SYMBOL INDEX (1041 symbols across 253 files) FILE: docs/app.js function resetFilters (line 225) | function resetFilters() { function syncFilterState (line 256) | function syncFilterState() { function loadBundledExample (line 271) | async function loadBundledExample() { function loadFromBlob (line 288) | async function loadFromBlob(blob, fileName) { function readBlobText (line 301) | async function readBlobText(blob, fileName) { function readResponseText (line 312) | async function readResponseText(response, fileName) { function ingestText (line 323) | function ingestText(text, fileName) { function makeRow (line 359) | function makeRow(index, cells, sampleHeaders) { function deriveEventType (line 400) | function deriveEventType(row) { function parseSampleField (line 432) | function parseSampleField(header, raw, evidence) { function rebuildChipGroups (line 453) | function rebuildChipGroups() { function renderChipList (line 460) | function renderChipList(container, counts, filterKey) { function render (line 491) | function render() { function applyFilters (line 501) | function applyFilters(rows) { function sortRows (line 546) | function sortRows(rows) { function sortableValue (line 569) | function sortableValue(row, key) { function updateSummary (line 579) | function updateSummary() { function renderTable (line 602) | function renderTable() { function renderDetail (line 683) | function renderDetail() { function detailCard (line 766) | function detailCard(label, value) { function detailPair (line 770) | function detailPair(label, value) { function reconcileSelection (line 774) | function reconcileSelection() { function findSelectedRow (line 781) | function findSelectedRow() { function exportFilteredRows (line 785) | function exportFilteredRows() { function countBy (line 800) | function countBy(rows, key) { function topCountValue (line 809) | function topCountValue(rows, key) { function toggleSetValue (line 822) | function toggleSetValue(set, value) { function setStatus (line 830) | function setStatus(message) { function passesNumericRange (line 834) | function passesNumericRange(value, min, max) { function passesNumericMinimum (line 850) | function passesNumericMinimum(value, min) { function parseNullableNumber (line 860) | function parseNullableNumber(raw) { function parseMaybeNumber (line 868) | function parseMaybeNumber(raw) { function formatNumber (line 876) | function formatNumber(value) { function presentOrX (line 888) | function presentOrX(value) { function normalizeSortNumber (line 892) | function normalizeSortNumber(value) { function zeroIfNull (line 902) | function zeroIfNull(value) { function stripLeadingHash (line 906) | function stripLeadingHash(value) { function escapeHtml (line 910) | function escapeHtml(value) { FILE: src/SGA/Algorithm/ClusterProcess.cpp function ClusterResult (line 30) | ClusterResult ClusterProcess::process(const SequenceWorkItem& item) function ClusterResult (line 106) | ClusterResult ClusterProcess::process(const ClusterVector& inSequences) FILE: src/SGA/Algorithm/ClusterProcess.h type ClusterParameters (line 21) | struct ClusterParameters type ClusterResult (line 32) | struct ClusterResult function class (line 38) | class ClusterProcess function class (line 56) | class ClusterPostProcess FILE: src/SGA/Algorithm/ConnectProcess.cpp function ConnectResult (line 33) | ConnectResult ConnectProcess::process(const SequenceWorkItemPair& workIt... FILE: src/SGA/Algorithm/ConnectProcess.h function class (line 21) | class ConnectResult function class (line 28) | class ConnectProcess function class (line 47) | class ConnectPostProcess FILE: src/SGA/Algorithm/DPAlignment.cpp function DPScoringScheme (line 45) | DPScoringScheme DPAlignment::getScoringScheme() const function DPOperation (line 147) | DPOperation DPAlignment::getPathOperationToCell(const std::string& s1, c... function DPPath (line 187) | DPPath DPAlignment::calculatePath(const std::string& s1, const std::stri... FILE: src/SGA/Algorithm/DPAlignment.h function min3 (line 14) | inline int min3(int a, int b, int c) function max3 (line 19) | inline int max3(int a, int b, int c) function class (line 26) | class EditDistanceScoring function class (line 35) | class SimilarityScoring type DPOperation (line 44) | enum DPOperation type DPPathNode (line 54) | struct DPPathNode function compare3 (line 133) | inline int compare3(int a, int b, int c) const type std (line 151) | typedef std::vector IntVector; type std (line 152) | typedef std::vector IntMatrix; FILE: src/SGA/Algorithm/ErrorCorrectProcess.cpp function ErrorCorrectResult (line 34) | ErrorCorrectResult ErrorCorrectProcess::process(const SequenceWorkItem& ... function ErrorCorrectResult (line 42) | ErrorCorrectResult ErrorCorrectProcess::correct(const SequenceWorkItem& ... function ErrorCorrectResult (line 79) | ErrorCorrectResult ErrorCorrectProcess::overlapCorrection(const Sequence... function ErrorCorrectResult (line 160) | ErrorCorrectResult ErrorCorrectProcess::overlapCorrectionNew(const Seque... function ErrorCorrectResult (line 209) | ErrorCorrectResult ErrorCorrectProcess::kmerCorrection(const SequenceWor... function ErrorCorrectResult (line 412) | ErrorCorrectResult ErrorCorrectProcess::threadingCorrection(const Sequen... FILE: src/SGA/Algorithm/ErrorCorrectProcess.h type ErrorCorrectAlgorithm (line 23) | enum ErrorCorrectAlgorithm type ECFlag (line 31) | enum ECFlag type ErrorCorrectParameters (line 40) | struct ErrorCorrectParameters function class (line 63) | class ErrorCorrectResult function class (line 79) | class ErrorCorrectProcess function class (line 102) | class ErrorCorrectPostProcess FILE: src/SGA/Algorithm/ExtensionDP.cpp function max3 (line 26) | inline int max3(int a, int b, int c) function min3 (line 32) | inline int min3(int a, int b, int c) function BandedDPColumn (line 92) | const BandedDPColumn* BandedDPColumn::getPreviousColumn() const function BandedDPColumn (line 192) | BandedDPColumn* ExtensionDP::createNewColumn(char b, const std::string& ... function ExtensionDPAlignment (line 376) | ExtensionDPAlignment ExtensionDP::findTrimmedAlignment(const BandedDPCol... function ExtensionDPAlignment (line 447) | ExtensionDPAlignment ExtensionDP::findGlocalAlignment(const BandedDPColu... FILE: src/SGA/Algorithm/ExtensionDP.h type std (line 30) | typedef std::vector CellVector; type ExtensionDPAlignment (line 34) | struct ExtensionDPAlignment function getBestRowIndex (line 68) | int getBestRowIndex() const; FILE: src/SGA/Algorithm/FMMergeProcess.cpp function FMMergeResult (line 30) | FMMergeResult FMMergeProcess::process(const SequenceWorkItem& item) FILE: src/SGA/Algorithm/FMMergeProcess.h type FMMergeResult (line 19) | struct FMMergeResult type FMMergeCandidate (line 33) | struct FMMergeCandidate type std (line 39) | typedef std::queue FMMergeQueue; function class (line 42) | class FMMergeProcess function class (line 74) | class FMMergePostProcess FILE: src/SGA/Algorithm/GapFillProcess.cpp function GapFillResult (line 54) | GapFillResult GapFillProcess::processScaffold(const std::string& scaffol... function GapFillReturnCode (line 143) | GapFillReturnCode GapFillProcess::processGap(size_t k, int estimatedSize... function AnchorSequence (line 190) | AnchorSequence GapFillProcess::findAnchor(size_t k, const std::string& s... function GapFillReturnCode (line 228) | GapFillReturnCode GapFillProcess::selectGapSequence(int estimatedSize, c... FILE: src/SGA/Algorithm/GapFillProcess.h type GapFillParameters (line 28) | struct GapFillParameters type GapFillResult (line 46) | struct GapFillResult type GapFillReturnCode (line 51) | enum GapFillReturnCode type GapFillStats (line 66) | struct GapFillStats function class (line 81) | class GapFillProcess function class (line 123) | class GapFillPostProcess FILE: src/SGA/Algorithm/HaplotypeBuilder.cpp function HaplotypeBuilderReturnCode (line 65) | HaplotypeBuilderReturnCode HaplotypeBuilder::run() function HaplotypeBuilderReturnCode (line 136) | HaplotypeBuilderReturnCode HaplotypeBuilder::parseWalks(HaplotypeBuilder... FILE: src/SGA/Algorithm/HaplotypeBuilder.h type AnchorSequence (line 20) | struct AnchorSequence type std (line 32) | typedef std::vector AnchorVector; type HaplotypeBuilderResult (line 35) | struct HaplotypeBuilderResult type HaplotypeBuilderReturnCode (line 41) | enum HaplotypeBuilderReturnCode function class (line 52) | class HaplotypeBuilder FILE: src/SGA/Algorithm/KmerOverlaps.cpp function MultipleAlignment (line 18) | MultipleAlignment KmerOverlaps::buildMultipleAlignment(const std::string... type KmerMatch (line 37) | struct KmerMatch type KmerMatchKey (line 58) | struct KmerMatchKey function SequenceOverlapPairVector (line 67) | SequenceOverlapPairVector KmerOverlaps::retrieveMatches(const std::strin... type SeedEdit (line 215) | struct SeedEdit method SeedEdit (line 217) | SeedEdit(int i, char b) : index(i), base(b) {} type ApproxSeed (line 224) | struct ApproxSeed function _approximateSeededMatch (line 240) | void _approximateSeededMatch(const std::string& in_query, function SequenceOverlapPairVector (line 454) | SequenceOverlapPairVector KmerOverlaps::approximateMatch(const std::stri... FILE: src/SGA/Algorithm/KmerOverlaps.h type SequenceOverlapPair (line 18) | struct SequenceOverlapPair type std (line 27) | typedef std::vector SequenceOverlapPairVector; function namespace (line 29) | namespace KmerOverlaps FILE: src/SGA/Algorithm/LRAlignment.cpp type LRAlignment (line 18) | namespace LRAlignment function bwaswAlignment (line 58) | void bwaswAlignment(const std::string& query, const BWT* pTargetBWT, c... function updateStack (line 272) | int updateStack(LRStack* pStack, function saveBestPositionHits (line 354) | void saveBestPositionHits(const SuffixArray* pQuerySA, LRStackEntry* u... function saveAllHits (line 402) | void saveAllHits(const SuffixArray* pQuerySA, const SampledSuffixArray... function saveTerminalHits (line 437) | void saveTerminalHits(const SuffixArray* pQuerySA, const SampledSuffix... function initializeDAWGHash (line 476) | void initializeDAWGHash(BWT* pQueryBWT, LRHash& hashTable) function mergeStackEntries (line 515) | void mergeStackEntries(LRStackEntry* u, LRStackEntry* v) function removeDuplicateCells (line 533) | void removeDuplicateCells(LRStackEntry* u, LRHash& hash) function fillCells (line 589) | int fillCells(const LRParams& params, int match_score, LRCell* c[4]) function resolveDuplicateHitsByID (line 625) | int resolveDuplicateHitsByID(const BWT* pTargetBWT, const SampledSuffi... function resolveDuplicateHits (line 688) | int resolveDuplicateHits(const BWT* pTargetBWT, const SampledSuffixArr... function cutTail (line 838) | void cutTail(LRStackEntry* u, const LRParams& params) function cutTailByScorePercent (line 861) | void cutTailByScorePercent(LRStackEntry* u, const LRParams& params) function cutTailByZBest (line 889) | void cutTailByZBest(LRStackEntry* u, const LRParams& params) function cutTailByStratifiedZBest (line 940) | void cutTailByStratifiedZBest(LRStackEntry* u, const LRParams& params) function MultiAlignment (line 1026) | MultiAlignment convertHitsToMultiAlignment(const std::string& query, function extendHitFullLength (line 1104) | void extendHitFullLength(LRHit& hit, uint8_t* pQueryPacked, uint8_t* p... FILE: src/SGA/Algorithm/LRAlignment.h function namespace (line 22) | namespace LRAlignment type LRHit (line 64) | struct LRHit FILE: src/SGA/Algorithm/OverlapAlgorithm.cpp function OverlapResult (line 19) | OverlapResult OverlapAlgorithm::overlapRead(const SeqRecord& read, int m... function OverlapResult (line 34) | OverlapResult OverlapAlgorithm::overlapReadInexact(const SeqRecord& read... function OverlapResult (line 138) | OverlapResult OverlapAlgorithm::alignReadDuplicate(const SeqRecord& read... function OverlapResult (line 153) | OverlapResult OverlapAlgorithm::overlapReadExact(const SeqRecord& read, ... FILE: src/SGA/Algorithm/OverlapAlgorithm.h type OverlapMode (line 21) | enum OverlapMode type OverlapResult (line 27) | struct OverlapResult function class (line 34) | class OverlapAlgorithm function setExactModeIrreducible (line 75) | void setExactModeIrreducible(bool b) { m_exactModeIrreducible = b; } function BWT (line 78) | const BWT* getBWT() const { return m_pBWT; } function BWT (line 79) | const BWT* getRBWT() const { return m_pRevBWT; } FILE: src/SGA/Algorithm/OverlapBlock.cpp function BWT (line 35) | const BWT* OverlapBlock::getExtensionBWT(const BWT* pBWT, const BWT* pRe... function AlphaCount64 (line 44) | AlphaCount64 OverlapBlock::getCanonicalExtCount(const BWT* pBWT, const B... function BWTInterval (line 62) | BWTInterval OverlapBlock::getCanonicalInterval() const function EdgeDir (line 114) | EdgeDir OverlapBlock::getEdgeDir() const function Overlap (line 123) | Overlap OverlapBlock::toOverlap(const std::string queryID, const std::st... function printBlockList (line 161) | void printBlockList(const OverlapBlockList* pList) function removeSubMaximalBlocks (line 170) | void removeSubMaximalBlocks(OverlapBlockList* pList, const BWT* pBWT, co... type TracingInterval (line 218) | struct TracingInterval function OverlapBlockList (line 232) | OverlapBlockList resolveOverlap(const OverlapBlock& A, const OverlapBloc... function partitionBlockList (line 434) | void partitionBlockList(int readLen, OverlapBlockList* pCompleteList, function removeContainmentBlocks (line 449) | void removeContainmentBlocks(int readLen, OverlapBlockList* pList) function MultiOverlap (line 462) | MultiOverlap blockListToMultiOverlap(const SeqRecord& record, OverlapBlo... function makeIdxString (line 504) | std::string makeIdxString(int64_t idx) FILE: src/SGA/Algorithm/OverlapBlock.h function isQueryRev (line 24) | struct AlignFlags function write (line 54) | void write(std::ostream& out) function read (line 59) | void read(std::istream& in) function setTargetRev (line 67) | void setTargetRev(bool b) { data.set(TARGETREV_BIT, b); } function setQueryComp (line 68) | void setQueryComp(bool b) { data.set(QUERYCOMP_BIT, b); } function sortSizeDescending (line 78) | struct OverlapBlock function sortIntervalLeft (line 148) | static bool sortIntervalLeft(const OverlapBlock& ob1, const OverlapBlock... type std (line 190) | typedef std::list OverlapBlockList; type OverlapBlockList (line 191) | typedef OverlapBlockList::iterator OBLIter; FILE: src/SGA/Algorithm/OverlapTools.h function namespace (line 17) | namespace OverlapTools FILE: src/SGA/Algorithm/QCProcess.cpp type KmerWindow (line 14) | struct KmerWindow method getCount (line 16) | int64_t getCount(bool bothStrand) const function QCResult (line 49) | QCResult QCProcess::process(const SequenceWorkItem& workItem) function DuplicateCheckResult (line 202) | DuplicateCheckResult QCProcess::performDuplicateCheck(const SequenceWork... FILE: src/SGA/Algorithm/QCProcess.h function setDefaults (line 20) | struct QCParameters function class (line 105) | class QCResult type DuplicateCheckResult (line 116) | enum DuplicateCheckResult function class (line 124) | class QCProcess function class (line 153) | class QCPostProcess FILE: src/SGA/Algorithm/ReadCluster.cpp function ClusterNode (line 30) | ClusterNode ReadCluster::addSeed(const std::string& sequence, bool bChec... function ClusterNodeVector (line 195) | ClusterNodeVector ReadCluster::getOutput() const FILE: src/SGA/Algorithm/ReadCluster.h function equal (line 17) | struct ClusterNode type std (line 34) | typedef std::queue ClusterNodeQueue; type std (line 35) | typedef std::vector ClusterNodeVector; type std (line 36) | typedef std::set ClusterIntervalSet; function class (line 39) | class ReadCluster FILE: src/SGA/Algorithm/SearchHistory.cpp function SearchHistoryLink (line 38) | SearchHistoryLink& SearchHistoryLink::operator=(SearchHistoryLink const&... function SearchHistoryLink (line 72) | SearchHistoryLink SearchHistoryNode::createChild(int var_pos, char var_b... function SearchHistoryLink (line 78) | SearchHistoryLink SearchHistoryNode::createRoot() function SearchHistoryVector (line 84) | SearchHistoryVector SearchHistoryNode::getHistoryVector() FILE: src/SGA/Algorithm/SearchHistory.h type SearchHistoryItem (line 15) | struct SearchHistoryItem type std (line 32) | typedef std::vector HistoryItemVector; function class (line 35) | class SearchHistoryVector function class (line 71) | class SearchHistoryLink function class (line 95) | class SearchHistoryNode FILE: src/SGA/Algorithm/SearchSeed.h type ExtendDirection (line 19) | enum ExtendDirection function isSeed (line 26) | struct SearchSeed FILE: src/SGA/Algorithm/StatsProcess.cpp function StatsResult (line 43) | StatsResult StatsProcess::process(const SequenceWorkItem& workItem) FILE: src/SGA/Algorithm/StatsProcess.h function class (line 19) | class StatsResult function class (line 31) | class StatsProcess function class (line 52) | class StatsPostProcess FILE: src/SGA/Algorithm/StringGraphGenerator.cpp function SGWalkVector (line 105) | SGWalkVector StringGraphGenerator::searchWalks() function Vertex (line 178) | Vertex* StringGraphGenerator::addTerminalVertex(const SeqRecord& record) FILE: src/SGA/Algorithm/StringGraphGenerator.h type GraphFrontier (line 22) | struct GraphFrontier type std (line 29) | typedef std::queue FrontierQueue; function class (line 31) | class StringGraphGenerator FILE: src/SGA/Algorithm/StringThreader.cpp function StringThreaderNode (line 66) | StringThreaderNode* StringThreaderNode::createChild(const std::string& l... function StringThreaderResult (line 133) | StringThreaderResult StringThreaderNode::getAlignment() const function StringVector (line 304) | StringVector StringThreader::getDeBruijnExtensions(StringThreaderNode* p... FILE: src/SGA/Algorithm/StringThreader.h type std (line 23) | typedef std::list STNodePtrList; type StringThreaderResult (line 26) | struct StringThreaderResult type std (line 31) | typedef std::vector StringThreaderResultVector; function getGlobalErrorRate (line 59) | double getGlobalErrorRate() const; FILE: src/SGA/Algorithm/VariationBuilderCommon.h type BubbleResultCode (line 21) | enum BubbleResultCode type BubbleResult (line 35) | struct BubbleResult type BuilderExtensionNode (line 46) | struct BuilderExtensionNode type std (line 55) | typedef std::queue BuilderExtensionQueue; type std (line 56) | typedef std::map StrIntMap; function namespace (line 59) | namespace VariationBuilderCommon FILE: src/SGA/Bigraph/Bigraph.cpp function Vertex (line 124) | Vertex* Bigraph::getVertex(VertexID id) const function VertexIDVec (line 443) | VertexIDVec Bigraph::getNonBranchingVertices() const function PathVector (line 464) | PathVector Bigraph::getLinearComponents() function Path (line 485) | Path Bigraph::constructLinearPath(VertexID id) function Path (line 524) | Path Bigraph::reversePath(const Path& path) function Vertex (line 533) | Vertex* Bigraph::getFirstVertex() const function VertexPtrVec (line 542) | VertexPtrVec Bigraph::getAllVertices() const FILE: src/SGA/Bigraph/Bigraph.h type std (line 29) | typedef std::unordered_map VertexPtrMap; type VertexPtrMap (line 32) | typedef VertexPtrMap::iterator VertexPtrMapIter; type VertexPtrMap (line 33) | typedef VertexPtrMap::const_iterator VertexPtrMapConstIter; type EdgePtrVec (line 38) | typedef EdgePtrVec Path; type std (line 39) | typedef std::vector PathVector; type std (line 40) | typedef std::vector VertexIDVec; type std (line 41) | typedef std::vector VertexPtrVec; function class (line 43) | class Bigraph FILE: src/SGA/Bigraph/Edge.cpp function EdgeDesc (line 13) | EdgeDesc Edge::getTwinDesc() const function Match (line 61) | Match Edge::getMatch() const function Overlap (line 69) | Overlap Edge::getOverlap() const FILE: src/SGA/Bigraph/Edge.h function setDir (line 26) | struct EdgeData function setComp (line 40) | void setComp(EdgeComp comp) function flipDir (line 48) | void flipDir() { m_data.flip(DIR_BIT); } function flipComp (line 49) | void flipComp() { m_data.flip(COMP_BIT); } function class (line 68) | class Edge FILE: src/SGA/Bigraph/EdgeDesc.h type EdgeDesc (line 16) | struct EdgeDesc FILE: src/SGA/Bigraph/GraphCommon.h type EdgeDir (line 18) | enum EdgeDir type EdgeComp (line 28) | enum EdgeComp type DotFlags (line 38) | enum DotFlags type GraphColor (line 47) | typedef uint8_t GraphColor; type std (line 56) | typedef std::string VertexID; type std (line 57) | typedef std::vector VertexIDVec; function EdgeDir (line 73) | inline EdgeDir correctDir(EdgeDir dir, EdgeComp comp) FILE: src/SGA/Bigraph/Vertex.cpp function MultiOverlap (line 158) | MultiOverlap Vertex::getMultiOverlap() const function EdgePtrVecIter (line 272) | EdgePtrVecIter Vertex::findEdge(const EdgeDesc& ed) function EdgePtrVecConstIter (line 283) | EdgePtrVecConstIter Vertex::findEdge(const EdgeDesc& ed) const function Edge (line 317) | Edge* Vertex::getEdge(const EdgeDesc& ed) function EdgePtrVec (line 325) | EdgePtrVec Vertex::findEdgesTo(VertexID id) function Edge (line 340) | Edge* Vertex::getLongestOverlapEdge(EdgeDir dir) const function EdgePtrVec (line 365) | EdgePtrVec Vertex::getEdges(EdgeDir dir) const function EdgePtrVec (line 379) | EdgePtrVec Vertex::getEdges() const FILE: src/SGA/Bigraph/Vertex.h type EdgeIDComp (line 32) | struct EdgeIDComp type EdgeLenComp (line 38) | struct EdgeLenComp type std (line 45) | typedef std::map EdgePtrMap; type std (line 46) | typedef std::vector EdgePtrVec; type std (line 47) | typedef std::set EdgeDescSet; type std (line 48) | typedef std::list EdgePtrList; type EdgePtrMap (line 49) | typedef EdgePtrMap::iterator EdgePtrMapIter; type EdgePtrMap (line 50) | typedef EdgePtrMap::const_iterator EdgePtrMapConstIter; type EdgePtrVec (line 51) | typedef EdgePtrVec::iterator EdgePtrVecIter; type EdgePtrVec (line 52) | typedef EdgePtrVec::const_iterator EdgePtrVecConstIter; type EdgePtrList (line 53) | typedef EdgePtrList::iterator EdgePtrListIter; type EdgePtrList (line 54) | typedef EdgePtrList::const_iterator EdgePtrListConstIter; function class (line 56) | class Vertex FILE: src/SGA/SGA/OverlapCommon.h function namespace (line 19) | namespace OverlapCommon FILE: src/SGA/SGA/index.cpp type opt (line 62) | namespace opt type option (line 82) | struct option function indexMain (line 98) | int indexMain(int argc, char** argv) function indexInMemoryBCR (line 119) | void indexInMemoryBCR() function indexInMemoryRopebwt (line 149) | void indexInMemoryRopebwt() function indexInMemorySAIS (line 190) | void indexInMemorySAIS() function indexOnDisk (line 219) | void indexOnDisk() function buildIndexForTable (line 248) | void buildIndexForTable(std::string prefix, const ReadTable* pRT, bool i... function parseIndexOptions (line 272) | void parseIndexOptions(int argc, char** argv) FILE: src/SGA/SGA/overlap.cpp type OutputType (line 28) | enum OutputType type opt (line 84) | namespace opt type option (line 107) | struct option function overlapMain (line 128) | int overlapMain(int argc, char** argv) function computeHitsSerial (line 213) | size_t computeHitsSerial(const std::string& prefix, const std::string& r... function computeHitsParallel (line 236) | size_t computeHitsParallel(int numThreads, const std::string& prefix, co... function convertHitsToASQG (line 267) | void convertHitsToASQG(const std::string& indexPrefix, const StringVecto... function parseOverlapOptions (line 327) | void parseOverlapOptions(int argc, char** argv) FILE: src/SGA/SQG/ASQG.cpp type ASQG (line 13) | namespace ASQG function RecordType (line 343) | RecordType getRecordType(const std::string& record) function writeFields (line 376) | void writeFields(std::ostream& out, const StringVector& fields) FILE: src/SGA/SQG/ASQG.h function namespace (line 16) | namespace ASQG type VertexRecord (line 63) | struct VertexRecord type EdgeRecord (line 88) | struct EdgeRecord FILE: src/SGA/SQG/SQG.cpp type SQG (line 12) | namespace SQG function StringVector (line 16) | StringVector tokenizeRecord(const std::string& record) function StringVector (line 22) | StringVector tokenizeTagValue(const std::string& tagValue) FILE: src/SGA/SQG/SQG.h function namespace (line 17) | namespace SQG FILE: src/SGA/StringGraph/CompleteOverlapSet.h type ExploreElement (line 21) | struct ExploreElement type CompareExploreElemOverlapLength (line 30) | struct CompareExploreElemOverlapLength type std (line 39) | typedef std::priority_queue EdgeDescList; type std (line 43) | typedef std::queue ExploreQueue; function class (line 45) | class CompleteOverlapSet FILE: src/SGA/StringGraph/GraphSearchTree.h type std (line 27) | typedef std::vector _EDGEPtrVector; function GraphSearchNode (line 40) | GraphSearchNode* getParent() const { return m_pParent; } function VERTEX (line 41) | VERTEX* getVertex() const { return m_pVertex; } function EDGE (line 43) | EDGE* getEdgeFromParent() const { return m_pEdgeFromParent; } type GraphSearchNode (line 62) | typedef GraphSearchNode _SearchNode; type typename (line 63) | typedef typename _SearchNode::GraphSearchNodePtrDeque _SearchNodePtrDeque; type typename (line 64) | typedef typename std::set<_SearchNode*> _SearchNodePtrSet; type std (line 65) | typedef std::vector WALK; type std (line 66) | typedef std::vector WALKVector; type std (line 68) | typedef std::vector VertexPtrVector; type std (line 69) | typedef std::vector VertexPtrVectorVector; FILE: src/SGA/StringGraph/RemovalAlgorithm.h function namespace (line 21) | namespace RemovalAlgorithm FILE: src/SGA/StringGraph/SGAlgorithms.cpp function Edge (line 16) | Edge* SGAlgorithms::createEdgesFromOverlap(StringGraph* pGraph, const Ov... function Overlap (line 181) | Overlap SGAlgorithms::inferTransitiveOverlap(const Overlap& ovrXY, const... type EDOPairCompare (line 232) | struct EDOPairCompare function EdgeDesc (line 329) | EdgeDesc SGAlgorithms::overlapToEdgeDesc(Vertex* pY, const Overlap& ovrXY) function EdgeDesc (line 348) | EdgeDesc SGAlgorithms::getEdgeDescFromEdge(Edge* pEdge) FILE: src/SGA/StringGraph/SGAlgorithms.h function namespace (line 18) | namespace SGAlgorithms FILE: src/SGA/StringGraph/SGSearch.h type SGDistanceFunction (line 20) | struct SGDistanceFunction type GraphSearchTree (line 29) | typedef GraphSearchTree SGSearchTree; type SGWalkBuilder (line 32) | struct SGWalkBuilder function namespace (line 53) | namespace SGSearch FILE: src/SGA/StringGraph/SGUtil.cpp function StringGraph (line 15) | StringGraph* SGUtil::loadASQG(const std::string& filename, const unsigne... function StringGraph (line 147) | StringGraph* SGUtil::loadASQG(std::stringstream& pReader, const unsigned... function StringGraph (line 279) | StringGraph* SGUtil::loadFASTA(const std::string& filename) FILE: src/SGA/StringGraph/SGUtil.h type Bigraph (line 17) | typedef Bigraph StringGraph; function namespace (line 19) | namespace SGUtil FILE: src/SGA/StringGraph/SGVisitors.h function previsit (line 21) | struct SGFastaVisitor function postvisit (line 30) | void postvisit(StringGraph* /*pGraph*/) {} type SGVisitorContig (line 38) | struct SGVisitorContig type SGTransitiveReductionVisitor (line 55) | struct SGTransitiveReductionVisitor type SGIdenticalRemoveVisitor (line 67) | struct SGIdenticalRemoveVisitor type SGContainRemoveVisitor (line 77) | struct SGContainRemoveVisitor type SGSmallRepeatResolveVisitor (line 96) | struct SGSmallRepeatResolveVisitor type SGOverlapRatioVisitor (line 108) | struct SGOverlapRatioVisitor type SGTrimVisitor (line 120) | struct SGTrimVisitor type SGDuplicateVisitor (line 133) | struct SGDuplicateVisitor type SGSuperRepeatVisitor (line 145) | struct SGSuperRepeatVisitor type SGSmoothingVisitor (line 156) | struct SGSmoothingVisitor type SGGraphStatsVisitor (line 182) | struct SGGraphStatsVisitor FILE: src/SGA/StringGraph/SGWalk.cpp function SGWalk (line 69) | SGWalk& SGWalk::operator=(const SGWalk& other) function Vertex (line 116) | Vertex* SGWalk::getStartVertex() const function Edge (line 467) | Edge* SGWalk::getFirstEdge() const function Edge (line 476) | Edge* SGWalk::getLastEdge() const function Vertex (line 485) | Vertex* SGWalk::getLastVertex() const function Edge (line 494) | Edge* SGWalk::getEdge(size_t idx) const function Vertex (line 501) | Vertex* SGWalk::getVertex(size_t idx) const function VertexPtrVec (line 511) | VertexPtrVec SGWalk::getVertices() const FILE: src/SGA/StringGraph/SGWalk.h type SGWalkType (line 18) | enum SGWalkType type SGWalkVertexPlacement (line 26) | struct SGWalkVertexPlacement type std (line 32) | typedef std::vector SGWalkVertexPlacementVector; FILE: src/SGA/SuffixTools/BWT.h type RLBWT (line 21) | typedef RLBWT BWT; FILE: src/SGA/SuffixTools/BWTAlgorithms.cpp function BWTInterval (line 14) | BWTInterval BWTAlgorithms::findInterval(const BWT* pBWT, const std::stri... function BWTInterval (line 36) | BWTInterval BWTAlgorithms::findIntervalWithCache(const BWT* pBWT, const ... function BWTInterval (line 67) | BWTInterval BWTAlgorithms::findInterval(const BWTIndexSet& indices, cons... function BWTIntervalPair (line 78) | BWTIntervalPair BWTAlgorithms::findIntervalPair(const BWT* pBWT, const B... function BWTIntervalPair (line 98) | BWTIntervalPair BWTAlgorithms::findIntervalPairWithCache(const BWT* pBWT, function AlphaCount64 (line 181) | AlphaCount64 BWTAlgorithms::calculateExactExtensions(const unsigned int ... function AlphaCount64 (line 219) | AlphaCount64 BWTAlgorithms::calculateDeBruijnExtensions(const std::strin... function AlphaCount64 (line 287) | AlphaCount64 BWTAlgorithms::calculateDeBruijnExtensionsSingleIndex(const... function _extractRankedPrefixes (line 456) | void _extractRankedPrefixes(const BWT* pBWT, BWTInterval interval, const... function RankedPrefixVector (line 484) | RankedPrefixVector BWTAlgorithms::extractRankedPrefixes(const BWT* pBWT,... FILE: src/SGA/SuffixTools/BWTAlgorithms.h type RankedPrefix (line 27) | struct RankedPrefix type std (line 32) | typedef std::vector RankedPrefixVector; function namespace (line 35) | namespace BWTAlgorithms FILE: src/SGA/SuffixTools/BWTCABauerCoxRosone.h function namespace (line 18) | namespace BWTCA type std (line 45) | typedef std::vector BCRVector; FILE: src/SGA/SuffixTools/BWTCARopebwt.h function namespace (line 15) | namespace BWTCA FILE: src/SGA/SuffixTools/BWTDiskConstruction.cpp type MergeItem (line 28) | struct MergeItem function buildBWTDisk (line 78) | void buildBWTDisk(const BWTDiskParameters& parameters) function MergeVector (line 165) | MergeVector computeInitialSAIS(const BWTDiskParameters& parameters) function MergeVector (line 228) | MergeVector computeInitialBCR(const BWTDiskParameters& parameters) function mergeIndependentIndices (line 281) | void mergeIndependentIndices(const std::string& readsFile1, const std::s... function removeReadsFromIndices (line 314) | void removeReadsFromIndices(const std::string& allReadsPrefix, const std... function mergeReadFiles (line 350) | void mergeReadFiles(const std::string& readsFile1, const std::string& re... function computeGapArray (line 385) | void computeGapArray(SeqReader* pReader, size_t n, const BWT* pBWT, bool... function merge (line 434) | int64_t merge(SeqReader* pReader, function writeMergedIndex (line 475) | void writeMergedIndex(const BWT* pBWTInternal, const MergeItem& external... function writeRemovalIndex (line 577) | void writeRemovalIndex(const BWT* pBWTInternal, const std::string& sai_i... function makeTempName (line 696) | std::string makeTempName(const std::string& prefix, int id, const std::s... function makeFilename (line 704) | std::string makeFilename(const std::string& prefix, const std::string& e... FILE: src/SGA/SuffixTools/BWTDiskConstruction.h type BWTDiskParameters (line 21) | struct BWTDiskParameters FILE: src/SGA/SuffixTools/BWTIndexSet.h type BWTIndexSet (line 24) | struct BWTIndexSet FILE: src/SGA/SuffixTools/BWTInterval.h type BWTInterval (line 19) | struct BWTInterval function write (line 53) | void write(std::ostream& out) function read (line 59) | void read(std::istream& in) type BWTIntervalPair (line 71) | struct BWTIntervalPair function sortFirstLower (line 84) | static bool sortFirstLower(const BWTIntervalPair& a, const BWTIntervalPa... function sortSecondLower (line 90) | static bool sortSecondLower(const BWTIntervalPair& a, const BWTIntervalP... FILE: src/SGA/SuffixTools/BWTIntervalCache.h function class (line 16) | class BWTIntervalCache FILE: src/SGA/SuffixTools/BWTReader.cpp function IBWTReader (line 14) | IBWTReader* BWTReader::createReader(const std::string& filename) FILE: src/SGA/SuffixTools/BWTReader.h type BWIOStage (line 17) | enum BWIOStage type BWFlag (line 27) | enum BWFlag function class (line 38) | class IBWTReader function namespace (line 51) | namespace BWTReader FILE: src/SGA/SuffixTools/BWTReaderAscii.h function class (line 21) | class BWTReaderAscii : public IBWTReader FILE: src/SGA/SuffixTools/BWTReaderBinary.h function class (line 22) | class BWTReaderBinary : public IBWTReader FILE: src/SGA/SuffixTools/BWTTraverse.h function getCurrChar (line 16) | struct TraverseElem type std (line 59) | typedef std::stack TraverseStack; type std (line 60) | typedef std::vector bool_vec; function namespace (line 62) | namespace BWTTraverse FILE: src/SGA/SuffixTools/BWTWriter.cpp function IBWTWriter (line 35) | IBWTWriter* BWTWriter::createWriter(const std::string& filename) FILE: src/SGA/SuffixTools/BWTWriter.h function class (line 19) | class IBWTWriter function namespace (line 33) | namespace BWTWriter FILE: src/SGA/SuffixTools/BWTWriterAscii.h function class (line 22) | class BWTWriterAscii : public IBWTWriter FILE: src/SGA/SuffixTools/BWTWriterBinary.h function class (line 23) | class BWTWriterBinary : public IBWTWriter FILE: src/SGA/SuffixTools/FMMarkers.h function getActualPosition (line 19) | struct LargeMarker type std (line 62) | typedef std::vector LargeMarkerVector; function getCountSum (line 68) | struct SmallMarker type std (line 94) | typedef std::vector SmallMarkerVector; FILE: src/SGA/SuffixTools/GapArray.cpp function GapArray (line 48) | GapArray* createGapArray(int storage) function updateGapArray (line 71) | void updateGapArray(const DNAString& w, const BWT* pBWTInternal, GapArra... function analyzeGapArray (line 107) | void analyzeGapArray(GapArray* pGapArray) FILE: src/SGA/SuffixTools/GapArray.h function class (line 18) | class GapArray function class (line 45) | class SimpleGapArray : public GapArray FILE: src/SGA/SuffixTools/HitData.h type Hit (line 17) | struct Hit type std (line 61) | typedef std::vector HitVector; FILE: src/SGA/SuffixTools/InverseSuffixArray.h type std (line 15) | typedef std::vector RankVector; type std (line 16) | typedef std::map RankCountMap; type std (line 17) | typedef std::map RankVectorMap; function class (line 19) | class InverseSuffixArray FILE: src/SGA/SuffixTools/Occurrence.h function class (line 24) | class Occurrence FILE: src/SGA/SuffixTools/PopulationIndex.cpp function StringVector (line 79) | StringVector PopulationIndex::getSamples() const function PopulationMember (line 123) | PopulationMember PopulationIndex::str2member(const std::string& line) FILE: src/SGA/SuffixTools/PopulationIndex.h type std (line 16) | typedef std::vector StringVector; type PopulationMember (line 18) | struct PopulationMember function class (line 32) | class PopulationIndex FILE: src/SGA/SuffixTools/QuickBWT.cpp function createQuickBWT (line 13) | void createQuickBWT(const std::string& str, BWT*& pBWT, SuffixArray*& pSA) FILE: src/SGA/SuffixTools/RLBWT.h function class (line 28) | class RLBWT FILE: src/SGA/SuffixTools/RLUnit.h function addCount (line 22) | struct RLUnit function subtractAlphaCount (line 76) | inline size_t subtractAlphaCount(AlphaCount64& ac, size_t max) const function subtractCount (line 89) | inline size_t subtractCount(char b, size_t& base_count, size_t max) const function incrementCount (line 101) | inline void incrementCount() function decrementCount (line 110) | inline void decrementCount() function setChar (line 127) | inline void setChar(char symbol) FILE: src/SGA/SuffixTools/RankProcess.cpp function RankResult (line 38) | RankResult RankProcess::process(const SequenceWorkItem& workItem) FILE: src/SGA/SuffixTools/RankProcess.h type std (line 18) | typedef std::vector RankVector; type RankResult (line 19) | struct RankResult FILE: src/SGA/SuffixTools/SACAInducedCopying.cpp function saca_induced_copying (line 25) | void saca_induced_copying(SuffixArray* pSA, const ReadTable* pRT, int nu... function induceSAl (line 141) | void induceSAl(const ReadTable* pRT, SuffixArray* pSA, char** p_array, i... function induceSAs (line 161) | void induceSAs(const ReadTable* pRT, SuffixArray* pSA, char** p_array, i... function countBuckets (line 183) | void countBuckets(const ReadTable* pRT, int64_t* counts, int K) function getBuckets (line 200) | void getBuckets(int64_t* counts, int64_t* buckets, int K, bool end) function setBit (line 214) | void setBit(char** p_array, size_t str_idx, size_t bit_idx, bool b) function getBit (line 220) | bool getBit(char** p_array, size_t str_idx, size_t bit_idx) function printType (line 225) | void printType(const ReadTable* pRT, char** p_array, size_t str_idx) FILE: src/SGA/SuffixTools/SAReader.cpp function SAElem (line 104) | SAElem SAReader::readElem() FILE: src/SGA/SuffixTools/SAReader.h type SAIOStage (line 18) | enum SAIOStage function class (line 28) | class SAReader FILE: src/SGA/SuffixTools/SAWriter.h function class (line 19) | class SAWriter FILE: src/SGA/SuffixTools/SBWT.h function class (line 25) | class SBWT function validate (line 71) | void validate() const; FILE: src/SGA/SuffixTools/STCommon.cpp function printMap (line 56) | void printMap(const std::map& m) function printVector (line 66) | void printVector(const std::vector& v) FILE: src/SGA/SuffixTools/STCommon.h type SAElem (line 36) | struct SAElem function setID (line 50) | inline void setID(uint64_t i) function setPos (line 61) | void setPos(uint64_t i) type std (line 104) | typedef std::vector SAElemVector; type std (line 105) | typedef std::pair SAElemPair; type std (line 106) | typedef std::vector SAElemPairVec; type std (line 107) | typedef std::set NumericIDSet; FILE: src/SGA/SuffixTools/STGlobals.h type std (line 24) | typedef std::string BWStr; type Label (line 25) | typedef uint32_t Label; type AIdx (line 26) | typedef uint8_t AIdx; type std (line 27) | typedef std::vector IntVector; type std (line 28) | typedef std::vector StringVector; FILE: src/SGA/SuffixTools/SampledSuffixArray.cpp function SAElem (line 44) | SAElem SampledSuffixArray::calcSA(int64_t idx, const BWT* pBWT) const FILE: src/SGA/SuffixTools/SampledSuffixArray.h type SSA_INT_TYPE (line 19) | typedef uint32_t SSA_INT_TYPE; type SSAFileType (line 21) | enum SSAFileType function class (line 27) | class SampledSuffixArray FILE: src/SGA/SuffixTools/SparseGapArray.h function set (line 40) | inline void set(size_t i, IntType c) function setCAS (line 47) | inline bool setCAS(size_t i, IntType oldV, IntType newV) function IntType (line 55) | inline IntType get(size_t i) const function getMax (line 60) | inline static size_t getMax() function class (line 82) | class SparseBaseStorage4 function class (line 183) | class SparseBaseStorage1 function resize (line 261) | void resize(size_t n) function attemptBaseIncrement (line 270) | bool attemptBaseIncrement(size_t i) function incrementOverflowSerial (line 305) | void incrementOverflowSerial(size_t i) function initOverflow (line 321) | void initOverflow(size_t i, OverflowStorage c) function incrementOverflow (line 327) | void incrementOverflow(size_t i) function get (line 335) | size_t get(size_t i) const function getBaseMax (line 361) | size_t getBaseMax() const type SparseGapArray (line 380) | typedef SparseGapArray SparseGapArray1; type SparseGapArray (line 381) | typedef SparseGapArray SparseGapArray4; type SparseGapArray (line 382) | typedef SparseGapArray, size_t> SparseGapArray8; type SparseGapArray (line 383) | typedef SparseGapArray, size_t> SparseGapArr... type SparseGapArray (line 384) | typedef SparseGapArray, size_t> SparseGapArr... FILE: src/SGA/SuffixTools/SuffixArray.h function class (line 17) | class SuffixArray FILE: src/SGA/SuffixTools/SuffixCompare.h function class (line 16) | class SuffixCompareRadix function class (line 95) | class SuffixCompareID function class (line 113) | class SuffixCompareIndex FILE: src/SGA/Util/Alphabet.h type BaseCount (line 39) | typedef uint64_t BaseCount; function namespace (line 41) | namespace DNA_ALPHABET function namespace (line 76) | namespace BWT_ALPHABET function namespace (line 111) | namespace IUPAC function clear (line 140) | inline void clear() function set (line 146) | inline void set(char b, Storage v) function setByIdx (line 152) | inline void setByIdx(size_t i, Storage v) function increment (line 159) | inline void increment(char b) function add (line 169) | inline void add(char b, Storage v) function subtract (line 179) | inline void subtract(char b, Storage v) function Storage (line 189) | inline Storage get(char b) const function Storage (line 195) | inline Storage getByIdx(const int i) const function getBase (line 201) | static char getBase(size_t i) function getMaxValue (line 207) | static size_t getMaxValue() function complement (line 214) | inline void complement() function getLessThan (line 230) | inline size_t getLessThan(char b) const function getNumNonZero (line 240) | uint8_t getNumNonZero() const function hasUniqueDNAChar (line 253) | inline bool hasUniqueDNAChar() function hasDNAChar (line 273) | inline bool hasDNAChar() function getMaxBase (line 285) | inline char getMaxBase() const function Storage (line 311) | inline Storage getMaxCount() const function getSum (line 337) | inline size_t getSum() const function getUniqueDNAChar (line 361) | inline char getUniqueDNAChar() type AlphaCountCompareDesc (line 450) | struct AlphaCountCompareDesc type AlphaCount (line 463) | typedef AlphaCount AlphaCount64; type AlphaCount (line 464) | typedef AlphaCount AlphaCount16; type AlphaCount (line 465) | typedef AlphaCount AlphaCount8; function alphacount_add16 (line 468) | inline void alphacount_add16(AlphaCount64& lhs, const AlphaCount16& rhs) function alphacount_subtract16 (line 477) | inline void alphacount_subtract16(AlphaCount64& lhs, const AlphaCount16&... function alphacount_add (line 489) | inline void alphacount_add(AlphaCount64& lhs, const AlphaCount8& rhs) function alphacount_subtract (line 498) | inline void alphacount_subtract(AlphaCount64& lhs, const AlphaCount8& rhs) FILE: src/SGA/Util/BWT4Codec.h function class (line 19) | class BWT4Codec FILE: src/SGA/Util/BWTCodec.h function class (line 19) | class BWTCodec FILE: src/SGA/Util/BitChar.cpp function printBinary (line 38) | void printBinary(std::ostream& out, const BitChar& bc) FILE: src/SGA/Util/BitChar.h type BitChar (line 14) | struct BitChar FILE: src/SGA/Util/BitVector.h function class (line 16) | class BitVector FILE: src/SGA/Util/BloomFilter.h function class (line 17) | class BloomFilter FILE: src/SGA/Util/ClusterReader.h type ClusterRecord (line 18) | struct ClusterRecord type std (line 25) | typedef std::vector ClusterVector; function class (line 27) | class ClusterReader FILE: src/SGA/Util/Contig.cpp function SequenceVector (line 51) | SequenceVector Contig::getVariants() const FILE: src/SGA/Util/Contig.h type UniqueFlag (line 14) | enum UniqueFlag function class (line 22) | class Contig FILE: src/SGA/Util/CorrectionThresholds.cpp function CorrectionThresholds (line 20) | CorrectionThresholds& CorrectionThresholds::Instance() FILE: src/SGA/Util/CorrectionThresholds.h function class (line 14) | class CorrectionThresholds FILE: src/SGA/Util/DNACodec.h function class (line 17) | class DNACodec FILE: src/SGA/Util/DNADouble.h function class (line 15) | class DNADouble FILE: src/SGA/Util/DNAString.cpp function DNAString (line 29) | DNAString& DNAString::operator=(const DNAString& dna) function DNAString (line 40) | DNAString& DNAString::operator=(const std::string& str) FILE: src/SGA/Util/DNAString.h function class (line 17) | class DNAString FILE: src/SGA/Util/EncodedString.h type typename (line 31) | typedef typename Codec::UNIT_TYPE StorageUnit; function resize (line 84) | void resize(size_t n) function append (line 92) | void append(const std::string& str) function append (line 102) | void append(const EncodedString& other) function swap (line 112) | void swap(EncodedString& other) function get (line 147) | inline char get(size_t idx) const function set (line 154) | inline void set(size_t idx, char b) function _copy (line 233) | void _copy(const EncodedString& other) function _copyUnitData (line 243) | void _copyUnitData(StorageUnit* pData, size_t num_units) function _append (line 251) | void _append(const char* pData, size_t n) function _append (line 260) | void _append(const EncodedString& other) function _alloc (line 270) | void _alloc(size_t n) function _realloc (line 280) | void _realloc(size_t n) function _dealloc (line 292) | void _dealloc() type EncodedString (line 312) | typedef EncodedString DNAEncodedString; type EncodedString (line 313) | typedef EncodedString BWTString; type EncodedString (line 314) | typedef EncodedString NoEncodingString; type std (line 316) | typedef std::vector DNAEncodedStringVector; FILE: src/SGA/Util/HashMap.h type std (line 23) | typedef std::hash StringHasher; type std (line 29) | typedef std::tr1::hash StringHasher; type StringHasher (line 44) | struct StringHasher FILE: src/SGA/Util/Interval.cpp function Interval (line 11) | Interval Interval::intersect(const Interval& r1, const Interval& r2) FILE: src/SGA/Util/Interval.h function isIntersecting (line 15) | struct Interval FILE: src/SGA/Util/IntervalTree.h type vector (line 59) | typedef vector intervalVector; type IntervalTTree (line 60) | typedef IntervalTTree intervalTree; function findOverlapping (line 172) | void findOverlapping(K start, K stop, intervalVector& overlapping) { function findContained (line 192) | void findContained(K start, K stop, intervalVector& contained) { FILE: src/SGA/Util/KmerDistribution.h function class (line 17) | class KmerDistribution FILE: src/SGA/Util/Match.cpp function SeqCoord (line 87) | SeqCoord Match::translate(const SeqCoord& c) const function SeqCoord (line 103) | SeqCoord Match::inverseTranslate(const SeqCoord& c) const function Match (line 141) | Match Match::infer(const Match& match_xy, const Match& match_xz) FILE: src/SGA/Util/Match.h function getNumDiffs (line 16) | struct Match function setNumDiffs (line 29) | void setNumDiffs(int n) { numDiff = n; } function calculateTranslation (line 32) | int calculateTranslation() const; type Overlap (line 83) | struct Overlap FILE: src/SGA/Util/Metrics.h type ErrorCount (line 15) | struct ErrorCount type std (line 24) | typedef std::map DataMap; function incrementSample (line 30) | void incrementSample(const Key& key) function incrementError (line 36) | void incrementError(const Key& key) function write (line 42) | void write(std::ostream* pWriter, const std::string& leader, const std::... FILE: src/SGA/Util/MultiAlignment.cpp type CigarIter (line 17) | struct CigarIter method updateAndEmit (line 23) | char updateAndEmit(char updateMode) method getCigarSymbol (line 81) | char getCigarSymbol() method getOutputBase (line 88) | char getOutputBase(char cigSym) method sortPosition (line 96) | static bool sortPosition(const CigarIter& a, const CigarIter& b) function MultiAlignment (line 465) | MultiAlignment MultiAlignmentTools::alignSequencesGlobal(const SeqItemVe... function MultiAlignment (line 491) | MultiAlignment MultiAlignmentTools::alignSequencesLocal(const SeqItemVec... FILE: src/SGA/Util/MultiAlignment.h type MAlignData (line 17) | struct MAlignData type std (line 33) | typedef std::vector MAlignDataVector; function class (line 35) | class MultiAlignment function namespace (line 83) | namespace MultiAlignmentTools FILE: src/SGA/Util/MultiOverlap.cpp function Overlap (line 63) | Overlap MultiOverlap::getOverlap(size_t idx) const function AlphaCount64 (line 444) | AlphaCount64 MultiOverlap::getAlphaCount(int idx) const function Pileup (line 466) | Pileup MultiOverlap::getPileup(int idx) const function Pileup (line 488) | Pileup MultiOverlap::getPileup(int idx, int numElems) const function Pileup (line 509) | Pileup MultiOverlap::getSingletonPileup(int base_idx, int ovr_idx) const function PileupVector (line 548) | PileupVector MultiOverlap::getPartitionedPileup(int idx, int num_parts) ... FILE: src/SGA/Util/MultiOverlap.h function class (line 17) | class MultiOverlap FILE: src/SGA/Util/NoCodec.h function class (line 14) | class NoCodec FILE: src/SGA/Util/Pileup.cpp function AlphaCount64 (line 30) | AlphaCount64 Pileup::getAlphaCount() const function DNADouble (line 42) | DNADouble Pileup::calculateSimpleAlphaProb() const function DNADouble (line 87) | DNADouble Pileup::calculateLikelihoodNoQuality(double p_error) const FILE: src/SGA/Util/Pileup.h function calculateSimpleConsensus (line 19) | struct PUElem type std (line 56) | typedef std::vector PileupVector; FILE: src/SGA/Util/PrimerScreen.h function class (line 15) | class PrimerScreen FILE: src/SGA/Util/Profiler.h function class (line 24) | class TimeTracker FILE: src/SGA/Util/Quality.cpp function DoubleVector (line 12) | DoubleVector Quality::uniformLogProbVector(double p_error, size_t n) FILE: src/SGA/Util/Quality.h type std (line 22) | typedef std::vector DoubleVector; function namespace (line 23) | namespace Quality FILE: src/SGA/Util/QualityCodec.h type QualityStorageUnit (line 16) | typedef uint8_t QualityStorageUnit; function encode (line 35) | inline uint8_t encode(char b) const function decode (line 53) | inline char decode(uint8_t c) const function getRequiredUnits (line 64) | inline size_t getRequiredUnits(size_t n) const function getCapacity (line 71) | inline size_t getCapacity(size_t n) const function getUnitIndex (line 78) | inline size_t getUnitIndex(size_t i) const function getUnitOffset (line 85) | inline size_t getUnitOffset(size_t i) const function getOffsetShift (line 93) | inline uint8_t getOffsetShift(size_t offset) const function getOffsetMask (line 99) | inline uint8_t getOffsetMask(size_t offset) const function store (line 105) | inline void store(UNIT_TYPE* pData, size_t i, char b) const function get (line 133) | inline char get(const UNIT_TYPE* pData, size_t i) const FILE: src/SGA/Util/QualityTable.h type QualityString (line 16) | struct QualityString type std (line 22) | typedef std::vector QualityStringVector; function class (line 24) | class QualityTable FILE: src/SGA/Util/QualityVector.cpp function DNADouble (line 45) | DNADouble QualityVector::get(size_t idx) const FILE: src/SGA/Util/QualityVector.h type std (line 17) | typedef std::vector APVec; function class (line 19) | class QualityVector FILE: src/SGA/Util/Read2Contig.h type Read2Contig (line 10) | struct Read2Contig { FILE: src/SGA/Util/ReadInfoTable.cpp function ReadInfo (line 85) | const ReadInfo ReadInfoTable::getReadInfo(size_t idx) const FILE: src/SGA/Util/ReadInfoTable.h type ReadInfoOption (line 17) | enum ReadInfoOption type ReadInfo (line 23) | struct ReadInfo FILE: src/SGA/Util/ReadTable.cpp function SeqItem (line 106) | const SeqItem& ReadTable::getRead(size_t idx) const function SeqItem (line 117) | const SeqItem& ReadTable::getRead(const std::string& id) const FILE: src/SGA/Util/ReadTable.h type std (line 17) | typedef std::vector ReadVector; type std (line 18) | typedef std::map ReadIndex; function class (line 20) | class ReadTable FILE: src/SGA/Util/ReadTableNew.cpp function SeqItem (line 75) | const SeqItem& ReadTable::getRead(size_t idx) const function SeqItem (line 99) | const SeqItem& ReadTable::getRead(const std::string& id) const FILE: src/SGA/Util/ReadTableNew.h type std (line 16) | typedef std::vector ReadVector; type std (line 17) | typedef std::map ReadIndex; function class (line 19) | class ReadTable FILE: src/SGA/Util/ReadTableS.h type std (line 18) | typedef std::vector ReadVector; type std (line 19) | typedef std::map ReadIndex; type std (line 20) | typedef std::vector BamAlignmentVector; function class (line 22) | class ReadTable FILE: src/SGA/Util/SGAStats.h function namespace (line 14) | namespace SGAStats FILE: src/SGA/Util/SeqCoord.cpp function SeqCoord (line 16) | SeqCoord SeqCoord::complement() const function QualityVector (line 55) | QualityVector SeqCoord::getSubvector(const QualityVector& vec) const FILE: src/SGA/Util/SeqCoord.h type SeqCoord (line 18) | struct SeqCoord function setEmpty (line 65) | inline void setEmpty() function setFull (line 72) | inline void setFull() function flip (line 97) | inline void flip() function flip (line 106) | static inline int flip(int p, int l) FILE: src/SGA/Util/SeqReader.h type RecordType (line 15) | enum RecordType function class (line 26) | class SeqReader FILE: src/SGA/Util/SimpleAllocator.h type SimplePool (line 20) | typedef SimplePool StorageType; type std (line 21) | typedef std::list StorageList; function dealloc (line 47) | void dealloc(void* /*ptr*/) FILE: src/SGA/Util/SimplePool.h function dealloc (line 53) | void dealloc(void* /*ptr*/) function isFull (line 58) | bool isFull() FILE: src/SGA/Util/StdAlnTools.cpp function LocalAlignmentResult (line 58) | LocalAlignmentResult StdAlnTools::localAlignment(const std::string& targ... FILE: src/SGA/Util/StdAlnTools.h function setDefaults (line 19) | struct GlobalAlnParams function setPacBio (line 35) | void setPacBio() type LocalAlignmentResult (line 54) | struct LocalAlignmentResult type std (line 71) | typedef std::vector LocalAlignmentResultVector; function namespace (line 73) | namespace StdAlnTools FILE: src/SGA/Util/Timer.h function class (line 16) | class Timer FILE: src/SGA/Util/Util.cpp function reverseComplement (line 19) | std::string reverseComplement(const std::string& seq) function reverseComplementIUPAC (line 31) | std::string reverseComplementIUPAC(const std::string& seq) function reverse (line 43) | std::string reverse(const std::string& seq) function complement (line 49) | std::string complement(const std::string& seq) function complementIUPAC (line 59) | std::string complementIUPAC(const std::string& seq) function prefix (line 69) | std::string prefix(const std::string& seq, const unsigned int len) function suffix (line 76) | std::string suffix(const std::string& seq, const unsigned int len) function calculateDustScore (line 86) | double calculateDustScore(const std::string& seq) function maxDustWindow (line 114) | double maxDustWindow(const std::string& seq, size_t windowSize, size_t m... function countDifferences (line 132) | int countDifferences(const std::string& s1, const std::string& s2, size_... function getDiffString (line 144) | std::string getDiffString(const std::string& s1, const std::string& s2) function randomBase (line 154) | char randomBase() function stripFilename (line 175) | std::string stripFilename(const std::string& filename) function stripExtension (line 185) | std::string stripExtension(const std::string& filename) function stripGzippedExtension (line 197) | std::string stripGzippedExtension(const std::string& filename) function stripDirectories (line 207) | std::string stripDirectories(const std::string& filename) function getFileExtension (line 218) | std::string getFileExtension(const std::string& filename) function writeFastaRecord (line 229) | void writeFastaRecord(std::ostream* pWriter, const std::string& id, cons... function isGzip (line 240) | bool isGzip(const std::string& filename) function isFastq (line 253) | bool isFastq(const std::string& filename) function getFilesize (line 260) | std::ifstream::pos_type getFilesize(const std::string& filename) function assertFileOpen (line 305) | void assertFileOpen(std::ifstream& fh, const std::string& fn) function assertFileOpen (line 315) | void assertFileOpen(std::ofstream& fh, const std::string& fn) function assertGZOpen (line 325) | void assertGZOpen(gzstreambase& gh, const std::string& fn) function StringVector (line 335) | StringVector split(std::string in, char delimiter) function splitKeyValue (line 352) | void splitKeyValue(std::string in, std::string& key, std::string& value) function getPairBasename (line 369) | std::string getPairBasename(const std::string& id) function getPairID (line 381) | std::string getPairID(const std::string& id) function getPairIndex (line 407) | int getPairIndex(const std::string& id) function debug_getReadDistFromNames (line 426) | size_t debug_getReadDistFromNames(const std::string& name1, const std::s... FILE: src/SGA/Util/Util.h type std (line 40) | typedef std::string Sequence; type std (line 41) | typedef std::string ContigID; type std (line 42) | typedef std::vector IntVec; type std (line 43) | typedef std::vector DoubleVec; type std (line 44) | typedef std::vector StringVector; type std (line 45) | typedef std::list StringList; type std (line 46) | typedef std::vector SequenceVector; type std (line 61) | typedef std::vector SeqItemVector; type SeqRecord (line 64) | struct SeqRecord function getPhredScore (line 97) | int getPhredScore(size_t i) const type std (line 115) | typedef std::vector SeqRecordVector; function string (line 145) | string makeKeyValue(std::string key, C value) function getBaseRank (line 187) | inline static uint8_t getBaseRank(char b) function complement (line 218) | inline char complement(char base) function complementIUPAC (line 240) | inline char complementIUPAC(char c) function isErrorRateAcceptable (line 273) | inline bool isErrorRateAcceptable(double er, double threshold) FILE: src/SGA/Util/VCFUtil.cpp function VCFClassification (line 144) | VCFClassification VCFRecord::classify() const function VCFReturnCode (line 174) | VCFReturnCode VCFUtil::generateVCFFromCancerVariant(const std::string& ref, type tm (line 412) | struct tm FILE: src/SGA/Util/VCFUtil.h type VCFClassification (line 17) | enum VCFClassification type VCFReturnCode (line 27) | enum VCFReturnCode type VCFRecord (line 39) | struct VCFRecord type std (line 84) | typedef std::vector VCFVector; type std (line 85) | typedef std::vector StringVector; type VCFCollection (line 88) | struct VCFCollection function namespace (line 94) | namespace VCFUtil FILE: src/SGA/Util/VariantIndex.cpp function VariantRecordVector (line 70) | VariantRecordVector VariantIndex::getNearVariants(const std::string& ref... FILE: src/SGA/Util/VariantIndex.h type VariantRecord (line 20) | struct VariantRecord type std (line 28) | typedef std::vector VariantRecordVector; type std (line 29) | typedef std::vector IntVector; type std (line 30) | typedef std::vector IntVectorVector; type std (line 33) | typedef std::map VariantIndexMap; function class (line 35) | class VariantIndex FILE: src/SGA/Util/Verbosity.h function class (line 14) | class Verbosity FILE: src/SGA/Util/bamreader.h function class (line 8) | class SVBamReader { FILE: src/SGA/Util/bucketSort.h type typename (line 18) | typedef typename std::iterator_traits::value_type base_value; type std (line 19) | typedef std::list base_list; type typename (line 20) | typedef typename base_list::iterator list_iterator; FILE: src/SGA/Util/gzstream.C function namespace (line 40) | namespace GZSTREAM_NAMESPACE { function underflow (line 84) | int gzstreambuf::underflow() { // used for input buffer only function flush_buffer (line 109) | int gzstreambuf::flush_buffer() { function overflow (line 119) | int gzstreambuf::overflow( int c) { // used for output buffer only function sync (line 131) | int gzstreambuf::sync() { function open (line 155) | void gzstreambase::open( const char* name, int open_mode) { function close (line 160) | void gzstreambase::close() { FILE: src/SGA/Util/gzstream.h function namespace (line 45) | namespace GZSTREAM_NAMESPACE { FILE: src/SGA/Util/mkqs.h function vecswap (line 30) | void vecswap(int i, int j, int n, T* x) function vecswap2 (line 45) | void vecswap2(T* a, T* b, int n) function inssort (line 67) | void inssort(T* a, int n, int d, const PrimarySorter& primarySorter, con... FILE: src/SGA/Util/old.AlignedContig.h function class (line 6) | class AlignedContig { FILE: src/SGA/Util/stdaln.c function AlnAln (line 232) | AlnAln *aln_init_AlnAln() function aln_free_AlnAln (line 241) | void aln_free_AlnAln(AlnAln *aa) type dpcell_t (line 321) | typedef struct type dpscore_t (line 326) | typedef struct function aln_init_score_array (line 332) | void aln_init_score_array(unsigned char *seq, int len, int row, int *sco... function aln_global_core (line 345) | int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, ... function aln_local_core (line 528) | int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, i... function AlnAln (line 777) | AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnPara... function AlnAln (line 857) | AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *a... function aln_extend_core (line 877) | int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, ... function main (line 1058) | int main() FILE: src/SGA/Util/stdaln.h type AlnParam (line 86) | typedef struct type path_t (line 97) | typedef struct type AlnAln (line 103) | typedef struct FILE: src/svaba/AlignedContig.cpp function r2cEscape (line 198) | std::string r2cEscape(const std::string& s) { function r2cCigarString (line 211) | std::string r2cCigarString(const SeqLib::Cigar& c) { type BpSupportEntry (line 359) | struct BpSupportEntry { function BreakPointPtrVector (line 615) | BreakPointPtrVector AlignedContig::getAllBreakPoints() const { FILE: src/svaba/AlignedContig.h function class (line 19) | class AlignedContig { type std (line 167) | typedef std::unordered_map ContigMap; type std (line 168) | typedef std::vector AlignedContigVec; FILE: src/svaba/BreakPoint.cpp function to_string (line 32) | static inline std::string to_string(SVType t) { function to_string (line 45) | static inline std::string to_string(SomaticState s) { function GenomicRegion (line 60) | GenomicRegion BreakPoint::BreakEndAsGenomicRegionLeft() const { function GenomicRegion (line 64) | GenomicRegion BreakPoint::BreakEndAsGenomicRegionRight() const { function HashVector (line 81) | HashVector BreakPoint::getBreakEndHashes() { function __myround (line 138) | double __myround(double x) { return std:: floor(x * 10) / 10; } function split_tabs (line 2440) | inline std::vector split_tabs(const std::string& s) { function to_long (line 2453) | inline long to_long(const std::string& s) { function to_int (line 2457) | inline int to_int(const std::string& s) { function to_double (line 2461) | inline double to_double(const std::string& s) { function parse_strand (line 2465) | inline char parse_strand(const std::string& s) { function upper (line 2469) | inline std::string upper(std::string v){ function SVType (line 2476) | inline SVType parse_svtype(const std::string& s_in) { function SomaticState (line 2489) | inline SomaticState parse_somatic(const std::string& s_in) { function stod_safe (line 2496) | inline double stod_safe(const std::string& s) { FILE: src/svaba/BreakPoint.h type class (line 16) | enum class type class (line 23) | enum class type class (line 33) | enum class function namespace (line 42) | namespace SeqLib { type BreakPoint (line 56) | struct BreakPoint type BreakEnd (line 57) | struct BreakEnd type std (line 59) | typedef std::vector HashVector; type std (line 60) | typedef std::vector BPVec; type std (line 61) | typedef std::shared_ptr BreakPointPtr; type std (line 62) | typedef std::vector BreakPointPtrVector; type std (line 64) | typedef std::unordered_set ReadNameSet; type BreakEnd (line 66) | struct BreakEnd { function class (line 105) | class BreakPoint { FILE: src/svaba/ContigAlignmentScore.cpp type svaba (line 28) | namespace svaba { function T (line 33) | inline T clip_range(T v, T lo, T hi) { function ContigAlignScore (line 39) | ContigAlignScore scoreContigAlignment(const SeqLib::BamRecord& r) { function tagContigAlignment (line 144) | void tagContigAlignment(SeqLib::BamRecord& r, const ContigAlignScore& ... function readContigConfTag (line 165) | double readContigConfTag(const SeqLib::BamRecord& r) { FILE: src/svaba/ContigAlignmentScore.h function namespace (line 24) | namespace svaba { FILE: src/svaba/DBSnpFilter.h function namespace (line 13) | namespace SeqLib { function class (line 17) | class DBSnpSite: public SeqLib::GenomicRegion { type SeqLib (line 31) | typedef SeqLib::GenomicRegionCollection DBC; function class (line 33) | class DBSnpFilter { FILE: src/svaba/DiscordantCluster.cpp type SeqLib (line 19) | namespace SeqLib { class BamHeader (line 20) | class BamHeader class GenomicRegion (line 21) | class GenomicRegion function DiscordantClusterMap (line 26) | DiscordantClusterMap DiscordantCluster::clusterReads(svabaReadPtrVector&... function GenomicRegion (line 613) | GenomicRegion DiscordantCluster::GetMateRegionOfOverlap(const GenomicReg... FILE: src/svaba/DiscordantCluster.h type std (line 14) | typedef std::unordered_map DiscordantReadMap; type std (line 15) | typedef std::vector svabaReadClusterVector; type std (line 16) | typedef std::vector DiscordantClusterVector; type std (line 17) | typedef std::unordered_map DiscordantClu... function isEmpty (line 46) | bool isEmpty() const; FILE: src/svaba/DiscordantRealigner.h function namespace (line 3) | namespace SeqLib { function class (line 10) | class DiscordantRealigner { FILE: src/svaba/Histogram.cpp function Bin (line 207) | Bin& Bin::operator++() function Bin (line 214) | Bin& Bin::operator--() { FILE: src/svaba/Histogram.h type SeqLib (line 16) | typedef SeqLib::TInterval BinInterval; type SeqLib (line 17) | typedef SeqLib::TIntervalTree BinIntervalTree; type std (line 18) | typedef std::vector BinIntervalVector; function class (line 26) | class Bin { FILE: src/svaba/KmerFilter.h type std (line 12) | typedef std::map KmerCountMap; function class (line 14) | class KmerFilter { FILE: src/svaba/LearnBamParams.cpp function extractReadGroups (line 24) | std::vector extractReadGroups(const SeqLib::BamHeader& hdr) { FILE: src/svaba/LearnBamParams.h function namespace (line 13) | namespace SeqLib { function class (line 23) | class BamReadGroup { function class (line 76) | class LearnBamParams { FILE: src/svaba/STCoverage.h function namespace (line 20) | namespace SeqLib { type std (line 24) | typedef std::unordered_map CovMap; function class (line 30) | class STCoverage { FILE: src/svaba/SvabaASQG.cpp type svabaASQG (line 13) | namespace svabaASQG function RecordType (line 343) | RecordType getRecordType(const std::string& record) function writeFields (line 376) | void writeFields(std::ostream& out, const StringVector& fields) FILE: src/svaba/SvabaASQG.h function namespace (line 16) | namespace svabaASQG type VertexRecord (line 63) | struct VertexRecord type EdgeRecord (line 88) | struct EdgeRecord FILE: src/svaba/SvabaAssemble.cpp function StringGraph (line 26) | StringGraph* assemble(std::stringstream& asqg_stream, int minOverlap, in... function walkExtra (line 115) | void walkExtra(StringGraph * pGraph, SGWalkVector& outWalks) { FILE: src/svaba/SvabaAssemble.h type AssemblyOptions (line 22) | struct AssemblyOptions { FILE: src/svaba/SvabaAssemblerConfig.h function namespace (line 38) | namespace svaba { FILE: src/svaba/SvabaAssemblerEngine.cpp function repeat (line 19) | static std::string repeat(char base, int count) { function ReadTable (line 270) | ReadTable* svabaAssemblerEngine::removeDuplicates(ReadTable* pRT) { FILE: src/svaba/SvabaAssemblerEngine.h function class (line 12) | class svabaAssemblerEngine FILE: src/svaba/SvabaBamWalker.cpp function debug_read (line 17) | inline void debug_read(std::string_view msg, function hasAdapter (line 36) | static bool hasAdapter(const svabaRead& r) { FILE: src/svaba/SvabaBamWalker.h function class (line 21) | class MateRegion: public SeqLib::GenomicRegion type SeqLib (line 31) | typedef SeqLib::GenomicRegionCollection MateRegionVector; function class (line 33) | class svabaBamWalker: public SeqLib::BamReader { FILE: src/svaba/SvabaDebug.h function _svaba_trace_match (line 34) | inline bool _svaba_trace_match(const std::string& cname) { function _svaba_read_trace_match (line 78) | inline bool _svaba_read_trace_match(const std::string& qname) { function std (line 132) | inline std::string _svaba_revcomp(const std::string& s) { function _svaba_kmer_match (line 146) | inline bool _svaba_kmer_match(const std::string& seq) { FILE: src/svaba/SvabaFileLoader.h function namespace (line 12) | namespace SeqLib { function class (line 18) | class SvabaFileLoader { FILE: src/svaba/SvabaLogger.h function class (line 11) | class SvabaLogger { FILE: src/svaba/SvabaModels.cpp type SvabaModels (line 8) | namespace SvabaModels { function LogLikelihood (line 11) | double LogLikelihood(double ref, function SomaticLOD (line 70) | double SomaticLOD(double aN, double dN, double aT, double dT, function SomaticLOD_withSplitErrors (line 86) | static inline double SomaticLOD_withSplitErrors(double aN, double dN, ... function GenotypeQuality (line 338) | int GenotypeQuality(const std::vector& PLs) { function GenotypeLikelihoods (line 356) | double GenotypeLikelihoods(int g, FILE: src/svaba/SvabaModels.h function namespace (line 5) | namespace SvabaModels { FILE: src/svaba/SvabaOptions.cpp function SvabaOptions (line 113) | SvabaOptions SvabaOptions::parse(int argc, char** argv) { FILE: src/svaba/SvabaOptions.h function class (line 161) | class SvabaOptions { FILE: src/svaba/SvabaOutputWriter.cpp function make_header_with_hd (line 27) | static SeqLib::BamHeader make_header_with_hd(const SeqLib::BamHeader& src, FILE: src/svaba/SvabaOutputWriter.h type SvabaSharedConfig (line 15) | struct SvabaSharedConfig type SvabaOutputWriter (line 17) | struct SvabaOutputWriter { FILE: src/svaba/SvabaOverlapAlgorithm.cpp function OverlapResult (line 21) | OverlapResult svabaOverlapAlgorithm::overlapRead(const SeqRecord& read, ... function OverlapResult (line 35) | OverlapResult svabaOverlapAlgorithm::overlapReadInexact(const SeqRecord&... function OverlapResult (line 169) | OverlapResult svabaOverlapAlgorithm::alignReadDuplicate(const SeqRecord&... function OverlapResult (line 184) | OverlapResult svabaOverlapAlgorithm::overlapReadExact(const SeqRecord& r... FILE: src/svaba/SvabaOverlapAlgorithm.h function class (line 33) | class svabaOverlapAlgorithm function setExactModeIrreducible (line 74) | void setExactModeIrreducible(bool b) { m_exactModeIrreducible = b; } function BWT (line 77) | const BWT* getBWT() const { return m_pBWT; } function BWT (line 78) | const BWT* getRBWT() const { return m_pRevBWT; } FILE: src/svaba/SvabaPostprocess.cpp type Opts (line 100) | struct Opts { type option (line 112) | struct option function printUsage (line 123) | void printUsage() { function Opts (line 145) | Opts parseOpts(int argc, char** argv) { function fileExists (line 177) | bool fileExists(const std::string& p) { function off_t (line 182) | off_t fileSize(const std::string& p) { function logLine (line 190) | void logLine(Args&&... args) { function shQuote (line 200) | std::string shQuote(const std::string& s) { type PgChainInfo (line 233) | struct PgChainInfo { function PgChainInfo (line 238) | PgChainInfo scanPgChain(const std::string& hdr_text) { function hasSvabaPostprocessPg (line 272) | bool hasSvabaPostprocessPg(const std::string& hdr_text) { function uniquifyId (line 281) | std::string uniquifyId(const std::string& base, function sanitizeHeaderValue (line 295) | std::string sanitizeHeaderValue(const std::string& s) { function appendSvabaPostprocessPg (line 307) | std::string appendSvabaPostprocessPg(const std::string& hdr_text, function stampedHeader (line 325) | SeqLib::BamHeader stampedHeader(const SeqLib::BamHeader& src, function readHeaderOnly (line 332) | SeqLib::BamHeader readHeaderOnly(const std::string& bam) { function isCoordinateSorted (line 351) | bool isCoordinateSorted(const std::string& bam) { function reheaderBamWithPg (line 380) | int reheaderBamWithPg(const std::string& bam, function indexBam (line 437) | int indexBam(const std::string& bam, const std::string& tag, int verbose) { function runSort (line 459) | int runSort(const std::string& in_bam, type DedupStats (line 492) | struct DedupStats { function mergeCommaTokens (line 507) | bool mergeCommaTokens(std::string& cur, std::string_view incoming) { function mergeZTagInto (line 541) | bool mergeZTagInto(SeqLib::BamRecord& existing, function DedupStats (line 571) | DedupStats streamDedup(const std::string& in_bam, function renameOrThrow (line 786) | void renameOrThrow(const std::string& from, const std::string& to) { function isDedupSuffix (line 793) | bool isDedupSuffix(const std::string& s) { function processSuffix (line 813) | void processSuffix(const std::string& id, function runPostprocess (line 938) | void runPostprocess(int argc, char** argv) { FILE: src/svaba/SvabaRead.cpp function r2c (line 19) | r2c svabaRead::GetR2C(const std::string& contig_name) const { FILE: src/svaba/SvabaRead.h type std (line 44) | typedef std::unordered_map R2CMap; type std (line 47) | typedef std::shared_ptr svabaReadPtr; type std (line 48) | typedef std::vector svabaReadPtrVector; function SetPrefix (line 80) | void SetPrefix(const std::string_view pref) { p = pref; } function SetDD (line 88) | void SetDD(int d) { dd = d; } function SeqLength (line 92) | int SeqLength() const; FILE: src/svaba/SvabaRegionProcessor.cpp function queryInterval (line 62) | inline std::pair queryInterval(const SeqLib::BamRecord& r) { function reciprocalOverlap (line 74) | inline double reciprocalOverlap(std::pair a, std::pair... function preferStandardChromosomes (line 82) | size_t preferStandardChromosomes(BamRecordPtrVector& alns, int maxStdChr) { function GRC (line 158) | GRC SvabaRegionProcessor::runMateCollectionLoop(const GenomicRegion& reg... FILE: src/svaba/SvabaRegionProcessor.h function namespace (line 18) | namespace SeqLib { function class (line 24) | class SvabaRegionProcessor { FILE: src/svaba/SvabaSharedConfig.h function class (line 19) | class SvabaSharedConfig { FILE: src/svaba/SvabaThreadUnit.cpp function make_header_with_hd (line 12) | static SeqLib::BamHeader make_header_with_hd(const SeqLib::BamHeader& src, FILE: src/svaba/SvabaThreadUnit.h function namespace (line 29) | namespace SeqLib { function class (line 35) | class svabaThreadUnit { FILE: src/svaba/SvabaUtils.cpp type svabaUtils (line 7) | namespace svabaUtils { function fileDateString (line 64) | std::string fileDateString() { function myreplace (line 129) | std::string myreplace(std::string &s, function hasRepeat (line 136) | bool hasRepeat(const std::string& seq) { function overlapSize (line 153) | int overlapSize(const SeqLib::BamRecord& query, const SeqLib::BamRecor... function print (line 186) | void print(std::stringstream& s, std::ofstream& log, bool cerr) { function runTimeString (line 194) | std::string runTimeString(int num_t_reads, int num_n_reads, int contig... function countJobs (line 224) | int countJobs(const std::string& regionFile, SeqLib::GRC &file_regions... function __bamOptParse (line 289) | std::string __bamOptParse(std::map& obam, st... function __openWriterBam (line 299) | bool __openWriterBam(const SeqLib::BamHeader& h, const std::string& na... function CalcMHWScore (line 320) | double CalcMHWScore(std::vector& scores) function weightedRandom (line 339) | int weightedRandom(const std::vector& cs) { function tokenize_delimited (line 352) | std::vector tokenize_delimited(const std::string& str, ch... function checkHeaderCompatibility (line 370) | void checkHeaderCompatibility(const SeqLib::BamHeader& bamHeader, function find_repeats (line 422) | std::vector> find_repeats(std::string_view seq, si... function parsePLString (line 463) | std::vector parsePLString(const std::string& pl_str) { function SubstringList (line 486) | SubstringList find_long_homopolymers(const std::string& s) { function SubstringList (line 516) | SubstringList find_long_dinuc_repeats(const std::string& s) { FILE: src/svaba/SvabaUtils.h type std (line 17) | typedef std::pair CountPair; type std (line 18) | typedef std::tuple Substring; type std (line 19) | typedef std::vector SubstringList; function namespace (line 23) | namespace svabaUtils { FILE: src/svaba/refilter.cpp type opt (line 45) | namespace opt { type option (line 77) | struct option function parseBreakOptions (line 113) | static void parseBreakOptions(int argc, char** argv) { function splitSampleHeader (line 153) | static std::pair function runRefilterBreakpoints (line 160) | void runRefilterBreakpoints(int argc, char** argv) { FILE: src/svaba/run_svaba.cpp type SvabaBatchWorkItem (line 58) | struct SvabaBatchWorkItem { method SvabaBatchWorkItem (line 64) | SvabaBatchWorkItem(const std::vector v) { function printTable (line 342) | void printTable(const TestOpts& opts, function runTest (line 412) | void runTest(int argc, char** argv) { FILE: src/svaba/threadpool.h function shutdown (line 39) | void shutdown(size_t numThreads) { function submit (line 86) | void submit(std::unique_ptr job){ function shutdown (line 91) | void shutdown(){ FILE: src/svaba/tovcf.cpp type ToVcfOpts (line 59) | struct ToVcfOpts { type option (line 119) | struct option function QualMode (line 137) | QualMode parse_qual_mode(const std::string& s) { function ToVcfOpts (line 146) | ToVcfOpts parse_cli(int argc, char** argv) { function splitSampleHeader (line 206) | std::pair splitSampleHeader(const std::string& ... function runToVCF (line 215) | void runToVCF(int argc, char** argv) { FILE: src/svaba/vcf.cpp function hash_string32 (line 69) | inline uint32_t hash_string32(const std::string& s) { function compareInfoFields (line 76) | bool compareInfoFields(const std::pair& lhs, function pairCompareDesc (line 86) | bool pairCompareDesc( function svtype_to_string (line 93) | std::string svtype_to_string(SVType t) { function max_allele_lo (line 108) | double max_allele_lo(const BreakPoint& bp) { function populate_sv_header (line 541) | void populate_sv_header(VCFHeader& h) { function populate_indel_header (line 609) | void populate_indel_header(VCFHeader& h) { class GenomicRegionWithID (line 756) | class GenomicRegionWithID : public SeqLib::GenomicRegion { method GenomicRegionWithID (line 758) | GenomicRegionWithID(int32_t c, uint32_t p1, uint32_t p2, int i, int p) function classify_symbolic_kind (line 1050) | std::string classify_symbolic_kind(const BreakPoint& bp) { function entry_lt_for_output (line 1065) | bool entry_lt_for_output(const VCFEntry& a, const VCFEntry& b) { function open_vcf_out (line 1077) | std::unique_ptr open_vcf_out(const std::string& path, bool... FILE: src/svaba/vcf.h function QualMode (line 60) | enum class QualMode { SUM_LO_PHRED, MAXLOD_PHRED, MISSING }; FILE: src/svabautils/AssemblyBamWalker.cpp type timespec (line 28) | struct timespec function __good_contig (line 32) | bool __good_contig(const SeqLib::BamRecordVector& brv, const SeqLib::Gen... function runAC (line 52) | bool runAC(const ContigElement * c) { FILE: src/svabautils/AssemblyBamWalker.h function class (line 12) | class AssemblyBamWalker: public SeqLib::BamReader { function AssemblyWalkerWorkItem (line 32) | struct ContigElement { FILE: src/svabautils/BamSplitter.h function class (line 8) | class BamSplitter: public SeqLib::BamReader FILE: src/svabautils/Fractions.h function class (line 12) | class FracRegion : public SeqLib::GenomicRegion { function class (line 27) | class Fractions { FILE: src/svabautils/PowerLawSim.cpp function PowerLawSim (line 14) | void PowerLawSim(faidx_t* findex, int num_breaks, double power_law, SeqL... function drawFromPower (line 203) | std::vector drawFromPower(double x0, double x1, double power, int n... function genRandomSequence (line 222) | void genRandomSequence(std::string& s, SeqLib::GenomicRegion& gr, int wi... FILE: src/svabautils/PowerLawSim.h type SVEvent (line 14) | struct SVEvent { FILE: src/svabautils/ReadSim.cpp function Indel (line 208) | Indel ReadSim::makeDelErrors(std::string& s, int del_size) { function Indel (line 239) | Indel ReadSim::makeDelErrors(std::string& s, int sstart, const std::stri... function Indel (line 279) | Indel ReadSim::makeInsErrors(std::string& s, bool keep_size, int indel_s... FILE: src/svabautils/ReadSim.h type Indel (line 10) | struct Indel { function class (line 34) | class ReadSim { FILE: src/svabautils/SeqFrag.h function class (line 12) | class SeqFrag { FILE: src/svabautils/SimGenome.h function class (line 8) | class SimGenome { FILE: src/svabautils/SimTrainerWalker.h function class (line 7) | class SimTrainerWalker : public SeqLib::BamReader { FILE: src/svabautils/assembly2vcf.cpp type bidx_delete (line 21) | struct bidx_delete { type option (line 26) | struct option type opt (line 71) | namespace opt { function runAssembly2VCF (line 92) | void runAssembly2VCF(int argc, char** argv) function parseAssembly2VCFOptions (line 188) | void parseAssembly2VCFOptions(int argc, char** argv) { FILE: src/svabautils/benchmark.cpp type opt (line 45) | namespace opt { type option (line 126) | struct option function runBenchmark (line 155) | void runBenchmark(int argc, char** argv) { function genBreaks (line 271) | std::string genBreaks() { function splitBam (line 397) | void splitBam() { function assemblyTest (line 427) | void assemblyTest() { function parseBenchmarkOptions (line 593) | void parseBenchmarkOptions(int argc, char** argv) { function parseErrorRates (line 680) | std::vector parseErrorRates(const std::string& s) { function errorRateString (line 698) | std::string errorRateString(const std::vector& v, const std::str... function realignBreaks (line 711) | void realignBreaks() { function realignRandomSegments (line 780) | void realignRandomSegments() { FILE: src/svabautils/snowmanutils.cpp function main (line 21) | int main(int argc, char** argv) { FILE: src/svabautils/snowtools.cpp function ParseFilterObject (line 16) | bool ParseFilterObject(const string& filterName, const Json::Value& filt... function string (line 47) | const string GetScriptContents(string script) { function main (line 84) | int main(int argc, char** argv) { FILE: src/svabautils/splitcounter.cpp type opt (line 21) | namespace opt { type option (line 30) | struct option function runSplitFasta (line 68) | void runSplitFasta(int argc, char** argv) { function runSplitCounter (line 129) | void runSplitCounter(int argc, char** argv) { function parseSplitCounterOptions (line 218) | void parseSplitCounterOptions(int argc, char** argv) { function parseFastaSplitOptions (line 249) | void parseFastaSplitOptions(int argc, char** argv) {