

FILE: UnitTests/SAUtils/GERP/GerpReaderTests.cs
  class GerpReaderTests (line 7) | public sealed class GerpReaderTests
    method TestReadGerpData (line 19) | [Fact]

FILE: UnitTests/SAUtils/GeneAnnotationsTest.cs
  class GeneAnnotationsTest (line 15) | public sealed class GeneAnnotationsTest
    method GetGeneAnnotations (line 17) | private static Dictionary<string, List<ISuppGeneItem>> GetGeneAnnotati...
    method ReadBackGeneAnnotations (line 45) | [Fact]

FILE: UnitTests/SAUtils/GenericScoreParserTests/GenericScoreParserTests.cs
  class GenericScoreParserTests (line 11) | public sealed class GenericScoreParserTests
    method TestParserNonNumericValues (line 19) | [Fact]
    method TestMaxScore (line 37) | [Fact]
    method TestMinScore (line 62) | [Fact]
    method TestNonConflictingScores (line 86) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/AlleleReaderTests.cs
  class AlleleReaderTests (line 12) | public sealed class AlleleReaderTests
    method GetAncestralAlleleStream (line 14) | private static Stream GetAncestralAlleleStream()
    method GetItems_test (line 31) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/ClinGenTests.cs
  class ClinGenTests (line 9) | public sealed class ClinGenTests
    method GetStream (line 11) | private static Stream GetStream()
    method GetItems (line 26) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/ClinVarXmlReaderTests.cs
  class ClinVarXmlReaderTests (line 17) | public sealed class ClinVarXmlReaderTests
    method GetSequenceProvider (line 19) | private static ISequenceProvider GetSequenceProvider(GenomeAssembly as...
    method BasicReadTest (line 28) | [Fact]
    method RCV000001373_NoExtraOmimId (line 52) | [Fact]
    method RCV000435546_NotMissing (line 68) | [Fact]
    method MissingAltAllele (line 78) | [Fact]
    method NonEnglishChars (line 95) | [Fact]
    method WrongPosition (line 110) | [Fact]
    method PubmedTest1 (line 134) | [Fact]
    method PubmedTest2 (line 150) | [Fact]
    method PubmedTest3 (line 166) | [Fact]
    method PubmedTest4 (line 182) | [Fact]
    method PubmedTest5 (line 198) | [Fact]
    method PubmedTest6 (line 216) | [Fact]
    method PubmedTest7_comma_trimming (line 233) | [Fact]
    method MultiScvPubmed (line 250) | [Fact]
    method NoClinVarItem_due_to_ref_mismatch (line 267) | [Fact]
    method ClinVarForRef (line 278) | [Fact]
    method MultiplePhenotypes (line 295) | [Fact]
    method MultipleOrigins (line 313) | [Fact]
    method SkipGeneralCitations (line 331) | [Fact]
    method IndelTest (line 355) | [Fact]
    method MultiScvPubmeds (line 382) | [Fact]
    method MultipleAlleleOrigins (line 400) | [Fact]
    method Discard_entries_with_unknown_variant_type (line 423) | [Fact]
    method EmptyRefAndAlt (line 434) | [Fact]
    method SkipMicrosattelite (line 445) | [Fact]
    method SkipAlus (line 456) | [Fact]
    method MissingClinvarInsertion (line 466) | [Fact]
    method MissingClinvarInsertionShift (line 483) | [Fact]
    method MissingClinvarInsertionShift2 (line 500) | [Fact]
    method AlternatePhenotype (line 516) | [Fact]
    method IupacBases (line 532) | [Fact]
    method OmitOmimFromAltPhenotypes (line 553) | [Fact]
    method TrimSpaceFromOmimIds (line 569) | [Fact]
    method ClinvarInsertion (line 586) | [Fact]
    method Remove9DigitsPubmedId (line 603) | [Fact]
    method CaptureGeneOmimId (line 618) | [Fact]
    method CapturePhenotypicSeriesOmimIDandUniq (line 633) | [Fact]
    method CapturePhenotypeSeriesOmimId (line 648) | [Fact]
    method RemoveDuplicationWithWrongRefSequence (line 663) | [Fact]
    method AllelicOmimIdsForSnvs (line 672) | [Fact]
    method AllelicOmimIdsForDeletions (line 688) | [Fact]
    method ExcludeAllelicOmimIdsFromTraits (line 704) | [Fact]
    method AllelicOmimIdsFromAttributeSetChrX (line 720) | [Fact]
    method AllelicOmimIdsFromAttributeSetChrY (line 738) | [Fact]
    method MultipleEntryRecordVariant1 (line 756) | [Fact]
    method MultipleEntryRecordVariant2 (line 769) | [Fact]
    method SkipMicrosatellitesWithoutAltAllele (line 782) | [Fact]
    method MissingClinvarInsertion2 (line 793) | [Fact]
    method Skip_entries_with_inconsistant_start_end (line 804) | [Fact]
    method Alternate_phenotypes (line 813) | [Fact]
    method Mising_entry (line 824) | [Fact]
    method Multiple_significance (line 835) | [Fact]
    method Multiple_significance_from_explanation (line 846) | [Fact]
    method Override_microsatellite_type (line 857) | [Fact]
    method OneRcv_oneVcv (line 868) | [Fact]
    method TwoRcv_oneVcv (line 882) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/ClinvarVariationParserTests.cs
  class ClinvarVariationParserTests (line 9) | public sealed class ClinvarVariationParserTests
    method InterpretedRecordsTest (line 11) | [Fact]
    method IncludedRecordTest (line 26) | [Fact]
    method SignificanceTest (line 38) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/CosmicCnvReaderTests.cs
  class CosmicCnvReaderTests (line 10) | public sealed class CosmicCnvReaderTests
    method GetColumnIndices_valid_header (line 12) | [Fact]
    method GetColumnIndices_missing_column (line 27) | [Fact]
    method GetEntries (line 41) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/CosmicItemTests.cs
  class CosmicItemTests (line 8) | public sealed class CosmicItemTests
    method GetCancerSiteCount_same_study (line 10) | [Fact]
    method GetTissueCount_different_studies (line 25) | [Fact]
    method GetCancerTypeCount_same_study (line 41) | [Fact]
    method GetCancerTypeCount_different_studies (line 57) | [Fact]
    method GetJsonString (line 73) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/DataSourceVersionTests.cs
  class DataSourceVersionTests (line 11) | public sealed class DataSourceVersionTests
    method ReadDataVersionFromFile (line 13) | [Fact]
    method GetSourceVersionTest (line 34) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/DbSnpReaderTests.cs
  class DbSnpReaderTests (line 13) | public sealed class DbSnpReaderTests
    method MissingEntry (line 15) | [Fact]
    method MissingEntry2 (line 28) | [Fact]
    method MissingDbsnpId (line 41) | [Fact]
    method NoMinorAllele (line 61) | [Obsolete("We should not have skipped unit tests.")]
    method DisregardZeroFreq (line 73) | [Obsolete("We should not have skipped unit tests.")]
    method GetStream (line 85) | private static Stream GetStream()
    method GetItems_test (line 101) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/DecipherReaderTest.cs
  class DecipherTests (line 9) | public sealed class DecipherTests
    method GetStream (line 11) | private static Stream GetStream()
    method GetItemsTest (line 28) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/DgvReaderTests.cs
  class DgvReaderTests (line 12) | public sealed class DgvReaderTests
    method CreateTruthDgvItemSequence (line 16) | private static IEnumerable<DgvItem> CreateTruthDgvItemSequence()
    method TestDbSnpReader (line 32) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/DgvTests.cs
  class DgvTests (line 10) | public sealed class DgvTests
    method ExtractDgvCnv (line 12) | [Fact]
    method ExtractDgvComplex (line 22) | [Fact]
    method EmptyObservedLossesAndGains (line 33) | [Fact]
    method EqualityAndHash (line 54) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/GlobalMinorReaderTests.cs
  class GlobalMinorReaderTests (line 11) | public sealed class GlobalMinorReaderTests
    method GetStream (line 13) | private static Stream GetStream()
    method GetItems_test (line 28) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/GmeReaderTests.cs
  class GmeTests (line 12) | public sealed class GmeTests
    method GetStream (line 14) | private static Stream GetStream()
    method GetItems_test (line 30) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/MergedCosmicReaderTests.cs
  class MergedCosmicReaderTests (line 9) | public sealed class MergedCosmicReaderTests
    method TwoStudyCosmicCoding (line 11) | [Fact]
    method IndelWithNoLeadingBase (line 32) | [Fact]
    method CosmicAltAllele (line 56) | [Fact]
    method CosmicAlleleSpecificIndel (line 67) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/OneKGenTests.cs
  class OneKGenTests (line 10) | public sealed class OneKGenTests
    method GetAlleleFrequency (line 12) | private static string GetAlleleFrequency(string jsonString, string des...
    method AlleleFrequencyTest (line 18) | [Fact]
    method MultiAltAlleleTest (line 35) | [Fact]
    method PrioritizingSymbolicAllele4Svs (line 64) | [Fact]
    method MissingSubPopulationFrequencies (line 82) | [Fact]
    method GetOneKgSvStream (line 95) | private static Stream GetOneKgSvStream()
    method OnekGenSvReader (line 112) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/ParserTestUtils.cs
  class ParserTestUtils (line 10) | public static class ParserTestUtils
    method GetSequenceProvider (line 12) | public static ISequenceProvider GetSequenceProvider(int position, stri...
    method GetRefMinorProvider (line 20) | public static IRefMinorProvider GetRefMinorProvider(List<(Chromosome c...

FILE: UnitTests/SAUtils/InputFileParsers/RefMinorTests.cs
  class RefMinorTests (line 18) | public sealed class RefMinorTests
    method GetStream (line 20) | private static Stream GetStream()
    method GetItems (line 36) | [Fact]
    method GetSequenceProvider (line 48) | private static ISequenceProvider GetSequenceProvider()
    method LoopBack (line 60) | [Fact]

FILE: UnitTests/SAUtils/InputFileParsers/TopMedReaderTests.cs
  class TopMedReaderTests (line 12) | public sealed class TopMedReaderTests
    method GetStream (line 14) | private static Stream GetStream()
    method GetItems_test (line 31) | [Fact]

FILE: UnitTests/SAUtils/MitoHeteroplasmy/MitoHeteroplasmyTests.cs
  class MitoHeteroplasmyTests (line 11) | public sealed class MitoHeteroplasmyTests
    method GetSequenceProvider (line 13) | private static ISequenceProvider GetSequenceProvider()
    method GetStream (line 20) | private static Stream GetStream()
    method ParseItems (line 36) | [Fact]
    method DeserializeStats (line 48) | [Fact]

FILE: UnitTests/SAUtils/MitoMap/MitoMapSvReaderTests.cs
  class MitoMapSvReaderTests (line 11) | public sealed class MitoMapSvReaderTests
    method ParseLine_AsExpected (line 19) | [Theory]

FILE: UnitTests/SAUtils/MitoMap/MitoMapVariantReaderTests.cs
  class MitoMapVariantReaderTests (line 13) | public sealed class MitoMapVariantReaderTests
    method GetAltAllelesTests (line 22) | [Fact]
    method GetNumFullLengthSequences_AsExpected (line 37) | [Theory]
    method ParseLine_AsExpected (line 51) | [Theory]

FILE: UnitTests/SAUtils/MitoMap/ParsingUtilitiesTests.cs
  class ParsingUtilitiesTests (line 7) | public sealed class ParsingUtilitiesTests
    method GetPubMedIds_AsExpected (line 19) | [Theory]
    method ExtractInternalIds_AsExpected (line 28) | [Theory]

FILE: UnitTests/SAUtils/NsaWriters/IntervalWriterReaderTests.cs
  class IntervalWriterReaderTests (line 18) | public sealed class IntervalWriterReaderTests
    method GetClinGenItems (line 20) | private static IEnumerable<ClinGenItem> GetClinGenItems()
    method Readback_clingen (line 31) | [Fact]

FILE: UnitTests/SAUtils/NsaWriters/NsaUtilitiesTests.cs
  class NsaUtilitiesTests (line 13) | public sealed class NsaUtilitiesTests
    method GetDupItemsStream (line 15) | private static Stream GetDupItemsStream()
    method RemoveConflictingAlleles_does_not_remove_duplicates (line 30) | [Fact]

FILE: UnitTests/SAUtils/NsaWriters/WriterReaderTests.cs
  class WriterReaderTests (line 23) | public sealed class WriterReaderTests
    method GetClinvarItems (line 25) | private static IEnumerable<ClinVarItem> GetClinvarItems()
    method GetSequenceProvider (line 54) | private static ISequenceProvider GetSequenceProvider()
    method Write_clinvar_basic (line 61) | [Fact]
    method GetDbsnpItems (line 111) | private static IEnumerable<DbSnpItem> GetDbsnpItems(int count)
    method GetParRegionItems (line 123) | private static IEnumerable<DbSnpItem> GetParRegionItems(int count)
    method GetAllASequenceProvider (line 135) | private static ISequenceProvider GetAllASequenceProvider()
    method Preload (line 144) | [Fact]
    method WriteParRegion (line 182) | [Fact]
    method GetAlternatePositions (line 213) | private static List<int> GetAlternatePositions(int start, int count)
    method WrongRefAllele_ThrowUserException (line 224) | [Fact]
    method WriteCustomSaItem (line 232) | private static void WriteCustomSaItem(CustomItem customItem)
    method RemoveConflictinItems (line 247) | [Fact]
    method GetChr22_17467787_17467799_genome (line 261) | private static Stream GetChr22_17467787_17467799_genome()
    method GetConflictingGnomadItems (line 278) | private static IEnumerable<ISupplementaryDataItem> GetConflictingGnoma...

FILE: UnitTests/SAUtils/Omim/OmimUtilitiesTests.cs
  class OmimUtilitiesTests (line 10) | public sealed class OmimUtilitiesTests
    method RemoveLinks_AsExpected (line 12) | [Theory]
    method RemoveFormatControl_AsExpected (line 35) | [Theory]
    method ExtractPhenotypeAndComments_AsExpected (line 42) | [Theory]
    method ExtractAndProcessItemDescription_AsExpected (line 59) | [Fact]

FILE: UnitTests/SAUtils/ParseUtils/SplitLineTests.cs
  class SplitLineTests (line 6) | public sealed class SplitLineTests
    method TestGetString (line 8) | [Theory]
    method TestParseInteger (line 23) | [Theory]
    method TestParseDouble (line 41) | [Theory]

FILE: UnitTests/SAUtils/ParseUtils/TsvIndicesTests.cs
  class TsvIndicesTests (line 6) | public class TsvIndicesTests
    method TestTsvIndices (line 8) | [Theory]

FILE: UnitTests/SAUtils/PhylopTests.cs
  class PhylopTests (line 15) | public sealed class PhylopTests
    method LoopbackTest (line 17) | [Fact]

FILE: UnitTests/SAUtils/PrimateAi/PrimateAiTests.cs
  class PrimateAiTests (line 15) | public sealed class PrimateAiTests
    method GetSequenceProvider (line 17) | private static ISequenceProvider GetSequenceProvider()
    method GetStream (line 24) | private static Stream GetStream()
    method ExtractEntries (line 48) | [Fact]
    method GetDuplicateItemStream (line 70) | private static Stream GetDuplicateItemStream()
    method ResolveDuplicates (line 83) | [Fact]

FILE: UnitTests/SAUtils/ProteinConservation/ParserTests.cs
  class ParserTests (line 8) | public sealed class ParserTests
    method GetStream (line 10) | private static Stream GetStream()
    method ReadItemsTest (line 27) | [Fact]

FILE: UnitTests/SAUtils/Revel/RevelParserTests.cs
  class RevelParserTests (line 10) | public sealed class RevelParserTests
    method GetStream (line 12) | private static Stream GetStream()
    method RevelReader_GetItems_AsExpected (line 32) | [Fact]

FILE: UnitTests/SAUtils/SaJsonSchemaTests.cs
  class SaJsonSchemaTests (line 10) | public sealed class SaJsonSchemaTests
    method Create_InitialJsonObject_AsExpected (line 14) | [Fact]
    method OutputKeyAnnotation_AsExpected (line 23) | [Fact]
    method ToString_AsExpected (line 33) | [Fact]
    method GetJsonString_AsExpected (line 54) | [Fact]
    method GetJsonString_DoubleValueHandling_AsExpected (line 66) | [Fact]
    method CheckAndGetBoolFromString_AsExpected (line 78) | [Fact]
    method CheckAndGetBoolFromString_InvalidValue_ThrowException (line 89) | [Fact]
    method CheckAndGetNullableDoubleFromString_GetNull_AsExpected (line 98) | [Fact]
    method CheckAndGetNullableDoubleFromString_NotANum_ThrowException (line 105) | [Fact]
    method GetJsonString__AsExpected (line 113) | [Fact]

FILE: UnitTests/SAUtils/SpliceAi/SpliceAiTests.cs
  class SpliceAiTests (line 23) | public sealed class SpliceAiTests
    method GetSpliceToNirvanaGenes (line 25) | private static Dictionary<string, string> GetSpliceToNirvanaGenes()
    method GetSequenceProvider (line 39) | private static ISequenceProvider GetSequenceProvider()
    method GetCacheSequenceProvider (line 49) | private static ISequenceProvider GetCacheSequenceProvider()
    method GetSpliceIntervals (line 57) | private static Dictionary<ushort, IntervalArray<byte>> GetSpliceInterv...
    method GetStream (line 89) | private static Stream GetStream()
    method GetPositionCachingStream (line 112) | private static Stream GetPositionCachingStream()
    method GetMultiGeneStream (line 133) | private static Stream GetMultiGeneStream()
    method GetMissingEntryStream (line 150) | private static Stream GetMissingEntryStream()
    method GetMultChromosomeStream (line 166) | private static Stream GetMultChromosomeStream()
    method Check_multi_chromosome_gene_update (line 186) | [Fact]
    method Parse_standard_lines (line 202) | [Fact]
    method MissingEntry (line 216) | [Fact]
    method GetMultiScoreStream (line 228) | private static Stream GetMultiScoreStream()
    method Parse_multiScore_entry (line 244) | [Fact]
    method Parse_multiGene_entry (line 256) | [Fact]
    method GetShiftableInsertionStream (line 269) | private static Stream GetShiftableInsertionStream()
    method Skip_shiftable_indels (line 286) | [Fact]
    method Check_position_caching (line 299) | [Fact]
    method GetCacheStream (line 310) | private static Stream GetCacheStream()
    method GetTranscripts (line 357) | private static ITranscript[] GetTranscripts(Chromosome chromosome, IGe...
    method GetSpliceIntervals_standard (line 367) | [Fact]
    method GetMultiGeneAtSameLocationStream (line 382) | private static Stream GetMultiGeneAtSameLocationStream()
    method Two_symbols_in_spliceAi (line 399) | [Fact]
    method GetInsertionStream (line 412) | private static Stream GetInsertionStream()
    method Parse_insertions (line 437) | [Fact]
    method GetDeletionStream (line 449) | private static Stream GetDeletionStream()
    method Parse_deletions (line 477) | [Fact]

FILE: UnitTests/SAUtils/gnomAD/GnomadGeneScoreTests.cs
  class GnomadGeneScoreTests (line 9) | public sealed class GnomadGeneScoreTests
    method GetStream (line 11) | private static Stream GetStream()
    method GetItems (line 26) | [Fact]
    method GetStream_with_duplicate_gene_entries (line 45) | private static Stream GetStream_with_duplicate_gene_entries()
    method GetNonDuplicateItems (line 59) | [Fact]
    method GetStream_resolve_without_loeuf (line 75) | private static Stream GetStream_resolve_without_loeuf()
    method ResolveDuplicateWithout_loeuf (line 90) | [Fact]

FILE: UnitTests/SAUtils/gnomAD/GnomadReaderTests.cs
  class GnomadReaderTests (line 17) | public sealed class GnomadReaderTests
    method GetGenomeStream (line 19) | private static Stream GetGenomeStream()
    method GetItems_test (line 37) | [Fact]
    method GetConflictingItemsStream (line 53) | private static Stream GetConflictingItemsStream()
    method IdentifyConflictingItems (line 69) | [Fact]
    method GetShiftingItemsStream (line 92) | private static Stream GetShiftingItemsStream()
    method LeftShiftingItems (line 107) | [Fact]
    method GetChr22ExomeStream (line 123) | private static Stream GetChr22ExomeStream()
    method GetChr22GenomeStream (line 141) | private static Stream GetChr22GenomeStream()
    method GetChr22_21006257_genome (line 182) | private static Stream GetChr22_21006257_genome()
    method GetChr22_21006257_exome (line 196) | private static Stream GetChr22_21006257_exome()
    method GetChr22_22055876_genome (line 224) | private static Stream GetChr22_22055876_genome()
    method GetChr22_22055876_exome (line 239) | private static Stream GetChr22_22055876_exome()
    method RemoveConflictingItems (line 254) | [Fact]
    method GetChr22_16689800_16689902_genome (line 269) | private static Stream GetChr22_16689800_16689902_genome()
    method DoNotReportCoverage_whenAnZero (line 284) | [Fact]
    method AddNullableInts (line 298) | [Theory]

FILE: UnitTests/SAUtils/gnomAD/GnomadSvBedParserTests.cs
  class GnomadSvBedParserTests (line 11) | public sealed class GnomadSvBedParserTests
    method GetStreamData (line 13) | private static Stream GetStreamData(string dataString)
    method TestGnomadSvBedParser (line 23) | [Fact]
    method TestUnknownChromosome (line 55) | [Fact]
    method TestInvalidStart (line 77) | [Fact]
    method TestInvalidEnd (line 90) | [Fact]
    method TestInvalidSvType (line 103) | [Fact]

FILE: UnitTests/SAUtils/gnomAD/GnomadSvItemTests.cs
  class GnomadSvItemTests (line 7) | public sealed class GnomadSvItemTests
    method TestGnomadSvItem (line 9) | [Fact]

FILE: UnitTests/SAUtils/gnomAD/GnomadSvTsvParserTests.cs
  class GnomadSvTsvParserTests (line 11) | public sealed class GnomadSvTsvParserTests
    method GetStreamData (line 13) | private static Stream GetStreamData(string dataString)
    method TestGnomadSvTsvParser (line 23) | [Fact]
    method TestUnknownChromosome (line 58) | [Fact]
    method TestInvalidStart (line 80) | [Fact]
    method TestInvalidEnd (line 92) | [Fact]
    method TestInvalidSvType (line 104) | [Fact]

FILE: UnitTests/SAUtils/gnomAD/LcrParserTests.cs
  class LcrParserTests (line 12) | public class LcrParserTests
    method GetGRCh37Stream (line 14) | private Stream GetGRCh37Stream()
    method GetGRCh37 (line 28) | private ISequenceProvider GetGRCh37()
    method GetGRCh38Stream (line 44) | private Stream GetGRCh38Stream()
    method GetGRCh38 (line 58) | private ISequenceProvider GetGRCh38()
    method GetGRCh37Lcrs (line 75) | [Fact]
    method GetGRCh38Lcrs (line 86) | [Fact]

FILE: UnitTests/SingleAnnotationLambda/SingleConfigTests.cs
  class SingleConfigTests (line 9) | public sealed class SingleConfigTests
    method Validate_Success (line 11) | [Fact]
    method Validate_NullId_ThrowException (line 19) | [Fact]
    method Validate_NullGenomeAssembly_ThrowException (line 27) | [Fact]
    method Validate_NullVariant_ThrowException (line 35) | [Fact]
    method GetConfig (line 43) | private static SingleConfig GetConfig() => new SingleConfig

FILE: UnitTests/SingleAnnotationLambda/SingleVariantTests.cs
  class SingleVariantTests (line 9) | public sealed class SingleVariantTests
    method GetVcfFields_AsExpected (line 11) | [Fact]
    method Validate_Success (line 44) | [Fact]
    method Validate_NullChromosome_ThrowException (line 52) | [Fact]
    method Validate_NullPosition_ThrowException (line 60) | [Fact]
    method Validate_NullReferenceAllele_ThrowException (line 68) | [Fact]
    method Validate_NullAlternateAlleles_ThrowException (line 76) | [Fact]
    method Validate_ZeroAlternateAlleles_ThrowException (line 84) | [Fact]
    method Validate_SampleNamesAndSampleFields_NoFormatField_ThrowException (line 92) | [Fact]
    method Validate_FormatField_NoSampleNamesAndSampleFields_ThrowException (line 101) | [Fact]
    method GetConfig (line 109) | private static SingleVariant GetConfig() => new SingleVariant

FILE: UnitTests/Tabix/BgzfBlockVcfReaderTests.cs
  class BgzfBlockVcfReaderTests (line 9) | public sealed class BgzfBlockVcfReaderTests
    method FindVariantsInBlock_NoVariants_ReturnFalse (line 14) | [Fact]
    method FindVariantsInBlock_ReturnTrue (line 25) | [Fact]
    method GetVcfPositions_MixedLineEndings_PartialEntries_MultipleChromosomes_ReturnTrue (line 38) | [Fact]
    method GetVcfPositions_MixedLineEndings_PartialEntries_MultipleChromosomes_ReturnFalse (line 45) | [Fact]
    method GetVcfPositions_SkipCorruptPositions (line 52) | [Fact]

FILE: UnitTests/Tabix/BinUtilitiesTests.cs
  class BinUtilitiesTests (line 8) | public sealed class BinUtilitiesTests
    method BottomBin_Nominal (line 10) | [Fact]
    method ConvertPositionToBin_Nominal (line 17) | [Fact]
    method OverlappingBinsWithVariants_EndBeforeBegin_ReturnEmptyList (line 24) | [Fact]
    method OverlappingBinsWithVariants_EndBeyondMaxRefLen_CorrectEnd (line 31) | [Fact]

FILE: UnitTests/Tabix/ReaderTests.cs
  class ReaderTests (line 10) | public sealed class ReaderTests
    method Read_Nominal (line 12) | [Fact]
    method Read_NotTabixFormat (line 45) | [Fact]

FILE: UnitTests/Tabix/SearchTests.cs
  class SearchTests (line 8) | public sealed class SearchTests
    method SearchTests (line 13) | public SearchTests()
    method HasVariants_IntervalBeforeReads_ReturnsFalse (line 25) | [Fact]
    method HasVariants_IntervalOverlapsReads_HasVcfPositionsOnIntervalTrue_ReturnsTrue (line 32) | [Fact]
    method HasVariants_IntervalOverlapsReads_ReturnsTrue (line 39) | [Fact]
    method HasVariants_NoOverlap_ReturnsFalse (line 46) | [Fact]
    method HasVariants_IntervalAfterReads_ReturnsFalse (line 53) | [Fact]
    method HasVariants_NullRefSeq_ReturnsFalse (line 60) | [Fact]

FILE: UnitTests/Tabix/SearchTestsLocalMother.cs
  class SearchTestsLocalMother (line 11) | public sealed class SearchTestsLocalMother
    method SearchTestsLocalMother (line 16) | public SearchTestsLocalMother()
    method HasVariants_IntervalBeforeReads_ReturnsFalse (line 36) | [Fact]
    method HasVariants_IntervalOverlapsReads_HasVcfPositionsOnIntervalTrue_ReturnsTrue (line 43) | [Fact]
    method HasVariants_IntervalOverlapsReads_ReturnsTrue (line 50) | [Fact]
    method HasVariants_NoOverlap_ReturnsFalse (line 57) | [Fact]
    method HasVariants_IntervalAfterReads_ReturnsTrue (line 64) | [Fact]
    method HasVariants_IntervalAfterReads_ReturnsFalse (line 71) | [Fact]

FILE: UnitTests/Tabix/SearchTestsRemoteMother.cs
  class SearchTestsRemoteMother (line 11) | public sealed class SearchTestsRemoteMother
    method SearchTestsRemoteMother (line 16) | public SearchTestsRemoteMother()
    method HasVariants_IntervalBeforeReads_ReturnsFalse (line 36) | [Fact]
    method HasVariants_IntervalOverlapsReads_HasVcfPositionsOnIntervalTrue_ReturnsTrue (line 43) | [Fact]
    method HasVariants_IntervalOverlapsReads_ReturnsTrue (line 50) | [Fact]
    method HasVariants_NoOverlap_ReturnsFalse (line 57) | [Fact]
    method HasVariants_IntervalAfterReads_ReturnsTrue (line 64) | [Fact]
    method HasVariants_IntervalAfterReads_ReturnsFalse (line 71) | [Fact]

FILE: UnitTests/Tabix/SearchUtilitiesTests.cs
  class SearchUtilitiesTests (line 8) | public sealed class SearchUtilitiesTests
    method SearchUtilitiesTests (line 12) | public SearchUtilitiesTests()
    method GetMinOffset_Nominal (line 25) | [Fact]
    method GetMinOffset_MissingBin (line 43) | [Fact]
    method GetMinOffset_MissingFirstBin (line 61) | [Fact]
    method GetMaxOffset_Nominal (line 79) | [Fact]
    method GetMaxOffset_MissingBin (line 95) | [Fact]
    method GetMaxOffset_MissingFirstBin (line 111) | [Fact]
    method GetMaxOffset_MissingAllOverlappingBins_ReturnMaxOffset (line 127) | [Fact]
    method GetMinOverlapOffset_SingleBin (line 140) | [Fact]
    method GetMinOverlapOffset_SingleBin_NullChunks (line 154) | [Fact]
    method GetOffset_Nominal (line 165) | [Fact]
    method GetOffset_HandleDiff_TabixIndex_And_RefIndex (line 182) | [Fact]
    method GetOffset_UnknownChromosome_ReturnMinusOne (line 202) | [Fact]
    method GetOffset_FixNegativeBeginCoordinate (line 210) | [Fact]
    method GetOffset_NoOverlappingBins_UseLinearIndex (line 232) | [Fact]
    method GetOffset_NoOverlappingBins_UseLinearIndex_WithTruncatedIndex_ReturnMinusOne (line 251) | [Fact]
    method GetFirstNonZeroValue_WithoutZeros (line 269) | [Fact]
    method GetFirstNonZeroValue_WithLeadingZeros (line 279) | [Fact]
    method GetFirstNonZeroValue_AllZeros_ReturnMinusOne (line 289) | [Fact]
    method GetTabixReferenceSequence_NullChromosome_ReturnNull (line 298) | [Fact]
    method GetTabixReferenceSequence_Nominal (line 315) | [Fact]
    method AdjustBegin_Nominal (line 332) | [Fact]
    method AdjustBegin_CorrectNegativeNumbers (line 339) | [Fact]
    method GetMinMaxFileOffset_Nominal (line 346) | [Fact]
    method GetIdToChunks (line 364) | private static Dictionary<int, Interval[]> GetIdToChunks()

FILE: UnitTests/Tabix/VirtualPositionTests.cs
  class VirtualPositionTests (line 6) | public sealed class VirtualPositionTests
    method VirtualPosition_LoopBack (line 8) | [Fact]

FILE: UnitTests/TestDataStructures/SimpleSequence.cs
  class SimpleSequence (line 8) | public sealed class SimpleSequence : ISequence
    method SimpleSequence (line 15) | public SimpleSequence(string s, int zeroBasedStartOffset = 0)
    method Substring (line 21) | public string Substring(int offset, int length)
  class SimpleSequenceProvider (line 29) | public sealed class SimpleSequenceProvider : ISequenceProvider
    method Annotate (line 34) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method PreLoad (line 39) | public void PreLoad(Chromosome chromosome, List<int> positions)
    method LoadChromosome (line 47) | public void LoadChromosome(Chromosome chromosome) { }
    method SimpleSequenceProvider (line 49) | public SimpleSequenceProvider(GenomeAssembly assembly, ISequence seque...
    method Dispose (line 57) | public void Dispose() { }

FILE: UnitTests/TestUtilities/AnnotationUtilities.cs
  class AnnotationUtilities (line 15) | public static class AnnotationUtilities
    method GetAnnotatedPosition (line 17) | internal static IAnnotatedPosition GetAnnotatedPosition(string cacheFi...
    method ParseVcfLine (line 33) | internal static IPosition ParseVcfLine(string vcfLine, IRefMinorProvid...
    method GetSimplePosition (line 40) | internal static SimplePosition GetSimplePosition(string vcfLine,
    method GetAnnotatorAndSequenceProvider (line 50) | private static (Annotator Annotator, ISequenceProvider SequenceProvide...

FILE: UnitTests/TestUtilities/ByteUtilities.cs
  class ByteUtilities (line 5) | public static class ByteUtilities
    method GetRandomBytes (line 7) | public static byte[] GetRandomBytes(int numBytes)

FILE: UnitTests/TestUtilities/ChromosomeUtilities.cs
  class ChromosomeUtilities (line 6) | public static class ChromosomeUtilities
    method ChromosomeUtilities (line 39) | static ChromosomeUtilities()
    method AddChromosome (line 49) | private static void AddChromosome(Chromosome chromosome)

FILE: UnitTests/TestUtilities/RandomPath.cs
  class RandomPath (line 5) | public static class RandomPath
    method GetRandomPath (line 7) | public static string GetRandomPath() => Path.Combine(Path.GetTempPath(...

FILE: UnitTests/TestUtilities/ResourceUtilities.cs
  class ResourceUtilities (line 6) | public static class ResourceUtilities
    method GetReadStream (line 8) | public static Stream GetReadStream(string path, bool checkMissingFile ...

FILE: UnitTests/TestUtilities/Resources.cs
  class Resources (line 6) | public static class Resources
    method TopPath (line 10) | public static string TopPath(string path) => Path.Combine(Top, path);
    method EndToEnd37 (line 11) | public static string EndToEnd37(string path) => Path.Combine(Top, "End...
    method InputFiles (line 12) | public static string InputFiles(string path) => Path.Combine(Top, "Inp...
    method ClinvarXmlFiles (line 13) | public static string ClinvarXmlFiles(string path) => Path.Combine(Top,...
    method VcvXmlFiles (line 14) | public static string VcvXmlFiles(string path) => Path.Combine(Top, "Cl...
    method SaGRCh37 (line 15) | public static string SaGRCh37(string path) => Path.Combine(Top, "SA", ...
    method SaPath (line 16) | public static string SaPath(string path) => Path.Combine(Top, "SA", pa...
    method Resources (line 19) | static Resources()
    method GetParentDirectory (line 25) | private static string GetParentDirectory(string directory)

FILE: UnitTests/TestUtilities/TestDataGenerator.cs
  class TestDataGenerator (line 15) | public static class TestDataGenerator
    method GenerateTestData (line 17) | public static void GenerateTestData(
    method GenerateRandomScoreData (line 45) | public static void GenerateRandomScoreData(
    method GetSequenceProvider (line 55) | public static ISequenceProvider GetSequenceProvider()
    method GetScoreReaderWithRandomData (line 61) | public static ScoreReader GetScoreReaderWithRandomData(
    method GetRandomSingleChromosomeData (line 104) | public static (

FILE: UnitTests/VariantAnnotation/Algorithms/SwapTests.cs
  class SwapTests (line 6) | public sealed class SwapTests
    method Swap_Int (line 8) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/AnnotatedPositionTests.cs
  class AnnotatedPositionTests (line 21) | public sealed class AnnotatedPositionTests
    method GetJsonString_DifferentOriginalChromosomeName (line 23) | [Fact]
    method GetJsonString_NullAnnotatedVariants (line 45) | [Fact]
    method GetJsonString_fisherStrand (line 60) | [Fact]
    method GetJsonString_StrelkaSomatic (line 84) | [Fact]
    method GetJsonString_custom_info (line 111) | [Fact]
    method GetJsonString_BreakEndEventId (line 143) | [Fact]
    method GetJsonString_LogOddsRatio (line 168) | [Fact]
    method GetSamples (line 193) | private static ISample[] GetSamples() => new ISample[] { Sample.EmptyS...
    method GetVariants (line 195) | private static IVariant[] GetVariants()
    method GetPosition (line 208) | private static IPosition GetPosition(string originalChromosomeName, IV...

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/AnnotatedVariantTests.cs
  class AnnotatedVariantTests (line 16) | public sealed class AnnotatedVariantTests
    method GetJsonString_RefMinor_WithTranscripts (line 20) | [Fact]
    method GetJsonString_RecomposedSnvAfterTrimming_IsRecomposedTrue (line 38) | [Fact]
    method AddRegulatoryRegion (line 54) | private static void AddRegulatoryRegion(IAnnotatedVariant annotatedVar...
    method AddTranscript (line 63) | private static void AddTranscript(IAnnotatedVariant annotatedVariant)
    method GetRefMinorVariant (line 74) | private static IVariant GetRefMinorVariant()

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/ConsequenceTests.cs
  class ConsequenceTests (line 12) | public sealed class ConsequenceTests
    method DetermineFlankingVariantEffects (line 14) | [Theory]
    method DetermineSmallVariantEffects_Tier1 (line 24) | [Theory]
    method DetermineSmallVariantEffects_Tier2 (line 46) | [Fact]
    method NeedsTranscriptVariant_NoConsequences_EvaluateByVariantType (line 67) | [Theory]
    method NeedsTranscriptVariant_Tier1 (line 91) | [Theory]
    method NeedsTranscriptVariant_Tier2_MatureMirnaVariant (line 101) | [Fact]
    method NeedsTranscriptVariant_Tier3 (line 109) | [Theory]
    method NeedsTranscriptVariant_Tier2_SV (line 141) | [Theory]
    method NeedsTranscriptVariant_CNV (line 153) | [Theory]
    method NeedsTranscriptVariant_STR (line 164) | [Theory]
    method DetermineSmallVariantEffects_Tier3 (line 175) | [Fact]
    method DetermineRegulatoryVariantEffects (line 243) | [Theory]
    method SvTheoryParameters (line 278) | public static IEnumerable<object[]> SvTheoryParameters()
    method DetermineStructuralVariantEffect (line 290) | [Theory]
    method GetFeatureVariantEffects (line 310) | private static IFeatureVariantEffects GetFeatureVariantEffects(bool is...

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvsCodingNomenclatureTests.cs
  class HgvsCodingNomenclatureTests (line 13) | public sealed class HgvsCodingNomenclatureTests
    method HgvsCodingNomenclatureTests (line 19) | public HgvsCodingNomenclatureTests()
    method GetForwardTranscript (line 26) | internal static ITranscript GetForwardTranscript()
    method GetForwardTranscriptWithoutUtr (line 53) | private static ITranscript GetForwardTranscriptWithoutUtr()
    method GetReverseTranscript (line 71) | internal static ITranscript GetReverseTranscript()
    method GetGapTranscript (line 96) | private static ITranscript GetGapTranscript()
    method GetHgvscAnnotation_in_intron_gap_substitution (line 143) | [Theory]
    method GetHgvscAnnotation_substitution_in_3UTR (line 166) | [Fact]
    method GetHgvscAnnotation_substitution_in_intron_before_TSS (line 175) | [Fact]
    method GetHgvscAnnotation_insertion_in_coding_region (line 184) | [Fact]
    method GetHgvscAnnotation_insertion_after_coding_region (line 196) | [Fact]
    method GetHgvscAnnotation_duplication_in_coding_region (line 208) | [Fact]
    method ApplyDuplicationAdjustments_NonCoding_Reverse (line 220) | [Fact]
    method ApplyDuplicationAdjustments_Coding_Forward (line 235) | [Fact]
    method GetHgvscAnnotation_Deletion_start_before_transcript (line 251) | [Fact]
    method GetHgvscAnnotation_Delin_start_from_Exon_end_in_intron (line 260) | [Fact]
    method GetHgvscAnnotation_inversion_start_from_Exon_end_in_intron (line 269) | [Fact]
    method GetHgvscAnnotation_Deletion_end_after_transcript (line 278) | [Fact]
    method GetHgvscAnnotation_Reference_no_hgvsc (line 287) | [Fact]
    method GetHgvscAnnotation_substitution_in_intron_of_reverse_gene (line 296) | [Fact]
    method GetHgvscAnnotation_substitution_after_stopCodon_of_reverse_gene (line 305) | [Fact]
    method GetHgvscAnnotation_deletion_of_reverse_gene (line 314) | [Fact]
    method GetHgvscAnnotation_insertion_at_last_position (line 323) | [Fact]
    method GetHgvscAnnotation_duplication_at_last_position (line 335) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvsProteinNomenclatureTests.cs
  class HgvsProteinNomenclatureTests (line 14) | public sealed class HgvsProteinNomenclatureTests
    method GetMockedTranscriptOnForwardStrand (line 18) | public static ITranscript GetMockedTranscriptOnForwardStrand()
    method GetHgvsProteinAnnotation_substitution (line 55) | [Fact]
    method GetHgvsProteinAnnotation_insertion (line 70) | [Fact]
    method GetHgvsProteinAnnotation_duplication_right_shifted (line 85) | [Fact]
    method GetHgvsProteinAnnotation_deletion (line 100) | [Fact]
    method GetHgvsProteinAnnotation_delIns (line 115) | [Fact]
    method GetHgvsProteinAnnotation_no_change (line 130) | [Fact]
    method GetHgvsProteinAnnotation_frameshift (line 145) | [Fact]
    method GetHgvsProteinAnnotation_frameshift_stop_gain (line 160) | [Fact]
    method GetHgvsProteinAnnotation_extension (line 175) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvsUtilitiesTests.cs
  class HgvsUtilitiesTests (line 11) | public sealed class HgvsUtilitiesTests
    method ShiftAndRotateAlleles_Rotated (line 13) | [Fact]
    method Rotate3Prime_Identity_Insertion (line 28) | [Fact]
    method Rotate3Prime_Identity_Deletion (line 43) | [Fact]
    method Rotate3Prime_Identity_WithNullAminoAcids (line 58) | [Fact]
    method IsAminoAcidDuplicate_True (line 73) | [Fact]
    method IsAminoAcidDuplicate_False (line 81) | [Fact]
    method IsAminoAcidDuplicate_False_WhenAminoAcidsNull (line 89) | [Fact]
    method IsAminoAcidDuplicate_False_StartEqualToAminoAcidLength (line 96) | [Fact]
    method GetNumAminoAcidsUntilStopCodon_FirstAminoAcidIsStop (line 103) | [Fact]
    method GetNumAminoAcidsUntilStopCodon_FoundExtraAminoAcids (line 116) | [Fact]
    method GetChangesAfterFrameshift_AfterFrameshift (line 129) | [Fact]
    method GetChangesAfterFrameshift_AtEndAfterFrameshift (line 139) | [Fact]
    method GetChangesAfterFrameshift_WhenStopRetained (line 149) | [Fact]
    method GetChangesAfterFrameshift_FirstAminoAcidIsStop (line 159) | [Fact]
    method GetAltPeptideSequence_Genomic (line 169) | [Fact]
    method GetCdnaPositionOffset_Intron_RltL_Reverse (line 186) | [Fact]
    method GetCdnaPositionOffset_Intron_ReqL_Reverse (line 198) | [Fact]
    method GetCdnaPositionOffset_Intron_LltR_Reverse (line 224) | [Fact]
    method GetCdnaPositionOffset_Intron_LeqR_Reverse (line 236) | [Fact]
    method GetCdnaPositionOffset_Gap_LeftSide_Forward (line 264) | [Fact]
    method GetCdnaPositionOffset_Gap_RightSide_Forward (line 276) | [Fact]
    method GetCdnaPositionOffset_Gap_LeftSide_Reverse (line 288) | [Fact]
    method GetCdnaPositionOffset_Gap_RightSide_Reverse (line 300) | [Fact]
    method GetCdnaPositionOffset_Intron_RltL_Forward (line 312) | [Fact]
    method GetCdnaPositionOffset_Intron_LltR_Forward (line 324) | [Fact]
    method GetCdnaPositionOffset_Intron_LeqR_Forward (line 336) | [Fact]
    method GetCdnaPositionOffset_Exon_Forward (line 348) | [Fact]
    method GetCdnaPositionOffset_Exon_Reverse (line 360) | [Fact]
    method GetCdnaPositionOffset_Gap_Forward_ReturnNull (line 385) | [Fact]
    method GetGenomicRefSequence (line 411) | private static ISequence GetGenomicRefSequence()
    method GetGenomicTranscript (line 418) | private static ITranscript GetGenomicTranscript()
    method GetReverseGapTranscript (line 433) | private static ITranscript GetReverseGapTranscript()
    method GetForwardGapTranscript (line 457) | private static ITranscript GetForwardGapTranscript()

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvscNotationTests.cs
  class HgvscNotationTests (line 6) | public sealed class HgvscNotationTests
    method ToString_substitution (line 9) | [Fact]
    method ToString_deletion_one_base (line 21) | [Fact]
    method ToString_deletion_multiple_base (line 33) | [Fact]
    method ToString_one_base_duplication (line 45) | [Fact]
    method ToString_multi_base_duplication (line 57) | [Fact]
    method ToString_insertion (line 69) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvsgNotationTests.cs
  class HgvsgNotationTests (line 11) | public sealed class HgvsgNotationTests
    method GetNotation_MT (line 17) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/HgvspNotationTests.cs
  class HgvspNotationTests (line 6) | public sealed class HgvspNotationTests
    method Missense_substitution (line 8) | [Fact]
    method Nonsense_substitution (line 15) | [Fact]
    method Silent_substitution (line 22) | [Fact]
    method StartLost_due_to_substitution (line 29) | [Fact]
    method One_aminoAcid_deletion (line 36) | [Fact]
    method Multiple_aminoAcid_deletion (line 43) | [Fact]
    method Deletion_gained_stop (line 50) | [Fact]
    method Unknown_start_equals_end (line 57) | [Fact]
    method Unknown_start_not_equals_end (line 63) | [Fact]
    method One_aminoAcid_duplication (line 69) | [Fact]
    method Multiple_aminoAcid_duplication (line 76) | [Fact]
    method One_aminoAcid_insertion (line 83) | [Fact]
    method Insert_stop_codon (line 90) | [Fact]
    method Insert_past_stop (line 96) | [Fact]
    method Multiple_aminoAcid_insertion (line 102) | [Fact]
    method Insertion_at_end (line 109) | [Fact]
    method Del_one_ins_two (line 116) | [Fact]
    method Del_two_ins_one (line 123) | [Fact]
    method Del_two_ins_stop (line 130) | [Fact]
    method Delins_becomes_substitution_of_Ter (line 137) | [Fact]
    method Frameshift_with_known_countToStop (line 144) | [Fact]
    method Frameshift_gains_immediate_stop (line 151) | [Fact]
    method Frameshift_unknown_countToStop (line 158) | [Fact]
    method Frameshift_due_to_insertion (line 165) | [Fact]
    method Start_lost_start_equals_end (line 172) | [Fact]
    method Start_lost_start_not_equals_end (line 179) | [Fact]
    method Stop_lost_with_countToEnd (line 186) | [Fact]
    method Stop_lost_without_countToEnd (line 194) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/ProteinChangeTests.cs
  class ProteinChangeTests (line 8) | public sealed class ProteinChangeTests
    method Substitution (line 10) | [Fact]
    method Single_base_deletion (line 25) | [Fact]
    method Frameshift (line 40) | [Fact]
    method Extension (line 55) | [Fact]
    method Duplication (line 70) | [Fact]
    method Insertion (line 85) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/RegulatoryRegionAnnotatorTests.cs
  class RegulatoryRegionAnnotatorTests (line 14) | public sealed class RegulatoryRegionAnnotatorTests
    method Annotate_Promoter (line 16) | [Fact]
    method GetRegulatoryRegion (line 31) | private static IRegulatoryRegion GetRegulatoryRegion()
    method GetVariant (line 37) | private static IVariant GetVariant()

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/AminoAcidTests.cs
  class AminoAcidTests (line 8) | public sealed class AminoAcidTests
    method AddUnknownAminoAcid_ExpectedResults (line 13) | [Fact]
    method AddUnknownAminoAcid_SameIfStopCodon (line 20) | [Fact]
    method Translate_ExpectedResults (line 27) | [Fact]
    method Translate_NullOrEmptyInput_ReturnEmpty (line 35) | [Fact]
    method Translate_NsInInput_ReturnEmpty (line 47) | [Fact]
    method ConvertAminoAcidToAbbreviation_ThrowException (line 59) | [Fact]
    method ConvertTripletToAminoAcid_StandardGeneticCode (line 65) | [Theory]
    method ConvertTripletToAminoAcid_VertebrateMitochondrialCode (line 76) | [Theory]
    method GetAbbreviations_ExpectedResults (line 87) | [Fact]
    method GetAbbreviations_SingleAA_ExpectedResults (line 93) | [Fact]
    method GetAbbreviations_NullOrEmptyInput_ReturnEmpty (line 99) | [Fact]
    method TranslateBases_ExpectedResults (line 106) | [Fact]
    method TranslateBases_NullInput_ReturnNull (line 114) | [Fact]
    class StandardGeneticCodeData (line 120) | private sealed class StandardGeneticCodeData : TheoryData<char, string[]>
      method StandardGeneticCodeData (line 122) | public StandardGeneticCodeData()
    class VertebrateMitochondrialCodeData (line 148) | private sealed class VertebrateMitochondrialCodeData : TheoryData<char...
      method VertebrateMitochondrialCodeData (line 150) | public VertebrateMitochondrialCodeData()

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/AnnotatedTranscriptTests.cs
  class AnnotatedTranscriptTests (line 12) | public sealed class AnnotatedTranscriptTests
    method SerializeJson_NominalUsage (line 14) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/CdnaSequenceTests.cs
  class CdnaSequenceTests (line 9) | public sealed class CdnaSequenceTests
    method RnaEdits_snv_forward_no_utr (line 11) | [Fact]
    method RnaEdits_snv_forward_with_utr (line 31) | [Fact]
    method RnaEdits_in_coding_sequence_reverse_insertion (line 57) | [Fact]
    method With_rnaEdits_reverse_deletion_utr (line 85) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/CodingSequenceTests.cs
  class CodingSequenceTests (line 10) | public sealed class CodingSequenceTests
    method Create (line 12) | [Fact]
    method Length_ReturnTrueLength_WhenGapsArePresent (line 41) | [Fact]
    method RnaEdits_snv_forward_no_utr (line 66) | [Fact]
    method RnaEdits_snv_forward_with_utr (line 91) | [Fact]
    method RnaEdits_snv_reverse_utr (line 121) | [Fact]
    method RnaEdits_insertion_in_utr (line 150) | [Fact]
    method RnaEdits_insertion_reverse_in_utr (line 175) | [Fact]
    method GetCodingSequence_InsertionGeneModel_InsertionRnaEdit (line 200) | [Fact]
    method RnaEdits_in_coding_sequence_reverse_insertion (line 230) | [Fact]
    method With_rnaEdits_snv_mnv (line 262) | [Fact]
    method With_rnaEdits_deletion (line 297) | [Fact]
    method With_rnaEdits_reverse_deletion_utr (line 332) | [Fact]
    method RnaEdits_deletion_reverse_utr (line 365) | [Fact]
    method RnaEdits_big_insertions_reverse (line 408) | [Fact]
    method RnaEdits_big_test_reverse (line 455) | [Fact]
    method RnaEdits_big_test (line 588) | [Fact]
    method GetCodingSequence_RnaEditInsertion_StartsCds_EndsUtr (line 719) | [Fact]
    method GetCodingSequence_RnaEditSnv_StartsUtr (line 759) | [Fact]
    method GetCodingSequence_NonZeroStartExonPhase_CdsBeforeFirstExon (line 793) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/CodonsTests.cs
  class CodonsTests (line 9) | public sealed class CodonsTests
    method Assign_WhenIntervalsNull_ReturnNull (line 11) | [Fact]
    method Assign_SNV_SuffixLenTooBig (line 21) | [Fact]
    method Assign_SNV (line 35) | [Fact]
    method Assign_MNV (line 49) | [Fact]
    method GetCodon_NullPrefixAndSuffix (line 64) | [Fact]
    method IsTriplet (line 72) | [Theory]
    method GetCodons_OutOfRangeIndexes_Adjusted (line 81) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/CompactIdTests.cs
  class CompactIdTests (line 11) | public sealed class CompactIdTests
    method Convert_ENSG (line 13) | [Fact]
    method Convert_ENST (line 20) | [Fact]
    method Convert_ENSP (line 27) | [Fact]
    method Convert_ENSESTG (line 34) | [Fact]
    method Convert_ENSESTP (line 41) | [Fact]
    method Convert_ENSR (line 48) | [Fact]
    method Convert_CCDS (line 55) | [Fact]
    method Convert_NR (line 62) | [Fact]
    method Convert_NM (line 69) | [Fact]
    method Convert_NP (line 76) | [Fact]
    method Convert_XR (line 83) | [Fact]
    method Convert_XM (line 90) | [Fact]
    method Convert_XP (line 97) | [Fact]
    method Convert_NullInput_ReturnsEmptyId (line 104) | [Fact]
    method Convert_Unknown (line 116) | [Fact]
    method Convert_OnlyNumbers (line 124) | [Fact]
    method Convert_OnlyNumbers_ThrowException_NumberTooLarge (line 131) | [Fact]
    method CompactId_IO_EndToEnd (line 141) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/FeatureVariantEffectsTests.cs
  class FeatureVariantEffectsTests (line 8) | public sealed class FeatureVariantEffectsTests
    method Ablation (line 10) | [Theory]
    method Amplification (line 23) | [Theory]
    method Truncation (line 37) | [Theory]
    method Elongation (line 50) | [Theory]
    method FivePrimeDuplicatedTranscript (line 65) | [Theory]
    method ThreePrimeDuplicatedTranscript (line 86) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/MappedPositionUtilitiesTests.cs
  class MappedPositionUtilitiesTests (line 9) | public sealed class MappedPositionUtilitiesTests
    method MappedPositionUtilitiesTests (line 86) | public MappedPositionUtilitiesTests()
    method FindRegion_Forward_Insertion (line 112) | [Fact]
    method FindRegion_Reverse_Deletion (line 124) | [Fact]
    method GetCdnaPositions_Forward_Insertion (line 136) | [Fact]
    method GetCdnaPositions_Reverse_Deletion (line 147) | [Fact]
    method GetCdnaPosition_Snv_AfterOutFrameRnaEditDeletion (line 157) | [Fact]
    method GetCdnaPosition_Snv_AfterInframeRnaEditInsertion (line 167) | [Fact]
    method GetCdnaPosition_Snv_AfterOutframeRnaEditInsertion (line 177) | [Fact]
    method GetCoveredCdnaPositions_Forward_StartBefore_EndExon (line 187) | [Fact]
    method GetCoveredCdnaPositions_Forward_StartIntron_EndExon (line 195) | [Fact]
    method GetCoveredCdnaPositions_Forward_StartExon_EndIntron (line 203) | [Fact]
    method GetCoveredCdnaPositions_Forward_StartExon_EndAfter (line 211) | [Fact]
    method GetCoveredCdnaPositions_Forward_StartBefore_EndAfter (line 219) | [Fact]
    method GetCoveredCdnaPositions_Forward_Insertion_StartAfter_EndExon (line 227) | [Fact]
    method GetCoveredCdnaPositions_Reverse_StartBefore_EndExon (line 250) | [Fact]
    method GetCoveredCdnaPositions_Reverse_StartIntron_EndExon (line 264) | [Fact]
    method GetCoveredCdnaPositions_Reverse_StartExon_EndIntron (line 279) | [Fact]
    method GetCoveredCdnaPositions_Reverse_StartExon_EndAfter (line 293) | [Fact]
    method GetCoveredCdnaPositions_Reverse_StartBefore_EndAfter (line 307) | [Fact]
    method GetCdsPosition_Forward_Insertion (line 315) | [Fact]
    method GetCdsPosition_Snv_AfterOutFrameRnaEditDeletion (line 327) | [Fact]
    method GetCdsPosition_Snv_AfterInframeRnaEditInsertion (line 338) | [Fact]
    method GetCdsPosition_Snv_AfterOutframeRnaEditInsertion (line 349) | [Fact]
    method GetCdsPosition_Forward_Insertion_WithStartExonPhase (line 360) | [Fact]
    method GetCdsPosition_Reverse_NoCodingRegion_Deletion (line 372) | [Fact]
    method GetCdsPosition_SilenceOutput_InsertionAfterCodingRegion_Forward (line 383) | [Fact]
    method GetCdsPosition_SilenceOutput_InsertionAfterCodingRegion_Reverse (line 396) | [Fact]
    method GetCdsPosition_SilenceOutput_InsertionBeforeCodingRegion_Reverse (line 409) | [Fact]
    method GetCdsPosition_DoNotSilenceOutput_Reverse (line 422) | [Fact]
    method GetProteinPosition_Forward_Insertion (line 435) | [Fact]
    method GetProteinPosition_Reverse_Deletion (line 444) | [Fact]
    method GetExon (line 453) | private static ITranscriptRegion GetExon() => new TranscriptRegion(Tra...
    method GetIntron (line 454) | private static ITranscriptRegion GetIntron() => new TranscriptRegion(T...
    method FoundExonEndpointInsertion_NotInsertion_ReturnFalse (line 456) | [Fact]
    method FoundExonEndpointInsertion_BothExons_ReturnFalse (line 462) | [Fact]
    method FoundExonEndpointInsertion_BothIntrons_ReturnFalse (line 468) | [Fact]
    method FoundExonEndpointInsertion_BothDefinedCdnaPositions_ReturnFalse (line 474) | [Fact]
    method FoundExonEndpointInsertion_BothUndefinedCdnaPositions_ReturnFalse (line 480) | [Fact]
    method FoundExonEndpointInsertion_UndefinedRegion_ReturnFalse (line 486) | [Fact]
    method FoundExonEndpointInsertion_OneIntron_OneExon_OneUndefinedPosition_ReturnTrue (line 492) | [Fact]
    method FixExonEndpointInsertion_VariantEnd_ExonEnd_Reverse (line 498) | [Fact]
    method FixExonEndpointInsertion_VariantStart_ExonStart_Reverse (line 511) | [Fact]
    method FixExonEndpointInsertion_VariantEnd_ExonEnd_Forward (line 525) | [Fact]
    method FixExonEndpointInsertion_VariantStart_ExonStart_Forward (line 538) | [Fact]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/StringExtensionsTests.cs
  class StringExtensionsTests (line 6) | public sealed class StringExtensionsTests
    method CommonPrefixLength (line 8) | [Theory]
    method CommonSuffixLength (line 19) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/TranscriptPositionalEffectTests.cs
  class TranscriptPositionalEffectTests (line 12) | public sealed class TranscriptPositionalEffectTests
    method TranscriptPositionalEffectTests (line 18) | public TranscriptPositionalEffectTests()
    method DetermineIntronicEffect_NullIntrons (line 80) | [Fact]
    method DetermineIntronicEffect_NotWithinFrameshiftIntron (line 100) | [Fact]
    method DetermineIntronicEffect_IsEndSpliceSite (line 117) | [Fact]
    method DetermineIntronicEffect_IsStartSpliceSite (line 125) | [Fact]
    method DetermineIntronicEffect_IsWithinFrameshiftIntron_NotInSpliceSite (line 133) | [Fact]
    method DetermineIntronicEffect_IsWithinIntron (line 143) | [Fact]
    method DetermineIntronicEffect_IsWithinSpliceSiteRegion (line 157) | [Fact]
    method DetermineExonicEffect_HasExonOverlap (line 167) | [Fact]
    method DetermineExonicEffect_AfterCoding (line 179) | [Fact]
    method DetermineExonicEffect_WithinCdna (line 190) | [Fact]
    method DetermineExonicEffect_WithinCds (line 201) | [Fact]
    method DetermineExonicEffect_OverlapWithMicroRna (line 212) | [Fact]
    method ExonOverlaps_NoOverlap (line 223) | [Fact]
    method IsMatureMirnaVariant_NullMirnas (line 237) | [Fact]
    method IsWithinCds_ReturnFalse (line 244) | [Fact]
    method IsWithinCds_ReturnTrue (line 252) | [Fact]
    method IsWithinCds_IsWithinFrameshiftIntron_OverlapCodingRegion_ReturnTrue (line 260) | [Fact]
    method IsWithinCds_IsWithinFrameshiftIntron_ReturnFalse (line 271) | [Fact]
    method IsAfterCoding_True_WhenInsertion (line 282) | [Fact]
    method IsBeforeCoding_True_WhenInsertion (line 289) | [Fact]
    method IsWithinCdna (line 296) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/TranscriptUtilitiesTests.cs
  class TranscriptUtilitiesTests (line 12) | public sealed class TranscriptUtilitiesTests
    method IsDuplicateWithinInterval_not_intertion (line 16) | [Fact]
    method IsDuplicateWithinInterval_outside_interval (line 23) | [Fact]
    method IsDuplicateWithinInterval_insertion_not_dup (line 35) | [Fact]
    method IsDuplicateWithinInterval_insertion_is_dup (line 49) | [Fact]
    method GenSimpleDeletionMock (line 63) | private static Mock<ISimpleVariant> GenSimpleDeletionMock()
    method GenSimpleInsertionMock (line 75) | private static Mock<ISimpleVariant> GenSimpleInsertionMock()

FILE: UnitTests/VariantAnnotation/AnnotatedPositions/Transcript/VariantEffectTests.cs
  class VariantEffectTests (line 9) | public sealed class VariantEffectTests
    method IsSpliceAcceptorVariant (line 11) | [Theory]
    method IsSpliceDonorVariant (line 40) | [Theory]
    method IsStartRetainedVariant (line 70) | [Theory]
    method IsFivePrimeUtrVariant (line 89) | [Theory]
    method IsStopLost_DeletionOverStopCodon_ReturnTrue (line 125) | [Fact]
    method IsCodingSequenceVariant_WithMoreSpecificConsequence_ReturnFalse (line 145) | [Theory]

FILE: UnitTests/VariantAnnotation/AnnotatorTests.cs
  class AnnotatorTest (line 15) | public sealed class AnnotatorTest
    method GetVariants (line 17) | private static IVariant[] GetVariants()
    method GetMitoVariants (line 30) | private static IVariant[] GetMitoVariants()
    method Annotate_conservation_annotation (line 43) | [Fact]
    method Annotate_mito_hg19 (line 66) | [Fact]
    method Annotate_mito_GRCh37 (line 89) | [Fact]
    method Annotate_null_position (line 116) | [Fact]
    method CheckAssemblyConsistency_Consistent (line 159) | [Fact]
    method CheckAssemblyConsistency_Inconsistent (line 179) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/EncodedTranscriptDataTests.cs
  class EncodedTranscriptDataTests (line 10) | public sealed class EncodedTranscriptDataTests
    method EncodedTranscriptData_EndToEnd (line 12) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/GeneTests.cs
  class GeneTests (line 13) | public sealed class GeneTests
    method Gene_EndToEnd (line 15) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/RegulatoryRegionTests.cs
  class RegulatoryRegionTests (line 15) | public sealed class RegulatoryRegionTests
    method RegulatoryRegion_EndToEnd (line 17) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/TranscriptRegionExtensionsTests.cs
  class TranscriptRegionExtensionsTests (line 7) | public sealed class TranscriptRegionExtensionsTests
    method TranscriptRegionExtensionsTests (line 12) | public TranscriptRegionExtensionsTests()
    method BinarySearch_Nominal (line 33) | [Theory]
    method BinarySearch_ReturnNegative_BeyondExons (line 44) | [Theory]
    method GetExonsAndIntrons_Forward_Internal (line 54) | [Fact]
    method GetExonsAndIntrons_Reverse_Gap_NIR_3592 (line 65) | [Fact]
    method GetExonsAndIntrons_Reverse_Internal (line 83) | [Fact]
    method GetExonsAndIntrons_Forward_StartBefore (line 94) | [Fact]
    method GetExonsAndIntrons_Forward_EndAfter (line 105) | [Fact]
    method GetExonsAndIntrons_Reverse_StartBefore_EndAfter (line 116) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/TranscriptRegionTests.cs
  class TranscriptRegionTests (line 11) | public sealed class TranscriptRegionTests
    method TranscriptRegion_EndToEnd (line 13) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/TranscriptTests.cs
  class TranscriptTests (line 15) | public sealed class TranscriptTests
    method Transcript_EndToEnd (line 17) | [Fact]
    method CreateIndices (line 109) | private static Dictionary<T, int> CreateIndices<T>(T[] objects)
    method GetTranscriptRegions (line 116) | private static ITranscriptRegion[] GetTranscriptRegions()
    method GetMicroRnas (line 127) | private static IInterval[] GetMicroRnas()

FILE: UnitTests/VariantAnnotation/Caches/DataStructures/TranslationTests.cs
  class TranslationTests (line 11) | public sealed class TranslationTests
    method Translation_EndToEnd (line 13) | [Fact]

FILE: UnitTests/VariantAnnotation/Caches/TranscriptCacheTests.cs
  class TranscriptCacheTests (line 18) | public sealed class TranscriptCacheTests
    method TranscriptCacheTests (line 24) | public TranscriptCacheTests()
    method GetOverlappingFlankingTranscripts_TwoOverlaps (line 34) | [Fact]
    method GetOverlappingFlankingTranscripts_NoOverlaps (line 44) | [Fact]
    method GetOverlappingRegulatoryRegions_OneOverlap (line 53) | [Fact]
    method GetOverlappingRegulatoryRegions_NoOverlaps (line 63) | [Fact]
    method Assembly_Get (line 72) | [Fact]
    method DataSourceVersions_Get (line 79) | [Fact]
    method GetDataSourceVersions (line 90) | [Fact]
    method GetRegulatoryRegions (line 99) | private static IRegulatoryRegion[] GetRegulatoryRegions()
    method GetTranscripts (line 115) | internal static ITranscript[] GetTranscripts()

FILE: UnitTests/VariantAnnotation/Caches/Utilities/RnaEditUtilitiesTests.cs
  class RnaEditUtilitiesTests (line 8) | public sealed class RnaEditUtilitiesTests
    method RnaEditTypes (line 10) | [Theory]

FILE: UnitTests/VariantAnnotation/Caches/Utilities/TranscriptUtilitiesTests.cs
  class TranscriptUtilitiesTests (line 8) | public sealed class TranscriptUtilitiesTests
    method TranscriptUtilitiesTests (line 12) | public TranscriptUtilitiesTests()
    method GetTotalExonLength_MultipleExons (line 17) | [Fact]
    method GetTranscriptRegions (line 25) | private static ITranscriptRegion[] GetTranscriptRegions()

FILE: UnitTests/VariantAnnotation/GeneFusions/Calling/GeneFusionCallerTests.cs
  class GeneFusionCallerTests (line 19) | public sealed class GeneFusionCallerTests
    method AddGeneFusionsToDictionary_ForwardFirst5PrimeUtr_ReverseFirstCds_ActualFusion (line 25) | [Fact]
    method AddGeneFusionsToDictionary_ForwardLast5PrimeUtr_ReverseIntronCds_ActualFusion (line 45) | [Fact]
    method AddGeneFusionsToDictionary_ForwardFirstCds_ReverseFirst3PrimeUtr_ActualFusion (line 65) | [Fact]
    method AddGeneFusionsToDictionary_ForwardIntronCds_ReverseLastCds_ActualFusion (line 85) | [Fact]
    method AddGeneFusionsToDictionary_ForwardLastCds_ReverseLast3PrimeUtr_ActualFusion (line 105) | [Fact]
    method AddGeneFusionsToDictionary_ForwardFirst3PrimeUtr_ReverseFirst5PrimeUtr_ActualFusion (line 125) | [Fact]
    method AddGeneFusionsToDictionary_ForwardLast3PrimeUtr_ReverseLast5PrimeUtr_ActualFusion (line 145) | [Fact]
    method AddGeneFusionsToDictionary_ReverseFirst5PrimeUtr_ForwardLastCds_ActualFusion (line 165) | [Fact]
    method AddGeneFusionsToDictionary_ReverseLast5PrimeUtr_ForwardFirstCds_ActualFusion (line 185) | [Fact]
    method AddGeneFusionsToDictionary_ReverseFirstCds_ForwardFirst3PrimeUtr_ActualFusion (line 205) | [Fact]
    method AddGeneFusionsToDictionary_ReverseLastCds_ForwardLast3PrimeUtr_ActualFusion (line 225) | [Fact]
    method AddGeneFusionsToDictionary_ReverseFirst3PrimeUtr_ForwardFirst5PrimeUtr_ActualFusion (line 245) | [Fact]
    method AddGeneFusionsToDictionary_ReverseLast3PrimeUtr_ForwardLast5PrimeUtr_ActualFusion (line 265) | [Fact]
    method AddGeneFusionsToDictionary_ForwardNonCodingFirstCdna_ReverseFirstCds_ActualFusion (line 285) | [Fact]
    method AddGeneFusionsToDictionary_ForwardNonCodingLastCdna_ReverseLastCds_ActualFusion (line 305) | [Fact]
    method AddGeneFusionsToDictionary_ForwardCds_ReverseCds_InFrame_ActualFusion (line 325) | [Fact]
    method AddGeneFusionsToDictionary_ForwardCds_ReverseCds_Imprecise_NotInFrame_ActualFusion (line 346) | [Fact]
    method FoundViableGeneFusion_ReturnTrue (line 367) | [Fact]
    method FoundViableGeneFusion_AffectedByOriginAdjacency_ReturnTrue (line 382) | [Fact]
    method FoundViableGeneFusion_SameGeneSymbol_ReturnFalse (line 402) | [Fact]
    method FoundViableGeneFusion_DifferentOriginOrientation_ReturnFalse (line 417) | [Fact]
    method FoundViableGeneFusion_DifferentPartnerOrientation_ReturnFalse (line 432) | [Fact]
    method FoundViableGeneFusion_DifferentTranscriptSource_ReturnFalse (line 447) | [Fact]
    method FoundViableGeneFusion_TranscriptsAlreadyOverlap_ReturnFalse (line 462) | [Fact]
    class GetCodonPositionData (line 477) | private sealed class GetCodonPositionData : TheoryData<int, int, byte?>
      method GetCodonPositionData (line 479) | public GetCodonPositionData()
    method GetCodonPosition_Forward_ExpectedResults (line 492) | [Theory]
    method DetermineInFrameFusion_ExpectedResults (line 502) | [Theory]
    method GetGeneSymbols_SameChromosome (line 523) | [Fact]
    method GetGeneSymbols_DifferentChromosomes (line 539) | [Fact]
    method AddGeneFusions_ExpectedResults (line 554) | [Fact]
    method GetAnnotatedVariants (line 581) | private IAnnotatedVariant[] GetAnnotatedVariants()
    method GetTranscriptIntervalForest (line 595) | private IntervalForest<ITranscript> GetTranscriptIntervalForest()

FILE: UnitTests/VariantAnnotation/GeneFusions/IO/GeneFusionIndexEntryTests.cs
  class GeneFusionIndexEntryTests (line 6) | public sealed class GeneFusionIndexEntryTests
    method Compare_ExpectedResults (line 8) | [Theory]

FILE: UnitTests/VariantAnnotation/GeneFusions/IO/GeneFusionSourceReaderTests.cs
  class GeneFusionSourceReaderTests (line 18) | public sealed class GeneFusionSourceReaderTests
    method CheckHeader_ExpectedResults (line 20) | [Theory]
    method AddAnnotations_ExpectedResults (line 31) | [Fact]
    method AddAnnotations_NoResults (line 66) | [Fact]
    method WriteGeneFusionSourceFile (line 88) | private static void WriteGeneFusionSourceFile(MemoryStream ms)

FILE: UnitTests/VariantAnnotation/GeneFusions/SA/GeneFusionPairTests.cs
  class GeneFusionPairTests (line 7) | public sealed class GeneFusionPairTests
    method Equals_ExpectedResults (line 13) | [Fact]
    method Equals_IGeneFusionPair_ExpectedResults (line 22) | [Fact]
    method GetHashCode_ExpectedResults (line 35) | [Fact]

FILE: UnitTests/VariantAnnotation/GeneFusions/SA/GeneFusionSourceCollectionTests.cs
  class GeneFusionSourceCollectionTests (line 6) | public sealed class GeneFusionSourceCollectionTests
    method Equals_ExpectedResults (line 20) | [Fact]
    method GetJsonEntry_ExpectedResults (line 29) | [Fact]
    method GetHashCode_ExpectedResults (line 39) | [Fact]

FILE: UnitTests/VariantAnnotation/GeneFusions/SA/GeneFusionSourceUtilitiesTests.cs
  class GeneFusionSourceUtilitiesTests (line 6) | public sealed class GeneFusionSourceUtilitiesTests
    method Convert_ExpectedResults (line 8) | [Theory]
    method Convert_UnknownSource_ReturnsNull (line 31) | [Fact]

FILE: UnitTests/VariantAnnotation/GeneFusions/Utilities/GeneFusionKeyTests.cs
  class GeneFusionKeyTests (line 6) | public sealed class GeneFusionKeyTests
    method Create_ExpectedResults (line 8) | [Fact]
    method Create_OneGeneIsNull_ReturnZero (line 19) | [Theory]

FILE: UnitTests/VariantAnnotation/GeneFusions/Utilities/IndexEntryExtensionsTests.cs
  class IndexEntryExtensionsTests (line 7) | public sealed class IndexEntryExtensionsTests
    method IndexEntryExtensionsTests (line 11) | public IndexEntryExtensionsTests()
    method GetIndex_Matches_ExpectedResults (line 23) | [Theory]
    method GetIndex_NotFound_ReturnNull (line 36) | [Theory]

FILE: UnitTests/VariantAnnotation/IO/Caches/CacheConstantsTests.cs
  class CacheConstantsTests (line 6) | public sealed class CacheConstantsTests
    method TranscriptPath_Null_WithNullPrefix (line 8) | [Fact]
    method TranscriptPath_NominalCase (line 15) | [Fact]
    method SiftPath_NominalCase (line 23) | [Fact]
    method PolyPhenPath_NominalCase (line 31) | [Fact]

FILE: UnitTests/VariantAnnotation/IO/Caches/CacheHeaderTests.cs
  class CacheHeaderTests (line 10) | public sealed class CacheHeaderTests
    method CacheHeader_EndToEnd (line 12) | [Fact]

FILE: UnitTests/VariantAnnotation/IO/Caches/TranscriptCacheReaderTests.cs
  class TranscriptCacheReaderTests (line 20) | public sealed class TranscriptCacheReaderTests
    method TranscriptCacheReaderTests (line 25) | public TranscriptCacheReaderTests()
    method TranscriptCacheReader_EndToEnd (line 62) | [Fact]
    method CheckIntervalArrays (line 91) | private static void CheckIntervalArrays<T>(IntervalArray<T>[] expected...
    method CheckChromosomeIntervals (line 117) | private static void CheckChromosomeIntervals(IEnumerable<IChromosomeIn...
    method CheckIntervals (line 135) | private static void CheckIntervals(IEnumerable<IInterval> expected, IE...
    method ReadItems_EndToEnd (line 151) | [Fact]
    method CheckGuard_InvalidGuard (line 178) | [Fact]
    method GetTranscripts (line 192) | private static ITranscript[] GetTranscripts(Chromosome chromosome, IGe...

FILE: UnitTests/VariantAnnotation/IO/JsonObjectTests.cs
  class JsonObjectTests (line 12) | public sealed class JsonObjectTests
    method ProcessBoolValue_True_TwoTimes (line 14) | [Fact]
    method AddBoolValue_True_TwoTimes (line 30) | [Fact]
    method AddIntValue_TwoTimes (line 44) | [Fact]
    method AddIntValue_NullInt (line 58) | [Fact]
    method AddDoubleValue_TwoTimes (line 70) | [Fact]
    method GetJsonDoubleString (line 84) | public static string GetJsonDoubleString()
    method AddDoubleValue_InvariantCulture (line 100) | [Fact]
    method AddDoubleValue_NullInt (line 111) | [Fact]
    method AddStringValue_TwoTimes (line 123) | [Fact]
    method AddStringValue_NullInt (line 137) | [Fact]
    method AddStringValues_TwoTimes (line 149) | [Fact]
    method AddStringValues_NullArray (line 167) | [Fact]
    method AddIntValues_TwoTimes (line 179) | [Fact]
    method AddIntValues_NullArray (line 197) | [Fact]
    method AddObjectValues_TwoTimes (line 209) | [Fact]
    method AddObjectValues_NullArray (line 231) | [Fact]
    method AddStringValues_EmptyArray (line 243) | [Fact]
    class Point (line 255) | private sealed class Point : IJsonSerializer
      method Point (line 260) | public Point(int x, int y)
      method SerializeJson (line 266) | public void SerializeJson(StringBuilder sb)

FILE: UnitTests/VariantAnnotation/IO/JsonWriterTests.cs
  class JsonWriterTests (line 14) | public sealed class JsonWriterTests
    method WriteJsonEntry_Nominal (line 16) | [Fact]

FILE: UnitTests/VariantAnnotation/IO/SampleExtensionsTests.cs
  class SampleExtensionsTests (line 7) | public sealed class SampleExtensionsTests
    method GetJsonString_Nominal (line 9) | [Fact]

FILE: UnitTests/VariantAnnotation/NSA/NsaIndexTests.cs
  class NsaIndexTests (line 12) | public sealed class NsaIndexTests
    method Query_chunks_in_same_chrom (line 14) | [Fact]
    method Query_chunks_in_different_chrom (line 51) | [Fact]

FILE: UnitTests/VariantAnnotation/NSA/RefMinorIndexTests.cs
  class RefMinorIndexTests (line 12) | public sealed class RefMinorIndexTests
    method CreateAndQuery_one_chromosome (line 14) | [Fact]
    method CreateAndQuery_multiple_chromosomes (line 34) | [Fact]
    method ReadBack (line 70) | [Fact]

FILE: UnitTests/VariantAnnotation/NSA/SuppAnnotationsOutputTests.cs
  class SuppAnnotationsOutputTests (line 8) | public sealed class SuppAnnotationsOutputTests
    method Output_positional_not_array (line 10) | [Fact]
    method Output_not_positional_not_array (line 20) | [Fact]
    method Output_not_positional_array (line 30) | [Fact]
    method Output_emptyJsonStrings_array (line 41) | [Fact]
    method Output_emptyJsonString_not_array (line 46) | [Fact]

FILE: UnitTests/VariantAnnotation/NSA/SuppIntervalUtilitiesTests.cs
  class SuppIntervalUtilitiesTests (line 9) | public sealed class SuppIntervalUtilitiesTests
    method GetOverlapFractions_NotNull_AsExpected (line 11) | [Theory]
    method GetOverlapFractions_ReturnNulls_DifferentChroms (line 28) | [Fact]
    method GetOverlapFractions_ReturnNulls_Insertion (line 39) | [Fact]
    method GetOverlapFractions_ReturnNulls_SaInsertion (line 50) | [Fact]
    method GetOverlapFractions_ReturnNulls_BreakEnd (line 61) | [Fact]

FILE: UnitTests/VariantAnnotation/ProviderTests/GsaProviderTests.cs
  class GsaProviderTests (line 24) | public sealed class GsaProviderTests
    method GetScoreReaderWithData (line 26) | private static (ScoreReader, Dictionary<Chromosome, List<Dictionary<st...
    method GetScoreProvider (line 55) | private static (ScoreProvider provider, Dictionary<Chromosome, List<Di...
    method GetPosition (line 63) | private static IAnnotatedPosition GetPosition(Chromosome chrom, int st...
    method TestAnnotateUsingScoreProvider (line 81) | [Fact]
    method TestSNVTypeAnnotationOnly (line 117) | [Fact]
    method TestUnknownPosition (line 137) | [Fact]
    method TestUnknownAssembly (line 151) | [Fact]

FILE: UnitTests/VariantAnnotation/ProviderTests/LcrProviderTests.cs
  class LcrProviderTests (line 16) | public class LcrProviderTests
    method GetNsiStream (line 18) | private Stream GetNsiStream()
    method GetAnnotatedVariant (line 42) | private IAnnotatedVariant GetAnnotatedVariant(Chromosome chromosome, i...
    method GetAnnotatedPosition (line 52) | private IAnnotatedPosition GetAnnotatedPosition(Chromosome chromosome,...
    method AddAnnotationsTest (line 65) | [Fact]

FILE: UnitTests/VariantAnnotation/ProviderTests/NsaProviderTests.cs
  class NsaProviderTests (line 20) | public sealed class NsaProviderTests
    method GetDbSnpProvider (line 22) | private static IAnnotationProvider GetDbSnpProvider()
    method GetClinVarProvider (line 52) | private static IAnnotationProvider GetClinVarProvider()
    method GetGmeProvider (line 80) | private static IAnnotationProvider GetGmeProvider()
    method GetPosition (line 109) | private static IAnnotatedPosition GetPosition(Chromosome chrom, int st...
    method Annotate_alleleSpecific (line 129) | [Fact]
    method Annotate_gme (line 145) | [Fact]
    method Annotate_notAlleleSpecific_isArray (line 161) | [Fact]

FILE: UnitTests/VariantAnnotation/ScoreFile/GenericScoreEncoderTests.cs
  class GenericScoreEncoderTests (line 9) | public sealed class GenericScoreEncoderTests
    method TestEncoderDecoder (line 11) | [Fact]
    method EncodeDecode (line 72) | private static double EncodeDecode(GenericScoreEncoder encoder, double...

FILE: UnitTests/VariantAnnotation/ScoreFile/GenericScoreEndToEndTests.cs
  class GenericScoreEndToEndTests (line 15) | public sealed class GenericScoreEndToEndTests
    method ScoreWriterTestRandomData (line 17) | [Fact]
    method ScoreWriterTestDeterministicData (line 145) | [Fact]
    method AssertTestData (line 220) | private static void AssertTestData(Dictionary<Chromosome, List<Diction...

FILE: UnitTests/VariantAnnotation/ScoreFile/GenericScoreTests.cs
  class GenericScoreTests (line 22) | public sealed class GenericScoreTests
    method TestScoreReader (line 24) | [Fact]
    method TestParRegion (line 77) | [Fact]
    method TestWriteUnknownAllele (line 125) | [Fact]
    method TestOutOfOrderWriting (line 174) | [Fact]
    method TestParRegion2 (line 215) | [Fact]
    method SchemaVersionTest (line 260) | [Fact]
    method TestHeader (line 304) | [Fact]
    method PrepareHeaderTestData (line 321) | private MemoryStream PrepareHeaderTestData(FileType fileType, uint gua...
    method GetSaItems (line 352) | private static IEnumerable<GenericScoreItem> GetSaItems(int count)
    method GetParRegionItems (line 366) | private static IEnumerable<GenericScoreItem> GetParRegionItems(int count)
    method WrongRefAllele_ThrowUserException (line 380) | [Fact]
    method WriteCustomSaItem (line 389) | private static void WriteCustomSaItem(GenericScoreItem customItem, boo...
    method GetChr22_17467787_17467799_genome (line 422) | private static Stream GetChr22_17467787_17467799_genome()
    method GetConflictingGnomadItems (line 442) | private static IEnumerable<GenericScoreItem> GetConflictingGnomadItems()
    method GetAllASequenceProvider (line 461) | public static ISequenceProvider GetAllASequenceProvider(GenomeAssembly...

FILE: UnitTests/VariantAnnotation/ScoreFile/HeaderTests.cs
  class HeaderTests (line 15) | public sealed class HeaderTests
    method TestFilePairId (line 17) | [Fact]
    method TestFileType (line 77) | [Fact]

FILE: UnitTests/VariantAnnotation/ScoreFile/ReaderSettingsTests.cs
  class ReaderSettingsTests (line 9) | public sealed class ReaderSettingsTests
    method TestReadWriteZeroToOne (line 11) | [Fact]
    method TestReadWriteGenericScoreEncoder (line 26) | [Fact]
    method TestReadUnknownEncoder (line 41) | [Fact]
    method AssertData (line 64) | private void AssertData(ExtendedBinaryWriter writer, ReaderSettings re...
    method GetReaderSettings (line 80) | private ReaderSettings GetReaderSettings(EncoderType encoderType, stri...

FILE: UnitTests/VariantAnnotation/ScoreFile/SaItemValidatorTests.cs
  class SaItemValidatorTests (line 10) | public sealed class SaItemValidatorTests
    method TestParRegion (line 12) | [Fact]
    method TestIncorrectReference (line 47) | [Fact]
    method TestCheckSnv (line 91) | [Fact]

FILE: UnitTests/VariantAnnotation/ScoreFile/ScoreEncoderTests.cs
  class ScoreEncoderTests (line 10) | public sealed class ScoreEncoderTests
    method TestEncoderDecoder (line 12) | [Fact]
    method TestByteRequired (line 83) | [Fact]
    method EncodeDecode (line 107) | private static double EncodeDecode(ZeroToOneScoreEncoder encoder, doub...

FILE: UnitTests/VariantAnnotation/ScoreFile/ScoreIndexTests.cs
  class ScoreIndexTests (line 13) | public sealed class ScoreIndexTests
    method ScoreIndexTest (line 15) | [Fact]
    method PositionToBlockIndexTest (line 87) | [Fact]
    method AddGetChromosomeBlocksTest (line 108) | [Fact]
    method TestGetNucleotidePosition (line 128) | [Fact]
    method GetScoreIndex (line 144) | private static (Stream stream, ScoreIndex scoreIndex) GetScoreIndex()
    method TestHeader (line 172) | [Fact]

FILE: UnitTests/VariantAnnotation/ScoreFile/ScoreJsonEncoderTests.cs
  class ScoreJsonEncoderTests (line 6) | public sealed class ScoreJsonEncoderTests
    method TestJsonRepresentation (line 8) | [Fact]

FILE: UnitTests/VariantAnnotation/Sequence/CompressedSequenceReaderTests.cs
  class CompressedSequenceReaderTests (line 8) | public sealed class CompressedSequenceReaderTests
    method GetCompressedSequence (line 10) | [Fact]

FILE: UnitTests/VariantAnnotation/Sequence/CompressedSequenceTests.cs
  class CompressedSequenceTests (line 8) | public sealed class CompressedSequenceTests
    method CompressedSequenceTests (line 13) | public CompressedSequenceTests()
    method Assembly_hg19 (line 29) | [Fact]
    method GetNumBufferBytes (line 35) | [Fact]
    method Substring (line 43) | [Theory]

FILE: UnitTests/VariantAnnotation/TranscriptAnnotation/BreakEndUtilitiesTests.cs
  class BreakEndUtilitiesTests (line 10) | public sealed class BreakEndUtilitiesTests
    method CreateFromTranslocation_Nominal (line 12) | [Theory]
    method CreateFromTranslocation_InvalidAltAllele_ThrowException (line 35) | [Fact]
    method CreateFromSymbolicAllele_Deletion (line 46) | [Fact]
    method CreateFromSymbolicAllele_Duplication (line 72) | [Fact]
    method CreateFromSymbolicAllele_Inversion (line 99) | [Fact]
    method CreateFromSymbolicAllele_Inversion_INV3 (line 119) | [Fact]
    method CreateFromSymbolicAllele_Inversion_INV5 (line 139) | [Fact]
    method CreateFromSymbolicAllele_UnhandledVariantType_ReturnNull (line 159) | [Fact]

FILE: UnitTests/VariantAnnotation/TranscriptAnnotation/FullTranscriptAnnotatorTests.cs
  class FullTranscriptAnnotatorTests (line 6) | public sealed class FullTranscriptAnnotatorTests
    method TryTrimAminoAcidsAndUpdateProteinPositions_AsExpected (line 8) | [Theory]

FILE: UnitTests/VariantAnnotation/TranscriptAnnotation/TranscriptAnnotationFactoryTests.cs
  class TranscriptAnnotationFactoryTests (line 14) | public sealed class TranscriptAnnotationFactoryTests
    method DecideAnnotationStatus_NoOverlap_ReturnNoAnnotation (line 16) | [Fact]
    method DecideAnnotationStatus_Flanking_ReturnFlankingAnnotation (line 25) | [Fact]
    method DecideAnnotationStatus_Reduced_TranscriptPartialOverlap_ReturnReducedAnnotation (line 34) | [Fact]
    method DecideAnnotationStatus_Full_PartialOverlap_ReturnFullAnnotation (line 43) | [Fact]
    method DecideAnnotationStatus_Full_CompleteOverlap_ReturnFullAnnotation (line 52) | [Fact]
    method DecideAnnotationStatus_ROH_Return_RohAnnotation (line 61) | [Fact]
    method GetAnnotatedTranscripts_ReturnEmptyList (line 70) | [Fact]
    method GetAnnotatedTranscripts_RohAnnotation_ReturnsCanonicalOnly (line 107) | [Fact]

FILE: UnitTests/VariantAnnotation/Utilities/DateTests.cs
  class DateTests (line 8) | public sealed class DateTests
    method GetTimeStamp_CheckFormat (line 10) | [Fact]
    method GetDate (line 18) | [Fact]

FILE: UnitTests/VariantAnnotation/Utilities/FormatUtilitiesTests.cs
  class FormatUtilitiesTests (line 6) | public sealed class FormatUtilitiesTests
    method SplitVersion_ReturnNull_WithNullInput (line 8) | [Fact]
    method SplitVersion (line 16) | [Theory]

FILE: UnitTests/VariantAnnotation/Utilities/GeneComparerTests.cs
  class GeneComparerTests (line 11) | public sealed class GeneComparerTests
    method GeneComparerTests (line 18) | public GeneComparerTests()
    method Equals_AsExpected (line 26) | [Fact]
    method GetHashCode_AsExpected (line 33) | [Fact]

FILE: UnitTests/Variants/BiDirectionalTrimmerTests.cs
  class BiDirectionalTrimmerTests (line 6) | public sealed class BiDirectionalTrimmerTests
    method Trim (line 8) | [Theory]

FILE: UnitTests/Variants/SimpleVariantTests.cs
  class SimpleVariantTests (line 7) | public sealed class SimpleVariantTests
    method SimpleVariant_Set (line 9) | [Fact]

FILE: UnitTests/Variants/VariantRotatorTests.cs
  class VariantRotatorTests (line 11) | public sealed class VariantRotatorTests
    method Right_Deletion_ForwardStrand (line 18) | [Fact]
    method Right_Deletion_ReverseStrand (line 36) | [Fact]
    method Right_Insertion (line 53) | [Fact]
    method Right_Identity_WhenRefSequenceNull (line 70) | [Fact]
    method Right_Identity_WhenNotInsertionOrDeletion (line 78) | [Fact]
    method Right_Identity_VariantBeforeTranscript_ForwardStrand (line 86) | [Fact]
    method Right_Identity_VariantBeforeTranscript_ReverseStrand (line 99) | [Fact]
    method Right_Identity_InsertionVariantBeforeTranscript_ForwardStrand (line 112) | [Fact]
    method Right_Identity_WithNoRotation (line 125) | [Fact]
    method GetDeletion (line 143) | private static ISimpleVariant GetDeletion() =>
    method GetInsertion (line 146) | private static ISimpleVariant GetInsertion() =>
    method Left_align_deletions (line 149) | [Theory]
    method Left_align_insertion (line 163) | [Theory]
    method Left_align_multiple_padding_bases (line 177) | [Fact]
    method CanNotLeftRotate (line 187) | [Theory]

FILE: UnitTests/Variants/VariantTests.cs
  class VariantTests (line 8) | public sealed class VariantTests
    method Variant_Set (line 10) | [Fact]

FILE: UnitTests/Vcf/Samples/BooleanExtensionsTests.cs
  class BooleanExtensionsTests (line 6) | public sealed class BooleanExtensionsTests
    method GetFailedFilter (line 8) | [Theory]

FILE: UnitTests/Vcf/Samples/FormatIndicesTests.cs
  class FormatIndicesTests (line 6) | public sealed class FormatIndicesTests
    method FormatIndicesTest (line 8) | [Fact]

FILE: UnitTests/Vcf/Samples/Legacy/LegacySampleFieldExtractorTests.cs
  class LegacySampleFieldExtractorTests (line 8) | public sealed class LegacySampleFieldExtractorTests
    method FormatIndicesTest (line 11) | [Fact]
    method AlleleDepths (line 45) | [Theory]
    method AlleleDepthsMultiAllelic (line 68) | [Theory]
    method FailedFilter (line 86) | [Theory]
    method Genotype (line 105) | [Theory]
    method GenotypeQuality (line 125) | [Theory]
    method TotalDepth (line 147) | [Theory]
    method PiscesTotalDepth (line 171) | [Fact]
    method VariantFrequency_Nominal (line 186) | [Theory]
    method VariantFrequency_ReturnNull (line 211) | [Theory]
    method Leftout_fields_return_null (line 232) | [Theory]
    method MajorChromosomeCopyTest (line 268) | [Fact]
    method EmptySamples (line 286) | [Fact]
    method VariantFrequencyNan (line 305) | [Theory]
    method SplitReadCounts (line 335) | [Fact]
    method EmptySample (line 354) | [Fact]

FILE: UnitTests/Vcf/Samples/SampleFieldExtractorTests.cs
  class SampleFieldExtractorTests (line 14) | public sealed class SampleFieldExtractorTests
    method NormalizeNulls (line 16) | [Fact]
    method ExtractSample_PEPE (line 29) | [Fact]
    method ExtractSample_DragenSomatic_AsExpected (line 45) | [Fact]
    method ExtractSample_DragenCNV_AsExpected (line 59) | [Fact]
    method ExtractSample_Custom_format (line 71) | [Fact]
    method ExtractSample_Custom_format_empty (line 85) | [Fact]
    method ExtractSample_DragenCNV_MCN_LOH_BC (line 99) | [Theory]
    method ExtractSample_ExpansionHunter (line 112) | [Fact]
    method ExtractSample_EmptySampleColumn_ReturnEmptySample (line 123) | [Fact]
    method ExtractSample_DotInSampleColumn_ReturnEmptySample (line 131) | [Fact]
    method ToSamples_SMN1_CNV (line 139) | [Fact]
    method ToSamples_Custom (line 189) | [Fact]
    method ToSamples_TooFewVcfColumns_ReturnNull (line 228) | [Fact]
    method ExtractSample_MitoHeteroplasmy_AsExpected (line 248) | [Fact]

FILE: UnitTests/Vcf/Samples/SampleParsingExtensionsTests.cs
  class SampleParsingExtensionsTests (line 6) | public sealed class SampleParsingExtensionsTests
    method GetString (line 8) | [Fact]
    method GetString_NullIndex_ReturnNull (line 16) | [Fact]
    method GetFloat (line 24) | [Fact]
    method GetFloat_NotFloat_ReturnNull (line 31) | [Fact]
    method GetFloat_NullString_ReturnNull (line 38) | [Fact]
    method GetDouble (line 46) | [Fact]
    method GetDouble_NotDouble_ReturnNull (line 53) | [Fact]
    method GetDouble_NullString_ReturnNull (line 60) | [Fact]
    method GetInteger (line 68) | [Fact]
    method GetInteger_NotInteger_ReturnNull (line 75) | [Fact]
    method GetInteger_NullString_ReturnNull (line 82) | [Fact]
    method GetStrings (line 90) | [Fact]
    method GetStrings_NullString_ReturnNull (line 97) | [Fact]
    method GetIntegers (line 105) | [Fact]
    method GetIntegers_NotInteger_ReturnNull (line 112) | [Fact]
    method GetIntegers_NullString_ReturnNull (line 119) | [Fact]

FILE: UnitTests/Vcf/Samples/SampleTests.cs
  class SampleTests (line 6) | public sealed class SampleTests
    method Sample_ReturnEmpty (line 8) | [Fact]

FILE: UnitTests/Vcf/Samples/TestUtilities.cs
  class TestUtilities (line 6) | public static class TestUtilities
    method GetSimplePositionUsingAlleleNum (line 8) | public static ISimplePosition GetSimplePositionUsingAlleleNum(int numA...

FILE: UnitTests/Vcf/Samples/VariantFrequencyTests.cs
  class VariantFrequencyTests (line 6) | public sealed class VariantFrequencyTests
    method GetVariantFrequencies_VF_OneAltAllele (line 8) | [Fact]
    method GetVariantFrequencies_VF_MultipleAltAlleles_ReturnNull (line 16) | [Fact]
    method GetVariantFrequencies_OverrideAD_UseVF (line 23) | [Fact]
    method GetVariantFrequencies_AD_WrongAlleleCount_ReturnNull (line 31) | [Fact]
    method GetVariantFrequencies_AD (line 38) | [Fact]
    method GetVariantFrequencies_AD_ZeroSumAlleleCount_ReturnZeros (line 46) | [Fact]
    method Evaluate (line 54) | private static void Evaluate(double[] expectedResults, double[] observ...

FILE: UnitTests/Vcf/StringExtensionsTests.cs
  class StringExtensionsTests (line 6) | public sealed class StringExtensionsTests
    method GetNullableValue_int (line 9) | [Theory]
    method GetNullableValue_double (line 18) | [Theory]
    method SplitToArray_int (line 29) | [Theory]

FILE: UnitTests/Vcf/VariantCreator/CnvCreatorTests.cs
  class CnvCreatorTests (line 9) | public sealed class CnvCreatorTests
    method Create_Dragen_3_3_DEL (line 11) | [Fact]
    method Create_Dragen_3_3_DUP (line 28) | [Fact]
    method Create_Canvas_TotalCopyNumber (line 45) | [Fact]
    method Create_Canvas_AlleleSpecificCopyNumber (line 62) | [Fact]

FILE: UnitTests/Vcf/VariantCreator/LegacyVariantIdTests.cs
  class LegacyVariantIdTests (line 10) | public sealed class LegacyVariantIdTests
    method Create_SmallVariants_ReturnVid (line 14) | [Theory]
    method Create_Reference_ReturnVid (line 36) | [Theory]
    method Create_TranslocationBreakend_ReturnVid (line 47) | [Theory]
    method Create_StructuralVariants_ReturnVid (line 59) | [Theory]
    method Create_LOH_ReturnsCnvVid (line 84) | [Fact]
    method GetSmallVariantVid_UnknownVariantType_ThrowsException (line 95) | [Fact]

FILE: UnitTests/Vcf/VariantCreator/ReferenceVariantCreatorTests.cs
  class ReferenceVariantCreatorTests (line 10) | public sealed class ReferenceVariantCreatorTests
    method Create_SinglePosition_NoGlobalMajorAllele_ReturnNull (line 15) | [Fact]
    method Create_SinglePosition_HasGlobalMajorAllele_ReturnVariant (line 22) | [Fact]
    method Create_MultiplePositions_NoGlobalMajorAllele_ReturnNull (line 29) | [Fact]
    method Create_MultiplePositions_HasGlobalMajorAllele_ReturnNull (line 36) | [Fact]
    method GetVariant (line 43) | private IVariant GetVariant(int start, int end, string refAllele, stri...

FILE: UnitTests/Vcf/VariantCreator/SmallVariantCreatorTests.cs
  class SmallVariantCreatorTests (line 8) | public sealed class SmallVariantCreatorTests
    method Create_Insertion_ReturnVariant (line 10) | [Fact]

FILE: UnitTests/Vcf/VariantCreator/VariantFactoryTests.cs
  class VariantFactoryTests (line 21) | public sealed class VariantFactoryTests
    method VariantFactoryTests (line 35) | public VariantFactoryTests()
    method ParseVcfLine (line 71) | private IPosition ParseVcfLine(string vcfLine)
    method CreateVariants_svDel (line 85) | [Fact]
    method CreateVariants_canvas_cnv (line 98) | [Fact]
    method CreateVariants_canvas_cnx (line 115) | [Fact]
    method CreateVariants_canvas_cnv_dup (line 135) | [Fact]
    method CreateVariants_dup (line 155) | [Fact]
    method CreateVariants_tandem_duplication (line 172) | [Fact]
    method CreateVariants_ROH (line 187) | [Fact]
    method CreateVariants_LegacyVid_DisableLeftAlignment_MultiAllelic_Deletions (line 202) | [Fact]
    method CreateVariants_NormalVid_EnableLeftAlignment_MultiAllelic_Deletions (line 217) | [Fact]
    method ToPosition_SNV (line 231) | [Fact]
    method ToPosition_insertion (line 245) | [Fact]
    method ToPosition_deletion (line 259) | [Fact]
    method ToPosition_CANVAS_LOH (line 273) | [Fact]
    method ToPosition_Manta_SmallDeletion (line 287) | [Fact]
    method ToPosition_CANVAS_CNnum (line 304) | [Fact]
    method ToPosition_SV_DUP (line 319) | [Fact]
    method ToPosition_SV_INS (line 333) | [Fact]
    method ToPosition_SV_INV (line 347) | [Fact]
    method ToPosition_SV_Translocation (line 361) | [Fact]
    method ToPosition_DRAGEN_LOH (line 375) | [Fact]
    method ToPosition_STR (line 396) | [Fact]
    method STR_without_num_throws_user_error (line 411) | [Fact]
    method ToPosition_indel (line 421) | [Fact]
    method ToPosition_MNV (line 435) | [Fact]
    method ToPosition_CNV_DUP (line 449) | [Fact]
    method ToPosition_CNV_DEL (line 464) | [Fact]
    method ToPosition_CustomSampleInfoFields (line 479) | [Fact]
    method ToPosition_ROH (line 498) | [Fact]
    method ToPosition_MultiAllelic_Deletions (line 513) | [Fact]
    method ToPosition_Giant_dbsnp155_variant (line 533) | [Fact]

FILE: UnitTests/Vcf/VariantCreator/VariantFactoryTestsWithLegacyVids.cs
  class VariantFactoryTestsWithLegacyVids (line 17) | public sealed class VariantFactoryTestsWithLegacyVids
    method VariantFactoryTestsWithLegacyVids (line 23) | public VariantFactoryTestsWithLegacyVids()
    method ParseVcfLine (line 30) | private IPosition ParseVcfLine(string vcfLine)
    method ToPosition_SNV (line 44) | [Fact]
    method ToPosition_insertion (line 58) | [Fact]
    method ToPosition_deletion (line 72) | [Fact]
    method ToPosition_CANVAS_LOH (line 86) | [Fact]
    method ToPosition_Manta_SmallDeletion (line 100) | [Fact]
    method ToPosition_CANVAS_CNnum (line 117) | [Fact]
    method ToPosition_SV_DUP (line 132) | [Fact]
    method ToPosition_SV_INS (line 146) | [Fact]
    method ToPosition_SV_INV (line 160) | [Fact]
    method ToPosition_SV_Translocation (line 174) | [Fact]
    method ToPosition_DRAGEN_LOH (line 188) | [Fact]
    method ToPosition_STR (line 210) | [Fact]
    method ToPosition_indel (line 226) | [Fact]
    method ToPosition_MNV (line 240) | [Fact]
    method ToPosition_CNV_DUP (line 254) | [Fact]
    method ToPosition_CNV_DEL (line 269) | [Fact]
    method ToPosition_ROH (line 285) | [Fact]
    method ToPosition_MultiAllelic_Deletions (line 300) | [Fact]

FILE: UnitTests/Vcf/VariantCreator/VariantIdTests.cs
  class VariantIdTests (line 10) | public sealed class VariantIdTests
    method VariantIdTests (line 15) | public VariantIdTests()
    method Create_SmallVariants_ReturnShortVid (line 34) | [Theory]
    method Create_TranslocationBreakend_ReturnShortVid (line 47) | [Fact]
    method Create_StructuralVariants_RecoverRefAllele_ReturnLongVid (line 55) | [Theory]

FILE: UnitTests/Vcf/VcfFilterTests.cs
  class VcfFilterTests (line 10) | public sealed class VcfFilterTests
    method FastForward_UcscNamingStyle_ChangeReaderStateCorrectly (line 13) | [Fact]
    method FastForward_EnsemblNamingStyle_ChangeReaderStateCorrectly (line 47) | [Fact]
    method GetNextLine_NoBufferedLine_ReadNextLine (line 81) | [Fact]
    method GetNextLine_ReturnBufferedLine (line 93) | [Fact]
    method PassedTheEnd_AsExpected (line 104) | [Fact]

FILE: UnitTests/Vcf/VcfInfoParserTests.cs
  class VcfInfoParserTests (line 7) | public sealed class VcfInfoParserTests
    method Parse_Somatic_Manta (line 9) | [Fact]
    method Parse_Somatic_Strelka (line 23) | [Fact]
    method Parse_GATK (line 31) | [Fact]
    method Parse_Breakend_Event_Id (line 41) | [Fact]
    method EmptyInfoField (line 49) | [Fact]

FILE: UnitTests/Vcf/VcfReaderTests.cs
  class VcfReaderTests (line 16) | public sealed class VcfReaderTests
    method AddLines (line 22) | private void AddLines(string[] lines)
    method ValidateVcfHeader_ExceptionThrown_NoFileFormat (line 35) | [Fact]
    method ValidateVcfHeader_ExceptionThrown_NoChromHeaderLine (line 45) | [Fact]
    method Sample_names_are_reported (line 55) | [Fact]
    method GetChromAndLengthInfo_ReturnEmptyArray_NoProperPrefix (line 72) | [Fact]
    method GetChromAndLengthInfo_ReturnEmptyArray_NoChromInfo (line 78) | [Fact]
    method GetChromAndLengthInfo_ReturnEmptyArray_NoLengthInfo (line 84) | [Fact]
    method CheckContigId_IncorrectAutoAndSexChromLength_ThrowException (line 90) | [Theory]
    method CheckContigId_InferredAssemblyIsUnknown_GivenIrregularChrom (line 103) | [Theory]
    method CheckContigId_IsRcrsMitochondrionTrue_InferredAssemblyIsUnknown_GivenRcrsChrMLength (line 119) | [Theory]
    method CheckContigId_IsRcrsMitochondrionFalse_InferredAssemblyIsUnknown_GivenNonRcrsChrMLength (line 135) | [Theory]
    method GetChromAndLength_AsExpect (line 152) | [Theory]
    method GetNextPosition (line 162) | [Fact]
    method CheckSampleConsistency_oneSample (line 197) | [Fact]
    method CheckSampleConsistency_noSample (line 224) | [Fact]

FILE: UnitTests/Vcf/VcfReaderUtilsTests.cs
  class VcfReaderUtilsTests (line 12) | public sealed class VcfReaderUtilsTests
    method ParseVcfLine_NonInformativeAlleles_Alone_NotFiltered (line 17) | [Fact]
    method ParseVcfLine_NonInformativeAlleles_WithNormalAllele_NotFiltered (line 47) | [Fact]
    method Test_crash_caused_by_variant_trimming (line 85) | [Fact]
    method ParseVcfLine_line_with_only_NonRef_is_refMinor (line 107) | [Fact]
    method ParseVcfLine_line_with_only_NonRef_is_not_refMinor (line 130) | [Fact]

FILE: VariantAnnotation.Interface/AnnotatedPositions/BioType.cs
  type BioType (line 3) | public enum BioType : byte

FILE: VariantAnnotation.Interface/AnnotatedPositions/ConsequenceTag.cs
  type ConsequenceTag (line 3) | public enum ConsequenceTag : byte
  class ConsequenceUtil (line 51) | public static class ConsequenceUtil
    method GetConsequence (line 53) | public static string GetConsequence(ConsequenceTag consequence)

FILE: VariantAnnotation.Interface/AnnotatedPositions/IAnnotatedGeneFusion.cs
  type IAnnotatedGeneFusion (line 7) | public interface IAnnotatedGeneFusion : IGeneFusionPair, IJsonSerializer

FILE: VariantAnnotation.Interface/AnnotatedPositions/IAnnotatedPosition.cs
  type IAnnotatedPosition (line 8) | public interface IAnnotatedPosition
    method GetJsonStringBuilder (line 14) | StringBuilder                   GetJsonStringBuilder();

FILE: VariantAnnotation.Interface/AnnotatedPositions/IAnnotatedRegulatoryRegion.cs
  type IAnnotatedRegulatoryRegion (line 6) | public interface IAnnotatedRegulatoryRegion:IJsonSerializer

FILE: VariantAnnotation.Interface/AnnotatedPositions/IAnnotatedTranscript.cs
  type IAnnotatedTranscript (line 6) | public interface IAnnotatedTranscript : IJsonSerializer
    method AddGeneFusions (line 22) | void AddGeneFusions(IAnnotatedGeneFusion[] geneFusions);
    method AddGeneFusionPairs (line 23) | void AddGeneFusionPairs(HashSet<IGeneFusionPair> geneKeys);
    method Initialize (line 25) | public void Initialize(ITranscript transcript, string referenceAminoAc...

FILE: VariantAnnotation.Interface/AnnotatedPositions/IAnnotatedVariant.cs
  type IAnnotatedVariant (line 8) | public interface IAnnotatedVariant
    method GetJsonStringBuilder (line 19) | StringBuilder                     GetJsonStringBuilder(string original...

FILE: VariantAnnotation.Interface/AnnotatedPositions/ICodingRegion.cs
  type ICodingRegion (line 6) | public interface ICodingRegion : IInterval, ISerializable

FILE: VariantAnnotation.Interface/AnnotatedPositions/ICompactId.cs
  type ICompactId (line 5) | public interface ICompactId : ISerializable
    method IsEmpty (line 7) | bool IsEmpty();

FILE: VariantAnnotation.Interface/AnnotatedPositions/IFeatureVariantEffects.cs
  type IFeatureVariantEffects (line 3) | public interface IFeatureVariantEffects
    method Ablation (line 5) | bool Ablation();
    method Amplification (line 6) | bool Amplification();
    method Truncation (line 7) | bool Truncation();
    method Elongation (line 8) | bool Elongation();
    method FivePrimeDuplicatedTranscript (line 9) | bool FivePrimeDuplicatedTranscript();
    method ThreePrimeDuplicatedTranscript (line 10) | bool ThreePrimeDuplicatedTranscript();

FILE: VariantAnnotation.Interface/AnnotatedPositions/IGene.cs
  type IGene (line 6) | public interface IGene : IChromosomeInterval, ISerializable

FILE: VariantAnnotation.Interface/AnnotatedPositions/IGeneFusion.cs
  type IGeneFusion (line 5) | public interface IGeneFusion : IJsonSerializer

FILE: VariantAnnotation.Interface/AnnotatedPositions/IGeneFusionPair.cs
  type IGeneFusionPair (line 3) | public interface IGeneFusionPair

FILE: VariantAnnotation.Interface/AnnotatedPositions/IMappedPosition.cs
  type IMappedPosition (line 3) | public interface IMappedPosition

FILE: VariantAnnotation.Interface/AnnotatedPositions/IRegulatoryRegion.cs
  type IRegulatoryRegion (line 7) | public interface IRegulatoryRegion : IChromosomeInterval, ISerializable

FILE: VariantAnnotation.Interface/AnnotatedPositions/IRnaEdit.cs
  type IRnaEdit (line 8) | public interface IRnaEdit : IInterval, ISerializable, IComparable<IRnaEdit>

FILE: VariantAnnotation.Interface/AnnotatedPositions/ITranscript.cs
  type ITranscript (line 8) | public interface ITranscript : IChromosomeInterval
    method Write (line 33) | void Write(IExtendedBinaryWriter writer, Dictionary<IGene, int> geneIn...
  type Source (line 38) | public enum Source : byte

FILE: VariantAnnotation.Interface/AnnotatedPositions/ITranscriptRegion.cs
  type ITranscriptRegion (line 6) | public interface ITranscriptRegion : IInterval, ISerializable
  type TranscriptRegionType (line 14) | public enum TranscriptRegionType : byte

FILE: VariantAnnotation.Interface/AnnotatedPositions/ITranslation.cs
  type ITranslation (line 5) | public interface ITranslation
    method Write (line 10) | void Write(IExtendedBinaryWriter writer, int peptideIndex);

FILE: VariantAnnotation.Interface/AnnotatedPositions/IVariantEffect.cs
  type IVariantEffect (line 3) | public interface IVariantEffect
    method IsStopLost (line 5) | bool IsStopLost();
    method IsStopRetained (line 6) | bool IsStopRetained();
    method IsStartLost (line 7) | bool IsStartLost();
    method IsFrameshiftVariant (line 8) | bool IsFrameshiftVariant();
    method IsMatureMirnaVariant (line 9) | bool IsMatureMirnaVariant();
    method IsSpliceDonorVariant (line 10) | bool IsSpliceDonorVariant();
    method IsSpliceAcceptorVariant (line 11) | bool IsSpliceAcceptorVariant();
    method IsStopGained (line 12) | bool IsStopGained();
    method IsInframeInsertion (line 13) | bool IsInframeInsertion();
    method IsInframeDeletion (line 14) | bool IsInframeDeletion();
    method IsMissenseVariant (line 15) | bool IsMissenseVariant();
    method IsProteinAlteringVariant (line 16) | bool IsProteinAlteringVariant();
    method IsSpliceRegionVariant (line 17) | bool IsSpliceRegionVariant();
    method IsIncompleteTerminalCodonVariant (line 18) | bool IsIncompleteTerminalCodonVariant();
    method IsStartRetained (line 19) | bool IsStartRetained();
    method IsSynonymousVariant (line 20) | bool IsSynonymousVariant();
    method IsCodingSequenceVariant (line 21) | bool IsCodingSequenceVariant();
    method IsFivePrimeUtrVariant (line 22) | bool IsFivePrimeUtrVariant();
    method IsThreePrimeUtrVariant (line 23) | bool IsThreePrimeUtrVariant();
    method IsNonCodingTranscriptExonVariant (line 24) | bool IsNonCodingTranscriptExonVariant();
    method IsWithinIntron (line 25) | bool IsWithinIntron();
    method IsNonsenseMediatedDecayTranscriptVariant (line 26) | bool IsNonsenseMediatedDecayTranscriptVariant();
    method IsNonCodingTranscriptVariant (line 27) | bool IsNonCodingTranscriptVariant();

FILE: VariantAnnotation.Interface/AnnotatedPositions/PredictionScore.cs
  class PredictionScore (line 3) | public sealed class PredictionScore
    method PredictionScore (line 8) | public PredictionScore(string prediction, double score)

FILE: VariantAnnotation.Interface/Caches/IPredictionCache.cs
  type IPredictionCache (line 6) | public interface IPredictionCache : IProvider
    method GetProteinFunctionPrediction (line 8) | PredictionScore GetProteinFunctionPrediction(int predictionIndex, char...

FILE: VariantAnnotation.Interface/Caches/ITranscriptCache.cs
  type ITranscriptCache (line 7) | public interface ITranscriptCache : IProvider

FILE: VariantAnnotation.Interface/Caches/RegulatoryRegionType.cs
  type RegulatoryRegionType (line 3) | public enum RegulatoryRegionType : byte

FILE: VariantAnnotation.Interface/Constants.cs
  class Constants (line 3) | public static class Constants

FILE: VariantAnnotation.Interface/GeneAnnotation/IGeneAnnotationProvider.cs
  type IGeneAnnotationProvider (line 6) | public interface IGeneAnnotationProvider : IProvider, IDisposable
    method Annotate (line 8) | string Annotate(string geneName);

FILE: VariantAnnotation.Interface/IAnnotationResources.cs
  type IAnnotationResources (line 9) | public interface IAnnotationResources : IDisposable
    method SingleVariantPreLoad (line 25) | void SingleVariantPreLoad(IPosition position);

FILE: VariantAnnotation.Interface/IAnnotator.cs
  type IAnnotator (line 8) | public interface IAnnotator
    method Annotate (line 11) | IAnnotatedPosition Annotate(IPosition position);
    method GetGeneAnnotations (line 12) | IEnumerable<string> GetGeneAnnotations();
    method EnableMitochondrialAnnotation (line 13) | void EnableMitochondrialAnnotation();

FILE: VariantAnnotation.Interface/IO/IJsonSerializer.cs
  type IJsonSerializer (line 5) | public interface IJsonSerializer
    method SerializeJson (line 7) | void SerializeJson(StringBuilder sb);

FILE: VariantAnnotation.Interface/IO/IJsonWriter.cs
  type IJsonWriter (line 6) | public interface IJsonWriter : IDisposable
    method WritePosition (line 8) | void WritePosition(IPosition position, string entry);

FILE: VariantAnnotation.Interface/IO/IVcfReader.cs
  type IVcfReader (line 5) | public interface IVcfReader : IDisposable

FILE: VariantAnnotation.Interface/IO/VcfCommon.cs
  class VcfCommon (line 5) | public static class VcfCommon
    method IsNonInformativeAltAllele (line 31) | public static bool IsNonInformativeAltAllele(string altAllele) => NonI...

FILE: VariantAnnotation.Interface/IVariantIdCreator.cs
  type IVariantIdCreator (line 5) | public interface IVariantIdCreator
    method Create (line 7) | string Create(ISequence sequence, VariantCategory category, string svT...
    method Normalize (line 10) | (int Start, string RefAllele, string AltAllele) Normalize(ISequence se...

FILE: VariantAnnotation.Interface/Positions/ICustomFields.cs
  type ICustomFields (line 6) | public interface ICustomFields: IJsonSerializer
    method Add (line 8) | void Add(string key, string value);
    method Clear (line 9) | void Clear();
    method IsEmpty (line 10) | bool IsEmpty();

FILE: VariantAnnotation.Interface/Positions/IInfoData.cs
  type IInfoData (line 6) | public interface IInfoData

FILE: VariantAnnotation.Interface/Positions/IPosition.cs
  type IPosition (line 5) | public interface IPosition : ISimplePosition

FILE: VariantAnnotation.Interface/Positions/ISample.cs
  type ISample (line 3) | public interface ISample

FILE: VariantAnnotation.Interface/Positions/ISimplePosition.cs
  type ISimplePosition (line 6) | public interface ISimplePosition : IChromosomeInterval

FILE: VariantAnnotation.Interface/Providers/IAnnotationProvider.cs
  type IAnnotationProvider (line 8) | public interface IAnnotationProvider : IProvider, IDisposable
    method Annotate (line 10) | void Annotate(IAnnotatedPosition annotatedPosition);
    method PreLoad (line 11) | void PreLoad(Chromosome chromosome, List<int> positions);

FILE: VariantAnnotation.Interface/Providers/IDataSourceVersion.cs
  type IDataSourceVersion (line 6) | public interface IDataSourceVersion : IJsonSerializer
    method Write (line 12) | void   Write(IExtendedBinaryWriter writer);

FILE: VariantAnnotation.Interface/Providers/IMitoHeteroplasmyProvider.cs
  type IMitoHeteroplasmyProvider (line 5) | public interface IMitoHeteroplasmyProvider : IProvider
    method GetVrfPercentiles (line 7) | double?[] GetVrfPercentiles(IVariant[] variants, double[] vrfs);

FILE: VariantAnnotation.Interface/Providers/IProvider.cs
  type IProvider (line 6) | public interface IProvider

FILE: VariantAnnotation.Interface/Providers/IRefMinorProvider.cs
  type IRefMinorProvider (line 6) | public interface IRefMinorProvider:IDisposable
    method GetGlobalMajorAllele (line 8) | string GetGlobalMajorAllele(Chromosome chromosome, int pos);

FILE: VariantAnnotation.Interface/Providers/ISequenceProvider.cs
  type ISequenceProvider (line 6) | public interface ISequenceProvider : IAnnotationProvider
    method LoadChromosome (line 11) | void LoadChromosome(Chromosome chromosome);

FILE: VariantAnnotation.Interface/Providers/ITranscriptAnnotationProvider.cs
  type ITranscriptAnnotationProvider (line 6) | public interface ITranscriptAnnotationProvider : IAnnotationProvider

FILE: VariantAnnotation.Interface/SA/INsaReader.cs
  type INsaReader (line 7) | public interface INsaReader : ISaMetadata, IDisposable
    method GetAnnotation (line 13) | void GetAnnotation(int position, List<(string refAllele, string altAll...
    method PreLoad (line 14) | void PreLoad(Chromosome chrom, List<int> positions);

FILE: VariantAnnotation.Interface/SA/INsiReader.cs
  type INsiReader (line 6) | public interface INsiReader : ISaMetadata
    method GetAnnotation (line 9) | IEnumerable<string> GetAnnotation(IVariant variant);

FILE: VariantAnnotation.Interface/SA/ISaMetadata.cs
  type ISaMetadata (line 6) | public interface ISaMetadata

FILE: VariantAnnotation.Interface/SA/ISupplementaryAnnotation.cs
  type ISupplementaryAnnotation (line 5) | public interface ISupplementaryAnnotation : IJsonSerializer

FILE: VariantAnnotation.Interface/SA/ISupplementaryDataItem.cs
  type ISupplementaryDataItem (line 5) | public interface ISupplementaryDataItem
    method GetJsonString (line 11) | string      GetJsonString();

FILE: VariantAnnotation.Interface/SA/ISupplementaryInterval.cs
  type ReportFor (line 3) | public enum ReportFor

FILE: VariantAnnotation.Interface/SA/IsuppGeneItem.cs
  type ISuppGeneItem (line 3) | public interface ISuppGeneItem
    method GetJsonString (line 6) | string GetJsonString();

FILE: VariantAnnotation.Interface/SA/IsuppIntervalItem.cs
  type ISuppIntervalItem (line 5) | public interface ISuppIntervalItem : IChromosomeInterval
    method GetJsonString (line 7) | string GetJsonString();

FILE: VariantAnnotation.Interface/VariantCategory.cs
  type VariantCategory (line 3) | public enum VariantCategory

FILE: VariantAnnotation/Algorithms/Swap.cs
  class Swap (line 3) | public static class Swap
    method Int (line 8) | public static void Int(ref int a, ref int b)

FILE: VariantAnnotation/AnnotatedPositions/AnnotatedPosition.cs
  class AnnotatedPosition (line 12) | public sealed class AnnotatedPosition : IAnnotatedPosition
    method Initialize (line 19) | public void Initialize(IPosition position, IAnnotatedVariant[] annotat...
    method GetJsonStringBuilder (line 27) | public StringBuilder GetJsonStringBuilder()
    method AddSuppIntervalToJsonObject (line 94) | private void AddSuppIntervalToJsonObject(JsonObject jsonObject)

FILE: VariantAnnotation/AnnotatedPositions/AnnotatedRegulatoryRegion.cs
  class AnnotatedRegulatoryRegion (line 9) | public sealed class AnnotatedRegulatoryRegion : IAnnotatedRegulatoryRegion
    method AnnotatedRegulatoryRegion (line 14) | public AnnotatedRegulatoryRegion(IRegulatoryRegion regulatoryRegion, L...
    method SerializeJson (line 20) | public void SerializeJson(StringBuilder sb)

FILE: VariantAnnotation/AnnotatedPositions/AnnotatedVariant.cs
  class AnnotatedVariant (line 11) | public sealed class AnnotatedVariant : IAnnotatedVariant
    method Initialize (line 24) | public void Initialize(IVariant variant)
    method GetJsonStringBuilder (line 37) | public StringBuilder GetJsonStringBuilder(string originalChromName)

FILE: VariantAnnotation/AnnotatedPositions/Consequence/Consequences.cs
  class Consequences (line 8) | public sealed class Consequences
    method GetConsequences (line 12) | public List<ConsequenceTag> GetConsequences() => _consequences;
    method Consequences (line 29) | public Consequences(VariantType variantType, IVariantEffect variantEff...
    method DetermineFlankingVariantEffects (line 65) | public static List<ConsequenceTag> DetermineFlankingVariantEffects(boo...
    method DetermineSmallVariantEffects (line 68) | public void DetermineSmallVariantEffects()
    method NeedsTranscriptVariant (line 77) | internal static bool NeedsTranscriptVariant(VariantType variantType, L...
    method NeedsTranscriptVariantByConsequences (line 81) | private static bool NeedsTranscriptVariantByConsequences(List<Conseque...
    method NeedsTranscriptVariantByVariantType (line 91) | private static bool NeedsTranscriptVariantByVariantType(VariantType va...
    method DetermineStructuralVariantEffect (line 107) | public void DetermineStructuralVariantEffect(IVariant variant)
    method DetermineRepeatExpansionEffect (line 118) | private void DetermineRepeatExpansionEffect(IVariant variant)
    method DetermineCopyNumberEffect (line 136) | private void DetermineCopyNumberEffect(VariantType variantType)
    method GetStructuralTier2Types (line 153) | private void GetStructuralTier2Types()
    method GetTier1Types (line 168) | private void GetTier1Types()
    method GetTier2Types (line 177) | private void GetTier2Types()
    method GetTier3Types (line 183) | private void GetTier3Types()
    method DetermineRegulatoryVariantEffects (line 191) | public void DetermineRegulatoryVariantEffects()

FILE: VariantAnnotation/AnnotatedPositions/HgvsCodingNomenclature.cs
  class HgvsCodingNomenclature (line 9) | public static class HgvsCodingNomenclature
    method GetHgvscAnnotation (line 11) | public static string GetHgvscAnnotation(ITranscript transcript, ISimpl...
    method ShiftDuplication (line 77) | internal static (int Start, int End, string RefAllele, int RegionStart...
    method GetGenomicChange (line 90) | public static GenomicChange GetGenomicChange(IInterval interval, bool ...
  type GenomicChange (line 126) | public enum GenomicChange

FILE: VariantAnnotation/AnnotatedPositions/HgvsProteinNomenclature.cs
  class HgvsProteinNomenclature (line 10) | public static class HgvsProteinNomenclature
    method GetHgvsProteinAnnotation (line 12) | public static string GetHgvsProteinAnnotation(
    method GetHgvsFrameshiftNotation (line 88) | private static string GetHgvsFrameshiftNotation(ISequence refSequence,...
    method IsHgvspNull (line 114) | private static bool IsHgvspNull(string transcriptAltAllele, int cdsSta...
    method GetProteinChange (line 124) | internal static ProteinChange GetProteinChange(int start, string refAm...
  type ProteinChange (line 151) | public enum ProteinChange

FILE: VariantAnnotation/AnnotatedPositions/HgvsUtilities.cs
  class HgvsUtilities (line 12) | public static class HgvsUtilities
    method ShiftAndRotateAlleles (line 14) | public static void ShiftAndRotateAlleles(ref int start, ref string ref...
    method Rotate3Prime (line 20) | internal static (int Start, string RefAminoAcids, string AltAminoAcids...
    method IsAminoAcidDuplicate (line 55) | public static bool IsAminoAcidDuplicate(int start, string altAminoAcid...
    method GetNumAminoAcidsUntilStopCodon (line 69) | public static int GetNumAminoAcidsUntilStopCodon(string altCds, string...
    method GetChangesAfterFrameshift (line 85) | public static (int Start, char RefAminoAcid, char AltAminoAcid) GetCha...
    method GetAltPeptideSequence (line 109) | public static string GetAltPeptideSequence(ISequence refSequence, int ...
    method GetPositionOffset (line 119) | public static PositionOffset GetPositionOffset(ITranscript transcript,...
    method GetPositionAndOffset (line 137) | internal static (int Position, int Offset) GetPositionAndOffset(int po...
    method GetIntronPositionAndOffset (line 160) | private static (int Position, int Offset) GetIntronPositionAndOffset(i...
    method GetGapPositionAndOffset (line 185) | private static (int Position, int Offset) GetGapPositionAndOffset(ITra...
    method GetCoordinate (line 188) | private static string GetCoordinate(int position, int codingRegionStar...
    method GetTranscriptAllele (line 197) | public static string GetTranscriptAllele(string variantAllele, bool on...
    method FormatDnaNotation (line 200) | public static string FormatDnaNotation(string start, string end, strin...
    method IsDuplicateWithinInterval (line 254) | public static bool IsDuplicateWithinInterval(ISequence refSequence, IS...

FILE: VariantAnnotation/AnnotatedPositions/HgvscNotation.cs
  class HgvscNotation (line 3) | public sealed class HgvscNotation
    method HgvscNotation (line 16) | public HgvscNotation(string referenceBases, string alternateBases, str...
    method SwapEndpoints (line 38) | private void SwapEndpoints()
    method ToString (line 47) | public override string ToString() => HgvsUtilities.FormatDnaNotation(_...

FILE: VariantAnnotation/AnnotatedPositions/HgvsgNotation.cs
  class HgvsgNotation (line 8) | public static class HgvsgNotation
    method GetNotation (line 13) | public static string GetNotation(string refseqAccession, ISimpleVarian...

FILE: VariantAnnotation/AnnotatedPositions/HgvspNotation.cs
  class HgvspNotation (line 5) | public static class HgvspNotation
    method GetDelInsNotation (line 7) | public static string GetDelInsNotation(string proteinId, int start, in...
    method GetInsertionNotation (line 17) | public static string GetInsertionNotation(string proteinId, int start,...
    method GetFrameshiftNotation (line 34) | public static string GetFrameshiftNotation(string proteinId, int start...
    method GetExtensionNotation (line 44) | public static string GetExtensionNotation(string proteinId, int start,...
    method GetDuplicationNotation (line 51) | public static string GetDuplicationNotation(string proteinId, int star...
    method GetStartLostNotation (line 59) | public static string GetStartLostNotation(string proteinId)
    method GetSilentNotation (line 65) | public static string GetSilentNotation(string hgvscNotation, int start...
    method GetSubstitutionNotation (line 70) | internal static string GetSubstitutionNotation(string proteinId, int s...
    method GetUnknownNotation (line 79) | internal static string GetUnknownNotation(string proteinId, int start,...
    method GetDeletionNotation (line 86) | internal static string GetDeletionNotation(string proteinId, int start...

FILE: VariantAnnotation/AnnotatedPositions/PositionOffset.cs
  type PositionOffset (line 3) | public sealed record PositionOffset(int Position, int Offset, string Val...

FILE: VariantAnnotation/AnnotatedPositions/RegulatoryRegionAnnotator.cs
  class RegulatoryRegionAnnotator (line 9) | public static class RegulatoryRegionAnnotator
    method Annotate (line 11) | public static IAnnotatedRegulatoryRegion Annotate(IVariant variant, IR...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/AminoAcids.cs
  class AminoAcids (line 8) | public sealed class AminoAcids
    type CodonConversion (line 52) | private enum CodonConversion : byte
    method AminoAcids (line 58) | public AminoAcids(bool isMitochondrial)
    method AddUnknownAminoAcid (line 146) | internal static string AddUnknownAminoAcid(string aminoAcids) => amino...
    method Translate (line 148) | public SequenceChange Translate(string referenceCodons, string alterna...
    method ConvertAminoAcidToAbbreviation (line 161) | public static string ConvertAminoAcidToAbbreviation(char aminoAcid)
    method ConvertTripletToAminoAcid (line 175) | internal char ConvertTripletToAminoAcid(string triplet)
    method GetAbbreviations (line 193) | public static string GetAbbreviations(string aminoAcids)
    method TranslateBases (line 212) | public string TranslateBases(string bases, bool forceNonTriplet)

FILE: VariantAnnotation/AnnotatedPositions/Transcript/AnnotatedConservationScore.cs
  class AnnotatedConservationScore (line 9) | public sealed class AnnotatedConservationScore : IJsonSerializer
    method AnnotatedConservationScore (line 13) | public AnnotatedConservationScore(IEnumerable<double> scores) => _scor...
    method SerializeJson (line 15) | public void SerializeJson(StringBuilder sb)

FILE: VariantAnnotation/AnnotatedPositions/Transcript/AnnotatedGeneFusion.cs
  type AnnotatedGeneFusion (line 8) | public sealed record AnnotatedGeneFusion(ITranscript transcript, int? ex...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/AnnotatedTranscript.cs
  class AnnotatedTranscript (line 12) | public sealed class AnnotatedTranscript : IAnnotatedTranscript
    method Initialize (line 30) | public void Initialize(ITranscript transcript, string referenceAminoAc...
    method SerializeJson (line 50) | public void SerializeJson(StringBuilder sb)
    method AddConsequences (line 104) | private void AddConsequences(JsonObject jsonObject)
    method GetBioType (line 109) | public static string GetBioType(BioType bioType) => bioType == BioType...
    method GetAminoAcidString (line 113) | private static string GetAminoAcidString(string a, string b)
    method GetCodonString (line 121) | private static string GetCodonString(string a, string b)
    method GetRangeString (line 129) | private static string GetRangeString(int start, int end)
    method GetFractionString (line 138) | private static string GetFractionString(int start, int end, int total)
    method AddGeneFusions (line 144) | public void AddGeneFusions(IAnnotatedGeneFusion[] geneFusions)
    method AddGeneFusionPairs (line 151) | public void AddGeneFusionPairs(HashSet<IGeneFusionPair> fusionPairs)

FILE: VariantAnnotation/AnnotatedPositions/Transcript/CdnaSequence.cs
  class CdnaSequence (line 11) | public sealed class CdnaSequence : ISequence
    method CdnaSequence (line 20) | public CdnaSequence(ISequence compressedSequence, ICodingRegion coding...
    method GetCdnaSequence (line 32) | public string GetCdnaSequence()
    method ApplyRnaEdits (line 57) | private void ApplyRnaEdits(StringBuilder sb)
    method Substring (line 96) | public string Substring(int offset, int length)

FILE: VariantAnnotation/AnnotatedPositions/Transcript/CodingSequence.cs
  class CodingSequence (line 6) | public sealed class CodingSequence : ISequence
    method CodingSequence (line 10) | public CodingSequence(ISequence compressedSequence, ICodingRegion codi...
    method GetCodingSequence (line 21) | public string GetCodingSequence()               => _sequence;
    method Substring (line 24) | public string Substring(int offset, int length) => _sequence.Substring...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/Codons.cs
  class Codons (line 7) | public static class Codons
    method GetCodons (line 9) | public static SequenceChange GetCodons(string transcriptAlternateAllele,
    method GetCodon (line 45) | public static string GetCodon(string allele, string prefix, string suf...
    method IsTriplet (line 54) | public static bool IsTriplet(int len) => Math.Abs(len) % 3 == 0;

FILE: VariantAnnotation/AnnotatedPositions/Transcript/CompactId.cs
  type CompactId (line 8) | public struct CompactId : ICompactId
    method IsEmpty (line 21) | public bool IsEmpty()           => _id == IdType.Unknown;
    method CompactId (line 23) | private CompactId(IdType id, byte version, uint info)
    method ToString (line 30) | public override string ToString() => ConvertToString(true);
    method Convert (line 34) | public static CompactId Convert(string s, byte version = NoVersion)
    method ToInfo (line 59) | private static uint ToInfo(int num, int len) => (uint)(num << 4 | (len...
    method GetCompactId (line 61) | private static CompactId GetCompactId(string s, int prefixLen, IdType ...
    method GetNumericalCompactId (line 68) | private static CompactId GetNumericalCompactId(int num, int paddedLength)
    method ConvertToString (line 74) | private string ConvertToString(bool showVersion)
    method GetVersion (line 83) | private string GetVersion(bool showVersion)
    method GetNumber (line 89) | private string GetNumber()
    method GetPrefix (line 96) | private string GetPrefix()
    method Write (line 134) | public void Write(IExtendedBinaryWriter writer)
    method Read (line 141) | public static CompactId Read(IBufferedBinaryReader reader)
  type IdType (line 150) | public enum IdType : byte

FILE: VariantAnnotation/AnnotatedPositions/Transcript/FeatureVariantEffects.cs
  class FeatureVariantEffects (line 7) | public sealed class FeatureVariantEffects : IFeatureVariantEffects
    method FeatureVariantEffects (line 22) | public FeatureVariantEffects(OverlapType overlapType, EndpointOverlapT...
    method Ablation (line 45) | public bool Ablation()      => (_lossOrDeletion || _isInsertionDeletio...
    method Amplification (line 46) | public bool Amplification() => _gainOrDuplication && _completelyOverlaps;
    method Truncation (line 47) | public bool Truncation()    => _isSv && _lossOrDeletion && _partialOve...
    method Elongation (line 48) | public bool Elongation()    => _isSv && _completelyWithin && (_gainOrD...
    method FivePrimeDuplicatedTranscript (line 50) | public bool FivePrimeDuplicatedTranscript()  => _gainOrDuplication && ...
    method ThreePrimeDuplicatedTranscript (line 51) | public bool ThreePrimeDuplicatedTranscript() => _gainOrDuplication && ...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/MappedPosition.cs
  class MappedPosition (line 5) | public sealed class MappedPosition : IMappedPosition
    method MappedPosition (line 27) | public MappedPosition(int cdnaStart, int cdnaEnd, int cdsStart, int cd...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/MappedPositionUtilities.cs
  class MappedPositionUtilities (line 8) | public static class MappedPositionUtilities
    method FindRegion (line 10) | public static (int Index, ITranscriptRegion Region) FindRegion(ITransc...
    method GetCdnaPositions (line 18) | public static (int CdnaStart, int CdnaEnd) GetCdnaPositions(ITranscrip...
    method GetCdnaPosition (line 33) | private static int GetCdnaPosition(ITranscriptRegion region, int varia...
    method GetCoveredCdnaPositions (line 46) | public static (int Start, int End) GetCoveredCdnaPositions(this ITrans...
    method GetCoveredRegion (line 68) | private static ITranscriptRegion GetCoveredRegion(this ITranscriptRegi...
    method GetCoveredCdnaPosition (line 74) | private static int GetCoveredCdnaPosition(int cdnaPosition, ITranscrip...
    method GetCoveredCdsAndProteinPositions (line 89) | public static (int CdsStart, int CdsEnd, int ProteinStart, int Protein...
    method GetProteinPosition (line 104) | public static int GetProteinPosition(int cdsPosition)
    method GetCdsPositions (line 110) | public static (int CdsStart, int CdsEnd) GetCdsPositions(ICodingRegion...
    method GetCdsPosition (line 126) | private static int GetCdsPosition(ICodingRegion codingRegion, int cdna...
    method FixExonEndpointInsertion (line 137) | internal static (int CdnaStart, int CdnaEnd) FixExonEndpointInsertion(...
    method FoundExonEndpointInsertion (line 160) | internal static bool FoundExonEndpointInsertion(bool isInsertion, int ...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/StringExtensions.cs
  class StringExtensions (line 5) | public static class StringExtensions
    method CommonPrefixLength (line 8) | public static int CommonPrefixLength(this string a, string b)
    method CommonSuffixLength (line 20) | public static int CommonSuffixLength(this string a, string b)

FILE: VariantAnnotation/AnnotatedPositions/Transcript/TranscriptPositionalEffect.cs
  class TranscriptPositionalEffect (line 8) | public sealed class TranscriptPositionalEffect
    method DetermineIntronicEffect (line 26) | public void DetermineIntronicEffect(ITranscriptRegion[] regions, IInte...
    method CheckSpliceSiteOverlap (line 73) | private void CheckSpliceSiteOverlap(IInterval variant, IInterval region)
    method CheckIntronOverlap (line 86) | private void CheckIntronOverlap(IInterval variant, bool isInsertion, I...
    method DetermineExonicEffect (line 99) | public void DetermineExonicEffect(ITranscript transcript, IInterval va...
    method IsMatureMirnaVariant (line 127) | internal static bool IsMatureMirnaVariant(int cdnaStart, int cdnaEnd, ...
    method IsAfterCoding (line 134) | internal static bool IsAfterCoding(int variantRefBegin, int variantRef...
    method IsBeforeCoding (line 147) | internal static bool IsBeforeCoding(int variantRefBegin, int variantRe...
    method IsWithinCdna (line 156) | internal static bool IsWithinCdna(int coveredCdnaStart, int coveredCdn...
    method IsWithinCds (line 159) | internal bool IsWithinCds(int coveredCdsBegin, int coveredCdsEnd, IInt...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/TranscriptUtilities.cs
  class TranscriptUtilities (line 7) | public static class TranscriptUtilities
    method GetAlternateCds (line 12) | public static string GetAlternateCds(ISequence refSequence, int cdsBeg...
    method GetUpstreamLength (line 31) | private static int GetUpstreamLength(int start, int length, int seqLen...
    method GetSplicedSequence (line 42) | private static string GetSplicedSequence(ISequence refSequence, ITrans...

FILE: VariantAnnotation/AnnotatedPositions/Transcript/VariantEffect.cs
  class VariantEffect (line 13) | public sealed class VariantEffect : IVariantEffect
    method VariantEffect (line 42) | public VariantEffect(TranscriptPositionalEffect transcriptEffect, ISim...
    method IsSpliceAcceptorVariant (line 75) | public bool IsSpliceAcceptorVariant()
    method IsSpliceDonorVariant (line 89) | public bool IsSpliceDonorVariant()
    method IsFivePrimeUtrVariant (line 103) | public bool IsFivePrimeUtrVariant()
    method IsFrameshiftVariant (line 127) | public bool IsFrameshiftVariant()
    method IsIncompleteTerminalCodonVariant (line 154) | public bool IsIncompleteTerminalCodonVariant()
    method IsInframeDeletion (line 178) | public bool IsInframeDeletion()
    method IsInframeInsertion (line 222) | public bool IsInframeInsertion()
    method IsTruncatedByStop (line 250) | private bool IsTruncatedByStop()
    method IsStartLost (line 266) | public bool IsStartLost()
    method IsMissenseVariant (line 300) | public bool IsMissenseVariant()
    method IsNonCodingTranscriptExonVariant (line 334) | public bool IsNonCodingTranscriptExonVariant()
    method IsNonsenseMediatedDecayTranscriptVariant (line 348) | public bool IsNonsenseMediatedDecayTranscriptVariant()
    method IsProteinAlteringVariant (line 361) | public bool IsProteinAlteringVariant()
    method IsSpliceRegionVariant (line 388) | public bool IsSpliceRegionVariant()
    method IsStopGained (line 411) | public bool IsStopGained()
    method IsStopLost (line 427) | public bool IsStopLost()
    method IsStopRetained (line 444) | public bool IsStopRetained()
    method IsStartRetained (line 462) | public bool IsStartRetained()
    method TrimPeptides (line 483) | private static string TrimPeptides(string alternateAminoAcids)
    method IsSynonymousVariant (line 494) | public bool IsSynonymousVariant()
    method IsThreePrimeUtrVariant (line 512) | public bool IsThreePrimeUtrVariant()
    method IsNonCodingTranscriptVariant (line 535) | public bool IsNonCodingTranscriptVariant()
    method IsCodingSequenceVariant (line 551) | public bool IsCodingSequenceVariant()
    method IsWithinIntron (line 570) | public bool IsWithinIntron() => _preCache.IsWithinIntron;
    method IsMatureMirnaVariant (line 575) | public bool IsMatureMirnaVariant()

FILE: VariantAnnotation/AnnotatedPositions/Transcript/VariantEffectCache.cs
  class VariantEffectCache (line 6) | public sealed class VariantEffectCache
    method VariantEffectCache (line 16) | public VariantEffectCache()
    method Add (line 26) | public void Add(ConsequenceTag consequence, bool result)
    method Get (line 37) | public bool Get(ConsequenceTag consequence)
    method Contains (line 45) | public bool Contains(ConsequenceTag consequence)

FILE: VariantAnnotation/Annotator.cs
  class Annotator (line 17) | public sealed class Annotator : IAnnotator
    method Annotator (line 32) | public Annotator(IAnnotationProvider taProvider,
    method GetAssembly (line 54) | private GenomeAssembly GetAssembly()
    method AddAssembly (line 69) | private static void AddAssembly(Dictionary<GenomeAssembly, List<string...
    method GetAssemblyErrorMessage (line 76) | private static string GetAssemblyErrorMessage(Dictionary<GenomeAssembl...
    method Annotate (line 85) | public IAnnotatedPosition Annotate(IPosition position)
    method TrackAffectedGenes (line 109) | private void TrackAffectedGenes(IAnnotatedPosition annotatedPosition)
    method AddGenesFromTranscripts (line 119) | private void AddGenesFromTranscripts(IList<IAnnotatedTranscript> trans...
    method IsFlankingTranscript (line 128) | private static bool IsFlankingTranscript(IAnnotatedTranscript transcript)
    method GetAnnotatedVariants (line 142) | internal static IAnnotatedVariant[] GetAnnotatedVariants(IVariant[] va...
    method GetGeneAnnotations (line 151) | public IEnumerable<string> GetGeneAnnotations()
    method EnableMitochondrialAnnotation (line 165) | public void EnableMitochondrialAnnotation() => _annotateMito = true;

FILE: VariantAnnotation/Caches/DataStructures/CodingRegion.cs
  class CodingRegion (line 6) | public sealed class CodingRegion : ICodingRegion
    method CodingRegion (line 14) | public CodingRegion(int start, int end, int cdnaStart, int cdnaEnd, in...
    method Read (line 23) | public static ICodingRegion Read(BufferedBinaryReader reader)
    method Write (line 34) | public void Write(IExtendedBinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/EncodedTranscriptData.cs
  class EncodedTranscriptData (line 6) | public sealed class EncodedTranscriptData
    method EncodedTranscriptData (line 50) | private EncodedTranscriptData(ushort info, byte contents)
    method GetEncodedTranscriptData (line 56) | public static EncodedTranscriptData GetEncodedTranscriptData(BioType b...
    method Read (line 79) | public static EncodedTranscriptData Read(BufferedBinaryReader reader)
    method Write (line 86) | internal void Write(IExtendedBinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/Gene.cs
  class Gene (line 9) | public sealed class Gene : IGene
    method Gene (line 20) | public Gene(Chromosome chromosome, int start, int end, bool onReverseS...
    method Read (line 33) | public static IGene Read(IBufferedBinaryReader reader, Dictionary<usho...
    method Write (line 47) | public void Write(IExtendedBinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/IndexEntry.cs
  type IndexEntry (line 5) | public struct IndexEntry
    method Read (line 10) | public void Read(BinaryReader reader)
    method Write (line 16) | public void Write(BinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/Prediction.cs
  class Prediction (line 7) | public sealed class Prediction
    method Prediction (line 18) | public Prediction(byte[] data, Entry[] lut)
    method GetPrediction (line 24) | public Entry GetPrediction(char newAminoAcid, int aaPosition)
    method GetIndex (line 38) | private static int GetIndex(char newAminoAcid, int aaPosition)
    method Write (line 59) | public void Write(BinaryWriter writer)
    method Read (line 65) | public static Prediction Read(ExtendedBinaryReader reader, Entry[] lut)
    class Entry (line 72) | public sealed class Entry
      method Entry (line 77) | public Entry(double score, byte enumIndex)
      method ReadEntry (line 83) | public static Entry ReadEntry(ExtendedBinaryReader reader)
      method Write (line 90) | public void Write(BinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/RegulatoryRegion.cs
  class RegulatoryRegion (line 10) | public sealed class RegulatoryRegion : IRegulatoryRegion
    method RegulatoryRegion (line 18) | public RegulatoryRegion(Chromosome chromosome, int start, int end, Com...
    method Read (line 27) | public static IRegulatoryRegion Read(IBufferedBinaryReader reader, Dic...
    method Write (line 38) | public void Write(IExtendedBinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/RnaEdit.cs
  class RnaEdit (line 7) | public sealed class RnaEdit : IRnaEdit
    method RnaEdit (line 14) | public RnaEdit(int start, int end, string bases)
    method Read (line 22) | public static IRnaEdit Read(BufferedBinaryReader reader)
    method Write (line 30) | public void Write(IExtendedBinaryWriter writer)
    method CompareTo (line 37) | public int CompareTo(IRnaEdit other)

FILE: VariantAnnotation/Caches/DataStructures/Transcript.cs
  class Transcript (line 13) | public sealed class Transcript : ITranscript
    method Transcript (line 38) | public Transcript(Chromosome chromosome, int start, int end, ICompactI...
    method Read (line 66) | public static ITranscript Read(BufferedBinaryReader reader,
    method Write (line 108) | public void Write(IExtendedBinaryWriter writer, Dictionary<IGene, int>...
    method ReadItems (line 150) | private static T[] ReadItems<T>(BufferedBinaryReader reader, Func<Buff...
    method WriteItems (line 158) | private static void WriteItems<T>(IExtendedBinaryWriter writer, T[] it...
    method ReadIndices (line 164) | private static T[] ReadIndices<T>(IBufferedBinaryReader reader, T[] ca...
    method WriteIndices (line 178) | private static void WriteIndices<T>(IExtendedBinaryWriter writer, T[] ...
    method GetIndex (line 184) | private static int GetIndex<T>(T item, IReadOnlyDictionary<T, int> ind...

FILE: VariantAnnotation/Caches/DataStructures/TranscriptRegion.cs
  class TranscriptRegion (line 6) | public sealed class TranscriptRegion : ITranscriptRegion
    method TranscriptRegion (line 15) | public TranscriptRegion(TranscriptRegionType type, ushort id, int star...
    method Read (line 25) | public static ITranscriptRegion Read(BufferedBinaryReader reader)
    method Write (line 38) | public void Write(IExtendedBinaryWriter writer)

FILE: VariantAnnotation/Caches/DataStructures/TranscriptRegionExtensions.cs
  class TranscriptRegionExtensions (line 7) | public static class TranscriptRegionExtensions
    method BinarySearch (line 9) | public static int BinarySearch(this ITranscriptRegion[] regions, int p...
    method GetExonsAndIntrons (line 27) | public static (int ExonStart, int ExonEnd, int IntronStart, int Intron...
    method FindDesiredRegionIds (line 39) | private static (int Start, int End) FindDesiredRegionIds(this ITranscr...
    method FindFirst (line 53) | private static int FindFirst(ITranscriptRegion[] regions, Func<Transcr...
    method FindLast (line 60) | private static int FindLast(ITranscriptRegion[] regions, Func<Transcri...
    method GetAffectedRegionIndex (line 67) | private static int GetAffectedRegionIndex(int index)

FILE: VariantAnnotation/Caches/DataStructures/Translation.cs
  class Translation (line 7) | public sealed class Translation : ITranslation
    method Translation (line 13) | public Translation(ICodingRegion codingRegion, CompactId proteinId, st...
    method Read (line 20) | public static ITranslation Read(BufferedBinaryReader reader, string[] ...
    method Write (line 30) | public void Write(IExtendedBinaryWriter writer, int peptideIndex)

FILE: VariantAnnotation/Caches/PredictionCache.cs
  class PredictionCache (line 10) | public sealed class PredictionCache : IPredictionCache
    method PredictionCache (line 18) | public PredictionCache(GenomeAssembly genomeAssembly, Prediction[] pre...
    method GetProteinFunctionPrediction (line 25) | public PredictionScore GetProteinFunctionPrediction(int predictionInde...

FILE: VariantAnnotation/Caches/TranscriptCache.cs
  class TranscriptCache (line 10) | public sealed class TranscriptCache : ITranscriptCache
    method TranscriptCache (line 18) | public TranscriptCache(IEnumerable<IDataSourceVersion> dataSourceVersi...

FILE: VariantAnnotation/Caches/TranscriptCacheData.cs
  class TranscriptCacheData (line 11) | public sealed class TranscriptCacheData
    method TranscriptCacheData (line 22) | public TranscriptCacheData(CacheHeader header, IGene[] genes, ITranscr...
    method GetCache (line 35) | public TranscriptCache GetCache()
    method GetDataSourceVersions (line 41) | private static IEnumerable<IDataSourceVersion> GetDataSourceVersions(C...

FILE: VariantAnnotation/Caches/TranscriptIntervalForestExtensions.cs
  class TranscriptIntervalForestExtensions (line 7) | public static class TranscriptIntervalForestExtensions
    method GetAllFlankingValues (line 9) | public static ITranscript[] GetAllFlankingValues(this IIntervalForest<...

FILE: VariantAnnotation/Caches/Utilities/ExonUtilities.cs
  class ExonUtilities (line 5) | public static class ExonUtilities
    method GetTotalExonLength (line 7) | public static int GetTotalExonLength(ITranscriptRegion[] regions)

FILE: VariantAnnotation/Caches/Utilities/GeneForestGenerator.cs
  class GeneForestGenerator (line 9) | public static class GeneForestGenerator
    method GetGeneForest (line 13) | public static IntervalForest<IGene> GetGeneForest(IntervalArray<ITrans...
    method GetGeneInterval (line 43) | private static Interval<IGene> GetGeneInterval(IGene gene) => new Inte...

FILE: VariantAnnotation/Caches/Utilities/RnaEditUtilities.cs
  class RnaEditUtilities (line 7) | public static class RnaEditUtilities
    method GetRnaEditType (line 9) | public static VariantType GetRnaEditType(IRnaEdit rnaEdit)
    method SetTypesAndSort (line 22) | public static void SetTypesAndSort(IRnaEdit[] rnaEdits)

FILE: VariantAnnotation/GeneAnnotation/GeneAnnotationProvider.cs
  class GeneAnnotationProvider (line 13) | public sealed class GeneAnnotationProvider : IGeneAnnotationProvider
    method Annotate (line 21) | public string Annotate(string geneName)
    method GeneAnnotationProvider (line 48) | public GeneAnnotationProvider(IEnumerable<Stream> dbStreams)
    method Dispose (line 56) | public void Dispose() {}

FILE: VariantAnnotation/GeneFusions/Calling/BreakEndAdjacency.cs
  type BreakEndAdjacency (line 3) | public sealed record BreakEndAdjacency(BreakPoint Origin, BreakPoint Par...

FILE: VariantAnnotation/GeneFusions/Calling/BreakEndAdjacencyFactory.cs
  class BreakEndAdjacencyFactory (line 10) | public static class BreakEndAdjacencyFactory
    method CreateAdjacencies (line 16) | public static BreakEndAdjacency[] CreateAdjacencies(ISimpleVariant var...
    method CreateFromTranslocation (line 21) | public static BreakEndAdjacency[] CreateFromTranslocation(ISimpleVaria...
    method ConvertTranslocation (line 26) | private static BreakEndAdjacency[] ConvertTranslocation(ISimpleVariant...
    method CreateFromSymbolicAllele (line 45) | public static BreakEndAdjacency[] CreateFromSymbolicAllele(IChromosome...
    method Flip (line 58) | private static BreakEndAdjacency Flip(this BreakEndAdjacency adjacency)
    method CreateFromDeletion (line 65) | private static BreakEndAdjacency[] CreateFromDeletion(IChromosomeInter...
    method CreateFromDuplication (line 75) | private static BreakEndAdjacency[] CreateFromDuplication(IChromosomeIn...
    method CreateFromInversion (line 85) | private static BreakEndAdjacency[] CreateFromInversion(IChromosomeInte...

FILE: VariantAnnotation/GeneFusions/Calling/BreakPoint.cs
  type BreakPoint (line 5) | public sealed record BreakPoint(Chromosome Chromosome, int Position, boo...

FILE: VariantAnnotation/GeneFusions/Calling/BreakPointTranscript.cs
  type BreakPointTranscript (line 5) | public sealed record BreakPointTranscript(ITranscript Transcript, int Ge...

FILE: VariantAnnotation/GeneFusions/Calling/GeneFusionCaller.cs
  class GeneFusionCaller (line 12) | public sealed class GeneFusionCaller
    method GeneFusionCaller (line 17) | public GeneFusionCaller(Dictionary<string, Chromosome> refNameToChromo...
    method AddGeneFusions (line 24) | public void AddGeneFusions(IAnnotatedVariant[] annotatedVariants, bool...
    method GetOverlappingTranscripts (line 55) | private ITranscript[] GetOverlappingTranscripts(BreakPoint bp) =>
    method AddGeneFusionsToDictionary (line 58) | internal static void AddGeneFusionsToDictionary(Dictionary<string, IAn...
    method EvaluateGeneFusionCandidate (line 82) | private static void EvaluateGeneFusionCandidate(List<IAnnotatedGeneFus...
    method GetGeneAndFusionKeys (line 114) | internal static (ulong FusionKey, string FirstGeneSymbol, uint FirstGe...
    method SortGenes (line 127) | private static (IGene FirstGene, IGene SecondGene) SortGenes(IGene ori...
    method DetermineInFrameFusion (line 142) | internal static bool DetermineInFrameFusion(BreakPointTranscript first...
    method GetCodonPosition (line 162) | internal static byte? GetCodonPosition(ITranscriptRegion region, ITran...
    method FoundViableGeneFusion (line 178) | internal static bool FoundViableGeneFusion(BreakEndAdjacency adjacency...

FILE: VariantAnnotation/GeneFusions/HGVS/HgvsRnaNomenclature.cs
  class HgvsRnaNomenclature (line 7) | public static class HgvsRnaNomenclature
    method GetHgvs (line 9) | public static string GetHgvs(BreakPointTranscript first, BreakPointTra...
    method GetHgvsRnaCoordinate (line 19) | private static string GetHgvsRnaCoordinate(BreakPointTranscript first)

FILE: VariantAnnotation/GeneFusions/IO/GeneFusionIndexEntry.cs
  type GeneFusionIndexEntry (line 6) | public readonly struct GeneFusionIndexEntry
    method GeneFusionIndexEntry (line 11) | public GeneFusionIndexEntry(ulong geneKey, ushort index)
    method Compare (line 17) | public int Compare(ulong geneKey)
    method Read (line 23) | public static GeneFusionIndexEntry Read(ref ReadOnlySpan<byte> byteSpan)
    method Write (line 30) | public void Write(ExtendedBinaryWriter writer)

FILE: VariantAnnotation/GeneFusions/IO/GeneFusionJsonReader.cs
  class GeneFusionJsonReader (line 19) | public sealed class GeneFusionJsonReader : IGeneFusionSaReader
    method GeneFusionJsonReader (line 31) | public GeneFusionJsonReader(Stream stream)
    method CheckHeader (line 41) | public static void CheckHeader(FileType fileType, ushort fileFormatVer...
    method LoadAnnotations (line 54) | public void LoadAnnotations()
    method AddAnnotations (line 76) | public void AddAnnotations(IGeneFusionPair[] fusionPairs, IList<ISuppl...
    method Dispose (line 92) | public void Dispose() => _reader.Dispose();

FILE: VariantAnnotation/GeneFusions/IO/GeneFusionSourceReader.cs
  class GeneFusionSourceReader (line 21) | public sealed class GeneFusionSourceReader : IGeneFusionSaReader
    method GeneFusionSourceReader (line 35) | public GeneFusionSourceReader(Stream stream)
    method CheckHeader (line 45) | internal static void CheckHeader(FileType fileType, ushort fileFormatV...
    method LoadAnnotations (line 58) | public void LoadAnnotations()
    method AddAnnotations (line 79) | public void AddAnnotations(IGeneFusionPair[] fusionPairs, IList<ISuppl...
    method Dispose (line 96) | public void Dispose() => _reader.Dispose();

FILE: VariantAnnotation/GeneFusions/IO/IGeneFusionSaReader.cs
  type IGeneFusionSaReader (line 8) | public interface IGeneFusionSaReader : ISaMetadata, IDisposable
    method LoadAnnotations (line 10) | void LoadAnnotations();
    method AddAnnotations (line 12) | void AddAnnotations(IGeneFusionPair[] fusionPairs, IList<ISupplementar...

FILE: VariantAnnotation/GeneFusions/SA/GeneFusionPair.cs
  type GeneFusionPair (line 5) | public sealed record GeneFusionPair

FILE: VariantAnnotation/GeneFusions/SA/GeneFusionSource.cs
  type GeneFusionSource (line 6) | public enum GeneFusionSource : byte

FILE: VariantAnnotation/GeneFusions/SA/GeneFusionSourceCollection.cs
  class GeneFusionSourceCollection (line 11) | public sealed class GeneFusionSourceCollection : IEquatable<GeneFusionSo...
    method GeneFusionSourceCollection (line 23) | public GeneFusionSourceCollection(bool isPseudogenePair, bool isParalo...
    method Write (line 33) | public void Write(ExtendedBinaryWriter writer)
    method GetFlags (line 40) | private byte GetFlags()
    method WriteSourceGroup (line 50) | private static void WriteSourceGroup(ExtendedBinaryWriter writer, Gene...
    method Read (line 62) | public static GeneFusionSourceCollection Read(ref ReadOnlySpan<byte> b...
    method ReadSources (line 74) | private static GeneFusionSource[] ReadSources(ref ReadOnlySpan<byte> b...
    method GetJsonEntry (line 90) | public string GetJsonEntry(IGeneFusionPair geneFusionPair, uint[] onco...
    method AddGenes (line 102) | private void AddGenes(IGeneFusionPair geneFusionPair, uint[] oncogeneK...
    method AddGene (line 114) | private static void AddGene(string key, uint geneKey, string geneSymbo...
    method AddGeneFusionSource (line 126) | private static void AddGeneFusionSource(string description, GeneFusion...
    method Equals (line 137) | public bool Equals(GeneFusionSourceCollection other)
    method GetHashCode (line 149) | public override int GetHashCode()

FILE: VariantAnnotation/GeneFusions/SA/GeneFusionSourceUtilities.cs
  class GeneFusionSourceUtilities (line 3) | public static class GeneFusionSourceUtilities
    method Convert (line 5) | public static string Convert(GeneFusionSource source)

FILE: VariantAnnotation/GeneFusions/Utilities/GeneFusionKey.cs
  class GeneFusionKey (line 5) | public static class GeneFusionKey
    method Create (line 7) | public static ulong Create(uint num, uint num2)
    method CreateGeneKey (line 14) | public static uint CreateGeneKey(string geneId)

FILE: VariantAnnotation/GeneFusions/Utilities/IndexEntryExtensions.cs
  class IndexEntryExtensions (line 5) | public static class IndexEntryExtensions
    method GetIndex (line 7) | public static ushort? GetIndex(this GeneFusionIndexEntry[] array, ulon...

FILE: VariantAnnotation/GenericScore/ChromosomeBlock.cs
  class ChromosomeBlock (line 6) | public sealed class ChromosomeBlock
    method ChromosomeBlock (line 12) | public ChromosomeBlock(List<ScoreIndexBlock> scoreIndexBlocks, int blo...
    method Add (line 23) | public void Add(ScoreIndexBlock indexBlock)
    method Get (line 34) | public ScoreIndexBlock Get(int blockNumber)
    method Write (line 44) | public void Write(ExtendedBinaryWriter writer)
    method Read (line 59) | public static ChromosomeBlock Read(ExtendedBinaryReader reader)

FILE: VariantAnnotation/GenericScore/EncoderType.cs
  type EncoderType (line 3) | public enum EncoderType: byte

FILE: VariantAnnotation/GenericScore/GenericScoreEncoder.cs
  class GenericScoreEncoder (line 8) | public sealed class GenericScoreEncoder : IScoreEncoder
    method GenericScoreEncoder (line 16) | public GenericScoreEncoder()
    method AddScore (line 22) | public ushort AddScore(double number)
    method EncodeToBytes (line 34) | public byte[] EncodeToBytes(double number)
    method DecodeFromBytes (line 45) | public double DecodeFromBytes(ReadOnlySpan<byte> encodedArray)
    method GetScore (line 51) | private double GetScore(ushort encodedNumber)
    method Write (line 56) | public void Write(ExtendedBinaryWriter writer)
    method Read (line 66) | public static GenericScoreEncoder Read(ExtendedBinaryReader reader)

FILE: VariantAnnotation/GenericScore/IScoreEncoder.cs
  type IScoreEncoder (line 6) | public interface IScoreEncoder
    method EncodeToBytes (line 9) | public byte[]      EncodeToBytes(double number);
    method DecodeFromBytes (line 10) | public double      DecodeFromBytes(ReadOnlySpan<byte> encodedArray);
    method Write (line 12) | public void Write(ExtendedBinaryWriter writer);

FILE: VariantAnnotation/GenericScore/MetaData.cs
  class MetaData (line 6) | public sealed class MetaData
    method CalculateCompressionRatio (line 29) | private static double CalculateCompressionRatio(uint compressedSize, u...
    method MetaData (line 34) | public MetaData()
    method AddIndexBlock (line 39) | public void AddIndexBlock(ushort chromosomeIndex, int blockNumber, lon...
    method AddChromosomeBlock (line 63) | public void AddChromosomeBlock(ushort chromosomeIndex)
    method TrackUnmatchedReferencePositions (line 81) | public void TrackUnmatchedReferencePositions()
    method PrintFormattedString (line 86) | private static void PrintFormattedString(ushort? chromosomeIndex, int?...
    method PrintWriteMetrics (line 109) | public void PrintWriteMetrics()

FILE: VariantAnnotation/GenericScore/ReaderSettings.cs
  class ReaderSettings (line 6) | public sealed class ReaderSettings
    method ReaderSettings (line 17) | public ReaderSettings(
    method Read (line 35) | public static ReaderSettings Read(ExtendedBinaryReader reader)
    method Write (line 69) | public void Write(ExtendedBinaryWriter writer)

FILE: VariantAnnotation/GenericScore/ScoreBlock.cs
  class ScoreBlock (line 7) | public sealed class ScoreBlock
    method ScoreBlock (line 17) | public ScoreBlock(ICompressionAlgorithm compressionAlgorithm, int bloc...
    method Clear (line 29) | private void Clear()
    method IsFull (line 35) | public bool IsFull()
    method Add (line 40) | public void Add(uint memoryIndex, byte[] variableArray, uint arraySize)
    method Write (line 46) | public (uint uncompressedSize, int compressedSize) Write(ExtendedBinar...

FILE: VariantAnnotation/GenericScore/ScoreIndex.cs
  class ScoreIndex (line 13) | public sealed class ScoreIndex
    method ScoreIndex (line 29) | public ScoreIndex(
    method Add (line 72) | public void Add(ushort chromIndex, long filePosition, int compressedSi...
    method AddChromosomeBlock (line 81) | public void AddChromosomeBlock(ushort chromIndex, int chromosomeStarti...
    method TrackUnmatchedReferencePositions (line 87) | public void TrackUnmatchedReferencePositions()
    method WriteHeader (line 92) | private void WriteHeader()
    method CheckHeader (line 99) | private static void CheckHeader(Header header)
    method ReadHeader (line 107) | private static (Header indexHeader, int filePairId) ReadHeader(Extende...
    method Write (line 125) | public void Write()
    method Read (line 151) | public static ScoreIndex Read(Stream stream, int dataFilePairId)
    method GetFilePosition (line 200) | public long GetFilePosition(ushort chromIndex, int position)
    method GetBlockNumber (line 219) | private int GetBlockNumber(ChromosomeBlock chromosomeBlock, int position)
    method GetBlockNumber (line 232) | public int GetBlockNumber(ushort chromosomeIndex, int position)
    method GetBytesToRead (line 238) | public int GetBytesToRead(ushort chromIndex, int blockNumber)
    method GetBlockLength (line 243) | public int GetBlockLength()
    method GetNucleotideCount (line 248) | public uint GetNucleotideCount()
    method GetNucleotidePosition (line 253) | public ushort? GetNucleotidePosition(string saItemAltAllele)
    method PositionToBlockLocation (line 259) | public (int blockNumber, int localBlockIndex) PositionToBlockLocation(...
    method PositionToBlockLocation (line 269) | private (int blockNumber, int localBlockIndex) PositionToBlockLocation...
    method PositionToBlockLocation (line 274) | public (int blockNumber, int localBlockIndex) PositionToBlockLocation(...
    method GetChromosomeBlocks (line 280) | public Dictionary<ushort, ChromosomeBlock> GetChromosomeBlocks()
    method GetLastBlockNumber (line 285) | public int GetLastBlockNumber(ushort chromosomeIndex)

FILE: VariantAnnotation/GenericScore/ScoreIndexBlock.cs
  class ScoreIndexBlock (line 5) | public sealed class ScoreIndexBlock
    method ScoreIndexBlock (line 10) | public ScoreIndexBlock(long filePosition, int bytesWritten)
    method Read (line 21) | public static ScoreIndexBlock Read(ExtendedBinaryReader reader)
    method Write (line 33) | public void Write(ExtendedBinaryWriter writer)

FILE: VariantAnnotation/GenericScore/ScoreJsonEncoder.cs
  class ScoreJsonEncoder (line 5) | public sealed class ScoreJsonEncoder
    method JsonRepresentation (line 10) | public string JsonRepresentation<T>(T data)
    method ScoreJsonEncoder (line 18) | public ScoreJsonEncoder(string jsonKey, string jsonSubKey)
    method Write (line 24) | public void Write(ExtendedBinaryWriter writer)
    method Read (line 30) | public static ScoreJsonEncoder Read(ExtendedBinaryReader reader)

FILE: VariantAnnotation/GenericScore/ScoreReader.cs
  class ScoreReader (line 15) | public sealed class ScoreReader : ISaMetadata
    method ScoreReader (line 32) | private ScoreReader(ScoreIndex scoreIndex, ExtendedBinaryReader dataFi...
    method Read (line 52) | public static ScoreReader Read(Stream dataStream, Stream indexStream)
    method CheckHeader (line 61) | private static void CheckHeader(Header header)
    method ReadHeader (line 73) | private static int ReadHeader(ExtendedBinaryReader dataFileReader)
    method GetUncompressedBlock (line 89) | private bool GetUncompressedBlock(ushort chromIndex, int position)
    method GetScore (line 111) | public double GetScore(ushort chromosomeIndex, int position, string al...
    method GetAnnotationJson (line 126) | public string GetAnnotationJson(ushort chromosomeIndex, int position, ...

FILE: VariantAnnotation/GenericScore/ZeroToOneScoreEncoder.cs
  class ZeroToOneScoreEncoder (line 7) | public sealed class ZeroToOneScoreEncoder : IScoreEncoder
    method ZeroToOneScoreEncoder (line 16) | public ZeroToOneScoreEncoder(int numberOfDigits, double maxScore)
    method Write (line 27) | public void Write(ExtendedBinaryWriter writer)
    method Read (line 33) | public static ZeroToOneScoreEncoder Read(ExtendedBinaryReader reader)
    method EncodeToBytes (line 38) | public byte[] EncodeToBytes(double number)
    method DecodeFromBytes (line 56) | public double DecodeFromBytes(ReadOnlySpan<byte> encodedArray)
    method TransformToUint (line 73) | private uint TransformToUint(double number)
    method TransformToDouble (line 79) | private double TransformToDouble(uint encodedNumber)

FILE: VariantAnnotation/IO/Caches/CacheHeader.cs
  class CacheHeader (line 6) | public sealed class CacheHeader : Header
    method CacheHeader (line 10) | public CacheHeader(Header header, TranscriptCacheCustomHeader customHe...
    method Write (line 17) | public new void Write(BinaryWriter writer)
    method Read (line 23) | public static CacheHeader Read(Stream stream)

FILE: VariantAnnotation/IO/Caches/Header.cs
  class Header (line 7) | public class Header
    method Header (line 16) | public Header(string identifier, ushort schemaVersion, ushort dataVers...
    method Write (line 27) | protected void Write(BinaryWriter writer)
    method Read (line 37) | protected static Header Read(BinaryReader reader)

FILE: VariantAnnotation/IO/Caches/PredictionCacheCustomHeader.cs
  class PredictionCacheCustomHeader (line 6) | public sealed class PredictionCacheCustomHeader
    method PredictionCacheCustomHeader (line 10) | public PredictionCacheCustomHeader(IndexEntry[] entries) => Entries = ...
    method Write (line 12) | public void Write(BinaryWriter writer)
    method Read (line 18) | public static PredictionCacheCustomHeader Read(BinaryReader reader)

FILE: VariantAnnotation/IO/Caches/PredictionCacheReader.cs
  class PredictionCacheReader (line 14) | public sealed class PredictionCacheReader : IDisposable
    method PredictionCacheReader (line 23) | public PredictionCacheReader(Stream stream, string[] predictionDescrip...
    method Dispose (line 35) | public void Dispose()
    method Read (line 44) | public IPredictionCache Read(ushort refIndex)
    method GetPredictions (line 51) | public Prediction[] GetPredictions(ushort refIndex)

FILE: VariantAnnotation/IO/Caches/PredictionHeader.cs
  class PredictionHeader (line 9) | public sealed class PredictionHeader : Header
    method PredictionHeader (line 14) | public PredictionHeader(Header header, PredictionCacheCustomHeader cus...
    method Write (line 22) | public new void Write(BinaryWriter writer)
    method Read (line 28) | public static PredictionHeader Read(Stream stream, BlockStream blockSt...
    method ReadLookupTable (line 48) | private static Prediction.Entry[] ReadLookupTable(ExtendedBinaryReader...

FILE: VariantAnnotation/IO/Caches/TranscriptCacheCustomHeader.cs
  class TranscriptCacheCustomHeader (line 5) | public sealed class TranscriptCacheCustomHeader
    method TranscriptCacheCustomHeader (line 10) | public TranscriptCacheCustomHeader(ushort vepVersion, long vepReleaseT...
    method Write (line 16) | public void Write(BinaryWriter writer)
    method Read (line 22) | public static TranscriptCacheCustomHeader Read(BinaryReader reader)

FILE: VariantAnnotation/IO/Caches/TranscriptCacheReader.cs
  class TranscriptCacheReader (line 15) | public sealed class TranscriptCacheReader : IDisposable
    method TranscriptCacheReader (line 20) | public TranscriptCacheReader(Stream stream)
    method Dispose (line 27) | public void Dispose() => _reader.Dispose();
    method Read (line 32) | public TranscriptCacheData Read(Dictionary<ushort, Chromosome> refInde...
    method ReadIntervals (line 44) | private static IntervalArray<T>[] ReadIntervals<T>(IBufferedBinaryRead...
    method ReadItems (line 69) | internal static T[] ReadItems<T>(IBufferedBinaryReader reader, Func<T>...
    method CheckGuard (line 81) | internal static void CheckGuard(IBufferedBinaryReader reader)

FILE: VariantAnnotation/IO/IntervalExtensions.cs
  class IntervalExtensions (line 6) | public static class IntervalExtensions
    method Read (line 8) | public static IInterval Read(IBufferedBinaryReader reader)
    method Write (line 15) | public static void Write(this IInterval interval, IExtendedBinaryWrite...

FILE: VariantAnnotation/IO/JsonCommon.cs
  class JsonCommon (line 3) | public static class JsonCommon

FILE: VariantAnnotation/IO/JsonObject.cs
  class JsonObject (line 9) | public sealed class JsonObject
    method JsonObject (line 23) | public JsonObject(StringBuilder sb) => _sb = sb;
    method AddKey (line 25) | private void AddKey(string description)
    method StartObjectWithKey (line 32) | public void StartObjectWithKey(string objectKey)
    method AddBoolValue (line 45) | public bool AddBoolValue(string description, bool b, bool outputFalse ...
    method AddIntValue (line 59) | public bool AddIntValue(string description, int? i)
    method AddUIntValue (line 72) | public bool AddUIntValue(string description, uint? i)
    method AddIntValues (line 85) | public void AddIntValues(string description, int[] values)
    method AddDoubleValue (line 96) | public bool AddDoubleValue(string description, double? d, string forma...
    method AddDoubleValues (line 108) | public void AddDoubleValues(string description, double[] values, strin...
    method AddStringValue (line 118) | public bool AddStringValue(string description, string s, bool useQuote...
    method AddStringValues (line 133) | public bool AddStringValues(string description, IEnumerable<string> va...
    method AddStringValues (line 163) | public bool AddStringValues(string description, IEnumerable<StringBuil...
    method AddObjectValue (line 195) | public void AddObjectValue<T>(string description, T value) where T : I...
    method AddObjectValues (line 207) | public bool AddObjectValues<T>(string description, IEnumerable<T> valu...
    method StartObject (line 231) | public void StartObject()
    method EndObject (line 238) | public void EndObject()
    method EndAllObjects (line 245) | public void EndAllObjects()

FILE: VariantAnnotation/IO/JsonWriter.cs
  class JsonWriter (line 15) | public sealed class JsonWriter : IJsonWriter
    method JsonWriter (line 25) | private JsonWriter(Stream jsonStream, Stream indexStream, string annot...
    method JsonWriter (line 30) | public JsonWriter(Stream jsonStream, Stream indexStream, IAnnotationRe...
    method GetProperWriter (line 34) | private static StreamWriter GetProperWriter(Stream jsonStream) => json...
    method JsonWriter (line 38) | public JsonWriter(StreamWriter writer, Stream indexStream, string anno...
    method WriteHeader (line 58) | private void WriteHeader(string annotator, string creationTime, string...
    method Dispose (line 83) | public void Dispose()
    method BeginSection (line 95) | private void BeginSection(string section)
    method EndSection (line 102) | private void EndSection(string section)
    method WritePosition (line 110) | public void WritePosition(IPosition position, string entry)
    method WritePosition (line 124) | public void WritePosition(IPosition position, StringBuilder sb)
    method WriteGenes (line 138) | public void WriteGenes(IEnumerable<string> annotatedGenes)
    method WriteFooter (line 168) | private void WriteFooter()

FILE: VariantAnnotation/IO/SampleExtensions.cs
  class SampleExtensions (line 6) | public static class SampleExtensions
    method GetJsonString (line 8) | public static string GetJsonString(this ISample sample)

FILE: VariantAnnotation/NSA/NgaReader.cs
  class NgaReader (line 15) | public sealed class NgaReader
    method NgaReader (line 23) | private NgaReader(IDataSourceVersion version, string jsonKey, bool isA...
    method Read (line 31) | public static NgaReader Read(Stream stream)
    method ReadHeader (line 61) | private static (IDataSourceVersion Version, string JsonKey, bool IsArr...
    method GetAnnotation (line 97) | public string GetAnnotation(string geneName) => _geneSymbolToJsonStrin...
    method GetJsonString (line 99) | private string GetJsonString(List<string> annotations)

FILE: VariantAnnotation/NSA/NsaBlock.cs
  class NsaBlock (line 9) | public sealed class NsaBlock:IDisposable
    method NsaBlock (line 26) | public NsaBlock(ICompressionAlgorithm compressionAlgorithm, int size)
    method Read (line 39) | public void Read(ExtendedBinaryReader reader)
    method ReadCompressedBytes (line 54) | public void ReadCompressedBytes(ExtendedBinaryReader reader)
    method WriteCompressedBytes (line 65) | public void WriteCompressedBytes(ExtendedBinaryWriter writer)
    method HasSpace (line 75) | public bool HasSpace(int length)
    method Add (line 80) | public void Add(byte[] data, int length, int position)
    method AddAnnotations (line 99) | public int AddAnnotations(List<int> vcfPositions, int j, List<Annotati...
    method Write (line 142) | public (int firstPosition, int lastPosition, int numBytes) Write(Exten...
    method Clear (line 158) | public void Clear()
    method Dispose (line 168) | public void Dispose()

FILE: VariantAnnotation/NSA/NsaIndex.cs
  class NsaIndex (line 10) | public sealed class NsaIndex
    method GetBlocks (line 25) | public Dictionary<ushort, List<NsaIndexBlock>> GetBlocks() => _chromBl...
    method GetChromBlocks (line 26) | public List<NsaIndexBlock> GetChromBlocks(ushort chromIndex) => _chrom...
    method NsaIndex (line 28) | public NsaIndex(ExtendedBinaryWriter indexWriter, GenomeAssembly assem...
    method Add (line 49) | public void Add(ushort chromIndex, int start, int end, long filePositi...
    method Write (line 63) | public void Write()
    method Write (line 78) | public void Write(Dictionary<ushort, List<NsaIndexBlock>>  chromBlocks)
    method NsaIndex (line 94) | public NsaIndex(Stream stream)
    method GetFileLocation (line 123) | public long GetFileLocation(ushort chromIndex, int start)
    method GetFileRange (line 132) | public (long startFilePosition, int chunkCount) GetFileRange(ushort ch...
    method BinarySearch (line 158) | private static int BinarySearch(List<NsaIndexBlock> chunks, int position)

FILE: VariantAnnotation/NSA/NsaIndexBlock.cs
  class NsaIndexBlock (line 6) | public sealed class NsaIndexBlock
    method NsaIndexBlock (line 13) | public NsaIndexBlock(int start, int end, long filePosition, int length)
    method NsaIndexBlock (line 21) | [Obsolete("Use a factory method instead of an extra constructor.")]
    method Write (line 30) | public void Write(ExtendedBinaryWriter writer)
    method CompareTo (line 38) | public int CompareTo(int position)

FILE: VariantAnnotation/NSA/NsaReader.cs
  class AnnotationItem (line 14) | public sealed class AnnotationItem
    method AnnotationItem (line 19) | public AnnotationItem(int position, byte[] data)
  class NsaReader (line 26) | public sealed class NsaReader : INsaReader
    method NsaReader (line 49) | public NsaReader(Stream dataStream, Stream indexStream, int blockSize ...
    method PreLoad (line 72) | public void PreLoad(Chromosome chrom, List<int> positions)
    method GetIndexBlocks (line 97) | public List<NsaIndexBlock> GetIndexBlocks(ushort chromIndex) => _index...
    method HasDataBlocks (line 99) | public bool HasDataBlocks(ushort chromIndex) {
    method GetCompressedBlocks (line 104) | public IEnumerable<NsaBlock> GetCompressedBlocks(ushort chromIndex)
    method ExtractAnnotations (line 119) | private void ExtractAnnotations(byte[] data, List<(string refAllele, s...
    method GetAnnotation (line 148) | public void GetAnnotation(int position, List<(string refAllele, string...
    method BinarySearch (line 156) | private int BinarySearch(int position)
    method Dispose (line 174) | public void Dispose()

FILE: VariantAnnotation/NSA/NsiReader.cs
  class NsiReader (line 23) | public sealed class NsiReader : INsiReader
    method NsiReader (line 31) | private NsiReader(GenomeAssembly assembly, IDataSourceVersion version,...
    method Read (line 40) | public static NsiReader Read(Stream stream)
    method ReadHeader (line 72) | private static (IDataSourceVersion, GenomeAssembly, string, ReportFor,...
    method GetAnnotation (line 95) | public IEnumerable<string> GetAnnotation(IVariant variant)
    method AddOverlapToAnnotation (line 118) | private static string AddOverlapToAnnotation(string jsonString, double...
    method OverlapsAny (line 127) | public bool OverlapsAny(IChromosomeInterval variant)

FILE: VariantAnnotation/NSA/NsiWriter.cs
  class NsiWriter (line 17) | public sealed class NsiWriter:IDisposable
    method NsiWriter (line 23) | public NsiWriter(Stream stream, DataSourceVersion version,
    method WriteHeader (line 36) | private void WriteHeader(DataSourceVersion version, GenomeAssembly ass...
    method Write (line 50) | public void Write(IEnumerable<ISuppIntervalItem> siItems)
    method Dispose (line 68) | public void Dispose()

FILE: VariantAnnotation/NSA/RefMinorDbReader.cs
  class RefMinorDbReader (line 11) | public sealed class RefMinorDbReader : IDisposable
    method RefMinorDbReader (line 19) | public RefMinorDbReader(Stream dbStream, Stream indexStream)
    method PreLoad (line 33) | private void PreLoad(Chromosome chrom)
    method GetGlobalMajorAllele (line 57) | public string GetGlobalMajorAllele(Chromosome chromosome, int position)
    method Dispose (line 67) | public void Dispose()

FILE: VariantAnnotation/NSA/RefMinorIndex.cs
  class RefMinorIndex (line 9) | public sealed class RefMinorIndex
    method RefMinorIndex (line 17) | public RefMinorIndex(ExtendedBinaryWriter writer, GenomeAssembly assem...
    method Add (line 32) | public void Add(ushort chromIndex, long location)
    method GetFileRange (line 49) | public (long location, int numBytes, int count) GetFileRange(ushort ch...
    method Write (line 54) | public void Write(long finalLocation)
    method RefMinorIndex (line 76) | public RefMinorIndex(ExtendedBinaryReader reader)

FILE: VariantAnnotation/NSA/SuppInterval.cs
  class SuppInterval (line 7) | public sealed class SuppInterval : ISuppIntervalItem
    method SuppInterval (line 14) | private SuppInterval(Chromosome chromosome, int start, int end, string...
    method Read (line 22) | public static SuppInterval Read(ExtendedBinaryReader reader)
    method GetJsonString (line 36) | public string GetJsonString() => _jsonString;

FILE: VariantAnnotation/NSA/SuppIntervalUtilities.cs
  class SuppIntervalUtilities (line 7) | public static class SuppIntervalUtilities
    method GetOverlapFractions (line 9) | public static (double? ReciprocalOverlap, double? AnnotationOverlap) G...

FILE: VariantAnnotation/NSA/SupplementaryAnnotation.cs
  class SupplementaryAnnotation (line 8) | public sealed class SupplementaryAnnotation:ISupplementaryAnnotation
    method SupplementaryAnnotation (line 16) | public SupplementaryAnnotation(string key, bool isArray, bool isPositi...
    method SerializeJson (line 32) | public void SerializeJson(StringBuilder sb)

FILE: VariantAnnotation/PerformanceMetrics.cs
  class PerformanceMetrics (line 9) | public sealed class PerformanceMetrics
    method ShowAnnotationEntry (line 16) | public void ShowAnnotationEntry(Chromosome chromosome, int numVariants)
    method ShowCacheLoad (line 28) | public void ShowCacheLoad()
    method ShowSaPositionScanLoad (line 35) | public void ShowSaPositionScanLoad(int numPositions)
    method GetPaddedField (line 43) | private static string GetPaddedField(string s, int fieldLength)
    method ShowAnnotationHeader (line 49) | public static void ShowAnnotationHeader() =>
    method ShowInitializationHeader (line 52) | public static void ShowInitializationHeader() =>
    method ShowSummaryTable (line 55) | public void ShowSummaryTable()
    method ShowSummaryEntry (line 69) | private void ShowSummaryEntry(string description, long entryTicks, lon...
    method GetTotalProcessTicks (line 77) | private static long GetTotalProcessTicks() => DateTime.Now.Ticks - Pro...
  class TimeKeeper (line 80) | public sealed class TimeKeeper
    method Stop (line 87) | public void Stop()
    method Start (line 93) | public void   Start()                         => _benchmark.Reset();
    method GetTime (line 94) | public string GetTime()                       => Benchmark.ToHumanRead...
    method GetIterationsPerSecond (line 95) | public double GetIterationsPerSecond(int num) => Benchmark.GetElapsedI...
  class MetricsCommon (line 98) | public static class MetricsCommon
    method DisplayHeader (line 103) | public static void DisplayHeader(string s)

FILE: VariantAnnotation/PhyloP/NpdIndex.cs
  class NpdIndex (line 10) | public sealed class NpdIndex
    method NpdIndex (line 22) | public NpdIndex(Stream stream, GenomeAssembly assembly, IDataSourceVer...
    method Add (line 34) | public void Add(ushort chromIndex, long location, int byteCount)
    method GetFileRange (line 39) | public (long location, int numBytes) GetFileRange(ushort chromIndex)
    method Write (line 44) | public void Write(Dictionary<double, byte> scoreMap)
    method NpdIndex (line 68) | public NpdIndex(ExtendedBinaryReader reader)

FILE: VariantAnnotation/PhyloP/NpdReader.cs
  class NpdReader (line 13) | public sealed class NpdReader:IDisposable
    method NpdReader (line 29) | public NpdReader(Stream dbStream, Stream indexStream)
    method PreLoad (line 55) | private void PreLoad(Chromosome chrom)
    method GetAnnotation (line 71) | public double? GetAnnotation(Chromosome chromosome, int position)
    method Dispose (line 81) | public void Dispose()

FILE: VariantAnnotation/Pools/AnnotatedPositionPool.cs
  class AnnotatedPositionPool (line 8) | public static class AnnotatedPositionPool
    method Get (line 13) | public static AnnotatedPosition Get(IPosition position, IAnnotatedVari...
    method Return (line 20) | public static void Return(AnnotatedPosition ap) => Pool.Return(ap);

FILE: VariantAnnotation/Pools/AnnotatedTranscriptPool.cs
  class AnnotatedTranscriptPool (line 8) | public static class AnnotatedTranscriptPool
    method Get (line 12) | public static AnnotatedTranscript Get(ITranscript transcript, string r...
    method Return (line 24) | public static void Return(AnnotatedTranscript annotatedTranscript) => ...

FILE: VariantAnnotation/Pools/AnnotatedVariantPool.cs
  class AnnotatedVariantPool (line 7) | public static class AnnotatedVariantPool
    method Get (line 12) | public static AnnotatedVariant Get(IVariant variant)
    method Return (line 19) | public static void Return(AnnotatedVariant av) => Pool.Return(av);

FILE: VariantAnnotation/Pools/VariantPool.cs
  class VariantPool (line 7) | public static class VariantPool
    method Get (line 12) | public static Variant Get(Chromosome chromosome, int start, int end, s...
    method Return (line 23) | public static void Return(Variant variant) => Pool.Return(variant);

FILE: VariantAnnotation/ProteinConservation/ProteinConservationCommon.cs
  class ProteinConservationCommon (line 3) | public static class ProteinConservationCommon

FILE: VariantAnnotation/ProteinConservation/ProteinConservationItem.cs
  class ProteinConservationItem (line 3) | public sealed class ProteinConservationItem
    method ProteinConservationItem (line 11) | public ProteinConservationItem(string chrom, string transcriptId, stri...

FILE: VariantAnnotation/ProteinConservation/ProteinConservationReader.cs
  class ProteinConservationReader (line 11) | public sealed class ProteinConservationReader:IDisposable
    method ProteinConservationReader (line 17) | public ProteinConservationReader(Stream stream)
    method GetItems (line 28) | public IEnumerable<TranscriptConservationScores> GetItems()
    method Dispose (line 39) | public void Dispose() =>_reader?.Dispose();

FILE: VariantAnnotation/ProteinConservation/TranscriptConservationScores.cs
  class TranscriptConservationScores (line 6) | public sealed class TranscriptConservationScores
    method TranscriptConservationScores (line 11) | public TranscriptConservationScores(string id, byte[] scores)
    method Read (line 18) | public static TranscriptConservationScores Read(ExtendedBinaryReader r...
    method Write (line 27) | public void Write(ExtendedBinaryWriter writer)
    method GetEmptyItem (line 34) | public static TranscriptConservationScores GetEmptyItem() => new Trans...
    method IsEmpty (line 36) | public bool IsEmpty() => string.IsNullOrEmpty(TranscriptId) && Conserv...

FILE: VariantAnnotation/Providers/ConservationScoreProvider.cs
  class ConservationScoreProvider (line 12) | public sealed class ConservationScoreProvider : IAnnotationProvider
    method ConservationScoreProvider (line 21) | public ConservationScoreProvider()
    method AddPhylopReader (line 26) | public ConservationScoreProvider AddPhylopReader(Stream dbStream, Stre...
    method Annotate (line 34) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method PreLoad (line 44) | public void PreLoad(Chromosome chromosome, List<int> positions)
    method Dispose (line 49) | public void Dispose()

FILE: VariantAnnotation/Providers/DataSourceVersion.cs
  class DataSourceVersion (line 10) | public sealed class DataSourceVersion : IDataSourceVersion, ISerializable
    method DataSourceVersion (line 17) | public DataSourceVersion(string name, string version, long releaseDate...
    method Read (line 25) | public static IDataSourceVersion Read(ExtendedBinaryReader reader)
    method Write (line 34) | public void Write(IExtendedBinaryWriter writer)
    method GetReleaseDate (line 42) | private string GetReleaseDate() => Date.GetDate(ReleaseDateTicks);
    method ToString (line 44) | public override string ToString() => "dataSource=" + Name + ",version:...
    method SerializeJson (line 46) | public void SerializeJson(StringBuilder sb)
  class DataSourceVersionComparer (line 59) | public sealed class DataSourceVersionComparer : EqualityComparer<IDataSo...
    method Equals (line 61) | public override bool Equals(IDataSourceVersion x, IDataSourceVersion y)
    method GetHashCode (line 69) | public override int GetHashCode(IDataSourceVersion obj)

FILE: VariantAnnotation/Providers/LcrProvider.cs
  class LcrProvider (line 10) | public class LcrProvider: IAnnotationProvider
    method LcrProvider (line 18) | public LcrProvider(Stream stream)
    method Dispose (line 25) | public void Dispose()
    method Annotate (line 30) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method PreLoad (line 38) | public void PreLoad(Chromosome chromosome, List<int> positions)

FILE: VariantAnnotation/Providers/NsaProvider.cs
  class NsaProvider (line 17) | public sealed class NsaProvider : IAnnotationProvider
    method NsaProvider (line 32) | public NsaProvider(INsaReader[] nsaReaders, INsiReader[] nsiReaders, I...
    method OrganizeReaders (line 47) | private static (List<ISaMetadata> Variant, List<ISaMetadata> Position,...
    method CheckDuplicateVariantKeys (line 84) | private static void CheckDuplicateVariantKeys(List<ISaMetadata> readers)
    method CheckDuplicatePositionKeys (line 90) | private static void CheckDuplicatePositionKeys(List<ISaMetadata> readers)
    method CheckJsonKey (line 96) | private static void CheckJsonKey(string jsonKey, string description, H...
    method GetReaderMetadata (line 102) | private static (GenomeAssembly Assembly, IEnumerable<IDataSourceVersio...
    method Annotate (line 120) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method GetGeneFusionAnnotations (line 127) | private void GetGeneFusionAnnotations(IAnnotatedPosition annotatedPosi...
    method LoadGeneFusions (line 141) | private void LoadGeneFusions()
    method GetGeneFusionPairs (line 147) | private static IGeneFusionPair[] GetGeneFusionPairs(IAnnotatedVariant ...
    method GetStructuralVariantAnnotations (line 154) | private void GetStructuralVariantAnnotations(IAnnotatedPosition annota...
    method AddPositionAndAlleleAnnotations (line 172) | private void AddPositionAndAlleleAnnotations(IAnnotatedPosition annota...
    method AddSmallAnnotations (line 183) | private void AddSmallAnnotations(IAnnotatedVariant annotatedVariant, b...
    method AddPositionalAnnotation (line 203) | private static void AddPositionalAnnotation(IEnumerable<(string refAll...
    method AddNonAlleleSpecificAnnotations (line 211) | private static void AddNonAlleleSpecificAnnotations(IEnumerable<(strin...
    method AddAlleleSpecificAnnotation (line 226) | private static void AddAlleleSpecificAnnotation(INsaReader nsaReader,
    method PreLoad (line 254) | public void PreLoad(Chromosome chromosome, List<int> positions)
    method DoPreload (line 261) | private static Task DoPreload(INsaReader nsaReader, Chromosome chromos...
    method Dispose (line 264) | public void Dispose()

FILE: VariantAnnotation/Providers/ProteinConservationProvider.cs
  class ProteinConservationProvider (line 9) | public sealed class ProteinConservationProvider:IDisposable
    method ProteinConservationProvider (line 16) | public ProteinConservationProvider(Stream stream)
    method Load (line 22) | public void Load()
    method GetConservationScore (line 31) | public int GetConservationScore(string transcriptId, int position)
    method Dispose (line 38) | public void Dispose() =>_reader?.Dispose();

FILE: VariantAnnotation/Providers/RefMinorProvider.cs
  class RefMinorProvider (line 8) | public sealed class RefMinorProvider : IRefMinorProvider
    method RefMinorProvider (line 12) | public RefMinorProvider(Stream dbStream, Stream indexStream)
    method GetGlobalMajorAllele (line 17) | public string GetGlobalMajorAllele(Chromosome chromosome, int pos) => ...
    method Dispose (line 19) | public void Dispose()

FILE: VariantAnnotation/Providers/ReferenceSequenceProvider.cs
  class ReferenceSequenceProvider (line 12) | public sealed class ReferenceSequenceProvider : ISequenceProvider
    method ReferenceSequenceProvider (line 25) | public ReferenceSequenceProvider(Stream stream)
    method Annotate (line 31) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method PreLoad (line 48) | public void PreLoad(Chromosome chromosome, List<int> positions)
    method LoadChromosome (line 53) | public void LoadChromosome(Chromosome chromosome)
    method Dispose (line 60) | public void Dispose() => _sequenceReader?.Dispose();

FILE: VariantAnnotation/Providers/ScoreProvider.cs
  class ScoreProvider (line 14) | public sealed class ScoreProvider : IAnnotationProvider
    method ScoreProvider (line 22) | public ScoreProvider(ScoreReader[] scoreReaders)
    method Annotate (line 28) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method GetReadersMetadata (line 55) | private (GenomeAssembly Assembly, IEnumerable<IDataSourceVersion> Vers...
    method PreLoad (line 74) | public void PreLoad(Chromosome chromosome, List<int> positions)
    method Dispose (line 78) | public void Dispose()

FILE: VariantAnnotation/Providers/TranscriptAnnotationProvider.cs
  class TranscriptAnnotationProvider (line 24) | public sealed class TranscriptAnnotationProvider : ITranscriptAnnotation...
    method TranscriptAnnotationProvider (line 46) | public TranscriptAnnotationProvider(string pathPrefix, ISequenceProvid...
    method InitiateCache (line 73) | private static (TranscriptCache Cache, IntervalArray<ITranscript>[] Tr...
    method CheckHeaderVersion (line 85) | private static void CheckHeaderVersion(Header header, GenomeAssembly r...
    method GetAssemblyErrorMessage (line 95) | private static string GetAssemblyErrorMessage(GenomeAssembly cacheAsse...
    method Annotate (line 104) | public void Annotate(IAnnotatedPosition annotatedPosition)
    method AddTranscripts (line 120) | private void AddTranscripts(IAnnotatedVariant[] annotatedVariants)
    method AddConservationScore (line 146) | private void AddConservationScore(IAnnotatedTranscript annotatedTransc...
    method PreLoad (line 167) | public void PreLoad(Chromosome chromosome, List<int> positions) => thr...
    method LoadPredictionCaches (line 169) | private void LoadPredictionCaches(ushort refIndex)
    method ClearCache (line 184) | private void ClearCache()
    method AddRegulatoryRegions (line 191) | private static void AddRegulatoryRegions(IAnnotatedVariant[] annotated...
    method SkipLargeVariants (line 221) | private static bool SkipLargeVariants(int begin, int end) => end - beg...
    method Dispose (line 223) | public void Dispose()

FILE: VariantAnnotation/Providers/VersionProvider.cs
  class VersionProvider (line 8) | public sealed class VersionProvider : IVersionProvider

FILE: VariantAnnotation/SA/CustomAnnotationCategories.cs
  type CustomAnnotationCategories (line 3) | public enum CustomAnnotationCategories:byte

FILE: VariantAnnotation/SA/JsonDataType.cs
  type JsonDataType (line 3) | public enum JsonDataType : byte
  class BacisJsonTypeExtension (line 12) | public static class BacisJsonTypeExtension
    method ToTypeString (line 14) | public static string ToTypeString(this JsonDataType jsonDataType)
    method GetSchemaKey (line 33) | public static string GetSchemaKey(this JsonDataType jsonDataType)
    method IsComplexType (line 46) | public static bool IsComplexType(this JsonDataType jsonDataType)

FILE: VariantAnnotation/SA/SaCommon.cs
  class SaCommon (line 3) | public static class SaCommon

FILE: VariantAnnotation/TranscriptAnnotation/FlankingTranscriptAnnotator.cs
  class FlankingTranscriptAnnotator (line 8) | public static class FlankingTranscriptAnnotator
    method GetAnnotatedTranscript (line 10) | public static IAnnotatedTranscript GetAnnotatedTranscript(int variantE...

FILE: VariantAnnotation/TranscriptAnnotation/FullTranscriptAnnotator.cs
  class FullTranscriptAnnotator (line 16) | public static class FullTranscriptAnnotator
    method GetAnnotatedTranscript (line 18) | public static IAnnotatedTranscript GetAnnotatedTranscript(ITranscript ...
    method AnnotateTranscript (line 51) | private static (VariantEffect VariantEffect, IMappedPosition Position,...
    method GetTranscriptRefAllele (line 99) | private static string GetTranscriptRefAllele(IMappedPosition position,...
    method GetCodingFromCdna (line 112) | private static string GetCodingFromCdna(ICodingRegion codingRegion, IS...
    method TryTrimAminoAcidsAndUpdateProteinPositions (line 118) | internal static (SequenceChange AaChange, int ProteinStart, int Protei...
    method GetCoveredAa (line 126) | private static SequenceChange GetCoveredAa(AminoAcids aminoAcids, stri...
    method GetCodingSequence (line 132) | private static ISequence GetCodingSequence(ITranscript transcript, ISe...
    method GetCdnaSequence (line 141) | private static ISequence GetCdnaSequence(ITranscript transcript, ISequ...
    method GetMappedPosition (line 148) | private static IMappedPosition GetMappedPosition(ITranscriptRegion[] r...
    method GetPositionalEffect (line 167) | private static TranscriptPositionalEffect GetPositionalEffect(ITranscr...
    method GetConsequences (line 182) | private static List<ConsequenceTag> GetConsequences(IInterval transcri...
    method GetPredictionScores (line 194) | private static (PredictionScore Sift, PredictionScore PolyPhen) GetPre...
    method NeedPredictionScore (line 207) | private static bool NeedPredictionScore(int proteinStart, int proteinE...
    method GetPredictionScore (line 218) | private static PredictionScore GetPredictionScore(int proteinPosition,...

FILE: VariantAnnotation/TranscriptAnnotation/ReducedTranscriptAnnotator.cs
  class ReducedTranscriptAnnotator (line 12) | public static class ReducedTranscriptAnnotator
    method GetAnnotatedTranscript (line 14) | public static IAnnotatedTranscript GetAnnotatedTranscript(ITranscript ...
    method GetMappedPosition (line 25) | private static IMappedPosition GetMappedPosition(ITranscriptRegion[] r...
    method GetConsequences (line 36) | private static List<ConsequenceTag> GetConsequences(IInterval transcri...

FILE: VariantAnnotation/TranscriptAnnotation/RohTranscriptAnnotator.cs
  class RohTranscriptAnnotator (line 6) | public static class RohTranscriptAnnotator
    method GetAnnotatedTranscript (line 8) | public static IAnnotatedTranscript GetAnnotatedTranscript(ITranscript ...

FILE: VariantAnnotation/TranscriptAnnotation/SequenceChange.cs
  type SequenceChange (line 3) | public struct SequenceChange
    method SequenceChange (line 8) | public SequenceChange(string reference, string alternate)

FILE: VariantAnnotation/TranscriptAnnotation/TranscriptAnnotationFactory.cs
  class TranscriptAnnotationFactory (line 11) | public static class TranscriptAnnotationFactory
    method GetAnnotatedTranscripts (line 16) | public static IList<IAnnotatedTranscript> GetAnnotatedTranscripts(IVar...
    method GetAnnotatedTranscript (line 36) | private static IAnnotatedTranscript GetAnnotatedTranscript(IVariant va...
    method DecideAnnotationStatus (line 65) | internal static Status DecideAnnotationStatus(IInterval variant, IInte...
    type Status (line 85) | public enum Status

FILE: VariantAnnotation/Utilities/BaseFormatting.cs
  class BaseFormatting (line 3) | public static class BaseFormatting
    method EmptyToDash (line 5) | public static string EmptyToDash(string bases) => bases == "" ? "-" : ...

FILE: VariantAnnotation/Utilities/Date.cs
  class Date (line 5) | public static class Date
    method GetDate (line 8) | public static string GetDate(long ticks) => new DateTime(ticks).ToStri...

FILE: VariantAnnotation/Utilities/FormatUtilities.cs
  class FormatUtilities (line 3) | public static class FormatUtilities
    method SplitVersion (line 5) | public static (string Id, byte Version) SplitVersion(string s)

FILE: VariantAnnotation/Utilities/GeneComparer.cs
  class GeneComparer (line 6) | public sealed class GeneComparer : EqualityComparer<IGene>
    method Equals (line 8) | public override bool Equals(IGene x, IGene y)
    method GetHashCode (line 20) | public override int GetHashCode(IGene obj)

FILE: Variants/AnnotationBehavior.cs
  class AnnotationBehavior (line 3) | public sealed class AnnotationBehavior
    method AnnotationBehavior (line 22) | private AnnotationBehavior(bool canonicalTranscriptOnly, bool minimalT...

FILE: Variants/BiDirectionalTrimmer.cs
  class BiDirectionalTrimmer (line 3) | public static class BiDirectionalTrimmer
    method Trim (line 5) | public static (int Start, string RefAllele, string AltAllele) Trim(int...

FILE: Variants/ISimpleVariant.cs
  type ISimpleVariant (line 5) | public interface ISimpleVariant : IChromosomeInterval

FILE: Variants/IVariant.cs
  type IVariant (line 3) | public interface IVariant : ISimpleVariant

FILE: Variants/RepeatExpansion.cs
  class RepeatExpansion (line 5) | public sealed class RepeatExpansion : IVariant
    method RepeatExpansion (line 25) | public RepeatExpansion(Chromosome chromosome, int start, int end, stri...

FILE: Variants/SimpleVariant.cs
  class SimpleVariant (line 5) | public sealed class SimpleVariant : ISimpleVariant
    method SimpleVariant (line 14) | public SimpleVariant(Chromosome chromosome, int start, int end, string...

FILE: Variants/Variant.cs
  class Variant (line 5) | public sealed class Variant : IVariant
    method Initialize (line 21) | public void Initialize(Chromosome chromosome, int start, int end, stri...

FILE: Variants/VariantRotator.cs
  class VariantRotator (line 7) | public static class VariantRotator
    method Right (line 11) | public static ISimpleVariant Right(ISimpleVariant simpleVariant, IInte...
    method GetDownstreamSeq (line 64) | private static string GetDownstreamSeq(IInterval simpleVariant, IInter...
    method GetRotatingBases (line 80) | private static string GetRotatingBases(ISimpleVariant simpleVariant, b...
    method VariantStartOverlapsRegion (line 87) | private static bool VariantStartOverlapsRegion(IInterval variant, IInt...

FILE: Variants/VariantType.cs
  type VariantType (line 3) | public enum VariantType

FILE: Variants/VariantUtils.cs
  class VariantUtils (line 6) | public static class VariantUtils
    method TrimAndLeftAlign (line 11) | public static (int start, string refAllele, string altAllele) TrimAndL...
    method TrimAndLeftAlign (line 36) | private static (int start, string refAllele, string altAllele) TrimAnd...
    method IfRefBaseMismatched (line 87) | private static bool IfRefBaseMismatched(int start, string refAllele, I...
    method IsLeftShiftPossible (line 93) | public static bool IsLeftShiftPossible(string refAllele, string altAll...
    method IsStructuralVariant (line 103) | private static bool IsStructuralVariant(string altAllele)

FILE: Vcf/IVcfFilter.cs
  type IVcfFilter (line 6) | public interface IVcfFilter
    method FastForward (line 8) | void FastForward(StreamReader reader);
    method GetNextLine (line 10) | string GetNextLine(StreamReader reader);
    method PassedTheEnd (line 12) | bool PassedTheEnd(Chromosome chromosome, int position);

FILE: Vcf/Info/CustomFields.cs
  class CustomFields (line 10) | public sealed class CustomFields:ICustomFields
    method Add (line 14) | public void Add(string key, string value)
    method Clear (line 19) | public void Clear()
    method IsEmpty (line 24) | public bool IsEmpty() =>_keyValues.Count == 0;
    method SerializeJson (line 26) | public void SerializeJson(StringBuilder sb)
    method ToString (line 39) | public override string ToString()

FILE: Vcf/Info/InfoData.cs
  type InfoData (line 6) | public sealed record InfoData(string BreakendEventId, int[] CiEnd, int[]...
  class InfoDataBuilder (line 10) | public sealed class InfoDataBuilder
    method Create (line 31) | public InfoData Create() =>
    method Reset (line 35) | public void Reset()

FILE: Vcf/Info/VcfInfoParser.cs
  class VcfInfoParser (line 8) | public static class VcfInfoParser
    method Parse (line 13) | public static IInfoData Parse(string infoField, HashSet<string> custom...
    method ExtractInfoFields (line 90) | private static Dictionary<string, string> ExtractInfoFields(string inf...

FILE: Vcf/NullVcfFilter.cs
  class NullVcfFilter (line 6) | public sealed class NullVcfFilter : IVcfFilter
    method FastForward (line 9) | public void FastForward(StreamReader reader)
    method GetNextLine (line 14) | public string GetNextLine(StreamReader reader) => reader.ReadLine();
    method PassedTheEnd (line 16) | public bool PassedTheEnd(Chromosome chromosome, int position) => false;

FILE: Vcf/Position.cs
  class Position (line 14) | public sealed class Position : IPosition
    method Initialize (line 34) | public void Initialize(Chromosome chromosome, int start, int end, stri...
    method CheckVariants (line 56) | private static (bool HasStructuralVariant, bool HasShortTandemRepeat) ...
    method ToPosition (line 73) | public static IPosition ToPosition(ISimplePosition simplePosition, IRe...
    method GetReferencePosition (line 110) | private static IPosition GetReferencePosition(ISimplePosition simplePo...
    method ExtractEnd (line 115) | private static int ExtractEnd(IInfoData infoData, int start, int refAl...

FILE: Vcf/PositionPool.cs
  class PositionPool (line 8) | public static class PositionPool
    method Get (line 12) | public static Position Get(Chromosome chromosome, int start, int end, ...
    method Return (line 23) | public static void Return(Position position) => Pool.Return(position);

FILE: Vcf/Sample/BooleanExtensions.cs
  class BooleanExtensions (line 3) | internal static class BooleanExtensions
    method GetFailedFilter (line 5) | internal static bool GetFailedFilter(this string ftField)
    method IsDeNovo (line 11) | internal static bool IsDeNovo(this string dnField)

FILE: Vcf/Sample/FormatIndices.cs
  class FormatIndices (line 6) | public sealed class FormatIndices
    method Clear (line 45) | private void Clear()
    method FormatIndices (line 86) | public FormatIndices(HashSet<string> customFields=null)
    method Set (line 96) | internal void Set(string formatColumn)

FILE: Vcf/Sample/Legacy/AlleleDepths.cs
  class AlleleDepths (line 5) | internal static class AlleleDepths
    method GetAlleleDepths (line 10) | public static int[] GetAlleleDepths(IntermediateSampleFields intermedi...
    method GetAlleleDepthsUsingTarTir (line 29) | private static int[] GetAlleleDepthsUsingTarTir(IntermediateSampleFiel...
    method GetAlleleDepthsUsingAlleleCounts (line 38) | private static int[] GetAlleleDepthsUsingAlleleCounts(IntermediateSamp...
    method GetAlleleCountString (line 68) | private static int? GetAlleleCountString(string s, IntermediateSampleF...
    method GetAlleleDepthsUsingAd (line 95) | private static int[] GetAlleleDepthsUsingAd(IntermediateSampleFields i...

FILE: Vcf/Sample/Legacy/FailedFilter.cs
  class FailedFilter (line 3) | internal static class FailedFilter
    method GetFailedFilter (line 5) | public static bool GetFailedFilter(IntermediateSampleFields intermedia...

FILE: Vcf/Sample/Legacy/Genotype.cs
  class Genotype (line 3) | internal static class Genotype
    method GetGenotype (line 5) | public static string GetGenotype(IntermediateSampleFields intermediate...

FILE: Vcf/Sample/Legacy/GenotypeQuality.cs
  class GenotypeQuality (line 5) | internal static class GenotypeQuality
    method GetGenotypeQuality (line 7) | public static int? GetGenotypeQuality(IntermediateSampleFields interme...

FILE: Vcf/Sample/Legacy/IntermediateSampleFields.cs
  class IntermediateSampleFields (line 6) | public sealed class IntermediateSampleFields
    method IntermediateSampleFields (line 32) | public IntermediateSampleFields(string[] vcfColumns, FormatIndices for...
    method GetString (line 54) | private static string GetString(int? index, string[] cols)
    method GetFloat (line 61) | private static float? GetFloat(string s)
    method GetDouble (line 68) | private static double? GetDouble(string s)
    method GetInteger (line 75) | private static int? GetInteger(string s)
    method GetLinkedIntegers (line 82) | private static (int?, int?) GetLinkedIntegers(string s, string s2)
    method GetStrings (line 90) | private static string[] GetStrings(string s) => s?.OptimizedSplit(',');
    method GetCopyNumber (line 92) | private static int? GetCopyNumber(string s, bool containsStr)
    method GetAlleleCounts (line 98) | private static (int?, int?, int?, int?, int?) GetAlleleCounts(string a...
    method GetFirstValue (line 110) | private static string GetFirstValue(string s) => GetStrings(s)?[0];

FILE: Vcf/Sample/Legacy/LegacySampleFieldExtractor.cs
  class LegacySampleFieldExtractor (line 7) | public sealed class LegacySampleFieldExtractor
    method LegacySampleFieldExtractor (line 13) | internal LegacySampleFieldExtractor(string[] vcfColumns, FormatIndices...
    method GetInfoDepth (line 20) | private static int? GetInfoDepth(string infoColumn)
    method ExtractSample (line 33) | internal ISample ExtractSample(string sampleColumn)

FILE: Vcf/Sample/Legacy/LegacyVariantFrequency.cs
  class LegacyVariantFrequency (line 5) | internal static class LegacyVariantFrequency
    method GetVariantFrequencies (line 9) | public static double[] GetVariantFrequencies(IntermediateSampleFields ...
    method GetVariantFrequenciesUsingVf (line 30) | private static double[] GetVariantFrequenciesUsingVf(IntermediateSampl...
    method GetVariantFrequenciesUsingAlleleCounts (line 36) | private static double[] GetVariantFrequenciesUsingAlleleCounts(Interme...
    method AreAllAltAllelesSingleBase (line 59) | internal static bool AreAllAltAllelesSingleBase(this string[] altAlleles)
    method GetAlleleCount (line 67) | private static int GetAlleleCount(IntermediateSampleFields sampleField...
    method GetVariantFrequenciesUsingTarTir (line 92) | private static double[] GetVariantFrequenciesUsingTarTir(IntermediateS...
    method GetVariantFrequenciesUsingAlleleDepths (line 103) | private static double[] GetVariantFrequenciesUsingAlleleDepths(Interme...
    method GetAlleleDepths (line 125) | private static (int[] AlleleDepths, bool AllValuesAreValid, int totalD...

FILE: Vcf/Sample/Legacy/ReadCounts.cs
  class ReadCounts (line 5) | internal static class ReadCounts
    method GetPairEndReadCounts (line 7) | public static int[] GetPairEndReadCounts(IntermediateSampleFields inte...
    method GetSplitReadCounts (line 24) | public static int[] GetSplitReadCounts(IntermediateSampleFields interm...

FILE: Vcf/Sample/Legacy/TotalDepth.cs
  class TotalDepth (line 5) | internal static class TotalDepth
    method GetTotalDepth (line 7) | public static int? GetTotalDepth(int? infoDepth, IntermediateSampleFie...
    method GetTotalDepthUsingTarTir (line 25) | private static int? GetTotalDepthUsingTarTir(IntermediateSampleFields ...
    method GetTotalDepthUsingAlleleCounts (line 27) | private static int? GetTotalDepthUsingAlleleCounts(IntermediateSampleF...
    method GetTotalDepthUsingDpi (line 29) | private static int? GetTotalDepthUsingDpi(IntermediateSampleFields int...
    method GetTotalDepthUsingDp (line 37) | private static int? GetTotalDepthUsingDp(IntermediateSampleFields inte...

FILE: Vcf/Sample/Sample.cs
  class Sample (line 7) | public sealed class Sample : ISample
    method Sample (line 40) | public Sample(int[] alleleDepths, float? artifactAdjustedQualityScore,...

FILE: Vcf/Sample/SampleFieldExtractor.cs
  class SampleFieldExtractor (line 13) | internal static class SampleFieldExtractor
    method ToSamples (line 15) | internal static ISample[]  ToSamples(this string[] vcfColumns, FormatI...
    method ExtractSample (line 36) | internal static ISample ExtractSample(string sampleColumn, FormatIndic...
    method GetLoh (line 98) | private static bool? GetLoh(int? copyNumber, int? minorHaplotypeCopyNu...
    method IsLegacyVariantCaller (line 105) | private static bool IsLegacyVariantCaller(FormatIndices formatIndices)
    method NormalizeNulls (line 119) | internal static void NormalizeNulls(this string[] cols)

FILE: Vcf/Sample/SampleParsingExtensions.cs
  class SampleParsingExtensions (line 6) | public static class SampleParsingExtensions
    method GetString (line 8) | internal static string GetString(this string[] cols, int? index) => in...
    method GetFloat (line 10) | internal static float? GetFloat(this string s)
    method GetDouble (line 17) | internal static double? GetDouble(this string s)
    method GetInteger (line 24) | internal static int? GetInteger(this string s)
    method GetStrings (line 31) | internal static string[] GetStrings(this string s) => s?.OptimizedSpli...
    method GetIntegers (line 33) | public static int[] GetIntegers(this string s, char delimiter = ',')

FILE: Vcf/Sample/VariantFrequency.cs
  class VariantFrequency (line 3) | internal static class VariantFrequency
    method GetVariantFrequencies (line 5) | public static double[] GetVariantFrequencies(double? vfField, int[] al...
    method GetVariantFrequenciesUsingVf (line 15) | private static double[] GetVariantFrequenciesUsingVf(double? vf, bool ...
    method GetVariantFrequenciesUsingAlleleDepths (line 21) | private static double[] GetVariantFrequenciesUsingAlleleDepths(int[] a...

FILE: Vcf/SimplePosition.cs
  class SimplePosition (line 9) | public sealed class SimplePosition : ISimplePosition
    method SimplePosition (line 22) | internal SimplePosition(Chromosome chromosome, int start, string refAl...
    method GetSimplePosition (line 30) | public static SimplePosition GetSimplePosition(Chromosome chromosome, ...

FILE: Vcf/StringExtensions.cs
  class StringExtensions (line 6) | public static class StringExtensions
    method GetNullableInt (line 10) | public static int? GetNullableInt(this string str)
    method GetNullableValue (line 16) | public static T? GetNullableValue<T>(this string str, TryParse<T> pars...
    method SplitToArray (line 29) | public static int[] SplitToArray(this string s)

FILE: Vcf/VariantCreator/CnvCreator.cs
  class CnvCreator (line 7) | public static class CnvCreator
    method Create (line 9) | public static IVariant Create(Chromosome chromosome, int start, int en...
    method GetVariantType (line 20) | private static VariantType GetVariantType(string altAllele)

FILE: Vcf/VariantCreator/LegacyVariantId.cs
  class LegacyVariantId (line 14) | public sealed class LegacyVariantId : IVariantIdCreator
    method LegacyVariantId (line 18) | public LegacyVariantId(Dictionary<string, Chromosome> refNameToChromos...
    method Create (line 20) | public string Create(ISequence sequence, VariantCategory category, str...
    method Normalize (line 43) | public (int Start, string RefAllele, string AltAllele) Normalize(ISequ...
    method GetSvVid (line 49) | private static string GetSvVid(Dictionary<string, Chromosome> refNameT...
    method ParseBreakendAltAllele (line 84) | private static (Chromosome Chromosome2, int Position2, bool IsSuffix1,...
    method GetCnvVid (line 125) | private static string GetCnvVid(Chromosome chromosome, int start, int ...
    method GetSmallVariantVid (line 144) | internal static string GetSmallVariantVid(Chromosome chromosome, int s...
    method GetInsertedAltAllele (line 164) | private static string GetInsertedAltAllele(string altAllele)
    method GetRepeatExpansionVid (line 184) | private static string GetRepeatExpansionVid(Chromosome chromosome, int...

FILE: Vcf/VariantCreator/ReferenceVariantCreator.cs
  class ReferenceVariantCreator (line 7) | public static class ReferenceVariantCreator
    method Create (line 9) | public static IVariant[] Create(IVariantIdCreator vidCreator, ISequenc...

FILE: Vcf/VariantCreator/RepeatExpansionCreator.cs
  class RepeatExpansionCreator (line 8) | public static class RepeatExpansionCreator
    method Create (line 10) | public static IVariant Create(Chromosome chromosome, int start, int en...

FILE: Vcf/VariantCreator/RohVariantCreator.cs
  class RohVariantCreator (line 7) | public static class RohVariantCreator
    method Create (line 9) | public static IVariant Create(Chromosome chromosome, int start, int en...

FILE: Vcf/VariantCreator/SmallVariantCreator.cs
  class SmallVariantCreator (line 8) | public static class SmallVariantCreator
    method Create (line 10) | public static IVariant Create(Chromosome chromosome, int start, int en...
    method GetVariantType (line 23) | public static VariantType GetVariantType(string refAllele, string altA...

FILE: Vcf/VariantCreator/StructuralVariantCreator.cs
  class StructuralVariantCreator (line 7) | public static class StructuralVariantCreator
    method Create (line 9) | public static IVariant Create(Chromosome chromosome, int start, int en...
    method GetVariantType (line 22) | public static VariantType GetVariantType(string altAllele, string svType)

FILE: Vcf/VariantCreator/VariantFactory.cs
  class VariantFactory (line 14) | public sealed class VariantFactory
    method VariantFactory (line 20) | public VariantFactory(ISequence sequence, IVariantIdCreator vidCreator...
    method CreateVariants (line 27) | public IVariant[] CreateVariants(Chromosome chromosome, int start, int...
    method GetVariantCategory (line 62) | internal static VariantCategory GetVariantCategory(string firstAltAlle...
    method IsBreakend (line 73) | private static bool IsBreakend(string altAllele) => altAllele.Contains...
    method IsSymbolicAllele (line 75) | private static bool IsSymbolicAllele(string altAllele) =>
    method GetVariant (line 78) | private IVariant GetVariant(Chromosome chromosome, int start, int end,...

FILE: Vcf/VariantCreator/VariantId.cs
  class VariantId (line 7) | public sealed class VariantId : IVariantIdCreator
    method Create (line 9) | public string Create(ISequence sequence, VariantCategory category, str...
    method Normalize (line 40) | public (int Start, string RefAllele, string AltAllele) Normalize(ISequ...
    method GetVid (line 43) | private static string GetVid(string chromosomeName, int paddedPosition...
    method GetLongVid (line 47) | private static string GetLongVid(string chromosomeName, int paddedPosi...

FILE: Vcf/VcfFilter.cs
  class VcfFilter (line 8) | public sealed class VcfFilter : IVcfFilter
    method VcfFilter (line 14) | public VcfFilter(GenomicRange genomicRange)
    method FastForward (line 20) | public void FastForward(StreamReader reader)
    method GetNextLine (line 41) | public string GetNextLine(StreamReader reader)
    method PassedTheEnd (line 53) | public bool PassedTheEnd(Chromosome chromosome, int position) => _geno...

FILE: Vcf/VcfReader.cs
  class VcfReader (line 15) | public sealed class VcfReader : IVcfReader
    method GetSampleNames (line 36) | public          string[]        GetSampleNames() => _sampleNames;
    method VcfReader (line 40) | private VcfReader(
    method Create (line 65) | public static VcfReader Create(StreamReader headerReader, StreamReader...
    method ParseHeader (line 76) | private void ParseHeader()
    method CheckContigId (line 93) | private void CheckContigId(string line)
    method GetChromAndLengthInfo (line 117) | internal static string[] GetChromAndLengthInfo(string line)
    method ValidateVcfHeader (line 125) | private void ValidateVcfHeader()
    method ExtractSampleNames (line 134) | private static string[] ExtractSampleNames(string line)
    method GetNextSimplePosition (line 146) | private ISimplePosition GetNextSimplePosition()
    method InconsistentSampleFields (line 175) | private bool InconsistentSampleFields(string[] vcfFields)
    method CheckVcfOrder (line 186) | private void CheckVcfOrder(string referenceName)
    method GetNextPosition (line 199) | public IPosition GetNextPosition() => Position.ToPosition(GetNextSimpl...
    method Dispose (line 203) | public void Dispose() => _reader?.Dispose();