SYMBOL INDEX (4516 symbols across 403 files)

FILE: src/main/java/com/github/lindenb/jbwa/jni/AlnRgn.java
  class AlnRgn (line 210) | public class AlnRgn {
    method AlnRgn (line 220) | public AlnRgn(String chrom, long pos, byte strand, String cigar, int m...
    method getChrom (line 231) | public String getChrom() {
    method getPos (line 235) | public long getPos() {
    method getStrand (line 239) | public char getStrand() {
    method getCigar (line 243) | public String getCigar() {
    method getMQual (line 247) | public int getMQual() {
    method getNm (line 251) | public int getNm() {
    method getAs (line 255) | public int getAs() {
    method getSecondary (line 259) | public int getSecondary() {
    method toString (line 263) | @Override

FILE: src/main/java/com/github/lindenb/jbwa/jni/BwaFrame.java
  class BwaFrame (line 240) | public class BwaFrame extends JFrame {
    class AlnTableModel (line 243) | private class AlnTableModel extends AbstractTableModel {
      method getColumnName (line 246) | @Override
      method getColumnCount (line 251) | @Override
      method getRowCount (line 256) | @Override
      method getValueAt (line 261) | @Override
      method getColumnClass (line 284) | @Override
      method isCellEditable (line 306) | @Override
      method clear (line 311) | void clear() {
      method addAll (line 316) | void addAll(AlnRgn rgn[]) {
    method BwaFrame (line 327) | private BwaFrame(File f, BwaIndex bwaIndex) {
    method doMenuClose (line 375) | private void doMenuClose() {
    method doMenuAlign (line 381) | private void doMenuAlign() {
    method main (line 402) | public static void main(String[] args) {

FILE: src/main/java/com/github/lindenb/jbwa/jni/BwaIndex.java
  class BwaIndex (line 212) | public class BwaIndex {
    method BwaIndex (line 215) | public BwaIndex(File index) throws IOException {
    method finalize (line 220) | @Override
    method close (line 225) | public native void close();
    method _open (line 228) | private static native long _open(String s) throws IOException;

FILE: src/main/java/com/github/lindenb/jbwa/jni/BwaMem.java
  class BwaMem (line 212) | public class BwaMem {
    method BwaMem (line 216) | public BwaMem(BwaIndex bwaIndex) {
    method updateScoringParameters (line 221) | public void updateScoringParameters(final int baseMismatchPen,
    method align (line 228) | public AlnRgn[] align(ShortRead read) throws IOException {
    method align (line 233) | public String[] align(final List<ShortRead> ks1, final List<ShortRead>...
    method align (line 243) | public String[] align(final ShortRead ks1[], final ShortRead ks2[]) th...
    method finalize (line 253) | @Override
    method dispose (line 258) | public native void dispose();
    method mem_opt_init (line 260) | private static native long mem_opt_init();
    method set_verbosity (line 272) | public native void set_verbosity(int verbosity);
    method update_score_parameters (line 274) | private native void update_score_parameters(int B, int Oi, int Od, int...
    method align (line 276) | private native AlnRgn[] align(BwaIndex bwaIndex, byte bases[]) throws ...
    method align2 (line 278) | private native String[] align2(BwaIndex bwaIndex, final ShortRead ks1[...

FILE: src/main/java/com/github/lindenb/jbwa/jni/KSeq.java
  class KSeq (line 212) | public class KSeq {
    method KSeq (line 215) | public KSeq(File f) throws IOException {
    method KSeq (line 219) | public KSeq() throws IOException {
    method next (line 223) | public native ShortRead next() throws IOException;
    method finalize (line 225) | @Override
    method dispose (line 230) | public native void dispose();
    method init (line 232) | private static native long init(String file);

FILE: src/main/java/com/github/lindenb/jbwa/jni/ShortRead.java
  class ShortRead (line 209) | public class ShortRead {
    method ShortRead (line 214) | public ShortRead(String name, byte[] seq, byte[] qual) {
    method getName (line 220) | public String getName() {
    method getBases (line 224) | public byte[] getBases() {
    method getQualities (line 228) | public byte[] getQualities() {
    method toString (line 232) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/ApplyBQSRAdaptor.java
  class ApplyBQSRAdaptor (line 50) | public class ApplyBQSRAdaptor {
    method applyBQSR (line 52) | public static List<BasicSamRecord> applyBQSR(RefContigInfo refContigInfo,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BQSRTableGather.java
  class BQSRTableGather (line 44) | public class BQSRTableGather {
    method gatherBQSRTables (line 46) | public static List<String> gatherBQSRTables(List<List<String>> reportL...
    method gatherBQSRTablesInParallel (line 69) | public static List<String> gatherBQSRTablesInParallel(final List<List<...
    class ForkJoinMergeTask (line 123) | private static class ForkJoinMergeTask extends RecursiveTask<Recalibra...
      method ForkJoinMergeTask (line 128) | public ForkJoinMergeTask(RecalibrationReport[] reports, int start, i...
      method compute (line 134) | public RecalibrationReport compute() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BaseRecalibratorAdapter.java
  class BaseRecalibratorAdapter (line 45) | public class BaseRecalibratorAdapter {
    method getRecalTableLines (line 47) | public static List<String> getRecalTableLines(RefContigInfo refContigI...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/BwaMemAdapter.java
  class BwaMemAdapter (line 46) | public class BwaMemAdapter {
    method getBwaIndexInstance (line 50) | private static BwaIndex getBwaIndexInstance(String bwaJNILibPath, Stri...
    method pairAlign (line 63) | public static List<BasicSamRecord> pairAlign(String bwaJNILibPath,
    method alignAndAddIntoResult (line 98) | private static void alignAndAddIntoResult(BwaIndex bwaIndex, List<Basi...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/HaplotypeCallerAdapter.java
  class HaplotypeCallerAdapter (line 60) | public class HaplotypeCallerAdapter {
    method getActiveRegions (line 62) | public static List<SerializableActiveRegionMapData> getActiveRegions(R...
    class StaticData (line 98) | public static class StaticData {
    method getStaticDataInstance (line 106) | public static StaticData getStaticDataInstance(RefContigInfo refContig...
    method callVariants (line 130) | public static List<VcfRecord> callVariants(RefContigInfo refContigInfo,
    method callVariants (line 139) | public static List<VcfRecord> callVariants(RefContigInfo refContigInfo,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/IndelRealignAdapter.java
  class IndelRealignAdapter (line 50) | public class IndelRealignAdapter {
    method realign (line 52) | public static List<BasicSamRecord> realign(RefContigInfo refContigInfo,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/MutectAdapter.java
  class MutectAdapter (line 50) | public class MutectAdapter {
    method callVariants (line 51) | public static List<VcfRecord> callVariants(RefContigInfo refContigInfo,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/CountSet.java
  class CountSet (line 34) | public class CountSet implements Cloneable, Set<Integer> {
    method CountSet (line 50) | public CountSet(final CountSet template) {
    method CountSet (line 60) | public CountSet(int initialCapacity) {
    method setTo (line 71) | public void setTo(int value) {
    method setTo (line 82) | public void setTo(int ... values) {
    method incAll (line 95) | public boolean incAll(final int delta) {
    method min (line 109) | public int min() {
    method max (line 121) | public int max() {
    method addRange (line 137) | public boolean addRange(final int fromValue, final int toValue) {
    method add (line 159) | public boolean add(final int value) {
    method addAll (line 176) | public boolean addAll(final int ... values) {
    method addAll (line 184) | @Override
    method addAll (line 205) | public boolean addAll(final int[] source, final int fromIndex, final i...
    method addAll (line 222) | public boolean addAll(final CountSet other) {
    method contains (line 231) | public boolean contains(final int value) {
    method ensureCapacity (line 242) | private void ensureCapacity(final int capacity) {
    method size (line 249) | @Override
    method isEmpty (line 254) | @Override
    method contains (line 259) | @Override
    method iterator (line 269) | @Override
    method toArray (line 274) | @Override
    method toArray (line 282) | @Override
    method toIntArray (line 305) | public int[] toIntArray() {
    method copyTo (line 317) | public void copyTo(final int[] dest, int offset) {
    method copyTo (line 332) | public void copyTo(final int[] dest) {
    method add (line 337) | @Override
    method remove (line 342) | @Override
    method remove (line 352) | public boolean remove(final int i) {
    method containsAll (line 362) | @Override
    method retainAll (line 371) | @Override
    method removeIndices (line 407) | private void removeIndices(final int fromIdx, final int toIdx) {
    method removeAll (line 412) | @Override
    method removeIndex (line 420) | private void removeIndex(int idx) {
    method clear (line 424) | @Override
    method clone (line 433) | @SuppressWarnings("all")
    method toString (line 438) | @Override
    class MyIterator (line 453) | private class MyIterator implements Iterator<Integer> {
      method hasNext (line 457) | @Override
      method next (line 462) | @Override
      method remove (line 469) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/DefaultHashMap.java
  class DefaultHashMap (line 29) | public class DefaultHashMap<K,V> extends HashMap<K,V> {
    method setDefaultValue (line 31) | public void setDefaultValue(V defaultValue) {
    method DefaultHashMap (line 35) | public DefaultHashMap(V defaultValue) {
    method get (line 38) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/IndexedSet.java
  class IndexedSet (line 42) | public class IndexedSet<E> extends AbstractSet<E> implements Set<E> {
    method IndexedSet (line 69) | public IndexedSet(final int initialCapacity) {
    method IndexedSet (line 86) | @SuppressWarnings("unchecked")
    method IndexedSet (line 117) | @SuppressWarnings("unchecked")
    method asList (line 151) | public List<E> asList() {
    method checkIndex (line 168) | protected void checkIndex(final int index) {
    method iterator (line 175) | @Override
    method size (line 184) | @Override
    method contains (line 194) | @Override
    method add (line 215) | @Override
    method remove (line 242) | @Override
    method clear (line 259) | @Override
    method equals (line 270) | @Override
    method equals (line 294) | public boolean equals(final IndexedSet<?> other) {
    method hashCode (line 308) | @Override
    method get (line 325) | public E get(final int index) {
    method indexOf (line 339) | public int indexOf(final E o) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/IntMaxHeap.java
  class IntMaxHeap (line 29) | public class IntMaxHeap {
    method IntMaxHeap (line 41) | public IntMaxHeap(final int initialCapacity) {
    method add (line 56) | public void add(final int v) {
    method addWithoutCheckingCapacity (line 66) | private void addWithoutCheckingCapacity(final int v) {
    method add (line 88) | public void add(final int ... v) {
    method ensureCapacity (line 96) | private void ensureCapacity(final int newSize) {
    method peek (line 108) | public int peek() {
    method remove (line 121) | public int remove() {
    method removeUpdate (line 132) | private void removeUpdate() {
    method isEmpty (line 185) | public boolean isEmpty() {
    method size (line 194) | public int size() {
    method clear (line 201) | public void clear() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/NestedIntegerArray.java
  class NestedIntegerArray (line 34) | public class NestedIntegerArray<T> {
    method NestedIntegerArray (line 46) | public NestedIntegerArray(final int... dimensions) {
    method getDimensions (line 66) | public int[] getDimensions() {
    method preallocateArray (line 79) | private void preallocateArray( Object[] subarray, int dimension, int d...
    method get (line 90) | public T get(final int... keys) {
    method put (line 120) | public boolean put(final T value, final int... keys) { // WARNING! val...
    method getAllValues (line 160) | public List<T> getAllValues() {
    method fillAllValues (line 166) | private void fillAllValues(final Object[] array, final List<T> result) {
    class Leaf (line 177) | public static class Leaf<T> {
      method Leaf (line 181) | public Leaf(final int[] keys, final T value) {
    method getAllLeaves (line 187) | public List<Leaf<T>> getAllLeaves() {
    method fillAllLeaves (line 193) | private void fillAllLeaves(final Object[] array, final int[] path, fin...
    method appendToPath (line 207) | private int[] appendToPath(final int[] path, final int newKey) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/Pair.java
  class Pair (line 27) | public class Pair<X,Y> {
    method Pair (line 32) | public Pair(X x, Y y) { first = x; second = y; }
    method set (line 34) | public void set(X x, Y y) { first = x; second = y; }
    method getFirst (line 39) | public X getFirst() { return first; }
    method getSecond (line 44) | public Y getSecond() { return second; }
    method equals (line 51) | @Override
    method hashCode (line 77) | @Override
    method toString (line 88) | public String toString() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/Permutation.java
  type Permutation (line 31) | public interface Permutation<E> {
    method isPartial (line 42) | public boolean isPartial();
    method isNonPermuted (line 49) | public boolean isNonPermuted();
    method toIndex (line 61) | public int toIndex(final int fromIndex);
    method fromIndex (line 71) | public int fromIndex(final int toIndex);
    method fromSize (line 78) | public int fromSize();
    method toSize (line 85) | public int toSize();
    method fromList (line 91) | public List<E> fromList();
    method toList (line 98) | public List<E> toList();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/basic/PrimitivePair.java
  class PrimitivePair (line 27) | public class PrimitivePair {
    class Int (line 30) | public static class Int {
      method Int (line 35) | public Int(int x, int y) { first = x; second = y; }
      method Int (line 36) | public Int() { first = second = 0; }
      method set (line 38) | public void set(int x, int y) { first = x; second = y; }
      method getFirst (line 43) | public int getFirst() { return first; }
      method getSecond (line 48) | public int getSecond() { return second; }
      method add (line 58) | public PrimitivePair.Int add(PrimitivePair.Int p) {
      method subtract (line 72) | public PrimitivePair.Int subtract(PrimitivePair.Int p) {
      method assignFrom (line 83) | public PrimitivePair.Int assignFrom(PrimitivePair.Int p ) {
    class Long (line 92) | public static class Long {
      method Long (line 97) | public Long(long x, long y) { first = x; second = y; }
      method Long (line 98) | public Long() { first = second = 0; }
      method set (line 100) | public void set(long x, long y) { first = x; second = y; }
      method getFirst (line 105) | public long getFirst() { return first; }
      method getSecond (line 110) | public long getSecond() { return second; }
      method add (line 120) | public PrimitivePair.Long add(PrimitivePair.Int p) {
      method add (line 134) | public PrimitivePair.Long add(PrimitivePair.Long p) {
      method subtract (line 148) | public PrimitivePair.Long subtract(PrimitivePair.Int p) {
      method subtract (line 162) | public PrimitivePair.Long subtract(PrimitivePair.Long p) {
      method assignFrom (line 173) | public PrimitivePair.Long assignFrom(PrimitivePair.Long p ) {
      method assignFrom (line 184) | public PrimitivePair.Long assignFrom(PrimitivePair.Int p ) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/RefContentProvider.java
  class RefContentProvider (line 33) | public class RefContentProvider {
    method RefContentProvider (line 64) | public RefContentProvider(SAMSequenceDictionary samSequenceDictionary,
    method getLocus (line 99) | public GenomeLoc getLocus() {
    method getReferenceContext (line 109) | public ReferenceContext getReferenceContext(GenomeLoc locus) {
    method getReferenceContext (line 133) | public ReferenceContext getReferenceContext(GenomeLoc locus, int overl...
    method getSamSequenceDictionary (line 139) | public SAMSequenceDictionary getSamSequenceDictionary() {
    method getOriginStartCoordinate (line 143) | public int getOriginStartCoordinate() {
    method getOriginEndCoordinate (line 147) | public int getOriginEndCoordinate() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/RefMetaDataTracker.java
  class RefMetaDataTracker (line 44) | public class RefMetaDataTracker {
    method RefMetaDataTracker (line 54) | public RefMetaDataTracker() {
    method RefMetaDataTracker (line 58) | public RefMetaDataTracker(final Collection<RODRecordList> allBindings) {
    method getValues (line 98) | public <T extends Feature> List<T> getValues(final Class<T> type) {
    method getValues (line 111) | public <T extends Feature> List<T> getValues(final Class<T> type, fina...
    method getFirstValue (line 129) | public <T extends Feature> T getFirstValue(final Class<T> type) {
    method getFirstValue (line 143) | public <T extends Feature> T getFirstValue(final Class<T> type, final ...
    method getPrioritizedValue (line 155) | public <T extends Feature> List<T> getPrioritizedValue(final Collectio...
    method getValues (line 186) | public <T extends Feature> List<T> getValues(final RodBinding<T> rodBi...
    method getValues (line 201) | public <T extends Feature> List<T> getValues(final Collection<RodBindi...
    method getValues (line 208) | public <T extends Feature> List<T> getValues(String name) {
    method getAllValues (line 218) | public <T extends Feature> List<T> getAllValues() {
    method getValues (line 237) | public <T extends Feature> List<T> getValues(final RodBinding<T> rodBi...
    method getValues (line 249) | public <T extends Feature> List<T> getValues(final Collection<RodBindi...
    method getFirstValue (line 265) | public <T extends Feature> T getFirstValue(final RodBinding<T> rodBind...
    method getFirstValue (line 279) | public <T extends Feature> T getFirstValue(final RodBinding<T> rodBind...
    method getFirstValue (line 292) | public <T extends Feature> T getFirstValue(final Collection<RodBinding...
    method getFirstValue (line 311) | public <T extends Feature> T getFirstValue(final Collection<RodBinding...
    method hasValues (line 326) | public boolean hasValues(final RodBinding rodBinding) {
    method getBoundRodTracks (line 336) | public List<RODRecordList> getBoundRodTracks() {
    method getNTracksWithBoundFeatures (line 345) | public int getNTracksWithBoundFeatures() {
    method hasValues (line 353) | protected boolean hasValues(final String name) {
    method getValues (line 357) | protected <T extends Feature> List<T> getValues(final Class<T> type, f...
    method getValues (line 361) | protected <T extends Feature> List<T> getValues(final Class<T> type, f...
    method getFirstValue (line 365) | protected <T extends Feature> T getFirstValue(final Class<T> type, fin...
    method getFirstValue (line 369) | protected <T extends Feature> T getFirstValue(final Class<T> type, fin...
    method safeGetFirst (line 389) | private <T extends Feature> T safeGetFirst(final List<T> l) {
    method addValues (line 393) | private <T extends Feature> List<T> addValues(final Collection<String>...
    method addValues (line 410) | private <T extends Feature> List<T> addValues(final String name,
    method getTrackDataByName (line 456) | private RODRecordList getTrackDataByName(final String name) {
    method getTrackDataByName (line 462) | private RODRecordList getTrackDataByName(final RodBinding binding) {
    method canonicalName (line 472) | private String canonicalName(final String name) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/reference/ReferenceContext.java
  class ReferenceContext (line 29) | public class ReferenceContext {
    method ReferenceContext (line 40) | public ReferenceContext(GenomeLoc locus, int contigId, byte[] bases) {
    method ReferenceContext (line 47) | public ReferenceContext(GenomeLoc locus, GenomeLoc window, int contigI...
    method getContigId (line 59) | public int getContigId() {
    method getLocus (line 68) | public GenomeLoc getLocus() {
    method getWindow (line 72) | public GenomeLoc getWindow() {
    method getBase (line 81) | public byte getBase() {
    method getBases (line 91) | public byte[] getBases() {
    method getForwardBases (line 95) | public byte[] getForwardBases() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/AlignmentContext.java
  class AlignmentContext (line 32) | public class AlignmentContext implements HasGenomeLocation {
    method AlignmentContext (line 43) | public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup) {
    method AlignmentContext (line 47) | public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, lo...
    method getBasePileup (line 67) | public ReadBackedPileup getBasePileup() {
    method hasPileupBeenDownsampled (line 76) | public boolean hasPileupBeenDownsampled() {
    method size (line 85) | public int size() {
    method getContig (line 89) | public String getContig() {
    method getPosition (line 93) | public long getPosition() {
    method getLocation (line 97) | public GenomeLoc getLocation() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/AlignmentStateMachine.java
  class AlignmentStateMachine (line 41) | public class AlignmentStateMachine {
    method AlignmentStateMachine (line 70) | public AlignmentStateMachine(final GATKSAMRecord read) {
    method initializeAsLeftEdge (line 82) | private void initializeAsLeftEdge() {
    method getRead (line 91) | public GATKSAMRecord getRead() {
    method getReferenceIndex (line 100) | public int getReferenceIndex() {
    method isLeftEdge (line 108) | public boolean isLeftEdge() {
    method isRightEdge (line 116) | public boolean isRightEdge() {
    method getReadOffset (line 125) | public int getReadOffset() {
    method getCurrentCigarElement (line 139) | public CigarElement getCurrentCigarElement() {
    method getCurrentCigarElementOffset (line 155) | public int getCurrentCigarElementOffset() {
    method getOffsetIntoCurrentCigarElement (line 170) | public int getOffsetIntoCurrentCigarElement() {
    method getCigarOperator (line 182) | public CigarOperator getCigarOperator() {
    method toString (line 186) | @Override
    method stepForwardOnGenome (line 219) | public CigarOperator stepForwardOnGenome() {
    method makePileupElement (line 300) | public final PileupElement makePileupElement() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/GATKSAMReadGroupRecord.java
  class GATKSAMReadGroupRecord (line 30) | public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
    method GATKSAMReadGroupRecord (line 41) | public GATKSAMReadGroupRecord(final String id) {
    method GATKSAMReadGroupRecord (line 45) | public GATKSAMReadGroupRecord(SAMReadGroupRecord record) {
    method getNGSPlatform (line 57) | public NGSPlatform getNGSPlatform() {
    method toString (line 66) | @Override
    method getSample (line 75) | @Override
    method setSample (line 84) | @Override
    method getPlatform (line 91) | @Override
    method setPlatform (line 100) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/GATKSAMRecord.java
  class GATKSAMRecord (line 43) | public class GATKSAMRecord extends SAMRecord implements Cloneable{
    method GATKSAMRecord (line 84) | public GATKSAMRecord(final SAMFileHeader header) {
    method GATKSAMRecord (line 92) | public GATKSAMRecord(final SAMRecord read) {
    method GATKSAMRecord (line 123) | public GATKSAMRecord(final SAMFileHeader header,
    method isStrandless (line 171) | public boolean isStrandless() {
    method setIsStrandless (line 179) | public void setIsStrandless(final boolean isStrandless) {
    method getReadNegativeStrandFlag (line 183) | @Override
    method setReadNegativeStrandFlag (line 188) | @Override
    method getReadString (line 200) | @Override
    method setReadString (line 207) | @Override
    method getReadGroup (line 217) | @Override
    method setReadGroup (line 236) | public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
    method hashCode (line 243) | @Override
    method equals (line 248) | @Override
    method setBaseQualities (line 261) | public void setBaseQualities( final byte[] quals, final EventType erro...
    method getBaseQualities (line 277) | public byte[] getBaseQualities( final EventType errorModel ) {
    method hasBaseIndelQualities (line 293) | public boolean hasBaseIndelQualities() {
    method getExistingBaseInsertionQualities (line 300) | public byte[] getExistingBaseInsertionQualities() {
    method getExistingBaseDeletionQualities (line 307) | public byte[] getExistingBaseDeletionQualities() {
    method getBaseInsertionQualities (line 317) | public byte[] getBaseInsertionQualities() {
    method getBaseDeletionQualities (line 333) | public byte[] getBaseDeletionQualities() {
    method getNGSPlatform (line 347) | public NGSPlatform getNGSPlatform() {
    method containsTemporaryAttribute (line 365) | public boolean containsTemporaryAttribute(Object key) {
    method setTemporaryAttribute (line 381) | public Object setTemporaryAttribute(Object key, Object value) {
    method getTemporaryAttribute (line 398) | public Object getTemporaryAttribute(Object key) {
    method isEmpty (line 413) | public boolean isEmpty() {
    method simplify (line 420) | public GATKSAMRecord simplify () {
    method getSoftStart (line 440) | public int getSoftStart() {
    method getSoftEnd (line 462) | public int getSoftEnd() {
    method resetSoftStartAndEnd (line 490) | public void resetSoftStartAndEnd() {
    method resetSoftStartAndEnd (line 499) | public void resetSoftStartAndEnd(int softStart, int softEnd) {
    method getOriginalAlignmentStart (line 511) | public int getOriginalAlignmentStart() {
    method getOriginalAlignmentEnd (line 522) | public int getOriginalAlignmentEnd() {
    method emptyRead (line 539) | public static GATKSAMRecord emptyRead(GATKSAMRecord read) {
    method createQualityModifiedRead (line 588) | public static GATKSAMRecord createQualityModifiedRead(final GATKSAMRec...
    method clone (line 615) | @Override
    method getAdaptorBoundary (line 642) | public int getAdaptorBoundary() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/IntervalLocusSamTraverser.java
  class IntervalLocusSamTraverser (line 37) | public class IntervalLocusSamTraverser {
    method IntervalLocusSamTraverser (line 43) | public IntervalLocusSamTraverser(SamContentProvider samContentProvider,
    method IntervalLocusSamTraverser (line 49) | public IntervalLocusSamTraverser(SamContentProvider samContentProvider,
    method getOverlappedIntervals (line 58) | private List<GenomeLoc> getOverlappedIntervals(GenomeLoc refLocus, Lis...
    method rewind (line 103) | public void rewind() {
    method hasNext (line 108) | public boolean hasNext() {
    method next (line 113) | public AlignmentContext next() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/LocusSamTraverser.java
  class LocusSamTraverser (line 37) | public class LocusSamTraverser {
    method LocusSamTraverser (line 53) | public LocusSamTraverser(SamContentProvider samContentProvider, Genome...
    method LocusSamTraverser (line 57) | public LocusSamTraverser(SamContentProvider samContentProvider, Genome...
    method rewind (line 72) | public void rewind() {
    method hasNext (line 81) | public boolean hasNext() {
    method next (line 85) | public AlignmentContext next() {
    class PileupTraker (line 146) | class PileupTraker {
      method PileupTraker (line 151) | PileupTraker(GATKSAMRecord read) {
      method stepForwardOnGenome (line 157) | void stepForwardOnGenome() {
      method isBeforeEnd (line 161) | boolean isBeforeEnd(int coordinate) {
      method isAfterStart (line 165) | boolean isAfterStart(int coordinate) {
    method forwardToCoordinate (line 175) | public void forwardToCoordinate(int newCoordinate) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/MergingPileupElementIterator.java
  class MergingPileupElementIterator (line 33) | class MergingPileupElementIterator<PE extends PileupElement> implements ...
    method MergingPileupElementIterator (line 36) | public MergingPileupElementIterator(PerSamplePileupElementTracker<PE> ...
    method hasNext (line 45) | public boolean hasNext() {
    method next (line 49) | public PE next() {
    method remove (line 57) | public void remove() {
    class PileupElementIteratorComparator (line 64) | private class PileupElementIteratorComparator implements Comparator<Pe...
      method compare (line 65) | public int compare(PeekableIterator<PE> lhs, PeekableIterator<PE> rh...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/PileupElement.java
  class PileupElement (line 36) | public class PileupElement implements Comparable<PileupElement> {
    method PileupElement (line 66) | public PileupElement(final GATKSAMRecord read, final int baseOffset,
    method PileupElement (line 90) | public PileupElement(final PileupElement toCopy) {
    method isDeletion (line 99) | public boolean isDeletion() {
    method isBeforeDeletionStart (line 111) | public boolean isBeforeDeletionStart() {
    method isAfterDeletionEnd (line 124) | public boolean isAfterDeletionEnd() {
    method getRead (line 132) | public GATKSAMRecord getRead() {
    method getOffset (line 143) | public int getOffset() {
    method getBase (line 154) | public byte getBase() {
    method getBaseIndex (line 158) | @Deprecated
    method getQual (line 167) | public byte getQual() {
    method getBaseInsertionQual (line 175) | public byte getBaseInsertionQual() {
    method getBaseDeletionQual (line 183) | public byte getBaseDeletionQual() {
    method getLengthOfImmediatelyFollowingIndel (line 200) | public int getLengthOfImmediatelyFollowingIndel() {
    method getNextIndelCigarElement (line 214) | private CigarElement getNextIndelCigarElement() {
    method getBasesOfImmediatelyFollowingInsertion (line 239) | public String getBasesOfImmediatelyFollowingInsertion() {
    method getMappingQual (line 253) | public int getMappingQual() {
    method toString (line 257) | public String toString() {
    method compareTo (line 261) | @Override
    method getCurrentCigarElement (line 285) | public CigarElement getCurrentCigarElement() {
    method getCurrentCigarOffset (line 297) | public int getCurrentCigarOffset() {
    method getOffsetInCurrentCigar (line 309) | public int getOffsetInCurrentCigar() {
    method getBetweenPrevPosition (line 326) | public LinkedList<CigarElement> getBetweenPrevPosition() {
    method getBetweenNextPosition (line 337) | public LinkedList<CigarElement> getBetweenNextPosition() {
    type Direction (line 342) | private enum Direction { PREV, NEXT }
    method getBetween (line 350) | private LinkedList<CigarElement> getBetween(final Direction direction) {
    method getPreviousOnGenomeCigarElement (line 387) | public CigarElement getPreviousOnGenomeCigarElement() {
    method getNextOnGenomeCigarElement (line 398) | public CigarElement getNextOnGenomeCigarElement() {
    method getNeighboringOnGenomeCigarElement (line 407) | private CigarElement getNeighboringOnGenomeCigarElement(final Directio...
    method hasOperator (line 428) | private boolean hasOperator(final CigarElement maybeCigarElement, fina...
    method isAfterInsertion (line 437) | public boolean isAfterInsertion() { return isAfter(getBetweenPrevPosit...
    method isBeforeInsertion (line 444) | public boolean isBeforeInsertion() { return isBefore(getBetweenNextPos...
    method isAfterSoftClip (line 451) | public boolean isAfterSoftClip() { return isAfter(getBetweenPrevPositi...
    method isBeforeSoftClip (line 458) | public boolean isBeforeSoftClip() { return isBefore(getBetweenNextPosi...
    method isNextToSoftClip (line 465) | public boolean isNextToSoftClip() { return isAfterSoftClip() || isBefo...
    method atEndOfCurrentCigar (line 475) | public boolean atEndOfCurrentCigar() {
    method atStartOfCurrentCigar (line 487) | public boolean atStartOfCurrentCigar() {
    method isAfter (line 498) | private boolean isAfter(final LinkedList<CigarElement> elements, final...
    method isBefore (line 509) | private boolean isBefore(final List<CigarElement> elements, final Ciga...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/PileupElementTracker.java
  class PileupElementTracker (line 36) | abstract class PileupElementTracker<PE extends PileupElement> implements...
    method size (line 37) | public abstract int size();
    method unorderedIterable (line 44) | public abstract Iterable<PE> unorderedIterable();
    method unorderedIterator (line 50) | public Iterator<PE> unorderedIterator() { return unorderedIterable().i...
    method copy (line 52) | public abstract PileupElementTracker<PE> copy();
  class UnifiedPileupElementTracker (line 55) | class UnifiedPileupElementTracker<PE extends PileupElement> extends Pile...
    method copy (line 58) | @Override
    method UnifiedPileupElementTracker (line 66) | public UnifiedPileupElementTracker() { pileup = new LinkedList<PE>(); }
    method UnifiedPileupElementTracker (line 67) | public UnifiedPileupElementTracker(List<PE> pileup) { this.pileup = pi...
    method add (line 69) | public void add(PE element) {
    method get (line 73) | public PE get(int index) {
    method size (line 77) | public int size() {
    method iterator (line 81) | public Iterator<PE> iterator() { return pileup.iterator(); }
    method unorderedIterable (line 82) | public Iterable<PE> unorderedIterable() { return this; }
  class PerSamplePileupElementTracker (line 85) | class PerSamplePileupElementTracker<PE extends PileupElement> extends Pi...
    method PerSamplePileupElementTracker (line 89) | public PerSamplePileupElementTracker() {
    method copy (line 93) | public PerSamplePileupElementTracker<PE> copy() {
    method getSamples (line 105) | public Collection<String> getSamples() {
    method getElements (line 109) | public PileupElementTracker<PE> getElements(final String sample) {
    method getElements (line 113) | public PileupElementTracker<PE> getElements(final Collection<String> s...
    method addElements (line 121) | public void addElements(final String sample, PileupElementTracker<PE> ...
    method iterator (line 126) | public Iterator<PE> iterator() { return new MergingPileupElementIterat...
    method size (line 128) | public int size() {
    method unorderedIterable (line 133) | public Iterable<PE> unorderedIterable() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/ReadBackedPileup.java
  type ReadBackedPileup (line 38) | public interface ReadBackedPileup extends Iterable<PileupElement>, HasGe...
    method getPileupWithoutDeletions (line 46) | public ReadBackedPileup getPileupWithoutDeletions();
    method getOverlappingFragmentFilteredPileup (line 56) | public ReadBackedPileup getOverlappingFragmentFilteredPileup();
    method getOverlappingFragmentFilteredPileup (line 66) | public ReadBackedPileup getOverlappingFragmentFilteredPileup(boolean d...
    method getPileupWithoutMappingQualityZeroReads (line 75) | public ReadBackedPileup getPileupWithoutMappingQualityZeroReads();
    method getPositiveStrandPileup (line 81) | public ReadBackedPileup getPositiveStrandPileup();
    method getNegativeStrandPileup (line 87) | public ReadBackedPileup getNegativeStrandPileup();
    method getBaseAndMappingFilteredPileup (line 95) | public ReadBackedPileup getBaseAndMappingFilteredPileup( int minBaseQ,...
    method getBaseFilteredPileup (line 102) | public ReadBackedPileup getBaseFilteredPileup( int minBaseQ );
    method getMappingFilteredPileup (line 109) | public ReadBackedPileup getMappingFilteredPileup( int minMapQ );
    method getDownsampledPileup (line 117) | public ReadBackedPileup getDownsampledPileup(int desiredCoverage);
    method getReadGroups (line 123) | public Collection<String> getReadGroups();
    method getPileupForReadGroup (line 130) | public ReadBackedPileup getPileupForReadGroup(String readGroupId);
    method getPileupForReadGroups (line 137) | public ReadBackedPileup getPileupForReadGroups(final HashSet<String> r...
    method getPileupForLane (line 145) | public ReadBackedPileup getPileupForLane(String laneID);
    method getSamples (line 151) | public Collection<String> getSamples();
    method getPileupForSamples (line 159) | public ReadBackedPileup getPileupForSamples(Collection<String> sampleN...
    method getPileupsForSamples (line 169) | public Map<String, ReadBackedPileup> getPileupsForSamples(Collection<S...
    method getPileupForSample (line 177) | public ReadBackedPileup getPileupForSample(String sampleName);
    method getNumberOfDeletions (line 184) | public int getNumberOfDeletions();
    method getNumberOfDeletionsAfterThisElement (line 191) | public int getNumberOfDeletionsAfterThisElement();
    method getNumberOfInsertionsAfterThisElement (line 198) | public int getNumberOfInsertionsAfterThisElement();
    method getNumberOfMappingQualityZeroReads (line 200) | public int getNumberOfMappingQualityZeroReads();
    method getNumberOfElements (line 205) | public int getNumberOfElements();
    method depthOfCoverage (line 210) | public int depthOfCoverage();
    method isEmpty (line 215) | public boolean isEmpty();
    method getLocation (line 220) | public GenomeLoc getLocation();
    method getBaseCounts (line 228) | public int[] getBaseCounts();
    method getPileupString (line 230) | public String getPileupString(Character ref);
    method getReads (line 236) | public List<GATKSAMRecord> getReads();
    method getOffsets (line 242) | public List<Integer> getOffsets();
    method getBases (line 248) | public byte[] getBases();
    method getQuals (line 254) | public byte[] getQuals();
    method getMappingQuals (line 260) | public int[] getMappingQuals();
    method getStartSortedPileup (line 267) | public ReadBackedPileup getStartSortedPileup();
    method toFragments (line 273) | public FragmentCollection<PileupElement> toFragments();
    method copy (line 280) | public ReadBackedPileup copy();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/ReadBackedPileupImpl.java
  class ReadBackedPileupImpl (line 45) | public class ReadBackedPileupImpl implements ReadBackedPileup {
    method ReadBackedPileupImpl (line 61) | public ReadBackedPileupImpl(GenomeLoc loc) {
    method ReadBackedPileupImpl (line 70) | public ReadBackedPileupImpl(GenomeLoc loc, List<PileupElement> pileup) {
    method ReadBackedPileupImpl (line 84) | @Deprecated
    method ReadBackedPileupImpl (line 89) | protected ReadBackedPileupImpl(GenomeLoc loc, PileupElementTracker<Pil...
    method ReadBackedPileupImpl (line 94) | public ReadBackedPileupImpl(GenomeLoc loc, Map<String, ReadBackedPileu...
    method createNewPileup (line 103) | protected ReadBackedPileupImpl createNewPileup(GenomeLoc loc, PileupEl...
    method getPileupWithoutDeletions (line 120) | @Override
    method getOverlappingFragmentFilteredPileup (line 158) | @Override
    method getOverlappingFragmentFilteredPileup (line 171) | @Override
    method getPileupWithoutMappingQualityZeroReads (line 228) | @Override
    method getPositiveStrandPileup (line 258) | public ReadBackedPileupImpl getPositiveStrandPileup() {
    method getNegativeStrandPileup (line 287) | public ReadBackedPileupImpl getNegativeStrandPileup() {
    method getBaseAndMappingFilteredPileup (line 319) | @Override
    method getBaseFilteredPileup (line 352) | @Override
    method getMappingFilteredPileup (line 364) | @Override
    method getReadGroups (line 374) | @Override
    method getPileupForReadGroup (line 388) | @Override
    method getPileupForReadGroups (line 423) | @Override
    method getPileupForLane (line 452) | @Override
    method getSamples (line 483) | public Collection<String> getSamples() {
    method getDownsampledPileup (line 506) | @Override
    method getPileupForSamples (line 553) | @Override
    method getPileupsForSamples (line 576) | @Override
    method getPileupForSample (line 609) | @Override
    method iterator (line 646) | @Override
    method getNumberOfDeletions (line 681) | @Override
    method getNumberOfMappingQualityZeroReads (line 694) | @Override
    method getNumberOfElements (line 712) | @Override
    method depthOfCoverage (line 720) | @Override
    method isEmpty (line 731) | @Override
    method getLocation (line 740) | @Override
    method getBaseCounts (line 751) | @Override
    method getPileupString (line 777) | @Override
    method getReads (line 799) | @Override
    method getNumberOfDeletionsAfterThisElement (line 808) | @Override
    method getNumberOfInsertionsAfterThisElement (line 818) | @Override
    method getOffsets (line 833) | @Override
    method getBases (line 847) | @Override
    method getQuals (line 862) | @Override
    method getMappingQuals (line 877) | @Override
    method quals2String (line 887) | static String quals2String(byte[] quals) {
    method getQualsString (line 898) | private String getQualsString() {
    method getStartSortedPileup (line 907) | @Override
    method toFragments (line 940) | @Override
    method copy (line 945) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/ReadSamTraverser.java
  class ReadSamTraverser (line 32) | public class ReadSamTraverser {
    method ReadSamTraverser (line 38) | public ReadSamTraverser(SamContentProvider samContentProvider) {
    method ReadSamTraverser (line 42) | public ReadSamTraverser(SamContentProvider samContentProvider, FilterU...
    method rewind (line 58) | public void rewind() {
    method hasNext (line 62) | public boolean hasNext() {
    method next (line 66) | public GATKSAMRecord next() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/RegionSamTraverser.java
  class RegionSamTraverser (line 35) | public class RegionSamTraverser {
    method RegionSamTraverser (line 44) | public RegionSamTraverser(SamContentProvider samContentProvider) {
    method RegionSamTraverser (line 48) | public RegionSamTraverser(SamContentProvider samContentProvider, Filte...
    method rewind (line 65) | public void rewind() {
    method getOverlappedReads (line 79) | public List<GATKSAMRecord> getOverlappedReads(GenomeLoc loc) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/SamContentProvider.java
  class SamContentProvider (line 38) | public class SamContentProvider {
    method SamContentProvider (line 45) | public SamContentProvider(SamRecordPartition samRecordPartition) {
    method SamContentProvider (line 66) | public SamContentProvider(List<GATKSAMRecord> gatksamRecords,
    method SamContentProvider (line 71) | public SamContentProvider(List<GATKSAMRecord> gatksamRecords,
    method getSamFileHeader (line 85) | public SAMFileHeader getSamFileHeader() {
    method getGatksamRecords (line 89) | public ArrayList<GATKSAMRecord> getGatksamRecords() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/BadCigarFilter.java
  class BadCigarFilter (line 34) | public class BadCigarFilter extends Filter {
    method filterOut (line 36) | public boolean filterOut(final SAMRecord rec) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/BadMateFilter.java
  class BadMateFilter (line 29) | public class BadMateFilter extends Filter {
    method filterOut (line 31) | public boolean filterOut(final SAMRecord rec) {
    method hasBadMate (line 35) | public static boolean hasBadMate(final SAMRecord rec) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/DuplicateReadFilter.java
  class DuplicateReadFilter (line 29) | public class DuplicateReadFilter extends Filter{
    method filterOut (line 31) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/FailsVendorQualityCheckFilter.java
  class FailsVendorQualityCheckFilter (line 29) | public class FailsVendorQualityCheckFilter extends Filter {
    method filterOut (line 30) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/Filter.java
  class Filter (line 29) | public abstract class Filter {
    method filterOut (line 30) | public abstract boolean filterOut(SAMRecord read);

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/FilterUtils.java
  class FilterUtils (line 34) | public class FilterUtils {
    method FilterUtils (line 47) | public FilterUtils() {
    method FilterUtils (line 51) | public FilterUtils(String[] filterNames) {
    method addFilter (line 56) | public void addFilter(Filter filter) {
    method addFilter (line 62) | public void addFilter(String filterName) {
    method addFilter (line 71) | public void addFilter(String[] filterNames) {
    method filter (line 83) | public boolean filter(SAMRecord read) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/HCMappingQualityFilter.java
  class HCMappingQualityFilter (line 29) | public class HCMappingQualityFilter extends Filter{
    method filterOut (line 32) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/InOriginIntervalFilter.java
  class InOriginIntervalFilter (line 32) | public class InOriginIntervalFilter extends Filter {
    method InOriginIntervalFilter (line 36) | public InOriginIntervalFilter(RefContentProvider refContentProvider) {
    method filterOut (line 40) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/MappingQualityUnavailableFilter.java
  class MappingQualityUnavailableFilter (line 30) | public class MappingQualityUnavailableFilter extends Filter{
    method filterOut (line 31) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/MappingQualityZeroFilter.java
  class MappingQualityZeroFilter (line 29) | public class MappingQualityZeroFilter extends Filter {
    method filterOut (line 30) | public boolean filterOut(SAMRecord rec) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/NegativeAlignmentStartFilter.java
  class NegativeAlignmentStartFilter (line 30) | public class NegativeAlignmentStartFilter extends Filter {
    method filterOut (line 32) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/NotPrimaryAlignmentFilter.java
  class NotPrimaryAlignmentFilter (line 29) | public class NotPrimaryAlignmentFilter extends Filter{
    method filterOut (line 31) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/SupplementaryReadFilter.java
  class SupplementaryReadFilter (line 29) | public class SupplementaryReadFilter extends Filter {
    method filterOut (line 31) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/UnmappedReadFilter.java
  class UnmappedReadFilter (line 29) | public class UnmappedReadFilter extends Filter{
    method filterOut (line 31) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/GATKFeature.java
  class GATKFeature (line 32) | public abstract class GATKFeature implements Feature, HasGenomeLocation {
    method GATKFeature (line 34) | public GATKFeature(String name) {
    method setName (line 40) | protected void setName(String name) {
    method getName (line 44) | public String getName() {
    method getLocation (line 48) | public abstract GenomeLoc getLocation();
    method getUnderlyingObject (line 51) | public abstract Object getUnderlyingObject();
    class TribbleGATKFeature (line 56) | public static class TribbleGATKFeature extends GATKFeature {
      method TribbleGATKFeature (line 61) | public TribbleGATKFeature(GenomeLocParser genomeLocParser,Feature f,...
      method getLocation (line 66) | public GenomeLoc getLocation() {
      method getChr (line 72) | @Override
      method getStart (line 78) | @Override
      method getEnd (line 87) | @Override
      method getUnderlyingObject (line 93) | public Object getUnderlyingObject() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/HomoSapiensConstants.java
  class HomoSapiensConstants (line 27) | public class HomoSapiensConstants {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RODContentProvider.java
  class RODContentProvider (line 40) | public class RODContentProvider {
    method RODContentProvider (line 47) | public RODContentProvider(String name, VcfRecordPartition partition, G...
    method RODContentProvider (line 65) | public RODContentProvider(String name, VCFHeader vcfFileHeader,
    method getVcfFileHeader (line 78) | public VCFHeader getVcfFileHeader() {
    method getFeatures (line 82) | public ArrayList<GATKFeature> getFeatures() {
    method getName (line 86) | public String getName() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RODNames.java
  class RODNames (line 27) | public class RODNames {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RODRecordList.java
  type RODRecordList (line 32) | public interface RODRecordList extends List<GATKFeature>, Comparable<ROD...
    method getLocation (line 33) | GenomeLoc getLocation();
    method getName (line 35) | String getName();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RODRecordListImpl.java
  class RODRecordListImpl (line 37) | public class RODRecordListImpl extends AbstractList<GATKFeature>
    method RODRecordListImpl (line 43) | public RODRecordListImpl(String name) {
    method RODRecordListImpl (line 63) | public RODRecordListImpl(String name, Collection<GATKFeature> data, Ge...
    method getLocation (line 81) | public GenomeLoc getLocation() {
    method getName (line 85) | public String getName() {
    method iterator (line 89) | public Iterator<GATKFeature> iterator() {
    method clear (line 93) | public void clear() {
    method isEmpty (line 97) | public boolean isEmpty() {
    method add (line 101) | public boolean add(GATKFeature record) {
    method get (line 106) | @Override
    method add (line 111) | public void add(GATKFeature record, boolean allowNameMismatch) {
    method add (line 119) | public void add(RODRecordList records) {
    method add (line 123) | public void add(RODRecordList records, boolean allowNameMismatch) {
    method size (line 128) | public int size() {
    method compareTo (line 143) | public int compareTo(RODRecordList that) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RODTraverser.java
  class RODTraverser (line 34) | public class RODTraverser {
    method RODTraverser (line 45) | public RODTraverser(RODContentProvider rodContentProvider) {
    method init (line 53) | public void init() {
    method getOverlap (line 59) | public RODRecordList getOverlap(GenomeLoc loc) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RefMetaTrackerTraverser.java
  class RefMetaTrackerTraverser (line 33) | public class RefMetaTrackerTraverser {
    method RefMetaTrackerTraverser (line 37) | public RefMetaTrackerTraverser(List<RODContentProvider> providerList) {
    method getOverlappedTracker (line 41) | public RefMetaDataTracker getOverlappedTracker(GenomeLoc loc) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/RodBinding.java
  class RodBinding (line 32) | public class RodBinding<T extends Feature> {
    method makeUnbound (line 51) | protected final static <T extends Feature> RodBinding<T> makeUnbound(C...
    method resetNameCounter (line 91) | final public static void resetNameCounter() {
    method countedVariableName (line 95) | final private static synchronized String countedVariableName(final Str...
    method RodBinding (line 106) | public RodBinding(Class<T> type, final String rawName, final String so...
    method RodBinding (line 121) | public RodBinding(Class<T> type, final String rawName) {
    method RodBinding (line 130) | private RodBinding(Class<T> type) {
    method isBound (line 143) | final public boolean isBound() {
    method getName (line 150) | final public String getName() {
    method getType (line 157) | final public Class<T> getType() {
    method getSource (line 164) | final public String getSource() {
    method getTags (line 172) | final public Tags getTags() {
    method getTribbleType (line 179) | final public String getTribbleType() {
    method toString (line 183) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/Tags.java
  class Tags (line 37) | public class Tags {
    method equals (line 54) | @Override
    method isEmpty (line 71) | public boolean isEmpty() {
    method getPositionalTags (line 80) | public List<String> getPositionalTags() {
    method getValue (line 90) | public String getValue(final String key) {
    method containsKey (line 100) | public boolean containsKey(final String key) {
    method addPositionalTag (line 109) | protected void addPositionalTag(final String... tags) {
    method addKeyValueTag (line 119) | protected void addKeyValueTag(final String key, final String value) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/VCFHeaderLineIterable.java
  class VCFHeaderLineIterable (line 38) | public class VCFHeaderLineIterable extends AbstractIterator<String> impl...
    method VCFHeaderLineIterable (line 42) | public VCFHeaderLineIterable(final VcfHeaderInfo vcfHeaderInfo) {
    method VCFHeaderLineIterable (line 46) | public VCFHeaderLineIterable(String[] vcfHeaderLines) {
    method advance (line 50) | @Override
    method close (line 59) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/header/StandardWESVCFHeader.java
  class StandardWESVCFHeader (line 31) | public class StandardWESVCFHeader {
    method getValues (line 32) | protected static String[] getValues() {
    method getHeader (line 140) | public static VCFHeader getHeader() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/data/vcf/header/StandardWGSVCFHeader.java
  class StandardWGSVCFHeader (line 31) | public class StandardWGSVCFHeader {
    method getValues (line 32) | private static String[] getValues() {
    method getHeader (line 163) | public static VCFHeader getHeader() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/ActiveRegionWalker.java
  class ActiveRegionWalker (line 37) | public abstract class ActiveRegionWalker extends Walker {
    method ActiveRegionWalker (line 41) | public ActiveRegionWalker(GenomeLocParser genomeLocParser,
    method run (line 50) | public void run() {
    method map (line 59) | protected abstract void map(ActiveRegionMapData activeRegionMapData);
    method onTraversalDone (line 61) | protected abstract void onTraversalDone();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/IntervalLocusWalker.java
  class IntervalLocusWalker (line 42) | public abstract class IntervalLocusWalker extends LocusWalker {
    method IntervalLocusWalker (line 48) | public IntervalLocusWalker(GenomeLocParser genomeLocParser,
    method run (line 57) | public void run() {
    method getIntervalLocusSamTraverser (line 76) | protected IntervalLocusSamTraverser getIntervalLocusSamTraverser() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/LocusWalker.java
  class LocusWalker (line 46) | public abstract class LocusWalker extends Walker {
    method LocusWalker (line 51) | public LocusWalker(GenomeLocParser genomeLocParser,
    method run (line 58) | public void run() {
    method getLocusSamTraverser (line 77) | protected LocusSamTraverser getLocusSamTraverser() {
    method getLocusWalkerFilterUtils (line 92) | protected FilterUtils getLocusWalkerFilterUtils() {
    method getFilter (line 101) | protected abstract List<Filter> getFilter();
    method map (line 103) | protected abstract void map(RefMetaDataTracker tracker,
    method onTraversalDone (line 107) | protected abstract void onTraversalDone();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/RODWalker.java
  class RODWalker (line 38) | public abstract class RODWalker extends Walker {
    method RODWalker (line 42) | public RODWalker(GenomeLocParser genomeLocParser,
    method run (line 49) | public void run() {
    method map (line 69) | protected abstract void map(final ReferenceContext ref,
    method onTraversalDone (line 72) | protected abstract void onTraversalDone();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/ReadWalker.java
  class ReadWalker (line 42) | public abstract class ReadWalker extends Walker {
    method ReadWalker (line 47) | public ReadWalker(GenomeLocParser genomeLocParser,
    method run (line 54) | public void run() {
    method getReadSamTraverser (line 79) | private ReadSamTraverser getReadSamTraverser() {
    method getReadWalkerFilterUtils (line 92) | private FilterUtils getReadWalkerFilterUtils() {
    method getFilter (line 100) | protected abstract List<Filter> getFilter();
    method map (line 102) | protected abstract void map(final ReferenceContext ref,
    method onTraversalDone (line 106) | protected abstract void onTraversalDone();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/engine/Walker.java
  class Walker (line 36) | public abstract class Walker {
    method Walker (line 45) | public Walker(GenomeLocParser genomeLocParser,
    method initialize (line 55) | protected abstract void initialize();
    method run (line 57) | public abstract void run();
    method getSampleName (line 59) | public String getSampleName() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/AlignmentContextUtils.java
  class AlignmentContextUtils (line 40) | public class AlignmentContextUtils {
    type ReadOrientation (line 47) | public enum ReadOrientation { COMPLETE, FORWARD, REVERSE }
    method AlignmentContextUtils (line 49) | private AlignmentContextUtils() {
    method stratify (line 61) | public static AlignmentContext stratify(AlignmentContext context, Read...
    method splitContextBySampleName (line 74) | public static Map<String, AlignmentContext> splitContextBySampleName(A...
    method splitContextBySampleName (line 87) | public static Map<String, AlignmentContext> splitContextBySampleName(A...
    method splitContextBySampleName (line 111) | public static Map<String, AlignmentContext> splitContextBySampleName(R...
    method joinContexts (line 116) | public static AlignmentContext joinContexts(Collection<AlignmentContex...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/AlignmentUtils.java
  class AlignmentUtils (line 43) | public class AlignmentUtils {
    method AlignmentUtils (line 49) | private AlignmentUtils() { }
    method startsOrEndsWithInsertionOrDeletion (line 57) | public static boolean startsOrEndsWithInsertionOrDeletion(final Cigar ...
    method createReadAlignedToRef (line 82) | public static GATKSAMRecord createReadAlignedToRef(final GATKSAMRecord...
    method getBasesCoveringRefInterval (line 151) | public static byte[] getBasesCoveringRefInterval(final int refStart, f...
    method calcNumDifferentBases (line 211) | public static int calcNumDifferentBases(final Cigar cigar, final byte[...
    class MismatchCount (line 242) | public static class MismatchCount {
    method mismatchingQualities (line 247) | public static long mismatchingQualities(GATKSAMRecord r, byte[] refSeq...
    method getMismatchCount (line 254) | public static MismatchCount getMismatchCount(GATKSAMRecord r, byte[] r...
    method getMismatchCount (line 274) | public static MismatchCount getMismatchCount(GATKSAMRecord r, byte[] r...
    method getNumAlignmentBlocks (line 352) | public static int getNumAlignmentBlocks(final SAMRecord r) {
    method getNumAlignedBasesCountingSoftClips (line 375) | public static int getNumAlignedBasesCountingSoftClips(final GATKSAMRec...
    method getNumHardClippedBases (line 395) | public static int getNumHardClippedBases(final SAMRecord r) {
    method calcNumHighQualitySoftClips (line 418) | public static int calcNumHighQualitySoftClips( final GATKSAMRecord rea...
    method calcAlignmentByteArrayOffset (line 451) | public static int calcAlignmentByteArrayOffset(final Cigar cigar, fina...
    method calcAlignmentByteArrayOffset (line 465) | public static int calcAlignmentByteArrayOffset(final Cigar cigar, fina...
    method readToAlignmentByteArray (line 539) | public static byte[] readToAlignmentByteArray(final Cigar cigar, final...
    method isReadGenomeLocUnmapped (line 599) | public static boolean isReadGenomeLocUnmapped(final SAMRecord r) {
    method isReadUnmapped (line 618) | public static boolean isReadUnmapped(final SAMRecord r) {
    method consolidateCigar (line 639) | public static Cigar consolidateCigar( final Cigar c ) {
    method needsConsolidation (line 676) | private static boolean needsConsolidation(final Cigar c) {
    method leftAlignIndel (line 715) | public static Cigar leftAlignIndel(Cigar cigar, final byte[] refSeq, f...
    method ensureLeftAlignmentHasGoodArguments (line 731) | private static void ensureLeftAlignmentHasGoodArguments(final Cigar ci...
    method countIndelElements (line 745) | private static int countIndelElements(final Cigar cigar) {
    method leftAlignSingleIndel (line 768) | public static Cigar leftAlignSingleIndel(Cigar cigar, final byte[] ref...
    method cigarHasZeroSizeElement (line 823) | protected static boolean cigarHasZeroSizeElement(final Cigar c) {
    method cleanUpCigar (line 840) | public static Cigar cleanUpCigar(final Cigar c) {
    method removeTrailingDeletions (line 858) | public static Cigar removeTrailingDeletions(final Cigar c) {
    method moveCigarLeft (line 874) | private static Cigar moveCigarLeft(Cigar cigar, int indexOfIndel) {
    method createIndelString (line 908) | private static byte[] createIndelString(final Cigar cigar, final int i...
    method trimCigarByReference (line 975) | public static Cigar trimCigarByReference(final Cigar cigar, final int ...
    method trimCigarByBases (line 995) | public static Cigar trimCigarByBases(final Cigar cigar, final int star...
    method trimCigar (line 1018) | private static Cigar trimCigar(final Cigar cigar, final int start, fin...
    method addCigarElements (line 1069) | protected static int addCigarElements(final List<CigarElement> dest, i...
    method calcFirstBaseMatchingReferenceInCigar (line 1088) | public static int calcFirstBaseMatchingReferenceInCigar(final Cigar ci...
    method applyCigarToCigar (line 1150) | public static Cigar applyCigarToCigar(final Cigar firstToSecond, final...
    method getTransformer (line 1184) | private static CigarPairTransform getTransformer(final CigarOperator o...
    class CigarPairTransform (line 1221) | private static class CigarPairTransform {
      method CigarPairTransform (line 1226) | private CigarPairTransform(CigarOperator op12, CigarOperator op23, C...
      method getCigarSet (line 1234) | private static EnumSet<CigarOperator> getCigarSet(final CigarOperato...
      method toString (line 1243) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/AlleleListUtils.java
  class AlleleListUtils (line 34) | public class AlleleListUtils {
    method alleleCount (line 38) | @Override
    method alleleIndex (line 43) | @Override
    method alleleAt (line 48) | @Override
    method equals (line 63) | public static <A extends Allele> boolean equals(final AlleleList<A> fi...
    method indexOfReference (line 99) | public static <A extends Allele> int indexOfReference(final AlleleList...
    method asList (line 118) | public static <A extends Allele> List<A> asList(final AlleleList<A> li...
    method emptyList (line 129) | @SuppressWarnings("unchecked")
    class AsList (line 137) | private static class AsList<A extends Allele> extends AbstractList<A> {
      method AsList (line 141) | private AsList(final AlleleList<A> list) {
      method get (line 146) | @Override
      method size (line 151) | @Override
    method permutation (line 169) | public static <A extends Allele> AlleleListPermutation<A> permutation(...
    class NonPermutation (line 176) | private static class NonPermutation<A extends Allele> implements Allel...
      method NonPermutation (line 180) | public NonPermutation(final AlleleList<A> original) {
      method isPartial (line 184) | @Override
      method isNonPermuted (line 189) | @Override
      method toIndex (line 194) | @Override
      method fromIndex (line 199) | @Override
      method fromSize (line 204) | @Override
      method toSize (line 209) | @Override
      method fromList (line 214) | @Override
      method toList (line 219) | @Override
      method alleleCount (line 225) | @Override
      method alleleIndex (line 230) | @Override
      method alleleAt (line 235) | @Override
    class ActualPermutation (line 241) | private static class ActualPermutation<A extends Allele> implements Al...
      method ActualPermutation (line 253) | private ActualPermutation(final AlleleList<A> original, final Allele...
      method isPartial (line 275) | @Override
      method isNonPermuted (line 280) | @Override
      method toIndex (line 285) | @Override
      method fromIndex (line 290) | @Override
      method fromSize (line 295) | @Override
      method toSize (line 300) | @Override
      method fromList (line 305) | @Override
      method toList (line 310) | @Override
      method alleleCount (line 315) | @Override
      method alleleIndex (line 320) | @Override
      method alleleAt (line 325) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/ArtificialSAMUtils.java
  class ArtificialSAMUtils (line 47) | public class ArtificialSAMUtils {
    method createArtificialBamFile (line 59) | public static void createArtificialBamFile(String filename, int number...
    method createArtificialSamFile (line 83) | public static void createArtificialSamFile(String filename, int number...
    method createArtificialSamHeader (line 106) | public static SAMFileHeader createArtificialSamHeader(int numberOfChro...
    method createArtificialSamHeader (line 125) | public static SAMFileHeader createArtificialSamHeader(final SAMSequenc...
    method createArtificialSamHeader (line 137) | public static SAMFileHeader createArtificialSamHeader() {
    method createDefaultReadGroup (line 149) | public static SAMFileHeader createDefaultReadGroup(SAMFileHeader heade...
    method createEnumeratedReadGroups (line 166) | public static SAMFileHeader createEnumeratedReadGroups(SAMFileHeader h...
    method createArtificialRead (line 194) | public static GATKSAMRecord createArtificialRead(SAMFileHeader header,...
    method createArtificialRead (line 233) | public static GATKSAMRecord createArtificialRead(SAMFileHeader header,...
    method createArtificialRead (line 260) | public static GATKSAMRecord createArtificialRead(SAMFileHeader header,...
    method createArtificialRead (line 282) | public static GATKSAMRecord createArtificialRead(byte[] bases, byte[] ...
    method createArtificialRead (line 287) | public static GATKSAMRecord createArtificialRead(Cigar cigar) {
    method createPair (line 298) | public final static List<GATKSAMRecord> createPair(SAMFileHeader heade...
    method ranIntInclusive (line 329) | private final static int ranIntInclusive(Random ran, int start, int st...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/BaseUtils.java
  class BaseUtils (line 35) | public class BaseUtils {
    type Base (line 37) | public enum Base {
      method Base (line 47) | private Base(final char base) {
    type BaseSubstitutionType (line 102) | public enum BaseSubstitutionType {
    method SNPSubstitutionType (line 114) | public static BaseSubstitutionType SNPSubstitutionType(byte base1, byt...
    method isTransition (line 120) | public static boolean isTransition(byte base1, byte base2) {
    method isTransversion (line 127) | public static boolean isTransversion(byte base1, byte base2) {
    method BaseUtils (line 134) | private BaseUtils() {
    method basesAreEqual (line 137) | static public boolean basesAreEqual(byte base1, byte base2) {
    method basesAreEqualIgnoreAmbiguous (line 148) | static public boolean basesAreEqualIgnoreAmbiguous(final byte base1, f...
    method basesAreEqualIgnoreAmbiguous (line 176) | static public boolean basesAreEqualIgnoreAmbiguous(final byte[] bases1...
    method extendedBasesAreEqual (line 183) | static public boolean extendedBasesAreEqual(byte base1, byte base2) {
    method containsBase (line 190) | static public boolean containsBase(final byte[] bases, final byte base) {
    method isUpperCase (line 198) | public static boolean isUpperCase(final byte[] bases) {
    method isUpperCase (line 205) | public static boolean isUpperCase(final byte base) {
    method convertIUPACtoN (line 209) | public static byte[] convertIUPACtoN(final byte[] bases, final boolean...
    method iupacToBases (line 230) | @Deprecated
    method basesToIUPAC (line 294) | static public byte basesToIUPAC(final byte base1, final byte base2) {
    method simpleBaseToBaseIndex (line 323) | static public int simpleBaseToBaseIndex(final byte base) {
    method simpleBaseToBaseIndex (line 335) | @Deprecated
    method extendedBaseToBaseIndex (line 340) | static public int extendedBaseToBaseIndex(byte base) {
    method isRegularBase (line 354) | @Deprecated
    method isRegularBase (line 359) | static public boolean isRegularBase(final byte base) {
    method isAllRegularBases (line 363) | static public boolean isAllRegularBases(final byte[] bases) {
    method isNBase (line 372) | static public boolean isNBase(byte base) {
    method baseIndexToSimpleBase (line 382) | static public byte baseIndexToSimpleBase(int baseIndex) {
    method simpleComplement (line 403) | static public byte simpleComplement(byte base) {
    method simpleComplement (line 422) | @Deprecated
    method simpleReverseComplement (line 433) | static public byte[] simpleReverseComplement(byte[] bases) {
    method simpleReverseComplement (line 449) | @Deprecated
    method simpleReverseComplement (line 466) | @Deprecated
    method convertToUpperCase (line 477) | static public void convertToUpperCase(final byte[] bases) {
    method mostFrequentBaseIndex (line 488) | static public int mostFrequentBaseIndex(int[] baseCounts) {
    method mostFrequentBaseIndexNotRef (line 498) | static public int mostFrequentBaseIndexNotRef(int[] baseCounts, int re...
    method mostFrequentBaseIndexNotRef (line 506) | static public int mostFrequentBaseIndexNotRef(int[] baseCounts, byte r...
    method mostFrequentSimpleBase (line 516) | static public byte mostFrequentSimpleBase(int[] baseCounts) {
    method mostFrequentBaseFraction (line 526) | static public double mostFrequentBaseFraction(byte[] sequence) {
    method getRandomBaseIndex (line 553) | static public int getRandomBaseIndex() {
    method getRandomBases (line 564) | @SuppressWarnings("unused")
    method fillWithRandomBases (line 579) | public static void fillWithRandomBases(final byte[] dest) {
    method fillWithRandomBases (line 594) | public static void fillWithRandomBases(final byte[] dest, final int fr...
    method getRandomBaseIndex (line 615) | static public int getRandomBaseIndex(int excludeBaseIndex) {
    method getComplement (line 625) | public static byte getComplement(byte base) {
    method compare (line 653) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/CGAAlignmentUtils.java
  class CGAAlignmentUtils (line 35) | public class CGAAlignmentUtils {
    method mismatchesInRefWindow (line 45) | public static int mismatchesInRefWindow(PileupElement p, ReferenceCont...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/CigarUtils.java
  class CigarUtils (line 39) | public class CigarUtils {
    method combineAdjacentCigarElements (line 47) | public static Cigar combineAdjacentCigarElements(Cigar rawCigar) {
    method invertCigar (line 72) | public static Cigar invertCigar (Cigar cigar) {
    method readHasNonClippedBases (line 90) | public static boolean readHasNonClippedBases(GATKSAMRecord read) {
    method isCigarValid (line 104) | public static boolean isCigarValid(Cigar cigar) {
    method countRefBasesBasedOnCigar (line 138) | public static final int countRefBasesBasedOnCigar(final GATKSAMRecord ...
    method calculateCigar (line 171) | public static Cigar calculateCigar(final byte[] refSeq, final byte[] a...
    method isSWFailure (line 204) | private static boolean isSWFailure(final SmithWaterman alignment) {
    method leftAlignCigarSequentially (line 232) | public static Cigar leftAlignCigarSequentially(final Cigar cigar, fina...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/DeprecatedToolChecks.java
  class DeprecatedToolChecks (line 30) | public class DeprecatedToolChecks {
    method isDeprecatedWalker (line 56) | public static boolean isDeprecatedWalker(final String walkerName) {
    method isDeprecatedAnnotation (line 65) | public static boolean isDeprecatedAnnotation(final String annotationNa...
    method getWalkerDeprecationInfo (line 74) | public static String getWalkerDeprecationInfo(final String walkerName) {
    method getAnnotationDeprecationInfo (line 83) | public static String getAnnotationDeprecationInfo(final String annotat...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/EventType.java
  type EventType (line 27) | public enum EventType {
    method EventType (line 35) | private EventType(String representation, String longRepresentation) {
    method eventFrom (line 46) | public static EventType eventFrom(int index) {
    method eventFrom (line 57) | public static EventType eventFrom(String representation) {
    method toString (line 65) | @Override
    method prettyPrint (line 70) | public String prettyPrint() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/FragmentUtils.java
  class FragmentUtils (line 48) | public final class FragmentUtils {
    method FragmentUtils (line 55) | private FragmentUtils() {}
    type ReadGetter (line 65) | public interface ReadGetter<T> {
      method get (line 72) | public GATKSAMRecord get(T object);
    method get (line 79) | @Override public GATKSAMRecord get(final GATKSAMRecord object) { retur...
    method get (line 86) | @Override public GATKSAMRecord get(final PileupElement object) { retur...
    method create (line 102) | private static <T> FragmentCollection<T> create(final Iterable<T> read...
    method create (line 159) | public static FragmentCollection<PileupElement> create(final ReadBacke...
    method create (line 170) | public static FragmentCollection<GATKSAMRecord> create(final List<GATK...
    method adjustQualsOfOverlappingPairedFragments (line 175) | public static void adjustQualsOfOverlappingPairedFragments( final List...
    method adjustQualsOfOverlappingPairedFragments (line 202) | public static void adjustQualsOfOverlappingPairedFragments(final GATKS...
    method mergeOverlappingPairedFragments (line 239) | public static List<GATKSAMRecord> mergeOverlappingPairedFragments( fin...
    method mergeOverlappingPairedFragments (line 269) | public static GATKSAMRecord mergeOverlappingPairedFragments(final GATK...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/GATKVariantContextUtils.java
  class GATKVariantContextUtils (line 61) | public class GATKVariantContextUtils {
    method overlapsRegion (line 96) | public static boolean overlapsRegion(final VariantContext variantConte...
    method homozygousAlleleList (line 120) | public static List<Allele> homozygousAlleleList(final Allele allele, f...
    method hasPLIncompatibleAlleles (line 128) | private static boolean hasPLIncompatibleAlleles(final Collection<Allel...
    method determineReferenceAllele (line 153) | public static Allele determineReferenceAllele(final List<VariantContex...
    method totalPloidy (line 175) | public static int totalPloidy(final VariantContext vc, final int defau...
    type GenotypeMergeType (line 189) | public enum GenotypeMergeType {
    type FilteredRecordMergeType (line 208) | public enum FilteredRecordMergeType {
    type MultipleAllelesMergeType (line 223) | public enum MultipleAllelesMergeType {
    method getMeanAltAlleleLength (line 239) | public static double getMeanAltAlleleLength(VariantContext vc) {
    method getLocation (line 280) | public static final GenomeLoc getLocation(GenomeLocParser genomeLocPar...
    method getSNPSubstitutionType (line 284) | public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(Va...
    method isTransition (line 293) | public static boolean isTransition(VariantContext context) {
    method isTransversion (line 300) | public static boolean isTransversion(VariantContext context) {
    method isTransition (line 304) | public static boolean isTransition(Allele ref, Allele alt) {
    method isTransversion (line 308) | public static boolean isTransversion(Allele ref, Allele alt) {
    method reverseComplement (line 318) | public static VariantContext reverseComplement(VariantContext vc) {
    method isTandemRepeat (line 371) | public static boolean isTandemRepeat(final VariantContext vc, final by...
    method getNumTandemRepeatUnits (line 393) | public static Pair<List<Integer>,byte[]> getNumTandemRepeatUnits(final...
    method getNumTandemRepeatUnits (line 430) | public static Pair<int[],byte[]> getNumTandemRepeatUnits(final byte[] ...
    method findRepeatedSubstring (line 466) | public static int findRepeatedSubstring(byte[] bases) {
    method findNumberOfRepetitions (line 495) | public static int findNumberOfRepetitions(byte[] repeatUnit, byte[] te...
    method isRepeatAllele (line 530) | protected static boolean isRepeatAllele(final Allele ref, final Allele...
    method basesAreRepeated (line 541) | protected static boolean basesAreRepeated(final String l, final String...
    type GenotypeAssignmentMethod (line 557) | public enum GenotypeAssignmentMethod {
    method subsetDiploidAlleles (line 601) | public static GenotypesContext subsetDiploidAlleles(final VariantConte...
    method determineLikelihoodIndexesToUse (line 624) | private static List<Integer> determineLikelihoodIndexesToUse(final Var...
    method getLikelihoodIndexes (line 644) | private static List<Integer> getLikelihoodIndexes(final VariantContext...
    method getAlleleIndexBitset (line 669) | private static boolean[] getAlleleIndexBitset(final VariantContext ori...
    method createGenotypesWithSubsettedLikelihoods (line 693) | private static GenotypesContext createGenotypesWithSubsettedLikelihood...
    method likelihoodsAreUninformative (line 747) | private static boolean likelihoodsAreUninformative(final double[] like...
    method updateGenotypeAfterSubsetting (line 760) | public static void updateGenotypeAfterSubsetting(final List<Allele> or...
    method subsetToRefOnly (line 807) | public static GenotypesContext subsetToRefOnly(final VariantContext vc...
    method assignDiploidGenotypes (line 842) | public static GenotypesContext assignDiploidGenotypes(final VariantCon...
    method splitVariantContextToBiallelics (line 860) | public static List<VariantContext> splitVariantContextToBiallelics(fin...
    method splitVariantContextToBiallelics (line 879) | public static List<VariantContext> splitVariantContextToBiallelics(fin...
    method removePLsAndAD (line 900) | public static Genotype removePLsAndAD(final Genotype g) {
    method simpleMerge (line 923) | public static VariantContext simpleMerge(final Collection<VariantConte...
    method simpleMerge (line 956) | public static VariantContext simpleMerge(final Collection<VariantConte...
    method stripPLsAndAD (line 1158) | public static GenotypesContext stripPLsAndAD(final GenotypesContext ge...
    method updatePLsAndAD (line 1176) | public static GenotypesContext updatePLsAndAD(final VariantContext sel...
    method fixGenotypesFromSubsettedAlleles (line 1201) | static private GenotypesContext fixGenotypesFromSubsettedAlleles(final...
    method fixADFromSubsettedAlleles (line 1218) | static private GenotypesContext fixADFromSubsettedAlleles(final Genoty...
    method fixAD (line 1246) | private static Genotype fixAD(final Genotype genotype, final boolean[]...
    method determineReferenceAllele (line 1268) | private static Allele determineReferenceAllele(final List<VariantConte...
    method contextMatchesLoc (line 1272) | public static boolean contextMatchesLoc(final VariantContext vc, final...
    method resolveIncompatibleAlleles (line 1276) | static private AlleleMapper resolveIncompatibleAlleles(final Allele re...
    method createAlleleMapping (line 1304) | private static Map<Allele, Allele> createAlleleMapping(final Allele re...
    method isUsableAlternateAllele (line 1326) | static private boolean isUsableAlternateAllele(final Allele allele) {
    method sortVariantContextsByPriority (line 1330) | public static List<VariantContext> sortVariantContextsByPriority(Colle...
    method mergeGenotypes (line 1343) | private static void mergeGenotypes(GenotypesContext mergedGenotypes, V...
    method ensureNoCallListsCapacity (line 1374) | private static synchronized void ensureNoCallListsCapacity(final int c...
    method noCallAlleles (line 1391) | public static List<Allele> noCallAlleles(final int ploidy) {
    method calculatePLindexFromUnorderedIndexes (line 1405) | protected static int calculatePLindexFromUnorderedIndexes(final int or...
    method mergedSampleName (line 1410) | public static String mergedSampleName(String trackName, String sampleN...
    method reverseTrimAlleles (line 1420) | public static VariantContext reverseTrimAlleles( final VariantContext ...
    method forwardTrimAlleles (line 1430) | public static VariantContext forwardTrimAlleles( final VariantContext ...
    method trimAlleles (line 1442) | public static VariantContext trimAlleles(final VariantContext inputVC,...
    method trimAlleles (line 1465) | protected static VariantContext trimAlleles(final VariantContext inputVC,
    method updateGenotypesWithMappedAlleles (line 1500) | protected static GenotypesContext updateGenotypesWithMappedAlleles(fin...
    method computeReverseClipping (line 1511) | public static int computeReverseClipping(final List<Allele> unclippedA...
    method computeForwardClipping (line 1563) | public static int computeForwardClipping(final List<Allele> unclippedA...
    method computeHardyWeinbergPvalue (line 1594) | public static double computeHardyWeinbergPvalue(VariantContext vc) {
    method requiresPaddingBase (line 1600) | public static boolean requiresPaddingBase(final List<String> alleles) {
    method subsetAttributes (line 1629) | private final static Map<String, Object> subsetAttributes(final Common...
    method pruneVariantContext (line 1644) | @Deprecated
    method pruneVariantContext (line 1649) | public static VariantContextBuilder pruneVariantContext(final VariantC...
    method allelesAreSubset (line 1668) | public static boolean allelesAreSubset(VariantContext vc1, VariantCont...
    method separateVariantContextsByType (line 1681) | public static Map<VariantContext.Type, List<VariantContext>> separateV...
    method purgeUnallowedGenotypeAttributes (line 1732) | public static VariantContext purgeUnallowedGenotypeAttributes(VariantC...
    class AlleleMapper (line 1749) | protected static class AlleleMapper {
      method AlleleMapper (line 1752) | public AlleleMapper(VariantContext vc)          { this.vc = vc; }
      method AlleleMapper (line 1753) | public AlleleMapper(Map<Allele, Allele> map)    { this.map = map; }
      method needsRemapping (line 1754) | public boolean needsRemapping()                 { return this.map !=...
      method values (line 1755) | public Collection<Allele> values()              { return map != null...
      method remap (line 1756) | public Allele remap(Allele a)                   { return map != null...
      method remap (line 1758) | public List<Allele> remap(List<Allele> as) {
      method getUniqueMappedAlleles (line 1770) | public List<Allele> getUniqueMappedAlleles() {
    class CompareByPriority (line 1777) | private static class CompareByPriority implements Comparator<VariantCo...
      method CompareByPriority (line 1779) | public CompareByPriority(List<String> priorityListOfVCs) {
      method getIndex (line 1783) | private int getIndex(VariantContext vc) {
      method compare (line 1789) | public int compare(VariantContext vc1, VariantContext vc2) {
    method makeFromAlleles (line 1804) | public static VariantContext makeFromAlleles(final String name, final ...
    method splitIntoPrimitiveAlleles (line 1827) | public static List<VariantContext> splitIntoPrimitiveAlleles(final Var...
    method equalSites (line 1880) | public static boolean equalSites(final VariantContext vc1, final Varia...
    method indexOfAllele (line 1912) | public static int indexOfAllele(final VariantContext vc, final Allele ...
    method indexOfAltAllele (line 1936) | public static int indexOfAltAllele(final VariantContext vc, final Alle...
    method indexOfEqualAllele (line 1942) | private static int indexOfEqualAllele(final VariantContext vc, final A...
    method indexOfSameAllele (line 1954) | private static int indexOfSameAllele(final VariantContext vc, final Al...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/GenomeLoc.java
  class GenomeLoc (line 43) | public class GenomeLoc implements Comparable<GenomeLoc>, Serializable, H...
    method isUnmapped (line 63) | public static final boolean isUnmapped(GenomeLoc loc) {
    method GenomeLoc (line 73) | public GenomeLoc(final String contig, final int contigIndex, final int...
    method GenomeLoc (line 83) | private GenomeLoc(final String contig) {
    method getLocation (line 90) | public final GenomeLoc getLocation() {
    method getStartLocation (line 94) | public final GenomeLoc getStartLocation() {
    method getStopLocation (line 98) | public final GenomeLoc getStopLocation() {
    method getContig (line 105) | public final String getContig() {
    method getContigIndex (line 109) | public final int getContigIndex() {
    method getStart (line 113) | public final int getStart() {
    method getStop (line 117) | public final int getStop() {
    method toString (line 121) | public final String toString() {
    method throughEndOfContigP (line 131) | private boolean throughEndOfContigP() {
    method atBeginningOfContigP (line 135) | private boolean atBeginningOfContigP() {
    method disjointP (line 139) | public final boolean disjointP(GenomeLoc that) {
    method discontinuousP (line 143) | public final boolean discontinuousP(GenomeLoc that) {
    method overlapsP (line 147) | public final boolean overlapsP(GenomeLoc that) {
    method contiguousP (line 151) | public final boolean contiguousP(GenomeLoc that) {
    method isUnmapped (line 160) | public final boolean isUnmapped() {
    method merge (line 169) | public GenomeLoc merge(GenomeLoc that) throws ReviewedGATKException {
    method endpointSpan (line 189) | public GenomeLoc endpointSpan(GenomeLoc that) throws ReviewedGATKExcep...
    method split (line 207) | public GenomeLoc[] split(final int splitPoint) {
    method union (line 213) | public GenomeLoc union(GenomeLoc that) {
    method intersect (line 217) | public GenomeLoc intersect(GenomeLoc that) throws ReviewedGATKException {
    method subtract (line 233) | public final List<GenomeLoc> subtract(final GenomeLoc that) {
    method containsP (line 305) | public final boolean containsP(GenomeLoc that) {
    method onSameContig (line 309) | public final boolean onSameContig(GenomeLoc that) {
    method distance (line 313) | public final int distance(final GenomeLoc that) {
    method isBetween (line 320) | public final boolean isBetween(final GenomeLoc left, final GenomeLoc r...
    method isBefore (line 330) | public final boolean isBefore(GenomeLoc that) {
    method startsAt (line 343) | public final boolean startsAt(GenomeLoc that) {
    method startsBefore (line 354) | public final boolean startsBefore(final GenomeLoc that) {
    method isPast (line 365) | public final boolean isPast(GenomeLoc that) {
    method minDistance (line 373) | public final int minDistance(final GenomeLoc that) {
    method distanceFirstStopToSecondStart (line 388) | private static int distanceFirstStopToSecondStart(GenomeLoc locFirst, ...
    method equals (line 399) | @Override
    method hashCode (line 412) | @Override
    method compareContigs (line 424) | public final int compareContigs(GenomeLoc that) {
    method compareTo (line 432) | public int compareTo(GenomeLoc that) {
    method endsAt (line 458) | public boolean endsAt(GenomeLoc that) {
    method size (line 468) | public int size() {
    method reciprocialOverlapFraction (line 487) | public final double reciprocialOverlapFraction(final GenomeLoc o) {
    method overlapPercent (line 494) | private final static double overlapPercent(final GenomeLoc gl1, final ...
    method sizeOfOverlap (line 498) | public long sizeOfOverlap(final GenomeLoc that) {
    method max (line 508) | public GenomeLoc max(final GenomeLoc other) {
    method setStart (line 522) | public GenomeLoc setStart(GenomeLoc loc, int start) {
    method setStop (line 535) | public GenomeLoc setStop(GenomeLoc loc, int stop) {
    method incPos (line 544) | public GenomeLoc incPos() {
    method incPos (line 554) | public GenomeLoc incPos(int by) {
    method merge (line 565) | public static <T extends GenomeLoc> GenomeLoc merge(final T a, final T...
    method merge (line 583) | public static <T extends GenomeLoc> GenomeLoc merge(final SortedSet<T>...
    method distanceAcrossContigs (line 612) | public long distanceAcrossContigs(GenomeLoc other, SAMFileHeader samFi...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/GenomeLocParser.java
  class GenomeLocParser (line 36) | public final class GenomeLocParser {
    type ValidationLevel (line 41) | public enum ValidationLevel {
    method initialValue (line 69) | @Override
    method getContigInfo (line 83) | private MRUCachingSAMSequenceDictionary getContigInfo() {
    method GenomeLocParser (line 92) | public GenomeLocParser(final ReferenceSequenceFile refFile) {
    method GenomeLocParser (line 101) | public GenomeLocParser(SAMSequenceDictionary seqDict) {
    method GenomeLocParser (line 111) | protected GenomeLocParser(SAMSequenceDictionary seqDict, final Validat...
    method contigIsInDictionary (line 130) | public final boolean contigIsInDictionary(final String contig) {
    method getContigInfo (line 140) | public final SAMSequenceRecord getContigInfo(final String contig) {
    method getContigIndex (line 152) | public final int getContigIndex(final String contig) {
    method getContigIndexWithoutException (line 156) | protected int getContigIndexWithoutException(final String contig) {
    method getContigs (line 167) | public final SAMSequenceDictionary getContigs() {
    method createGenomeLoc (line 184) | public GenomeLoc createGenomeLoc(String contig, final int start, final...
    method createGenomeLoc (line 194) | public GenomeLoc createGenomeLoc(final String contig, final int start,...
    method createGenomeLoc (line 203) | public GenomeLoc createGenomeLoc(String contig, int index, final int s...
    method createGenomeLoc (line 217) | public GenomeLoc createGenomeLoc(final String contig, int index, final...
    method createGenomeLoc (line 233) | public GenomeLoc createGenomeLoc(final String contig, final int pos) {
    method validateGenomeLoc (line 252) | protected String validateGenomeLoc(final String contig, final int cont...
    method isValidGenomeLoc (line 289) | public boolean isValidGenomeLoc(String contig, int start, int stop, bo...
    method isValidGenomeLoc (line 301) | public boolean isValidGenomeLoc(String contig, int start, int stop) {
    method vglHelper (line 305) | private void vglHelper(final String msg) {
    method parseGenomeLoc (line 325) | public GenomeLoc parseGenomeLoc(final String str) {
    method parsePosition (line 374) | protected int parsePosition(final String pos) {
    method createGenomeLoc (line 411) | public GenomeLoc createGenomeLoc(final SAMRecord read) {
    method createGenomeLocUnclipped (line 429) | public GenomeLoc createGenomeLocUnclipped(final SAMRecord read) {
    method createGenomeLoc (line 446) | public GenomeLoc createGenomeLoc(final Feature feature) {
    method createOverEntireContig (line 457) | public GenomeLoc createOverEntireContig(final String contigName) {
    method createGenomeLocAtStart (line 469) | public GenomeLoc createGenomeLocAtStart(final GenomeLoc loc, final int...
    method createPaddedGenomeLoc (line 494) | public GenomeLoc createPaddedGenomeLoc(final GenomeLoc loc, final int ...
    method createGenomeLocAtStop (line 508) | public GenomeLoc createGenomeLocAtStop(final GenomeLoc loc, final int ...
    method createGenomeLocOnContig (line 530) | public GenomeLoc createGenomeLocOnContig(final String contig, final in...
    method createGenomeLocOnContig (line 546) | public GenomeLoc createGenomeLocOnContig(final String contig, final in...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/GenomeLocSortedSet.java
  class GenomeLocSortedSet (line 43) | public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
    method GenomeLocSortedSet (line 59) | public GenomeLocSortedSet(final GenomeLocParser parser) {
    method GenomeLocSortedSet (line 70) | public GenomeLocSortedSet(final GenomeLocParser parser, final GenomeLo...
    method GenomeLocSortedSet (line 84) | public GenomeLocSortedSet(final GenomeLocParser parser, final Collecti...
    method getGenomeLocParser (line 96) | public GenomeLocParser getGenomeLocParser() {
    method iterator (line 105) | public Iterator<GenomeLoc> iterator() {
    method size (line 114) | public int size() {
    method coveredSize (line 122) | public long coveredSize() {
    method sizeBeforeLoc (line 135) | public long sizeBeforeLoc(GenomeLoc loc) {
    method isEmpty (line 155) | public boolean isEmpty() {
    method overlaps (line 165) | public boolean overlaps(final GenomeLoc loc) {
    method overlapsAtOrImmediatelyAfterCachedIndex (line 186) | private boolean overlapsAtOrImmediatelyAfterCachedIndex(final GenomeLo...
    method getOverlapping (line 208) | public List<GenomeLoc> getOverlapping(final GenomeLoc loc) {
    method getOverlappingFullSearch (line 248) | protected List<GenomeLoc> getOverlappingFullSearch(final GenomeLoc loc) {
    method add (line 268) | public boolean add(final GenomeLoc loc) {
    method addRegion (line 280) | public boolean addRegion(final GenomeLoc loc) {
    method add (line 292) | public boolean add(final GenomeLoc loc, final boolean mergeIfIntervalO...
    method mergeOverlappingIntervalsFromAdd (line 331) | private boolean mergeOverlappingIntervalsFromAdd(final GenomeLoc loc, ...
    method subtractRegions (line 351) | public GenomeLocSortedSet subtractRegions(GenomeLocSortedSet toRemoveS...
    method remove (line 400) | public void remove(GenomeLoc location) {
    method createSetFromSequenceDictionary (line 412) | public static GenomeLocSortedSet createSetFromSequenceDictionary(final...
    method createSetFromList (line 428) | public static GenomeLocSortedSet createSetFromList(GenomeLocParser par...
    method clone (line 440) | public GenomeLocSortedSet clone() {
    method toList (line 453) | public List<GenomeLoc> toList() {
    method toString (line 457) | public String toString() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/GenotypingGivenAllelesUtils.java
  class GenotypingGivenAllelesUtils (line 39) | public class GenotypingGivenAllelesUtils {
    method composeGivenAllelesVariantContextFromRod (line 50) | public static VariantContext composeGivenAllelesVariantContextFromRod(...
    method composeGivenHaplotypes (line 85) | public static List<Haplotype> composeGivenHaplotypes(final Haplotype r...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/HasGenomeLocation.java
  type HasGenomeLocation (line 29) | public interface HasGenomeLocation {
    method getLocation (line 30) | public GenomeLoc getLocation();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/HelpConstants.java
  class HelpConstants (line 27) | public class HelpConstants {
    method forumPost (line 59) | public static String forumPost(String post) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/LRUCache.java
  class LRUCache (line 30) | public class LRUCache<K,V> extends LinkedHashMap<K,V> {
    method LRUCache (line 33) | public LRUCache(int capacity) {
    method removeEldestEntry (line 38) | protected boolean removeEldestEntry(final Map.Entry entry) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/MRUCachingSAMSequenceDictionary.java
  class MRUCachingSAMSequenceDictionary (line 31) | final class MRUCachingSAMSequenceDictionary {
    method MRUCachingSAMSequenceDictionary (line 46) | public MRUCachingSAMSequenceDictionary(final SAMSequenceDictionary dic...
    method getDictionary (line 59) | public SAMSequenceDictionary getDictionary() {
    method hasContig (line 69) | public final boolean hasContig(final String contig) {
    method hasContigIndex (line 79) | public final boolean hasContigIndex(final int contigIndex) {
    method getSequence (line 90) | public final SAMSequenceRecord getSequence(final String contig) {
    method getSequence (line 104) | public final SAMSequenceRecord getSequence(final int index) {
    method getSequenceIndex (line 118) | public final int getSequenceIndex(final String contig) {
    method isCached (line 132) | protected boolean isCached(final String contig) {
    method isCached (line 142) | protected boolean isCached(final int index) {
    method updateCache (line 155) | private SAMSequenceRecord updateCache(final String contig, int index) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/MannWhitneyU.java
  class MannWhitneyU (line 39) | public class MannWhitneyU {
    method MannWhitneyU (line 50) | public MannWhitneyU(ExactMode mode, boolean dither) {
    method MannWhitneyU (line 60) | public MannWhitneyU() {
    method MannWhitneyU (line 64) | public MannWhitneyU(boolean dither) {
    method MannWhitneyU (line 68) | public MannWhitneyU(ExactMode mode) {
    method add (line 78) | public void add(Number n, USet set) {
    method getR1R2 (line 87) | public Pair<Long, Long> getR1R2() {
    method runOneSidedTest (line 105) | public Pair<Double, Double> runOneSidedTest(USet lessThanOther) {
    method runTwoSidedTest (line 127) | public Pair<Double, Double> runTwoSidedTest() {
    method calculateP (line 149) | protected static Pair<Double, Double> calculateP(int n, int m, long u,...
    method calculatePFromTable (line 169) | public static Pair<Double, Double> calculatePFromTable(int n, int m, l...
    method calculatePNormalApproximation (line 184) | public static Pair<Double, Double> calculatePNormalApproximation(int n...
    method getZApprox (line 201) | private static double getZApprox(int n, int m, long u) {
    method calculatePUniformApproximation (line 219) | public static double calculatePUniformApproximation(int n, int m, long...
    method uniformSumHelper (line 246) | private static double uniformSumHelper(double z, int m, int n, int k) {
    method calculateTwoSidedU (line 264) | public static Pair<Long, USet> calculateTwoSidedU(TreeSet<Pair<Number,...
    method calculateOneSidedU (line 300) | public static long calculateOneSidedU(TreeSet<Pair<Number, USet>> obse...
    method calculatePRecursively (line 326) | public static Pair<Double, Double> calculatePRecursively(int n, int m,...
    method calculatePRecursivelyDoNotCheckValuesEvenThoughItIsSlow (line 367) | protected static double calculatePRecursivelyDoNotCheckValuesEvenThoug...
    method countSequences (line 378) | protected static long countSequences(int n, int m, long u) {
    method cpr (line 397) | private static double cpr(int n, int m, long u) {
    method cumulativeCPR (line 411) | private static double cumulativeCPR(int n, int m, long u) {
    method getObservations (line 431) | protected TreeSet<Pair<Number, USet>> getObservations() {
    method getSetSizes (line 440) | protected Pair<Integer, Integer> getSetSizes() {
    method validateObservations (line 450) | protected static boolean validateObservations(TreeSet<Pair<Number, USe...
    class DitheringComparator (line 476) | private static class DitheringComparator implements Comparator<Pair<Nu...
      method DitheringComparator (line 478) | public DitheringComparator() {
      method equals (line 481) | @Override
      method compare (line 486) | @Override
    class NumberedPairComparator (line 502) | private static class NumberedPairComparator implements Comparator<Pair...
      method NumberedPairComparator (line 504) | public NumberedPairComparator() {
      method equals (line 507) | @Override
      method compare (line 512) | @Override
    type USet (line 518) | public enum USet {SET1, SET2}
    type ExactMode (line 520) | public enum ExactMode {POINT, CUMULATIVE}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/MathUtils.java
  class MathUtils (line 37) | public class MathUtils {
    method MathUtils (line 42) | private MathUtils() {
    class Log10Cache (line 59) | public static class Log10Cache {
      method get (line 65) | public static double get(final int n) {
      method ensureCacheContains (line 84) | public static synchronized void ensureCacheContains(final int n) {
    method randomIntegerInRange (line 105) | public static int randomIntegerInRange( final int min, final int max ) {
    class JacobianLogTable (line 112) | private static class JacobianLogTable {
      method get (line 116) | public static double get(final double difference) {
      method initialize (line 123) | private static synchronized void initialize() {
    method fastRound (line 140) | public static int fastRound(final double d) {
    method approximateLog10SumLog10 (line 144) | public static double approximateLog10SumLog10(final double[] vals) {
    method approximateLog10SumLog10 (line 158) | public static double approximateLog10SumLog10(final double[] vals, fin...
    method approximateLog10SumLog10 (line 174) | public static double approximateLog10SumLog10(final double[] vals, fin...
    method approximateLog10SumLog10 (line 193) | public static double approximateLog10SumLog10(final double a, final do...
    method approximateLog10SumLog10 (line 197) | public static double approximateLog10SumLog10(double small, double big) {
    method sum (line 221) | public static double sum(final double[] values) {
    method sum (line 228) | public static long sum(final int[] x) {
    method sum (line 235) | public static int sum(final byte[] x) {
    method percentage (line 242) | public static double percentage(int x, int base) {
    method ratio (line 246) | public static double ratio(final int num, final int denom) {
    method ratio (line 258) | public static double ratio(final long num, final long denom) {
    method toLog10 (line 276) | public static double[] toLog10(final double[] prRealSpace) {
    method log10sumLog10 (line 284) | public static double log10sumLog10(final double[] log10p, final int st...
    method log10sumLog10 (line 288) | public static double log10sumLog10(final double[] log10p, final int st...
    method sumLog10 (line 313) | public static double sumLog10(final double[] log10values) {
    method log10sumLog10 (line 317) | public static double log10sumLog10(final double[] log10values) {
    method wellFormedDouble (line 321) | public static boolean wellFormedDouble(final double val) {
    method bound (line 325) | public static double bound(final double value, final double minBoundar...
    method isBounded (line 329) | public static boolean isBounded(final double val, final double lower, ...
    method isPositive (line 333) | public static boolean isPositive(final double val) {
    method isPositiveOrZero (line 337) | public static boolean isPositiveOrZero(final double val) {
    method isNegativeOrZero (line 341) | public static boolean isNegativeOrZero(final double val) {
    method isNegative (line 345) | public static boolean isNegative(final double val) {
    method compareDoubles (line 356) | public static byte compareDoubles(final double a, final double b) {
    method compareDoubles (line 368) | public static byte compareDoubles(final double a, final double b, fina...
    method normalDistribution (line 385) | public static double normalDistribution(final double mean, final doubl...
    method normalDistributionLog10 (line 403) | public static double normalDistributionLog10(final double mean, final ...
    method square (line 418) | public static double square(final double x) {
    method binomialCoefficient (line 430) | public static double binomialCoefficient(final int n, final int k) {
    method log10BinomialCoefficient (line 437) | public static double log10BinomialCoefficient(final int n, final int k) {
    method binomialProbability (line 460) | public static double binomialProbability(final int n, final int k, fin...
    method log10BinomialProbability (line 467) | public static double log10BinomialProbability(final int n, final int k...
    method binomialProbability (line 477) | public static double binomialProbability(final int n, final int k) {
    method log10BinomialProbability (line 484) | public static double log10BinomialProbability(final int n, final int k) {
    method fastGenerateUniqueHashFromThreeIntegers (line 497) | static Long fastGenerateUniqueHashFromThreeIntegers(final int one, fin...
    method binomialCumulativeProbability (line 522) | public static double binomialCumulativeProbability(final int n, final ...
    method log1mexp (line 583) | public static double log1mexp(final double a) {
    method log10OneMinusPow10 (line 605) | public static double log10OneMinusPow10(final double a) {
    method log10MultinomialCoefficient (line 620) | public static double log10MultinomialCoefficient(final int n, final in...
    method log10MultinomialProbability (line 647) | public static double log10MultinomialProbability(final int n, final in...
    method multinomialCoefficient (line 671) | public static double multinomialCoefficient(final int[] k) {
    method multinomialProbability (line 694) | public static double multinomialProbability(final int[] k, final doubl...
    method rms (line 713) | public static double rms(final byte[] x) {
    method rms (line 730) | public static double rms(final int[] x) {
    method rms (line 747) | public static double rms(final Double[] x) {
    method rms (line 758) | public static double rms(final Collection<Integer> l) {
    method distanceSquared (line 769) | public static double distanceSquared(final double[] x, final double[] ...
    method round (line 777) | public static double round(final double num, final int digits) {
    method normalizeFromLog10 (line 791) | public static double[] normalizeFromLog10(final double[] array, final ...
    method normalizeFromLog10 (line 804) | public static double[] normalizeFromLog10(final double[] array, final ...
    method normalizeFromLog10 (line 847) | public static double[] normalizeFromLog10(final double[] array) {
    method normalizeFromRealSpace (line 860) | public static double[] normalizeFromRealSpace(final double[] array) {
    method maxElementIndex (line 873) | public static int maxElementIndex(final double[] array) {
    method maxElementIndex (line 877) | public static int maxElementIndex(final double[] array, final int star...
    method maxElementIndex (line 893) | public static int maxElementIndex(final double[] array, final int endI...
    method maxElementIndex (line 897) | public static int maxElementIndex(final int[] array) {
    method maxElementIndex (line 901) | public static int maxElementIndex(final byte[] array) {
    method maxElementIndex (line 905) | public static int maxElementIndex(final int[] array, final int endInde...
    method maxElementIndex (line 917) | public static int maxElementIndex(final byte[] array, final int endInd...
    method arrayMax (line 930) | public static int arrayMax(final int[] array) {
    method arrayMax (line 935) | public static double arrayMax(final double[] array) {
    method arrayMax (line 939) | public static double arrayMax(final double[] array, final int endIndex) {
    method arrayMin (line 943) | public static double arrayMin(final double[] array) {
    method arrayMin (line 947) | public static int arrayMin(final int[] array) {
    method arrayMin (line 951) | public static byte arrayMin(final byte[] array) {
    method arrayMin (line 960) | public static int arrayMin(final List<Integer> array) {
    method median (line 973) | public static <T extends Comparable<? super T>> T median(final List<T>...
    method minElementIndex (line 997) | public static int minElementIndex(final double[] array) {
    method minElementIndex (line 1010) | public static int minElementIndex(final byte[] array) {
    method minElementIndex (line 1023) | public static int minElementIndex(final int[] array) {
    method arrayMaxInt (line 1036) | public static int arrayMaxInt(final List<Integer> array) {
    method sum (line 1048) | public static int sum(final List<Integer> list ) {
    method average (line 1056) | public static double average(final List<Long> vals, final int maxI) {
    method average (line 1070) | public static double average(final List<Long> vals) {
    method countOccurrences (line 1074) | public static int countOccurrences(final char c, final String s) {
    method countOccurrences (line 1082) | public static <T> int countOccurrences(T x, List<T> l) {
    method countOccurrences (line 1092) | public static int countOccurrences(byte element, byte[] array) {
    method countOccurrences (line 1102) | public static int countOccurrences(final boolean element, final boolea...
    method sampleIndicesWithReplacement (line 1120) | static public ArrayList<Integer> sampleIndicesWithReplacement(final in...
    method sampleIndicesWithoutReplacement (line 1139) | static public ArrayList<Integer> sampleIndicesWithoutReplacement(final...
    method sliceListByIndices (line 1160) | static public <T> ArrayList<T> sliceListByIndices(final List<Integer> ...
    method logDotProduct (line 1177) | public static double logDotProduct(final double [] x, final double[] y) {
    method goodLog10ProbVector (line 1202) | public static boolean goodLog10ProbVector(final double[] vector, final...
    method goodLog10Probability (line 1223) | public static boolean goodLog10Probability(final double result) {
    method goodLog10Probability (line 1234) | public static boolean goodLog10Probability(final double result, final ...
    method goodProbability (line 1244) | public static boolean goodProbability(final double result) {
    class RunningAverage (line 1257) | public static class RunningAverage {
      method add (line 1262) | public void add(double obs) {
      method addAll (line 1269) | public void addAll(Collection<Number> col) {
      method mean (line 1275) | public double mean() {
      method stddev (line 1279) | public double stddev() {
      method var (line 1283) | public double var() {
      method observationCount (line 1287) | public long observationCount() {
      method clone (line 1291) | public RunningAverage clone() {
      method merge (line 1299) | public void merge(RunningAverage other) {
    method max (line 1312) | static public double max(double x0, double x1, double x2) {
    method lnToLog10 (line 1323) | public static double lnToLog10(final double ln) {
    method HI (line 1336) | private static final int HI(final double x) {
    method LO (line 1344) | private static final int LO(final double x) {
    method lnGamma (line 1352) | private static double lnGamma(final double x) {
    method log10Gamma (line 1473) | public static double log10Gamma(final double x) {
    method factorial (line 1477) | public static double factorial(final int x) {
    method log10Factorial (line 1482) | public static double log10Factorial(final int x) {
    class Log10FactorialCache (line 1492) | private static class Log10FactorialCache {
      method size (line 1499) | public static int size() { return CACHE_SIZE; }
      method get (line 1501) | public static double get(final int n) {
      method initialize (line 1507) | private static synchronized void initialize() {
    method addArrays (line 1527) | public static int[] addArrays(final int[] a, final int[] b) {
    method vectorSum (line 1540) | public static double[] vectorSum(final double[]x, final double[] y) {
    method vectorDiff (line 1557) | public static int[] vectorDiff(final int[]x, final int[] y) {
    method log10LinearRange (line 1579) | public static List<Integer> log10LinearRange(final int start, final in...
    method log10OneMinusX (line 1609) | public static double log10OneMinusX(final double x) {
    method randomSubset (line 1625) | public static <T> List<T> randomSubset(final List<T> list, final int N) {
    method randomSample (line 1638) | public static <T> List<T> randomSample(final List<T> list, final int N) {
    method dirichletMultinomial (line 1654) | public static double dirichletMultinomial(final double[] dirichletPara...
    method dirichletMultinomial (line 1671) | public static double dirichletMultinomial(double[] params, int[] count...
    method exponentialDistribution (line 1675) | public static ExponentialDistribution exponentialDistribution( final d...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/NGSPlatform.java
  type NGSPlatform (line 34) | public enum NGSPlatform {
    method NGSPlatform (line 52) | NGSPlatform(final String... BAM_PL_NAMES) {
    method getDefaultPlatform (line 67) | public final String getDefaultPlatform() {
    method fromRead (line 80) | public static NGSPlatform fromRead(final GATKSAMRecord read) {
    method fromReadGroupPL (line 92) | public static NGSPlatform fromReadGroupPL(final String plFromRG) {
    method isKnown (line 115) | public static boolean isKnown(final String platform) {
    method knownPlatformsString (line 124) | public static String knownPlatformsString() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/QualityUtils.java
  class QualityUtils (line 29) | public class QualityUtils {
    method QualityUtils (line 72) | private QualityUtils() {
    method qualToProb (line 94) | public static double qualToProb(final byte qual) {
    method qualToProb (line 108) | public static double qualToProb(final double qual) {
    method qualToProbLog10 (line 126) | public static double qualToProbLog10(final byte qual) {
    method qualToErrorProb (line 140) | public static double qualToErrorProb(final double qual) {
    method qualToErrorProb (line 158) | public static double qualToErrorProb(final byte qual) {
    method qualToErrorProbLog10 (line 176) | public static double qualToErrorProbLog10(final byte qual) {
    method qualToErrorProbLog10 (line 190) | public static double qualToErrorProbLog10(final double qual) {
    method errorProbToQual (line 210) | public static byte errorProbToQual(final double errorRate) {
    method errorProbToQual (line 226) | public static byte errorProbToQual(final double errorRate, final byte ...
    method trueProbToQual (line 251) | public static byte trueProbToQual(final double trueProb, final byte ma...
    method phredScaleCorrectRate (line 268) | public static double phredScaleCorrectRate(final double trueRate) {
    method phredScaleLog10CorrectRate (line 282) | public static double phredScaleLog10CorrectRate(final double trueRateL...
    method phredScaleErrorRate (line 295) | public static double phredScaleErrorRate(final double errorRate) {
    method phredScaleLog10ErrorRate (line 309) | public static double phredScaleLog10ErrorRate(final double errorRateLo...
    method boundQual (line 334) | public static byte boundQual(final int qual, final byte maxQual) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/RandomGenerator.java
  class RandomGenerator (line 29) | public class RandomGenerator {
    method getRandomGenerator (line 34) | public static Random getRandomGenerator() {
    method resetRandomGenerator (line 38) | public static void resetRandomGenerator() {
    method resetRandomGenerator (line 42) | public static void resetRandomGenerator(long seed) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/ReadUtils.java
  class ReadUtils (line 51) | public class ReadUtils {
    method ReadUtils (line 57) | private ReadUtils() {
    type ClippingTail (line 66) | public enum ClippingTail {
    type ReadAndIntervalOverlap (line 134) | public enum ReadAndIntervalOverlap {NO_OVERLAP_CONTIG, NO_OVERLAP_LEFT...
    method isBaseInsideAdaptor (line 150) | public static boolean isBaseInsideAdaptor(final GATKSAMRecord read, lo...
    method getAdaptorBoundary (line 184) | public static int getAdaptorBoundary(final SAMRecord read) {
    method hasWellDefinedFragmentSize (line 204) | public static boolean hasWellDefinedFragmentSize(final SAMRecord read) {
    method is454Read (line 237) | public static boolean is454Read(GATKSAMRecord read) {
    method isIonRead (line 247) | public static boolean isIonRead(GATKSAMRecord read) {
    method isSOLiDRead (line 257) | public static boolean isSOLiDRead(GATKSAMRecord read) {
    method isIlluminaRead (line 267) | public static boolean isIlluminaRead(GATKSAMRecord read) {
    method isPlatformRead (line 279) | public static boolean isPlatformRead(GATKSAMRecord read, String name) {
    method sortReadsByCoordinate (line 298) | public final static List<GATKSAMRecord> sortReadsByCoordinate(List<GAT...
    method getFirstInsertionOffset (line 312) | public final static int getFirstInsertionOffset(SAMRecord read) {
    method getLastInsertionOffset (line 328) | public final static int getLastInsertionOffset(SAMRecord read) {
    method getReadAndIntervalOverlapType (line 343) | public static ReadAndIntervalOverlap getReadAndIntervalOverlapType(GAT...
    method getReadCoordinateForReferenceCoordinate (line 397) | public static int getReadCoordinateForReferenceCoordinate(GATKSAMRecor...
    method getReadCoordinateForReferenceCoordinateUpToEndOfRead (line 401) | public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead...
    method getReadCoordinateForReferenceCoordinate (line 406) | public static int getReadCoordinateForReferenceCoordinate(final int al...
    method getReadCoordinateForReferenceCoordinate (line 443) | public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoor...
    method getReadCoordinateForReferenceCoordinate (line 447) | public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoor...
    method isInsideRead (line 563) | public static boolean isInsideRead(final GATKSAMRecord read, final int...
    method readIsEntirelyInsertion (line 573) | public static boolean readIsEntirelyInsertion(GATKSAMRecord read) {
    method readStartsWithInsertion (line 584) | public static CigarElement readStartsWithInsertion(final Cigar cigarFo...
    method readStartsWithInsertion (line 595) | public static CigarElement readStartsWithInsertion(final Cigar cigarFo...
    method getCoverageDistributionOfReads (line 616) | public static int [] getCoverageDistributionOfReads(List<GATKSAMRecord...
    method getCoverageDistributionOfRead (line 638) | public static int [] getCoverageDistributionOfRead(GATKSAMRecord read,...
    method getBothReadToLociMappings (line 685) | public static Pair<HashMap<Integer, HashSet<GATKSAMRecord>> , HashMap<...
    method createRandomReadQuals (line 723) | public static byte[] createRandomReadQuals(int length) {
    method createRandomReadBases (line 738) | public static byte[] createRandomReadBases(int length, boolean allowNs) {
    method createRandomRead (line 766) | public static GATKSAMRecord createRandomRead(int length) {
    method createRandomRead (line 770) | public static GATKSAMRecord createRandomRead(int length, boolean allow...
    method prettyPrintSequenceRecords (line 777) | public static String prettyPrintSequenceRecords ( SAMSequenceDictionar...
    method getReferenceCoordinateForReadCoordinate (line 792) | public static long getReferenceCoordinateForReadCoordinate(GATKSAMReco...
    method getCigarOperatorForAllBases (line 824) | public static Map<CigarOperator, ArrayList<Integer>> getCigarOperatorF...
    method convertReadBasesToString (line 857) | public static String convertReadBasesToString(GATKSAMRecord read) {
    method convertReadQualToString (line 871) | public static String convertReadQualToString(byte[] quals) {
    method convertReadQualToString (line 885) | public static String convertReadQualToString(GATKSAMRecord read) {
    method getBasesReverseComplement (line 895) | public static String getBasesReverseComplement(byte[] bases) {
    method getBasesReverseComplement (line 909) | public static String getBasesReverseComplement(GATKSAMRecord read) {
    method getMaxReadLength (line 918) | public static int getMaxReadLength( final List<GATKSAMRecord> reads ) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/RecalUtils.java
  class RecalUtils (line 52) | public class RecalUtils {
    method initializeCovariates (line 98) | public static Pair<ArrayList<Covariate>, ArrayList<Covariate>> initial...
    method addRequiredCovariatesToList (line 116) | private static ArrayList<Covariate> addRequiredCovariatesToList() {
    type SOLID_RECAL_MODE (line 124) | public enum SOLID_RECAL_MODE {
      method recalModeFromString (line 142) | public static SOLID_RECAL_MODE recalModeFromString(String recalMode) {
    type SOLID_NOCALL_STRATEGY (line 156) | public enum SOLID_NOCALL_STRATEGY {
      method nocallStrategyFromString (line 170) | public static SOLID_NOCALL_STRATEGY nocallStrategyFromString(String ...
    method parsePlatformForRead (line 188) | public static void parsePlatformForRead(final GATKSAMRecord read, fina...
    method isColorSpaceConsistent (line 220) | public static boolean isColorSpaceConsistent(final SOLID_NOCALL_STRATE...
    method hasNoCallInColorSpace (line 267) | private static boolean hasNoCallInColorSpace(final byte[] colorSpace) {
    method getNextBaseFromColor (line 287) | private static byte getNextBaseFromColor(GATKSAMRecord read, final byt...
    method isColorSpaceConsistent (line 310) | public static boolean isColorSpaceConsistent(final GATKSAMRecord read,...
    method computeCovariates (line 337) | public static ReadCovariates computeCovariates(final GATKSAMRecord rea...
    method computeCovariates (line 355) | public static void computeCovariates(final GATKSAMRecord read, final C...
    method performColorOne (line 369) | private static byte performColorOne(byte base) {
    method performColorTwo (line 394) | private static byte performColorTwo(byte base) {
    method performColorThree (line 419) | private static byte performColorThree(byte base) {
    method combineTables (line 446) | public static void combineTables(final NestedIntegerArray<RecalDatum> ...
    method incrementDatumOrPutIfNecessary (line 474) | public static void incrementDatumOrPutIfNecessary(final NestedIntegerA...
    method createDatumObject (line 500) | private static RecalDatum createDatumObject(final byte reportedQual, f...
    method generateReportTables (line 506) | private static List<GATKReportTable> generateReportTables(final Recali...
    method parseCovariateName (line 582) | private static String parseCovariateName(final Covariate covariate) {
    method covariateNames (line 592) | public static String covariateNames(final Covariate[] requestedCovaria...
    method getRecalibrationReport (line 599) | public static GATKReport getRecalibrationReport(final RecalibrationArg...
    method createRecalibrationGATKReport (line 618) | private static GATKReport createRecalibrationGATKReport(final GATKRepo...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/SampleListUtils.java
  class SampleListUtils (line 36) | public class SampleListUtils {
    method sampleCount (line 40) | @Override
    method sampleIndex (line 45) | @Override
    method sampleAt (line 50) | @Override
    method emptyList (line 61) | public static SampleList emptyList() {
    method equals (line 74) | public static boolean equals(final SampleList first, final SampleList ...
    method asList (line 102) | public static List<String> asList(final SampleList list) {
    method asSet (line 115) | public static Set<String> asSet(final SampleList list) {
    method singletonList (line 127) | public static SampleList singletonList(final String sampleName) {
    class AsList (line 154) | private static class AsList extends AbstractList<String> {
      method AsList (line 158) | private AsList(final SampleList list) {
      method get (line 163) | @Override
      method size (line 168) | @Override
    class AsSet (line 177) | private static class AsSet extends AbstractSet<String> {
      method AsSet (line 181) | private AsSet(final SampleList list) {
      method iterator (line 186) | @Override
      method size (line 210) | @Override
      method contains (line 215) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/SequenceComplexity.java
  class SequenceComplexity (line 27) | public class SequenceComplexity {
    method findBasesInShortUnitRepeats (line 46) | public static boolean[] findBasesInShortUnitRepeats(final byte[] bases...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/TextFormattingUtils.java
  class TextFormattingUtils (line 41) | public class TextFormattingUtils {
    method wordWrap (line 60) | public static List<String> wordWrap(String text, int width ) {
    class CaseInsensitiveComparator (line 78) | public static class CaseInsensitiveComparator implements Comparator<St...
      method compare (line 85) | public int compare(String lhs, String rhs) {
    method loadResourceBundle (line 99) | public static ResourceBundle loadResourceBundle(String bundleName) {
    method getWordStarts (line 124) | public static List<Integer> getWordStarts(String line) {
    method splitFixedWidth (line 142) | public static String[] splitFixedWidth(String line, List<Integer> colu...
    method splitWhiteSpace (line 165) | public static String[] splitWhiteSpace(String line) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/Utils.java
  class Utils (line 47) | public class Utils {
    method xor (line 60) | public static boolean xor(final boolean x, final boolean y) {
    method optimumHashSize (line 73) | public static int optimumHashSize ( int maxElements ) {
    method equals (line 85) | public static boolean equals(Object lhs, Object rhs) {
    method cons (line 89) | public static <T> List<T> cons(final T elt, final List<T> l) {
    method warnUser (line 96) | public static void warnUser(final String msg) {
    method warnUser (line 100) | public static void warnUser(final Logger logger, final String msg) {
    method prettyPrintWarningMessage (line 114) | private static void prettyPrintWarningMessage(Logger logger, String me...
    method joinMap (line 139) | public static <L,R> String joinMap(String keyValueSeperator, String re...
    method split (line 156) | public static ArrayList<String> split(String str, String delimiter) {
    method split (line 168) | public static ArrayList<String> split(String str, String delimiter, in...
    method join (line 189) | public static String join(String separator, String[] strings) {
    method join (line 193) | public static String join(String separator, String[] strings, int star...
    method join (line 205) | public static String join(String separator, int[] ints) {
    method list2Array (line 219) | public static int[] list2Array(List<Integer> list) {
    method append (line 236) | public static <T> List<T> append(final List<T> left, T ... elts) {
    method join (line 249) | public static String join(String separator, double[] doubles) {
    method join (line 273) | public static <T> String join(final String separator, final Collection...
    method asList (line 299) | public static List<Integer> asList(final int ... values) {
    method asList (line 322) | public static List<Double> asList(final double ... values) {
    method join (line 339) | public static <T> String join(final String separator, final T ... obje...
    method dupString (line 349) | public static String dupString(final String s, int nCopies) {
    method dupString (line 359) | public static String dupString(char c, int nCopies) {
    method dupBytes (line 365) | public static byte[] dupBytes(byte b, int nCopies) {
    method trim (line 372) | public static String trim(String str, char ch) {
    method escapeExpressions (line 393) | public static String[] escapeExpressions(String args) {
    method escapeExpressions (line 409) | private static String[] escapeExpressions(String args, String delimite...
    method concatArrays (line 432) | public static String[] concatArrays(String[] A, String[] B) {
    method concat (line 443) | public static byte[] concat(final byte[] ... allBytes) {
    method appendArray (line 463) | public static String[] appendArray(String[] A, String... B) {
    method sorted (line 467) | public static <T extends Comparable<T>> List<T> sorted(Collection<T> c) {
    method sorted (line 471) | public static <T extends Comparable<T>> List<T> sorted(Collection<T> c...
    method sorted (line 478) | public static <T extends Comparable<T>, V> List<V> sorted(Map<T,V> c) {
    method sorted (line 482) | public static <T extends Comparable<T>, V> List<V> sorted(Map<T,V> c, ...
    method reverse (line 500) | static public byte[] reverse(byte[] bases) {
    method reverse (line 510) | static public <T> List<T> reverse(final List<T> l) {
    method reverse (line 522) | static public int[] reverse(int[] bases) {
    method reverse (line 538) | static public String reverse(String bases) {
    method isFlagSet (line 542) | public static boolean isFlagSet(int value, int flag) {
    method resolveHostname (line 550) | public static String resolveHostname() {
    method arrayFromArrayWithLength (line 561) | public static byte [] arrayFromArrayWithLength(byte[] array, int lengt...
    method fillArrayWithByte (line 568) | public static void fillArrayWithByte(byte[] array, byte value) {
    method setupWriter (line 580) | public static SAMFileHeader setupWriter(final SAMFileHeader originalHe...
    method nCombinations (line 601) | public static <T> int nCombinations(final Collection<T>[] options) {
    method nCombinations (line 609) | public static <T> int nCombinations(final List<List<T>> options) {
    method makePermutations (line 633) | public static <T> List<List<T>> makePermutations(final List<T> objects...
    method formattedNoveltyRate (line 659) | public static String formattedNoveltyRate(final int known, final int a...
    method formattedPercent (line 670) | public static String formattedPercent(final long x, final long total) {
    method formattedRatio (line 681) | public static String formattedRatio(final long num, final long denom) {
    method addAll (line 707) | public static <T> boolean addAll(Collection<T> dest, T ... elements) {
    method makeIdentityFunctionMap (line 718) | public static <T> Map<T, T> makeIdentityFunctionMap(Collection<T> valu...
    method groupList (line 733) | public static <T> List<List<T>> groupList(final List<T> list, final in...
    method calcMD5 (line 747) | public static String calcMD5(final String s) {
    method calcMD5 (line 757) | public static String calcMD5(final byte[] bytes) {
    method endsWith (line 779) | public static boolean endsWith(final byte[] big, final byte[] suffix) {
    method longestCommonPrefix (line 792) | public static int longestCommonPrefix(final byte[] seq1, final byte[] ...
    method longestCommonSuffix (line 812) | public static int longestCommonSuffix(final byte[] seq1, final byte[] ...
    method trimArray (line 833) | public static byte[] trimArray(final byte[] seq, final int trimFromFro...
    method listFromPrimitives (line 846) | public static List<Integer> listFromPrimitives(final int[] ar) {
    method equalRange (line 870) | public static boolean equalRange(final byte[] left, final int leftOffs...
    method skimArray (line 899) | public static <T> T skimArray(final T original, final boolean[] remove) {
    method skimArray (line 930) | public static <T> T skimArray(final T source, final int sourceOffset, ...
    method skimArray (line 973) | public static <T> T skimArray(final T source, final int sourceOffset, ...
    method skimArrayBuildResultArray (line 1045) | private static <T> T skimArrayBuildResultArray(final T dest, final int...
    method skimArrayDetermineDestArrayClass (line 1059) | private static <T> Class<T> skimArrayDetermineDestArrayClass(final T d...
    method deepCloneArray (line 1092) | public static <T>  T deepCloneArray(final T array) {
    method calculateArrayDimensions (line 1109) | private static int calculateArrayDimensions(final Class<?> clazz) {
    method deepCloneArrayUnchecked (line 1116) | private static <T> T deepCloneArrayUnchecked(final T array, final Clas...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/clip/ClippingOp.java
  class ClippingOp (line 46) | public class ClippingOp {
    method ClippingOp (line 49) | public ClippingOp(int start, int stop) {
    method getLength (line 55) | public int getLength() {
    method apply (line 66) | public GATKSAMRecord apply(ClippingRepresentation algorithm, GATKSAMRe...
    method revertSoftClippedBases (line 163) | private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
    method getNewAlignmentStartOffset (line 198) | private int getNewAlignmentStartOffset(final Cigar __cigar, final Ciga...
    method softClip (line 245) | private Cigar softClip(final Cigar __cigar, final int __startClipEnd, ...
    method hardClip (line 349) | private GATKSAMRecord hardClip(GATKSAMRecord read, int start, int stop) {
    method hardClipCigar (line 386) | private CigarShift hardClipCigar(Cigar cigar, int start, int stop) {
    method cleanHardClippedCigar (line 493) | private CigarShift cleanHardClippedCigar(final Cigar cigar) {
    method calcHardSoftOffset (line 566) | private int calcHardSoftOffset(final Cigar cigar) {
    method calculateAlignmentStartShift (line 583) | private int calculateAlignmentStartShift(Cigar oldCigar, Cigar newCiga...
    method calculateHardClippingAlignmentShift (line 589) | private int calculateHardClippingAlignmentShift(CigarElement cigarElem...
    class CigarShift (line 602) | private static class CigarShift {
      method CigarShift (line 607) | private CigarShift(Cigar cigar, int shiftFromStart, int shiftFromEnd) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/clip/ClippingRepresentation.java
  type ClippingRepresentation (line 27) | public enum ClippingRepresentation {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/clip/ReadClipper.java
  class ReadClipper (line 68) | public class ReadClipper {
    method ReadClipper (line 85) | public ReadClipper(final GATKSAMRecord read) {
    method addOp (line 103) | public void addOp(ClippingOp op) {
    method getOps (line 113) | public List<ClippingOp> getOps() {
    method wasClipped (line 121) | public boolean wasClipped() {
    method getRead (line 130) | public GATKSAMRecord getRead() {
    method clipRead (line 140) | public GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
    method hardClipByReferenceCoordinatesLeftTail (line 171) | private GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(int refSt...
    method hardClipByReferenceCoordinatesLeftTail (line 174) | public static GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(GAT...
    method hardClipByReferenceCoordinatesRightTail (line 187) | private GATKSAMRecord hardClipByReferenceCoordinatesRightTail(int refS...
    method hardClipByReferenceCoordinatesRightTail (line 190) | public static GATKSAMRecord hardClipByReferenceCoordinatesRightTail(GA...
    method hardClipByReadCoordinates (line 201) | private GATKSAMRecord hardClipByReadCoordinates(int start, int stop) {
    method hardClipByReadCoordinates (line 208) | public static GATKSAMRecord hardClipByReadCoordinates(GATKSAMRecord re...
    method hardClipBothEndsByReferenceCoordinates (line 222) | private GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left,...
    method hardClipBothEndsByReferenceCoordinates (line 235) | public static GATKSAMRecord hardClipBothEndsByReferenceCoordinates(GAT...
    method clipLowQualEnds (line 250) | private GATKSAMRecord clipLowQualEnds(ClippingRepresentation algorithm...
    method hardClipLowQualEnds (line 276) | private GATKSAMRecord hardClipLowQualEnds(byte lowQual) {
    method hardClipLowQualEnds (line 279) | public static GATKSAMRecord hardClipLowQualEnds(GATKSAMRecord read, by...
    method clipLowQualEnds (line 282) | public static GATKSAMRecord clipLowQualEnds(GATKSAMRecord read, byte l...
    method hardClipSoftClippedBases (line 292) | private GATKSAMRecord hardClipSoftClippedBases () {
    method hardClipSoftClippedBases (line 325) | public static GATKSAMRecord hardClipSoftClippedBases (GATKSAMRecord re...
    method hardClipToRegion (line 338) | public static GATKSAMRecord hardClipToRegion( final GATKSAMRecord read...
    method hardClipToRegionIncludingClippedBases (line 352) | public static GATKSAMRecord hardClipToRegionIncludingClippedBases( fin...
    method hardClipToRegion (line 358) | private static GATKSAMRecord hardClipToRegion( final GATKSAMRecord rea...
    method hardClipToRegion (line 373) | public static List<GATKSAMRecord> hardClipToRegion( final List<GATKSAM...
    method hardClipAdaptorSequence (line 391) | private GATKSAMRecord hardClipAdaptorSequence () {
    method hardClipAdaptorSequence (line 399) | public static GATKSAMRecord hardClipAdaptorSequence (GATKSAMRecord rea...
    method hardClipLeadingInsertions (line 409) | private GATKSAMRecord hardClipLeadingInsertions() {
    method hardClipLeadingInsertions (line 424) | public static GATKSAMRecord hardClipLeadingInsertions(GATKSAMRecord re...
    method revertSoftClippedBases (line 433) | private GATKSAMRecord revertSoftClippedBases() {
    method revertSoftClippedBases (line 447) | public static GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
    method revertSoftClippedBases (line 460) | public static GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read,...
    method hardClipLowQualitySoftClips (line 471) | public static GATKSAMRecord hardClipLowQualitySoftClips(GATKSAMRecord ...
    method hardClipByReferenceCoordinates (line 519) | protected GATKSAMRecord hardClipByReferenceCoordinates(int refStart, i...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/downsampling/AlleleBiasedDownsamplingUtils.java
  class AlleleBiasedDownsamplingUtils (line 43) | public class AlleleBiasedDownsamplingUtils {
    class PileupElementList (line 46) | private final static class PileupElementList extends ArrayList<PileupE...
    method createAlleleBiasedBasePileup (line 55) | public static ReadBackedPileup createAlleleBiasedBasePileup(final Read...
    method calculateAlleleCounts (line 106) | private static int[] calculateAlleleCounts(final PileupElementList[] a...
    method scoreAlleleCounts (line 114) | private static int scoreAlleleCounts(final int[] alleleCounts) {
    method runSmartDownsampling (line 142) | protected static int[] runSmartDownsampling(final int[] alleleCounts, ...
    method downsampleElements (line 182) | protected static List<PileupElement> downsampleElements(final List<Pil...
    method selectAlleleBiasedReads (line 218) | public static <A extends Allele> List<GATKSAMRecord> selectAlleleBiase...
    method downsampleElements (line 254) | protected static List<GATKSAMRecord> downsampleElements(final List<GAT...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/downsampling/Downsampler.java
  class Downsampler (line 30) | public abstract class Downsampler<T> {
    method submit (line 44) | public abstract void submit( final T item );
    method submit (line 52) | public void submit( final Collection<T> items ) {
    method hasFinalizedItems (line 67) | public abstract boolean hasFinalizedItems();
    method consumeFinalizedItems (line 74) | public abstract List<T> consumeFinalizedItems();
    method hasPendingItems (line 82) | public abstract boolean hasPendingItems();
    method peekFinalized (line 90) | public abstract T peekFinalized();
    method peekPending (line 98) | public abstract T peekPending();
    method size (line 109) | public abstract int size();
    method getNumberOfDiscardedItems (line 117) | public int getNumberOfDiscardedItems() {
    method signalEndOfInput (line 125) | public abstract void signalEndOfInput();
    method clearItems (line 130) | public abstract void clearItems();
    method resetStats (line 135) | public void resetStats() {
    method doNotDiscardItem (line 148) | protected boolean doNotDiscardItem( final Object item ) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/downsampling/DownsamplingUtils.java
  class DownsamplingUtils (line 36) | public class DownsamplingUtils {
    method DownsamplingUtils (line 37) | private DownsamplingUtils() { }
    method levelCoverageByPosition (line 56) | public static List<GATKSAMRecord> levelCoverageByPosition(final List<G...
    method partitionReadsBySampleAndStart (line 81) | private static Map<String, Map<Integer, List<GATKSAMRecord>>> partitio...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/downsampling/LIBSDownsamplingInfo.java
  class LIBSDownsamplingInfo (line 27) | public class LIBSDownsamplingInfo {
    method LIBSDownsamplingInfo (line 31) | public LIBSDownsamplingInfo(boolean performDownsampling, int toCoverag...
    method isPerformDownsampling (line 36) | public boolean isPerformDownsampling() {
    method getToCoverage (line 40) | public int getToCoverage() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/downsampling/LevelingDownsampler.java
  class LevelingDownsampler (line 36) | public class LevelingDownsampler<T extends List<E>, E> extends Downsampl...
    method LevelingDownsampler (line 54) | public LevelingDownsampler( final int targetSize ) {
    method LevelingDownsampler (line 68) | public LevelingDownsampler( final int targetSize, final int minElement...
    method submit (line 78) | @Override
    method submit (line 83) | @Override
    method hasFinalizedItems (line 88) | @Override
    method consumeFinalizedItems (line 93) | @Override
    method hasPendingItems (line 105) | @Override
    method peekFinalized (line 110) | @Override
    method peekPending (line 115) | @Override
    method size (line 120) | @Override
    method signalEndOfInput (line 129) | @Override
    method clearItems (line 135) | @Override
    method levelGroups (line 141) | private void levelGroups() {
    method downsampleOneGroup (line 187) | private void downsampleOneGroup( final T group, final int numItemsToKe...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/fragments/FragmentCollection.java
  class FragmentCollection (line 31) | public class FragmentCollection<T> {
    method FragmentCollection (line 35) | public FragmentCollection(final Collection<T> singletons, final Collec...
    method getSingletonReads (line 45) | public Collection<T> getSingletonReads() {
    method getOverlappingPairs (line 54) | public Collection<List<T>> getOverlappingPairs() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/haplotype/EventMap.java
  class EventMap (line 49) | public class EventMap extends TreeMap<Integer, VariantContext> {
    method EventMap (line 61) | public EventMap(final Haplotype haplotype, final byte[] ref, final Gen...
    method EventMap (line 76) | public EventMap(final Collection<VariantContext> stateForTesting) {
    method processCigarForInitialEvents (line 85) | protected void processCigarForInitialEvents() {
    method addVC (line 183) | protected void addVC(final VariantContext vc) {
    method addVC (line 193) | public void addVC(final VariantContext vc, final boolean merge) {
    method makeBlock (line 217) | protected VariantContext makeBlock(final VariantContext vc1, final Var...
    method replaceClumpedEventsWithBlockSubstitutions (line 254) | protected void replaceClumpedEventsWithBlockSubstitutions() {
    method updateToBlockSubstitutionIfBetter (line 273) | protected boolean updateToBlockSubstitutionIfBetter(final List<Variant...
    method getNeighborhood (line 311) | protected List<VariantContext> getNeighborhood(final VariantContext le...
    method getStartPositions (line 334) | public Set<Integer> getStartPositions() {
    method getVariantContexts (line 343) | public Collection<VariantContext> getVariantContexts() {
    method getNumberOfEvents (line 352) | public int getNumberOfEvents() {
    method toString (line 356) | @Override
    method buildEventMapsForHaplotypes (line 375) | public static TreeSet<Integer> buildEventMapsForHaplotypes(final List<...
    class VariantContextComparator (line 399) | private static class VariantContextComparator implements Comparator<Va...
      method compare (line 400) | @Override
    method getAllVariantContexts (line 412) | public static TreeSet<VariantContext> getAllVariantContexts(final List...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/haplotype/Haplotype.java
  class Haplotype (line 43) | public class Haplotype extends Allele {
    method Haplotype (line 58) | public Haplotype(final byte[] bases, final boolean isRef) {
    method Haplotype (line 67) | public Haplotype(final byte[] bases) {
    method Haplotype (line 81) | public Haplotype(final byte[] bases, final boolean isRef, final int al...
    method Haplotype (line 92) | public Haplotype(final Allele allele) {
    method Haplotype (line 96) | public Haplotype(final byte[] bases, final GenomeLoc loc) {
    method trim (line 113) | public Haplotype trim(final GenomeLoc loc) {
    method equals (line 138) | @Override
    method hashCode (line 143) | @Override
    method getEventMap (line 148) | public EventMap getEventMap() {
    method setEventMap (line 152) | public void setEventMap(final EventMap eventMap) {
    method toString (line 156) | @Override
    method getGenomeLocation (line 166) | public GenomeLoc getGenomeLocation() {
    method setGenomeLocation (line 170) | public void setGenomeLocation(GenomeLoc genomeLocation) {
    method getStartPosition (line 174) | public long getStartPosition() {
    method getStopPosition (line 178) | public long getStopPosition() {
    method getAlignmentStartHapwrtRef (line 182) | public int getAlignmentStartHapwrtRef() {
    method setAlignmentStartHapwrtRef (line 186) | public void setAlignmentStartHapwrtRef(final int alignmentStartHapwrtR...
    method getCigar (line 196) | public Cigar getCigar() {
    method getConsolidatedPaddedCigar (line 206) | public Cigar getConsolidatedPaddedCigar(final int padSize) {
    method setCigar (line 221) | public void setCigar(final Cigar cigar) {
    method insertAllele (line 227) | public Haplotype insertAllele(final Allele refAllele, final Allele alt...
    class Event (line 242) | private static class Event {
      method Event (line 247) | public Event(final Allele ref, final Allele alt, final int pos) {
    method getScore (line 259) | public double getScore() {
    method setScore (line 270) | public void setScore(double score) {
    method compare (line 283) | @Override
    method makeHaplotypeListFromAlleles (line 299) | public static LinkedHashMap<Allele, Haplotype> makeHaplotypeListFromAl...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/interval/IntervalMergingRule.java
  type IntervalMergingRule (line 27) | public enum IntervalMergingRule {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/interval/IntervalSetRule.java
  type IntervalSetRule (line 27) | public enum IntervalSetRule {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/interval/IntervalUtils.java
  class IntervalUtils (line 39) | public class IntervalUtils {
    method isUnmapped (line 46) | public static boolean isUnmapped(String interval) {
    method mergeListsBySetOperator (line 57) | public static List<GenomeLoc> mergeListsBySetOperator(List<GenomeLoc> ...
    method sortAndMergeIntervals (line 109) | public static GenomeLocSortedSet sortAndMergeIntervals(GenomeLocParser...
    method equateIntervals (line 134) | public static String equateIntervals(List<GenomeLoc> masterArg, List<G...
    method toInterval (line 167) | private static htsjdk.samtools.util.Interval toInterval(GenomeLoc loc,...
    method mergeIntervalLocations (line 179) | public static List<GenomeLoc> mergeIntervalLocations(final List<Genome...
    method intervalSize (line 202) | public static long intervalSize(final List<GenomeLoc> locs) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/ArrayLoglessPairHMM.java
  class ArrayLoglessPairHMM (line 32) | public class ArrayLoglessPairHMM extends PairHMM {
    method initialize (line 70) | @Override
    method subComputeReadLikelihoodGivenHaplotypeLog10 (line 105) | @Override
    method initializePriors (line 197) | public void initializePriors(final byte[] haplotypeBases, final byte[]...
    method initializeProbabilities (line 220) | protected static void initializeProbabilities(final double[][] transit...
    method padMatchAndInsertArrays (line 230) | private void padMatchAndInsertArrays(final int padPosition) {
    method padDeleteArrays (line 250) | private void padDeleteArrays(final int haplotypeLength, final int padP...
    method clearArraySolutionPosition (line 265) | private void clearArraySolutionPosition() {
    method clearPreviouslyCachedInfo (line 280) | private void clearPreviouslyCachedInfo(final int fillLength) {
    method applyPreviouslyCachedInfo (line 294) | private void applyPreviouslyCachedInfo(int indK) {
    method recordNewCacheInfo (line 311) | private void recordNewCacheInfo(int indK) {
    method updateArrays (line 327) | private void updateArrays(final int readLength,
    method updateArrayCell (line 361) | private void updateArrayCell( final int indK, final double prior, fina...
    method rotateArrayReferences (line 373) | private void rotateArrayReferences() {
    method rotateCacheArrays (line 395) | private void rotateCacheArrays() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/Log10PairHMM.java
  class Log10PairHMM (line 35) | public class Log10PairHMM extends N2MemoryPairHMM {
    method Log10PairHMM (line 50) | public Log10PairHMM(final boolean doExactLog10) {
    method isDoingExactLog10Calculations (line 58) | public boolean isDoingExactLog10Calculations() {
    method initialize (line 65) | @Override
    method subComputeReadLikelihoodGivenHaplotypeLog10 (line 79) | @Override
    method initializeMatrixValues (line 112) | protected void initializeMatrixValues(final byte[] haplotypeBases) {
    method finalLikelihoodCalculation (line 119) | protected double finalLikelihoodCalculation() {
    method initializePriors (line 137) | public void initializePriors(final byte[] haplotypeBases, final byte[]...
    method initializeProbabilities (line 160) | protected void initializeProbabilities(final byte[] insertionGOP, fina...
    method myLog10SumLog10 (line 180) | protected double myLog10SumLog10(final double[] values) {
    method updateCell (line 195) | protected void updateCell( final int indI, final int indJ, final doubl...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/LoglessPairHMM.java
  class LoglessPairHMM (line 30) | public class LoglessPairHMM extends N2MemoryPairHMM {
    method subComputeReadLikelihoodGivenHaplotypeLog10 (line 40) | @Override
    method initializePriors (line 100) | protected void initializePriors(final byte[] haplotypeBases, final byt...
    method initializeProbabilities (line 123) | protected static void initializeProbabilities(final double[][] transit...
    method updateCell (line 138) | protected void updateCell( final int indI, final int indJ, final doubl...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/N2MemoryPairHMM.java
  class N2MemoryPairHMM (line 27) | abstract class N2MemoryPairHMM extends PairHMM {
    method doNotUseTristateCorrection (line 37) | public void doNotUseTristateCorrection() {
    method initialize (line 49) | @Override
    method dumpMatrices (line 64) | protected void dumpMatrices() {
    method dumpMatrix (line 75) | private void dumpMatrix(final String name, final double[][] matrix) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/PairHMM.java
  class PairHMM (line 39) | public abstract class PairHMM {
    type HMM_IMPLEMENTATION (line 47) | public enum HMM_IMPLEMENTATION {
    method doNotUseTristateCorrection (line 70) | protected void doNotUseTristateCorrection() {
    method initialize (line 91) | public void initialize(final int readMaxLength, final int haplotypeMax...
    method finalizeRegion (line 113) | public void finalizeRegion() {
    method initialize (line 126) | public void initialize(final List<Haplotype> haplotypes, final Map<Str...
    method findMaxReadLength (line 130) | private int findMaxReadLength(final GATKSAMRecord... reads) {
    method findMaxAlleleLength (line 140) | private int findMaxAlleleLength(final List<? extends Allele> alleles) {
    method findMaxReadLength (line 150) | protected int findMaxReadLength(final List<GATKSAMRecord> reads) {
    method findMaxHaplotypeLength (line 161) | protected int findMaxHaplotypeLength(final Collection<Haplotype> haplo...
    method computeLikelihoods (line 183) | public void computeLikelihoods(final ReadLikelihoods.Matrix<Haplotype>...
    method computeReadLikelihoodGivenHaplotypeLog10 (line 251) | protected final double computeReadLikelihoodGivenHaplotypeLog10(final ...
    method subComputeReadLikelihoodGivenHaplotypeLog10 (line 308) | protected abstract double subComputeReadLikelihoodGivenHaplotypeLog10(...
    method findFirstPositionWhereHaplotypesDiffer (line 327) | public static int findFirstPositionWhereHaplotypesDiffer(final byte[] ...
    method setNumberOfThreads (line 346) | public static void setNumberOfThreads(final int numThreads) {
    method getLikelihoodArray (line 355) | public double[] getLikelihoodArray() {
    method close (line 362) | public void close() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/PairHMMIndelErrorModel.java
  class PairHMMIndelErrorModel (line 50) | public class PairHMMIndelErrorModel {
    method PairHMMIndelErrorModel (line 88) | public PairHMMIndelErrorModel(byte indelGOP, byte indelGCP, boolean de...
    method getContextHomopolymerLength (line 138) | static private void getContextHomopolymerLength(final byte[] refBytes,...
    method fillGapProbabilities (line 170) | private void fillGapProbabilities(final int[] hrunProfile,
    method trimHaplotypes (line 195) | protected static Map<Allele, Haplotype> trimHaplotypes(final Map<Allel...
    method mustClipDownstream (line 240) | protected static boolean mustClipDownstream(final GATKSAMRecord read, ...
    method mustClipUpstream (line 251) | protected static boolean mustClipUpstream(final GATKSAMRecord read, fi...
    method computeGeneralReadHaplotypeLikelihoods (line 255) | public synchronized double[][] computeGeneralReadHaplotypeLikelihoods(...
    method useSoftClippedBases (line 447) | private boolean useSoftClippedBases(GATKSAMRecord read, long eventStar...
    method getDiploidHaplotypeLikelihoods (line 462) | private static double[] getDiploidHaplotypeLikelihoods(final int numHa...
    method computeDiploidReadHaplotypeLikelihoods (line 495) | public synchronized double[] computeDiploidReadHaplotypeLikelihoods(fi...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/pairhmm/PairHMMModel.java
  class PairHMMModel (line 30) | public class PairHMMModel {
    method PairHMMModel (line 36) | private PairHMMModel() {
    method qualToTransProbs (line 129) | public static void qualToTransProbs(final double[] dest, final byte in...
    method qualToTransProbs (line 153) | @SuppressWarnings("unused")
    method qualToTransProbs (line 180) | @SuppressWarnings("unused")
    method qualToTransProbs (line 211) | @SuppressWarnings("unused")
    method qualToTransProbsLog10 (line 229) | public static void qualToTransProbsLog10(final double[] dest, final by...
    method qualToTransProbsLog10 (line 253) | @SuppressWarnings("unused")
    method qualToTransProbsLog10 (line 279) | @SuppressWarnings("unused")
    method qualToTransProbsLog10 (line 309) | @SuppressWarnings("unused")
    method createTransitionMatrix (line 323) | public static double[][] createTransitionMatrix(final int maxReadLengt...
    method matchToMatchProb (line 344) | public static double matchToMatchProb(final byte insQual, final byte d...
    method matchToMatchProbLog10 (line 361) | public static double matchToMatchProbLog10(final byte insQual, final b...
    method matchToMatchProb (line 381) | public static double matchToMatchProb(final int insQual, final int del...
    method matchToMatchProbLog10 (line 414) | public static double matchToMatchProbLog10(final int insQual, final in...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReport.java
  class GATKReport (line 41) | public class GATKReport {
    method GATKReport (line 52) | public GATKReport() {
    method GATKReport (line 60) | public GATKReport(String filename) {
    method GATKReport (line 69) | public GATKReport(File file) {
    method GATKReport (line 77) | public GATKReport(GATKReportTable... tables) {
    method loadReport (line 87) | private void loadReport(File file) {
    method addTable (line 121) | public void addTable(final String tableName, final String tableDescrip...
    method addTable (line 133) | public void addTable(final String tableName, final String tableDescrip...
    method addTable (line 143) | public void addTable(GATKReportTable table) {
    method addTables (line 147) | public void addTables(List<GATKReportTable> gatkReportTableV2s) {
    method hasTable (line 158) | public boolean hasTable(String tableName) {
    method getTable (line 168) | public GATKReportTable getTable(String tableName) {
    method print (line 180) | public void print(PrintStream out) {
    method getTables (line 186) | public Collection<GATKReportTable> getTables() {
    method concat (line 196) | public void concat(GATKReport input) {
    method setVersion (line 207) | public void setVersion(GATKReportVersion version) {
    method getVersion (line 211) | public GATKReportVersion getVersion() {
    method isSameFormat (line 223) | public boolean isSameFormat(GATKReport report) {
    method equals (line 243) | public boolean equals(GATKReport report) {
    method newSimpleReport (line 279) | public static GATKReport newSimpleReport(final String tableName, final...
    method newSimpleReportWithDescription (line 290) | public static GATKReport newSimpleReportWithDescription(final String t...
    method newSimpleReport (line 325) | public static GATKReport newSimpleReport(final String tableName, final...
    method addRow (line 345) | public void addRow(final Object... values) {
    method addRowList (line 366) | public void addRowList(final List<Object> values) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReportColumn.java
  class GATKReportColumn (line 32) | public class GATKReportColumn {
    method GATKReportColumn (line 48) | public GATKReportColumn(final String columnName, final String format) {
    method getColumnFormat (line 67) | public GATKReportColumnFormat getColumnFormat() {
    method isRightAlign (line 89) | protected static boolean isRightAlign(final String value) {
    method formatValue (line 99) | private String formatValue(final Object obj) {
    method getDataType (line 113) | public GATKReportDataType getDataType() {
    method getColumnName (line 117) | public String getColumnName() {
    method getFormat (line 121) | public String getFormat() {
    method updateFormatting (line 125) | public void updateFormatting(final Object value) {
    method updateMaxWidth (line 135) | private void updateMaxWidth(final String formatted) {
    method updateFormat (line 139) | private void updateFormat(final String formatted) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReportColumnFormat.java
  class GATKReportColumnFormat (line 27) | public class GATKReportColumnFormat {
    type Alignment (line 28) | public static enum Alignment { LEFT, RIGHT }
    method GATKReportColumnFormat (line 32) | public GATKReportColumnFormat(int width, Alignment alignment) {
    method getWidth (line 37) | public int getWidth() {
    method getAlignment (line 41) | public Alignment getAlignment() {
    method getNameFormat (line 45) | public String getNameFormat() {
    method getValueFormat (line 49) | public String getValueFormat() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReportDataType.java
  type GATKReportDataType (line 31) | public enum GATKReportDataType {
    method GATKReportDataType (line 69) | private GATKReportDataType(String dataTypeString) {
    method toString (line 81) | @Override
    method fromObject (line 93) | public static GATKReportDataType fromObject(Object object) {
    method fromFormatString (line 128) | public static GATKReportDataType fromFormatString(String format) {
    method getDefaultValue (line 143) | public Object getDefaultValue() {
    method isEqual (line 167) | public boolean isEqual(Object a, Object b) {
    method Parse (line 189) | Object Parse(Object obj) {
    method getDefaultFormatString (line 215) | public String getDefaultFormatString() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReportTable.java
  class GATKReportTable (line 47) | public class GATKReportTable {
    type TableDataHeaderFields (line 75) | public enum TableDataHeaderFields {
      method TableDataHeaderFields (line 82) | TableDataHeaderFields(int index) {
      method index (line 86) | public int index() {
    type TableSortingWay (line 91) | public enum TableSortingWay {
    type TableNameHeaderFields (line 97) | public enum TableNameHeaderFields {
      method TableNameHeaderFields (line 103) | TableNameHeaderFields(int index) {
      method index (line 107) | public int index() {
    method GATKReportTable (line 119) | public GATKReportTable(BufferedReader reader, GATKReportVersion versio...
    method GATKReportTable (line 207) | public GATKReportTable(Iterator<String> lineIter, GATKReportVersion ve...
    method GATKReportTable (line 281) | public GATKReportTable(final String tableName, final String tableDescr...
    method GATKReportTable (line 293) | public GATKReportTable(final String tableName, final String tableDescr...
    method GATKReportTable (line 317) | public GATKReportTable(final GATKReportTable tableToCopy, final boolea...
    method isValidName (line 331) | private boolean isValidName(String name) {
    method isValidDescription (line 344) | private boolean isValidDescription(String description) {
    method addRowID (line 356) | public void addRowID(final String ID) {
    method addRowID (line 366) | public void addRowID(final String ID, final boolean populateFirstColum...
    method addRowIDMapping (line 376) | public void addRowIDMapping(final String ID, final int index) {
    method addRowIDMapping (line 387) | public void addRowIDMapping(final Object ID, final int index, final bo...
    method removeRowIDMapping (line 400) | public void removeRowIDMapping(final Object ID) {
    method addColumn (line 409) | public void addColumn(String columnName) {
    method addColumn (line 419) | public void addColumn(String columnName, String format) {
    method verifyEntry (line 430) | private void verifyEntry(final int rowIndex, final int colIndex) {
    method expandTo (line 441) | private void expandTo(final int rowIndex, final boolean updateRowIdMap) {
    method set (line 462) | public void set(final Object rowID, final String columnName, final Obj...
    method set (line 478) | public void set(final int rowIndex, final int colIndex, Object value) {
    method containsRowID (line 502) | public boolean containsRowID(final Object rowID) {
    method getRowIDs (line 509) | public Collection<Object> getRowIDs() {
    method increment (line 520) | public void increment(final Object rowID, final String columnName) {
    method findRowByData (line 543) | public int findRowByData(final Object... columnValues) {
    method fixType (line 566) | private Object fixType(final Object value, final GATKReportColumn colu...
    method get (line 603) | public Object get(final Object rowID, final String columnName) {
    method get (line 614) | public Object get(final int rowIndex, final String columnName) {
    method get (line 625) | public Object get(int rowIndex, int columnIndex) {
    method write (line 635) | void write(final PrintStream out) {
    method writeRow (line 718) | private void writeRow(final PrintStream out, final Object[] row) {
    method transIntoLines (line 743) | public String[] transIntoLines() {
    method writeRowIntoBuffer (line 828) | private void writeRowIntoBuffer(final StringBuilder sBuilder, final Ob...
    method getNumRows (line 853) | public int getNumRows() {
    method getNumColumns (line 857) | public int getNumColumns() {
    method getColumnInfo (line 861) | public List<GATKReportColumn> getColumnInfo() {
    method getTableName (line 865) | public String getTableName() {
    method getTableDescription (line 869) | public String getTableDescription() {
    method concat (line 878) | public void concat(final GATKReportTable table) {
    method isSameFormat (line 899) | public boolean isSameFormat(final GATKReportTable table) {
    method equals (line 920) | public boolean equals(final GATKReportTable table) {
    method getOrderedRows (line 940) | private List<Object[]> getOrderedRows() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/reports/GATKReportVersion.java
  type GATKReportVersion (line 29) | public enum GATKReportVersion {
    method GATKReportVersion (line 62) | private GATKReportVersion(String versionString) {
    method toString (line 66) | @Override
    method equals (line 71) | public boolean equals(GATKReportVersion that) {
    method fromHeader (line 81) | public static GATKReportVersion fromHeader(String header) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignment.java
  class GlobalEdgeGreedySWPairwiseAlignment (line 36) | public final class GlobalEdgeGreedySWPairwiseAlignment extends SWPairwis...
    method GlobalEdgeGreedySWPairwiseAlignment (line 47) | public GlobalEdgeGreedySWPairwiseAlignment(final byte[] reference, fin...
    method GlobalEdgeGreedySWPairwiseAlignment (line 60) | public GlobalEdgeGreedySWPairwiseAlignment(final byte[] reference, fin...
    method GlobalEdgeGreedySWPairwiseAlignment (line 67) | public GlobalEdgeGreedySWPairwiseAlignment(byte[] reference, byte[] al...
    method align (line 77) | @Override
    method debugMatrix (line 133) | private void debugMatrix(final int[][] matrix) {
    method makeCigarForStrictPrefixAndSuffix (line 151) | private Cigar makeCigarForStrictPrefixAndSuffix(final byte[] reference...
    method calculateCigar (line 186) | protected SWPairwiseAlignmentResult calculateCigar(final int matchingP...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/smithwaterman/Parameters.java
  class Parameters (line 27) | public final class Parameters {
    method Parameters (line 41) | public Parameters(final int w_match, final int w_mismatch, final int w...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/smithwaterman/SWPairwiseAlignment.java
  class SWPairwiseAlignment (line 38) | public class SWPairwiseAlignment implements SmithWaterman {
    type State (line 47) | protected enum State {
    type OVERHANG_STRATEGY (line 57) | public enum OVERHANG_STRATEGY {
    method SWPairwiseAlignment (line 102) | @Deprecated
    method SWPairwiseAlignment (line 116) | public SWPairwiseAlignment(byte[] seq1, byte[] seq2, Parameters parame...
    method SWPairwiseAlignment (line 131) | public SWPairwiseAlignment(final byte[] seq1, final byte[] seq2, final...
    method SWPairwiseAlignment (line 142) | protected SWPairwiseAlignment(final Parameters parameters) {
    method SWPairwiseAlignment (line 155) | public SWPairwiseAlignment(byte[] seq1, byte[] seq2, SWParameterSet na...
    method SWPairwiseAlignment (line 159) | public SWPairwiseAlignment(byte[] seq1, byte[] seq2) {
    method getCigar (line 163) | @Override
    method getAlignmentStart2wrt1 (line 166) | @Override
    method align (line 175) | protected void align(final byte[] reference, final byte[] alternate) {
    method calculateMatrix (line 197) | protected void calculateMatrix(final byte[] reference, final byte[] al...
    method calculateMatrix (line 210) | protected void calculateMatrix(final byte[] reference, final byte[] al...
    class SWPairwiseAlignmentResult (line 324) | protected final class SWPairwiseAlignmentResult {
      method SWPairwiseAlignmentResult (line 327) | public SWPairwiseAlignmentResult(final Cigar cigar, final int alignm...
    method calculateCigar (line 341) | protected SWPairwiseAlignmentResult calculateCigar(final int[][] sw, f...
    method makeElement (line 459) | protected CigarElement makeElement(final State state, final int length) {
    method wd (line 471) | private int wd(final byte x, final byte y) {
    method printAlignment (line 475) | public void printAlignment(byte[] ref, byte[] read) {
    method printAlignment (line 479) | public void printAlignment(byte[] ref, byte[] read, int width) {
    method print_cautiously (line 578) | private static void print_cautiously(StringBuilder s, int start, int w...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/smithwaterman/SWParameterSet.java
  type SWParameterSet (line 27) | public enum SWParameterSet {
    method SWParameterSet (line 38) | SWParameterSet(final Parameters parameters) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/smithwaterman/SmithWaterman.java
  type SmithWaterman (line 29) | public interface SmithWaterman {
    method getCigar (line 35) | public Cigar getCigar();
    method getAlignmentStart2wrt1 (line 41) | public int getAlignmentStart2wrt1();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/transformers/BQSRReadTransformer.java
  class BQSRReadTransformer (line 35) | public class BQSRReadTransformer extends ReadTransformer {
    method BQSRReadTransformer (line 41) | public BQSRReadTransformer(GATKReport recalTable) {
    method getOrderingConstraint (line 45) | @Override
    method initializeSub (line 50) | @Override
    method enabled (line 68) | @Override
    method apply (line 76) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/transformers/MisencodedBaseQualityReadTransformer.java
  class MisencodedBaseQualityReadTransformer (line 34) | public class MisencodedBaseQualityReadTransformer extends ReadTransformer {
    method initializeSub (line 44) | @Override
    method enabled (line 51) | @Override
    method apply (line 56) | @Override
    method fixMisencodedQuals (line 65) | protected static GATKSAMRecord fixMisencodedQuals(final GATKSAMRecord ...
    method checkForMisencodedQuals (line 76) | protected static void checkForMisencodedQuals(final GATKSAMRecord read) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/transformers/ReadTransformer.java
  class ReadTransformer (line 51) | abstract public class ReadTransformer {
    method ReadTransformer (line 62) | protected ReadTransformer() {
    method getOrderingConstraint (line 68) | public OrderingConstraint getOrderingConstraint() {
    method initialize (line 79) | public final void initialize(final ApplicationTime overrideTime,
    method initializeSub (line 96) | protected abstract void initializeSub(Map<String, Object> args, final ...
    method enabled (line 105) | public boolean enabled() {
    method isInitialized (line 114) | public final boolean isInitialized() {
    method getApplicationTime (line 123) | public final ApplicationTime getApplicationTime() {
    method apply (line 137) | abstract public GATKSAMRecord apply(final GATKSAMRecord read);
    method toString (line 139) | @Override
    type ApplicationTime (line 147) | public static enum ApplicationTime {
    type OrderingConstraint (line 172) | public enum OrderingConstraint {
    class ReadTransformerComparator (line 189) | public static class ReadTransformerComparator implements Comparator<Re...
      method compare (line 191) | public int compare(final ReadTransformer r1, final ReadTransformer r...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/vcfWriter/GVCFWriter.java
  class GVCFWriter (line 42) | public class GVCFWriter implements VariantContextWriter {
    method parsePartitions (line 65) | protected static List<HomRefBlock> parsePartitions(final List<Integer>...
    method GVCFWriter (line 100) | public GVCFWriter(final List<Integer> GQPartitions, final int defaultP...
    method writeHeader (line 112) | @Override
    method close (line 120) | @Override
    method close (line 133) | public void close(final boolean closeUnderlyingWriter) {
    method addHomRefSite (line 144) | protected VariantContext addHomRefSite(final VariantContext vc, final ...
    method genotypeCanBeMergedInCurrentBlock (line 166) | private boolean genotypeCanBeMergedInCurrentBlock(final Genotype g) {
    method emitCurrentBlock (line 174) | private void emitCurrentBlock() {
    method blockToVCF (line 190) | private VariantContext blockToVCF(final HomRefBlock block) {
    method createNewBlock (line 219) | private HomRefBlock createNewBlock(final VariantContext vc, final Geno...
    method add (line 245) | @Override
    method getResultGVCFWriter (line 277) | public List<VariantContext> getResultGVCFWriter() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/utils/vcfWriter/HomRefBlock.java
  class HomRefBlock (line 36) | final class HomRefBlock {
    method HomRefBlock (line 53) | public HomRefBlock(final VariantContext startingVC, final int minGQ, f...
    method HomRefBlock (line 71) | public HomRefBlock(final int minGQ, final int maxGQ, final int ploidy) {
    method add (line 86) | public void add(final int pos, final Genotype g) {
    method withinBounds (line 114) | public boolean withinBounds(final int GQ) {
    method getMinGQ (line 119) | public int getMinGQ() { return MathUtils.arrayMin(GQs); }
    method getMedianGQ (line 121) | public int getMedianGQ() { return MathUtils.median(GQs); }
    method getMinDP (line 123) | public int getMinDP() { return MathUtils.arrayMin(DPs); }
    method getMedianDP (line 125) | public int getMedianDP() { return MathUtils.median(DPs); }
    method getMinPLs (line 127) | public int[] getMinPLs() { return minPLs; }
    method getGQUpperBound (line 129) | protected int getGQUpperBound() { return maxGQ; }
    method getGQLowerBound (line 130) | protected int getGQLowerBound() { return minGQ; }
    method isContiguous (line 132) | public boolean isContiguous(final VariantContext vc) {
    method getStartingVC (line 136) | public VariantContext getStartingVC() { return startingVC; }
    method getStart (line 137) | public int getStart() { return startingVC.getStart(); }
    method getStop (line 138) | public int getStop() { return stop; }
    method getRef (line 139) | public Allele getRef() { return ref; }
    method getSize (line 140) | public int getSize() { return getStop() - getStart() + 1; }
    method toString (line 142) | @Override
    method toVCFHeaderLine (line 150) | public VCFHeaderLine toVCFHeaderLine() {
    method getPloidy (line 158) | public int getPloidy() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/SerializableActiveRegionMapData.java
  class SerializableActiveRegionMapData (line 49) | public class SerializableActiveRegionMapData implements Serializable {
    method SerializableActiveRegionMapData (line 57) | public SerializableActiveRegionMapData(ActiveRegionMapData activeRegio...
    method getVCInTrackerInLocus (line 77) | private List<VariantContext> getVCInTrackerInLocus(final RefMetaDataTr...
    method toActiveRegionMapData (line 86) | public ActiveRegionMapData toActiveRegionMapData(GenomeLocParser parser,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/BAQ.java
  class BAQ (line 63) | public class BAQ {
    type CalculationMode (line 67) | public enum CalculationMode {
    type QualityMode (line 74) | public enum QualityMode {
    method convertFromPhredScale (line 99) | private double convertFromPhredScale(double x) { return (Math.pow(10,(...
    method getMinBaseQual (line 106) | public byte getMinBaseQual() {
    method getGapOpenProb (line 115) | public double getGapOpenProb() {
    method getGapExtensionProb (line 119) | public double getGapExtensionProb() {
    method getBandWidth (line 123) | public int getBandWidth() {
    method BAQ (line 130) | public BAQ() {
    method BAQ (line 137) | public BAQ(final double gapOpenPenalty) {
    method BAQ (line 152) | public BAQ(final double d, final double e, final int b, final byte min...
    method initializeCachedData (line 164) | private void initializeCachedData() {
    method calcEpsilon (line 182) | protected double calcEpsilon( byte ref, byte read, byte qualB ) {
    method hmm_glocal (line 192) | public int hmm_glocal(final byte[] ref, final byte[] query, int qstart...
    method stateIsIndel (line 368) | public static boolean stateIsIndel(int state) {
    method stateAlignedPosition (line 373) | public static int stateAlignedPosition(int state) {
    method set_u (line 385) | private static int set_u(final int b, final int i, final int k) {
    method getBAQTag (line 402) | public static byte[] getBAQTag(SAMRecord read) {
    method encodeBQTag (line 407) | public static String encodeBQTag(SAMRecord read, byte[] baq) {
    method addBAQTag (line 427) | public static void addBAQTag(SAMRecord read, byte[] baq) {
    method hasBAQTag (line 437) | public static boolean hasBAQTag(SAMRecord read) {
    method calcBAQFromTag (line 449) | public static byte[] calcBAQFromTag(SAMRecord read, boolean overwriteO...
    method calcBAQFromTag (line 481) | public static byte calcBAQFromTag(SAMRecord read, int offset, boolean ...
    class BAQCalculationResult (line 502) | public static class BAQCalculationResult {
      method BAQCalculationResult (line 506) | public BAQCalculationResult(SAMRecord read, byte[] ref) {
      method BAQCalculationResult (line 510) | public BAQCalculationResult(byte[] bases, byte[] quals, byte[] ref) {
    method calcBAQFromHMM (line 522) | public BAQCalculationResult calcBAQFromHMM(SAMRecord read, RefContentP...
    method calcBAQFromHMM (line 542) | public BAQCalculationResult calcBAQFromHMM(byte[] ref, byte[] query, b...
    method calculateQueryRange (line 566) | private final Pair<Integer,Integer> calculateQueryRange(SAMRecord read) {
    method calcBAQFromHMM (line 601) | public BAQCalculationResult calcBAQFromHMM(SAMRecord read, byte[] ref,...
    method capBaseByBAQ (line 644) | public byte capBaseByBAQ( byte oq, byte bq, int state, int expectedPos...
    method baqRead (line 666) | public byte[] baqRead(SAMRecord read, RefContentProvider refContentPro...
    method excludeReadFromBAQ (line 708) | public boolean excludeReadFromBAQ(SAMRecord read) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/BaseRecalibrator.java
  class BaseRecalibrator (line 62) | public class BaseRecalibrator extends ReadWalker {
    method BaseRecalibrator (line 95) | public BaseRecalibrator(GenomeLocParser genomeLocParser,
    method initialize (line 102) | @Override
    method initializeRecalibrationEngine (line 127) | private void initializeRecalibrationEngine() {
    method isLowQualityBase (line 135) | private boolean isLowQualityBase( final GATKSAMRecord read, final int ...
    method getFilter (line 139) | @Override
    method map (line 152) | @Override
    method nEvents (line 198) | protected static int nEvents(final int[]... hasEvents) {
    method calculateSkipArray (line 206) | protected boolean[] calculateSkipArray( final GATKSAMRecord read, fina...
    method badSolidOffset (line 216) | protected boolean badSolidOffset( final GATKSAMRecord read, final int ...
    method calculateKnownSites (line 220) | protected static boolean[] calculateKnownSites( final GATKSAMRecord re...
    method calculateIsSNP (line 245) | protected static int[] calculateIsSNP( final GATKSAMRecord read, final...
    method calculateIsIndel (line 281) | protected static int[] calculateIsIndel( final GATKSAMRecord read, fin...
    method updateIndel (line 324) | private static void updateIndel(final int[] indel, final int index, fi...
    method calculateFractionalErrorArray (line 330) | protected static double[] calculateFractionalErrorArray( final int[] e...
    method calculateAndStoreErrorsInBlock (line 365) | private static void calculateAndStoreErrorsInBlock( final int iii,
    method flatBAQArray (line 384) | protected  static byte[] flatBAQArray(final GATKSAMRecord read) {
    method calculateBAQArray (line 395) | private byte[] calculateBAQArray( final GATKSAMRecord read ) {
    method onTraversalDone (line 400) | @Override
    method getReport (line 410) | public GATKReport getReport() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/QualQuantizer.java
  class QualQuantizer (line 42) | public class QualQuantizer {
    method QualQuantizer (line 69) | protected QualQuantizer(final int minInterestingQual) {
    method QualQuantizer (line 94) | public QualQuantizer(final List<Long> nObservationsPerQual, final int ...
    class QualInterval (line 116) | protected final class QualInterval implements Comparable<QualInterval> {
      method QualInterval (line 124) | protected QualInterval(final int qStart, final int qEnd, final long ...
      method QualInterval (line 128) | protected QualInterval(final int qStart, final int qEnd, final long ...
      method QualInterval (line 132) | protected QualInterval(final int qStart, final int qEnd, final long ...
      method QualInterval (line 136) | public QualInterval(final int qStart, final int qEnd, final long nOb...
      method getName (line 150) | public String getName() {
      method toString (line 154) | @Override
      method getErrorRate (line 162) | public double getErrorRate() {
      method getQual (line 174) | public byte getQual() {
      method hasFixedQual (line 184) | public boolean hasFixedQual() {
      method compareTo (line 188) | @Override
      method merge (line 204) | public QualInterval merge(final QualInterval toMerge) {
      method getPenalty (line 221) | public double getPenalty() {
      method calcPenalty (line 239) | private double calcPenalty(final double globalErrorRate) {
    method quantize (line 272) | private TreeSet<QualInterval> quantize() {
    method mergeLowestPenaltyIntervals (line 298) | private void mergeLowestPenaltyIntervals(final TreeSet<QualInterval> i...
    method intervalsToMap (line 337) | private List<Byte> intervalsToMap(final TreeSet<QualInterval> interval...
    method getNQualsInHistogram (line 352) | private final int getNQualsInHistogram() {
    method getOriginalToQuantizedMap (line 356) | public List<Byte> getOriginalToQuantizedMap() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/QuantizationInfo.java
  class QuantizationInfo (line 36) | public class QuantizationInfo {
    method QuantizationInfo (line 41) | private QuantizationInfo(List<Byte> quantizedQuals, List<Long> empiric...
    method QuantizationInfo (line 47) | public QuantizationInfo(List<Byte> quantizedQuals, List<Long> empirica...
    method QuantizationInfo (line 51) | public QuantizationInfo(final RecalibrationTables recalibrationTables,...
    method quantizeQualityScores (line 70) | public void quantizeQualityScores(int nLevels) {
    method noQuantization (line 75) | public void noQuantization() {
    method getQuantizedQuals (line 81) | public List<Byte> getQuantizedQuals() {
    method getQuantizationLevels (line 85) | public int getQuantizationLevels() {
    method calculateQuantizationLevels (line 89) | private static int calculateQuantizationLevels(List<Byte> quantizedQua...
    method generateReportTable (line 101) | public GATKReportTable generateReportTable(boolean sortByCols) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/ReadCovariates.java
  class ReadCovariates (line 35) | public class ReadCovariates {
    method initialValue (line 51) | @Override protected LRUCache<Integer, int[][][]> initialValue() {
    method clearKeysCache (line 60) | public static void clearKeysCache() {
    method ReadCovariates (line 74) | public ReadCovariates(final int readLength, final int numberOfCovariat...
    method setCovariateIndex (line 87) | public void setCovariateIndex(final int index) {
    method addCovariate (line 103) | public void addCovariate(final int mismatch, final int insertion, fina...
    method getKeySet (line 116) | public int[] getKeySet(final int readPosition, final EventType errorMo...
    method getKeySet (line 120) | public int[][] getKeySet(final EventType errorModel) {
    method getMismatchesKeySet (line 130) | protected int[][] getMismatchesKeySet() { return getKeySet(EventType.B...
    method getInsertionsKeySet (line 131) | protected int[][] getInsertionsKeySet() { return getKeySet(EventType.B...
    method getDeletionsKeySet (line 132) | protected int[][] getDeletionsKeySet() { return getKeySet(EventType.BA...
    method getMismatchesKeySet (line 134) | protected int[] getMismatchesKeySet(final int readPosition) {
    method getInsertionsKeySet (line 138) | protected int[] getInsertionsKeySet(final int readPosition) {
    method getDeletionsKeySet (line 142) | protected int[] getDeletionsKeySet(final int readPosition) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/ReadRecalibrationInfo.java
  class ReadRecalibrationInfo (line 31) | public final class ReadRecalibrationInfo {
    method ReadRecalibrationInfo (line 39) | public ReadRecalibrationInfo(final GATKSAMRecord read,
    method getQual (line 76) | public byte getQual(final EventType eventType, final int offset) {
    method getErrorFraction (line 98) | public double getErrorFraction(final EventType eventType, final int of...
    method getRead (line 111) | public GATKSAMRecord getRead() {
    method skip (line 120) | public boolean skip(final int offset) {
    method getCovariatesValues (line 128) | public ReadCovariates getCovariatesValues() {
    method validOffset (line 137) | private boolean validOffset(final int offset) {
    method validQual (line 141) | private boolean validQual(final byte result) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/RecalDatum.java
  class RecalDatum (line 32) | public class RecalDatum {
    method RecalDatum (line 74) | public RecalDatum(final long _numObservations, final double _numMismat...
    method RecalDatum (line 89) | public RecalDatum(final RecalDatum copy) {
    method combine (line 102) | public synchronized void combine(final RecalDatum other) {
    method setEstimatedQReported (line 109) | public synchronized void setEstimatedQReported(final double estimatedQ...
    method getEstimatedQReported (line 118) | public final double getEstimatedQReported() {
    method getEstimatedQReportedAsByte (line 121) | public final byte getEstimatedQReportedAsByte() {
    method getEmpiricalErrorRate (line 135) | public double getEmpiricalErrorRate() {
    method setEmpiricalQuality (line 147) | public synchronized void setEmpiricalQuality(final double empiricalQua...
    method getEmpiricalQuality (line 155) | public final double getEmpiricalQuality() {
    method getEmpiricalQuality (line 159) | public synchronized final double getEmpiricalQuality(final double cond...
    method getEmpiricalQualityAsByte (line 166) | public final byte getEmpiricalQualityAsByte() {
    method toString (line 176) | @Override
    method stringForCSV (line 181) | public String stringForCSV() {
    method getNumObservations (line 191) | public final long getNumObservations() {
    method setNumObservations (line 195) | public final synchronized void setNumObservations(final long numObserv...
    method getNumMismatches (line 201) | public final double getNumMismatches() {
    method setNumMismatches (line 205) | public final synchronized void setNumMismatches(final double numMismat...
    method incrementNumObservations (line 211) | public final synchronized void incrementNumObservations(final long by) {
    method incrementNumMismatches (line 216) | public final synchronized void incrementNumMismatches(final double by) {
    method increment (line 221) | public final synchronized void increment(final long incObservations, f...
    method increment (line 227) | public final synchronized void increment(final boolean isError) {
    method calcExpectedErrors (line 243) | private double calcExpectedErrors() {
    method calcEmpiricalQuality (line 250) | private synchronized void calcEmpiricalQuality(final double conditiona...
    method bayesianEstimateOfEmpiricalQuality (line 267) | static public double bayesianEstimateOfEmpiricalQuality(final long nOb...
    method log10QempPrior (line 316) | static protected double log10QempPrior(final double Qempirical, final ...
    method log10QempLikelihood (line 325) | static protected double log10QempLikelihood(final double Qempirical, l...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/RecalibrationArgumentCollection.java
  class RecalibrationArgumentCollection (line 39) | public class RecalibrationArgumentCollection {
    method generateReportTable (line 147) | public GATKReportTable generateReportTable(final String covariateNames) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/RecalibrationEngine.java
  class RecalibrationEngine (line 36) | public class RecalibrationEngine {
    method makeAndCaptureTable (line 54) | private synchronized RecalibrationTables makeAndCaptureTable() {
    method initialValue (line 60) | @Override
    method getUpdatableRecalibrationTables (line 78) | protected RecalibrationTables getUpdatableRecalibrationTables() {
    method RecalibrationEngine (line 94) | public RecalibrationEngine(final Covariate[] covariates, final int num...
    method updateDataForRead (line 107) | public void updateDataForRead( final ReadRecalibrationInfo recalInfo ) {
    method finalizeData (line 144) | public void finalizeData() {
    method mergeThreadLocalRecalibrationTables (line 180) | private RecalibrationTables mergeThreadLocalRecalibrationTables() {
    method getFinalRecalibrationTables (line 207) | public RecalibrationTables getFinalRecalibrationTables() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/RecalibrationTables.java
  class RecalibrationTables (line 34) | public final class RecalibrationTables {
    type TableType (line 35) | public enum TableType {
    method RecalibrationTables (line 46) | public RecalibrationTables(final Covariate[] covariates) {
    method RecalibrationTables (line 50) | public RecalibrationTables(final Covariate[] covariates, final int num...
    method getReadGroupTable (line 68) | public NestedIntegerArray<RecalDatum> getReadGroupTable() {
    method getQualityScoreTable (line 72) | public NestedIntegerArray<RecalDatum> getQualityScoreTable() {
    method getTable (line 76) | public NestedIntegerArray<RecalDatum> getTable(final int index) {
    method numTables (line 80) | public int numTables() {
    method isEmpty (line 87) | public boolean isEmpty() {
    method makeQualityScoreTable (line 104) | public NestedIntegerArray<RecalDatum> makeQualityScoreTable() {
    method combine (line 111) | public void combine(final RecalibrationTables toMerge) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/ContextCovariate.java
  class ContextCovariate (line 39) | public class ContextCovariate implements StandardCovariate {
    method initialize (line 57) | @Override
    method recordValues (line 78) | @Override
    method getValue (line 117) | @Override
    method formatKey (line 122) | @Override
    method keyFromValue (line 130) | @Override
    method createMask (line 135) | private static int createMask(final int contextSize) {
    method contextWith (line 151) | private static ArrayList<Integer> contextWith(final byte[] bases, fina...
    method keyFromContext (line 206) | public static int keyFromContext(final String dna) {
    method keyFromContext (line 218) | private static int keyFromContext(final byte[] dna, final int start, f...
    method contextFromKey (line 238) | public static String contextFromKey(final int key) {
    method maximumKeyValue (line 257) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/Covariate.java
  type Covariate (line 35) | public interface Covariate {
    method initialize (line 42) | public void initialize(final RecalibrationArgumentCollection RAC);
    method recordValues (line 50) | public void recordValues(final GATKSAMRecord read, final ReadCovariate...
    method getValue (line 58) | public Object getValue(final String str);
    method formatKey (line 66) | public String formatKey(final int key);
    method keyFromValue (line 77) | public int keyFromValue(final Object value);
    method maximumKeyValue (line 84) | public int maximumKeyValue();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/CycleCovariate.java
  class CycleCovariate (line 36) | public class CycleCovariate implements StandardCovariate {
    method initialize (line 46) | @Override
    method recordValues (line 55) | @Override
    method getValue (line 184) | @Override
    method formatKey (line 189) | @Override
    method keyFromValue (line 197) | @Override
    method maximumKeyValue (line 202) | @Override
    method keyFromCycle (line 207) | private int keyFromCycle(final int cycle) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/ExperimentalCovariate.java
  type ExperimentalCovariate (line 27) | public interface ExperimentalCovariate extends Covariate {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/QualityScoreCovariate.java
  class QualityScoreCovariate (line 32) | public class QualityScoreCovariate implements RequiredCovariate {
    method initialize (line 35) | @Override
    method recordValues (line 38) | @Override
    method getValue (line 50) | @Override
    method formatKey (line 55) | @Override
    method keyFromValue (line 60) | @Override
    method maximumKeyValue (line 65) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/ReadGroupCovariate.java
  class ReadGroupCovariate (line 36) | public class ReadGroupCovariate implements RequiredCovariate {
    method initialize (line 44) | @Override
    method recordValues (line 49) | @Override
    method getValue (line 59) | @Override
    method formatKey (line 64) | @Override
    method keyFromValue (line 71) | @Override
    method getKeyMap (line 80) | public Set<Map.Entry<String, Integer>> getKeyMap() {
    method keyForReadGroup (line 84) | private int keyForReadGroup(final String readGroupId) {
    method maximumKeyValue (line 108) | @Override
    method readGroupValueFromRG (line 120) | private String readGroupValueFromRG(final GATKSAMReadGroupRecord rg) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/RepeatCovariate.java
  class RepeatCovariate (line 39) | public abstract class RepeatCovariate implements ExperimentalCovariate {
    method initialize (line 47) | @Override
    method initialize (line 53) | public void initialize(final int MAX_STR_UNIT_LENGTH, final int MAX_RE...
    method recordValues (line 58) | @Override
    method findTandemRepeatUnits (line 87) | public Pair<byte[], Integer> findTandemRepeatUnits(byte[] readBases, i...
    method getValue (line 150) | @Override
    method formatKey (line 155) | @Override
    method getCovariateValueFromUnitAndLength (line 162) | protected abstract String getCovariateValueFromUnitAndLength(final byt...
    method keyFromValue (line 165) | @Override
    method getKeyMap (line 174) | public Set<Map.Entry<String, Integer>> getKeyMap() {
    method keyForRepeat (line 178) | private int keyForRepeat(final String repeatID) {
    method getRUandNRfromCovariate (line 209) | public static Pair<String,Integer> getRUandNRfromCovariate(final Strin...
    method getBasesFromRUandNR (line 230) | public static String getBasesFromRUandNR(final String repeatUnit, fina...
    method getBasesFromRUandNR (line 240) | public static String  getBasesFromRUandNR(final String covariateValue) {
    method maximumKeyValue (line 245) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/RepeatLengthCovariate.java
  class RepeatLengthCovariate (line 27) | public class RepeatLengthCovariate extends RepeatCovariate {
    method getCovariateValueFromUnitAndLength (line 29) | protected String getCovariateValueFromUnitAndLength(final byte[] repea...
    method maximumKeyValue (line 33) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/RepeatUnitAndLengthCovariate.java
  class RepeatUnitAndLengthCovariate (line 27) | public class RepeatUnitAndLengthCovariate extends RepeatCovariate {
    method getCovariateValueFromUnitAndLength (line 29) | protected String getCovariateValueFromUnitAndLength(final byte[] repea...
    method maximumKeyValue (line 33) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/RepeatUnitCovariate.java
  class RepeatUnitCovariate (line 27) | public class RepeatUnitCovariate extends RepeatCovariate {
    method getCovariateValueFromUnitAndLength (line 29) | protected String getCovariateValueFromUnitAndLength(final byte[] repea...
    method maximumKeyValue (line 35) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/RequiredCovariate.java
  type RequiredCovariate (line 27) | public interface RequiredCovariate extends Covariate {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/baserecalibrator/covariate/StandardCovariate.java
  type StandardCovariate (line 27) | public interface StandardCovariate extends Covariate {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/genotypegvcfs/GenotypeGVCFs.java
  class GenotypeGVCFs (line 73) | public class GenotypeGVCFs extends RODWalker implements AnnotatorCompati...
    method getDbsnpRodBinding (line 83) | public RodBinding<VariantContext> getDbsnpRodBinding() {
    method getCompRodBindings (line 97) | public List<RodBinding<VariantContext>> getCompRodBindings() { return ...
    method getSnpEffRodBinding (line 98) | public RodBinding<VariantContext> getSnpEffRodBinding() { return null; }
    method getResourceRodBindings (line 99) | public List<RodBinding<VariantContext>> getResourceRodBindings() { ret...
    method alwaysAppendDbsnpId (line 100) | public boolean alwaysAppendDbsnpId() { return false; }
    method GenotypeGVCFs (line 104) | public GenotypeGVCFs(GenomeLocParser genomeLocParser,
    method initialize (line 112) | @Override
    method getSamplesListFromContentProvider (line 128) | private SampleList getSamplesListFromContentProvider() {
    method createUAC (line 144) | private UnifiedArgumentCollection createUAC() {
    method getVCInTrackerInLocus (line 150) | private List<VariantContext> getVCInTrackerInLocus(String rodName, fin...
    method map (line 159) | @Override
    method regenotypeVC (line 183) | protected VariantContext regenotypeVC(final RefMetaDataTracker tracker...
    method addGenotypingAnnotations (line 236) | private VariantContext addGenotypingAnnotations(final Map<String, Obje...
    method cleanupGenotypeAnnotations (line 258) | private List<Genotype> cleanupGenotypeAnnotations(final VariantContext...
    method onTraversalDone (line 308) | @Override
    method getResultVcfRecords (line 313) | public List<VariantContext> getResultVcfRecords() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/genotypegvcfs/ReferenceConfidenceVariantContextMerger.java
  class ReferenceConfidenceVariantContextMerger (line 52) | public class ReferenceConfidenceVariantContextMerger {
    method combineAnnotationValues (line 54) | private static Comparable combineAnnotationValues( final List<Comparab...
    method merge (line 68) | public static VariantContext merge(final List<VariantContext> VCs, fin...
    method determineReferenceAlleleGivenReferenceBase (line 167) | private static Allele determineReferenceAlleleGivenReferenceBase(final...
    method removeStaleAttributesAfterMerge (line 182) | private static void removeStaleAttributesAfterMerge(final Map<String, ...
    method addReferenceConfidenceAttributes (line 197) | private static void addReferenceConfidenceAttributes(final Map<String,...
    method remapAlleles (line 236) | private static List<Allele> remapAlleles(final List<Allele> vcAlleles,...
    method replaceWithNoCalls (line 276) | private static List<Allele> replaceWithNoCalls(final List<Allele> alle...
    method mergeRefConfidenceGenotypes (line 294) | private static void mergeRefConfidenceGenotypes(final GenotypesContext...
    method generatePL (line 338) | private static int[] generatePL(final Genotype g, final int[] genotype...
    method getIndexesOfRelevantAlleles (line 355) | protected static int[] getIndexesOfRelevantAlleles(final List<Allele> ...
    method generateAD (line 386) | protected static int[] generateAD(final int[] originalAD, final int[] ...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActiveRegion.java
  class ActiveRegion (line 45) | public class ActiveRegion implements HasGenomeLocation, Serializable {
    method ActiveRegion (line 110) | public ActiveRegion(final GenomeLoc activeRegionLoc, final List<Activi...
    method ActiveRegion (line 145) | public ActiveRegion(final GenomeLoc activeRegionLoc, final GenomeLocPa...
    method toString (line 149) | @Override
    method getActiveRegionReference (line 157) | public byte[] getActiveRegionReference(final RefContentProvider refCon...
    method getActiveRegionReference (line 171) | public byte[] getActiveRegionReference(final RefContentProvider refCon...
    method getFullReference (line 178) | public byte[] getFullReference(final RefContentProvider refContentProv...
    method getFullReference (line 185) | public byte[] getFullReference(final RefContentProvider refContentProv...
    method getReference (line 200) | public byte[] getReference(final RefContentProvider refContentProvider...
    method getLocation (line 219) | @Override
    method getExtendedLoc (line 229) | public GenomeLoc getExtendedLoc() {
    method getReadSpanLoc (line 240) | public GenomeLoc getReadSpanLoc() {
    method getSupportingStates (line 250) | public List<ActivityProfileState> getSupportingStates() {
    method getExtension (line 261) | public int getExtension() {
    method setReads (line 265) | public void setReads(List<GATKSAMRecord> reads) {
    method getReads (line 276) | public List<GATKSAMRecord> getReads() {
    method size (line 285) | public int size() {
    method add (line 297) | public void add(final GATKSAMRecord read) {
    method readOverlapsRegion (line 324) | public boolean readOverlapsRegion(final GATKSAMRecord read) {
    method addAll (line 334) | public void addAll(final Collection<GATKSAMRecord> reads) {
    method clearReads (line 343) | public void clearReads() {
    method removeAll (line 353) | public void removeAll(final Set<GATKSAMRecord> readsToRemove) {
    method equalExceptReads (line 371) | protected boolean equalExceptReads(final ActiveRegion other) {
    method isActive (line 384) | public boolean isActive() {
    method splitAndTrimToIntervals (line 399) | protected List<ActiveRegion> splitAndTrimToIntervals(final GenomeLocSo...
    method trim (line 418) | public ActiveRegion trim(final GenomeLoc span, final int extension) {
    method trim (line 437) | public ActiveRegion trim(final GenomeLoc span) {
    method trim (line 463) | public ActiveRegion trim(final GenomeLoc span, final GenomeLoc extende...
    method setFinalized (line 494) | public void setFinalized(final boolean value) {
    method isFinalized (line 498) | public boolean isFinalized() {
    method getGenomeLocParser (line 502) | public GenomeLocParser getGenomeLocParser() {
    method setGenomeLocParser (line 506) | public void setGenomeLocParser(GenomeLocParser genomeLocParser) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActiveRegionFinder.java
  class ActiveRegionFinder (line 75) | public class ActiveRegionFinder extends LocusWalker {
    method ActiveRegionFinder (line 128) | public ActiveRegionFinder(GenomeLocParser genomeLocParser,
    method setGVCFArg (line 138) | private void setGVCFArg(boolean useGVCF) {
    method initialize (line 144) | @Override
    method getSamplesListFromContentProvider (line 191) | private SampleList getSamplesListFromContentProvider() {
    method emitReferenceConfidence (line 202) | private boolean emitReferenceConfidence() {
    method map (line 213) | @Override
    method getFilter (line 249) | @Override
    method onTraversalDone (line 257) | @Override
    method prepActiveRegionsForProcessing (line 283) | private void prepActiveRegionsForProcessing(final RegionSamTraverser r...
    method prepActiveRegionForProcessing (line 295) | private ActiveRegionMapData prepActiveRegionForProcessing(final Active...
    method getResultActiveRegions (line 311) | public List<ActiveRegionMapData> getResultActiveRegions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActiveRegionMapData.java
  class ActiveRegionMapData (line 32) | public final class ActiveRegionMapData {
    method ActiveRegionMapData (line 38) | public ActiveRegionMapData(ActiveRegion activeRegion, RefMetaDataTrack...
    method ActiveRegionMapData (line 46) | public ActiveRegionMapData(ActiveRegion activeRegion, RefMetaDataTrack...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActiveRegionTrimmer.java
  class ActiveRegionTrimmer (line 39) | class ActiveRegionTrimmer {
    method initialize (line 97) | void initialize(final GenomeLocParser glp, final boolean debug, final ...
    method checkUserArguments (line 114) | private void checkUserArguments() {
    class Result (line 128) | public static class Result {
      method getIdealSpan (line 171) | @SuppressWarnings("unused")
      method getPadding (line 205) | @SuppressWarnings("unused")
      method getUsableExtension (line 232) | @SuppressWarnings("unused")
      method Result (line 281) | protected Result(final boolean emitReferenceConfidence, final boolea...
      method isVariationPresent (line 310) | public boolean isVariationPresent() {
      method needsTrimming (line 317) | public boolean needsTrimming() {
      method getCallableRegion (line 327) | public ActiveRegion getCallableRegion() {
      method hasLeftFlankingRegion (line 343) | public boolean hasLeftFlankingRegion() {
      method hasRightFlankingRegion (line 352) | public boolean hasRightFlankingRegion() {
      method nonVariantLeftFlankRegion (line 363) | public ActiveRegion nonVariantLeftFlankRegion() {
      method nonVariantRightFlankRegion (line 374) | public ActiveRegion nonVariantRightFlankRegion() {
      method noTrimming (line 385) | protected static Result noTrimming(final boolean emitReferenceConfid...
      method noVariation (line 398) | protected static Result noVariation(final boolean emitReferenceConfi...
    method trim (line 417) | public Result trim(final ActiveRegion originalRegion,
    method nonVariantTargetRegions (line 476) | private Pair<GenomeLoc, GenomeLoc> nonVariantTargetRegions(final Activ...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActivityProfile.java
  class ActivityProfile (line 37) | public class ActivityProfile {
    method ActivityProfile (line 62) | public ActivityProfile(final GenomeLocParser parser, final int maxProb...
    method toString (line 72) | @Override
    method getMaxProbPropagationDistance (line 90) | public int getMaxProbPropagationDistance() {
    method size (line 99) | public int size() {
    method isEmpty (line 108) | public boolean isEmpty() {
    method getSpan (line 117) | public GenomeLoc getSpan() {
    method getContigIndex (line 121) | public int getContigIndex() {
    method getStop (line 125) | public int getStop() {
    method getStateList (line 134) | protected List<ActivityProfileState> getStateList() {
    method getProbabilitiesAsArray (line 143) | protected double[] getProbabilitiesAsArray() {
    method getLocForOffset (line 159) | protected GenomeLoc getLocForOffset(final GenomeLoc relativeLoc, final...
    method getCurrentContigLength (line 173) | private int getCurrentContigLength() {
    method add (line 190) | public void add(final ActivityProfileState state) {
    method incorporateSingleState (line 219) | private void incorporateSingleState(final ActivityProfileState stateTo...
    method processState (line 255) | protected Collection<ActivityProfileState> processState(final Activity...
    method popReadyActiveRegions (line 301) | public List<ActiveRegion> popReadyActiveRegions(final int activeRegion...
    method popNextReadyActiveRegion (line 342) | private ActiveRegion popNextReadyActiveRegion(final int activeRegionEx...
    method findEndOfRegion (line 395) | private int findEndOfRegion(final boolean isActiveRegion, final int st...
    method findBestCutSite (line 426) | private int findBestCutSite(final int startSearchIdx, final int endOfA...
    method findFirstActivityBoundary (line 459) | private int findFirstActivityBoundary(final int startSearchIdx, final ...
    method getProb (line 481) | private double getProb(final int index) {
    method isMinimum (line 494) | private boolean isMinimum(final int index) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ActivityProfileState.java
  class ActivityProfileState (line 31) | public class ActivityProfileState implements Serializable {
    type Type (line 37) | public enum Type implements Serializable {
    method ActivityProfileState (line 48) | public ActivityProfileState(final GenomeLoc loc, final double isActive...
    method ActivityProfileState (line 62) | public ActivityProfileState(final GenomeLoc loc, final double isActive...
    method getOffset (line 81) | public int getOffset(final GenomeLoc regionStartLoc) {
    method getLoc (line 91) | public GenomeLoc getLoc() {
    method toString (line 95) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/AlleleList.java
  type AlleleList (line 29) | public interface AlleleList<A extends Allele> {
    method alleleCount (line 31) | public int alleleCount();
    method alleleIndex (line 33) | public int alleleIndex(final A allele);
    method alleleAt (line 35) | public A alleleAt(final int index);

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/AlleleListPermutation.java
  type AlleleListPermutation (line 30) | public interface AlleleListPermutation<A extends Allele> extends Permuta...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/AssemblyResult.java
  class AssemblyResult (line 30) | public class AssemblyResult {
    method AssemblyResult (line 40) | public AssemblyResult(final Status status, final SeqGraph graph) {
    method setThreadingGraph (line 51) | public void setThreadingGraph(final ReadThreadingGraph threadingGraph) {
    method getThreadingGraph (line 55) | public ReadThreadingGraph getThreadingGraph() {
    method getStatus (line 59) | public Status getStatus() { return status; }
    method getGraph (line 60) | public SeqGraph getGraph() { return graph; }
    method getKmerSize (line 62) | public int getKmerSize() {
    type Status (line 70) | public enum Status {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/AssemblyResultSet.java
  class AssemblyResultSet (line 48) | public class AssemblyResultSet {
    method AssemblyResultSet (line 67) | public AssemblyResultSet() {
    method setDebug (line 80) | void setDebug(final boolean newValue) {
    method trimTo (line 93) | public AssemblyResultSet trimTo(final ActiveRegion trimmedActiveRegion) {
    method calculateOriginalByTrimmedHaplotypes (line 118) | private Map<Haplotype, Haplotype> calculateOriginalByTrimmedHaplotypes...
    method getReferenceHaplotype (line 171) | public Haplotype getReferenceHaplotype() {
    method isVariationPresent (line 184) | public boolean isVariationPresent() {
    method debugDump (line 194) | public void debugDump(final PrintWriter pw) {
    method add (line 236) | public boolean add(final Haplotype h) {
    method add (line 261) | public boolean add(final Haplotype h, final AssemblyResult ar) {
    method add (line 295) | public boolean add(final AssemblyResult ar) {
    method getRegionForGenotyping (line 315) | public ActiveRegion getRegionForGenotyping() {
    method setRegionForGenotyping (line 324) | public void setRegionForGenotyping(final ActiveRegion regionForGenotyp...
    method getFullReferenceWithPadding (line 333) | public byte[] getFullReferenceWithPadding() {
    method setFullReferenceWithPadding (line 342) | public void setFullReferenceWithPadding(final byte[] fullReferenceWith...
    method getPaddedReferenceLoc (line 351) | public GenomeLoc getPaddedReferenceLoc() {
    method setPaddedReferenceLoc (line 360) | public void setPaddedReferenceLoc(final GenomeLoc paddedReferenceLoc) {
    method getHaplotypeCount (line 369) | public int getHaplotypeCount() {
    method getHaplotypeList (line 382) | public List<Haplotype> getHaplotypeList() {
    method getMaximumKmerSize (line 392) | public int getMaximumKmerSize() {
    method hasMultipleKmerSizes (line 403) | public boolean hasMultipleKmerSizes() {
    method getMinimumKmerSize (line 413) | public int getMinimumKmerSize() {
    method getUniqueReadThreadingGraph (line 425) | public ReadThreadingGraph getUniqueReadThreadingGraph(final int kmerSi...
    method wasTrimmed (line 436) | public boolean wasTrimmed() {
    method resetVariationPresent (line 443) | public void resetVariationPresent() {
    method debugDump (line 453) | public void debugDump(final Logger logger) {
    method updateReferenceHaplotype (line 482) | private void updateReferenceHaplotype(final Haplotype newHaplotype) {
    method getVariationEvents (line 499) | public TreeSet<VariantContext> getVariationEvents() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/BandPassActivityProfile.java
  class BandPassActivityProfile (line 35) | public class BandPassActivityProfile extends ActivityProfile {
    method BandPassActivityProfile (line 44) | public BandPassActivityProfile(final GenomeLocParser parser, final Gen...
    method BandPassActivityProfile (line 49) | public BandPassActivityProfile(final GenomeLocParser parser, final Gen...
    method BandPassActivityProfile (line 66) | public BandPassActivityProfile(final GenomeLocParser parser, final Gen...
    method determineFilterSize (line 79) | protected static int determineFilterSize(final double[] kernel, final ...
    method makeKernel (line 91) | protected static double[] makeKernel(final int filterSize, final doubl...
    method getMaxProbPropagationDistance (line 108) | @Override
    method getBandSize (line 117) | public int getBandSize() {
    method getFilteredSize (line 125) | public int getFilteredSize() {
    method getSigma (line 133) | public double getSigma() {
    method getKernel (line 141) | protected double[] getKernel() {
    method processState (line 149) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ConsensusAlleleCounter.java
  class ConsensusAlleleCounter (line 52) | public class ConsensusAlleleCounter {
    method ConsensusAlleleCounter (line 58) | public ConsensusAlleleCounter(final boolean doMultiAllelicCalls,
    method computeConsensusAlleles (line 74) | public List<Allele> computeConsensusAlleles(ReferenceContext ref,
    method countConsensusAlleles (line 84) | private Map<String, Integer> countConsensusAlleles(ReferenceContext ref,
    method consensusCountsToAlleles (line 208) | private List<Allele> consensusCountsToAlleles(final ReferenceContext ref,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/DiploidGenotype.java
  type DiploidGenotype (line 29) | public enum DiploidGenotype {
    method DiploidGenotype (line 43) | @Deprecated
    method DiploidGenotype (line 48) | private DiploidGenotype(byte base1, byte base2) {
    method isHomRef (line 53) | public boolean isHomRef(byte r) {
    method isHomVar (line 57) | public boolean isHomVar(byte r) {
    method isHetRef (line 61) | public boolean isHetRef(byte r) {
    method isHom (line 68) | public boolean isHom() {
    method isHet (line 72) | public boolean isHet() {
    method createHomGenotype (line 81) | public static DiploidGenotype createHomGenotype(byte hom) {
    method createDiploidGenotype (line 94) | public static DiploidGenotype createDiploidGenotype(byte base1, byte b...
    method createDiploidGenotype (line 110) | public static DiploidGenotype createDiploidGenotype(int baseIndex1, in...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/DiploidSNPGenotypeLikelihoods.java
  class DiploidSNPGenotypeLikelihoods (line 72) | public class DiploidSNPGenotypeLikelihoods implements Cloneable {
    method DiploidSNPGenotypeLikelihoods (line 97) | public DiploidSNPGenotypeLikelihoods(double PCR_error_rate) {
    method clone (line 108) | protected Object clone() throws CloneNotSupportedException {
    method setToZero (line 114) | protected void setToZero() {
    method getLikelihoods (line 122) | public double[] getLikelihoods() {
    method add (line 145) | public int add(ReadBackedPileup pileup, boolean ignoreBadBases, boolea...
    method add (line 160) | public int add(PileupElement elt, boolean ignoreBadBases, boolean capB...
    method add (line 169) | public int add(List<PileupElement> overlappingPair, boolean ignoreBadB...
    method add (line 198) | private int add(byte obsBase1, byte qual1, byte obsBase2, byte qual2, ...
    method add (line 225) | private int add(byte obsBase1, byte qual1, byte obsBase2, byte qual2) {
    method inCache (line 237) | protected boolean inCache(byte observedBase1, byte qualityScore1, byte...
    method getCachedGenotypeLikelihoods (line 241) | protected DiploidSNPGenotypeLikelihoods getCachedGenotypeLikelihoods(b...
    method calculateCachedGenotypeLikelihoods (line 249) | protected DiploidSNPGenotypeLikelihoods calculateCachedGenotypeLikelih...
    method setCache (line 255) | protected void setCache( DiploidSNPGenotypeLikelihoods[][][][][] cache,
    method getCache (line 267) | protected DiploidSNPGenotypeLikelihoods getCache(DiploidSNPGenotypeLik...
    method calculateGenotypeLikelihoods (line 277) | protected DiploidSNPGenotypeLikelihoods calculateGenotypeLikelihoods(b...
    method computeLog10Likelihoods (line 321) | protected double[] computeLog10Likelihoods(byte observedBase1, byte qu...
    method log10PofObservingBaseGivenChromosome (line 357) | protected double log10PofObservingBaseGivenChromosome(byte observedBas...
    method qualToUse (line 386) | private static byte qualToUse(PileupElement p, boolean ignoreBadBases,...
    method toString (line 415) | public String toString() {
    method validate (line 434) | public boolean validate() {
    method validate (line 438) | public boolean validate(boolean throwException) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ExactACcounts.java
  class ExactACcounts (line 29) | public final class ExactACcounts {
    method ExactACcounts (line 33) | public ExactACcounts(final int[] counts) {
    method getCounts (line 37) | public int[] getCounts() {
    method equals (line 41) | @Override
    method hashCode (line 46) | @Override
    method toString (line 53) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GeneralPloidyGenotypeLikelihoods.java
  class GeneralPloidyGenotypeLikelihoods (line 45) | public abstract class GeneralPloidyGenotypeLikelihoods {
    method GeneralPloidyGenotypeLikelihoods (line 75) | public GeneralPloidyGenotypeLikelihoods(final List<Allele> alleles, fi...
    class SumIterator (line 131) | public static class SumIterator {
      method SumIterator (line 147) | public SumIterator(final int[] finalState,final int restrictSumTo) {
      method SumIterator (line 162) | public SumIterator(final int numAlleles, final int numChromosomes) {
      method getInitialStateVector (line 167) | private static int[] getInitialStateVector(final int nAlleles, final...
      method setInitialStateVector (line 173) | public void setInitialStateVector(final int[] stateVector) {
      method next (line 188) | public void next() {
      method next (line 195) | private boolean next(final int[] finalState, int initialDim) {
      method reset (line 222) | public void reset() {
      method getCurrentVector (line 230) | public int[] getCurrentVector() {
      method getCurrentAltVector (line 234) | public int[] getCurrentAltVector() {
      method getLinearIndex (line 241) | public int getLinearIndex() {
      method hasNext (line 245) | public boolean hasNext() {
    method getAlleles (line 250) | public List<Allele> getAlleles() { return alleles;}
    method getLikelihoods (line 257) | public double[] getLikelihoods() {
    method setLogPLs (line 268) | public void setLogPLs(final int idx, final double pl) {
    method renormalize (line 272) | public void renormalize() {
    method getMostLikelyACCount (line 279) | public Pair<int[],Double> getMostLikelyACCount() {
    method subsetToAlleles (line 311) | public static double[] subsetToAlleles(final double[] oldLikelihoods, ...
    method getLinearIndex (line 376) | public static int getLinearIndex(int[] vectorIdx, int numAlleles, int ...
    method getAlleleCountFromPLIndex (line 405) | public static int[] getAlleleCountFromPLIndex(final int nAlleles, fina...
    method getNumLikelihoodElements (line 416) | public static int getNumLikelihoodElements(int numAlleles, int ploidy) {
    method fillGLVectorSizeCache (line 422) | private static int[][] fillGLVectorSizeCache(int maxAlleles, int maxPl...
    method toString (line 449) | public String toString() {
    method computeLikelihoods (line 477) | public void computeLikelihoods(ErrorModel errorModel,
    method calculateACConformationAndUpdateQueue (line 537) | private double calculateACConformationAndUpdateQueue(final ExactACset ...
    method getLikelihoodOfConformation (line 594) | public abstract void getLikelihoodOfConformation(final ExactACset ACset,
    method add (line 601) | public abstract int add(ReadBackedPileup pileup, UnifiedArgumentCollec...
    method updateACset (line 604) | public static void updateACset(final int[] newSetCounts,
    method fillCache (line 637) | private void fillCache() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypeAlleleCounts.java
  class GenotypeAlleleCounts (line 79) | public class GenotypeAlleleCounts implements Comparable<GenotypeAlleleCo...
    method GenotypeAlleleCounts (line 128) | private GenotypeAlleleCounts(final int ploidy, final int index, final ...
    method log10CombinationCount (line 140) | public double log10CombinationCount() {
    method calculateLog10CombinationCount (line 152) | private double calculateLog10CombinationCount() {
    method ploidy (line 167) | public int ploidy() {
    method increase (line 183) | protected void increase(final int times) {
    method increase (line 196) | protected void increase() {
    method next (line 266) | protected GenotypeAlleleCounts next() {
    method distinctAlleleCount (line 328) | public int distinctAlleleCount() {
    method alleleIndexAt (line 341) | public int alleleIndexAt(final int rank) {
    method alleleRankFor (line 359) | public int alleleRankFor(final int index) {
    method toUnphasedGenotypeString (line 383) | public String toUnphasedGenotypeString() {
    method toString (line 397) | @Override
    method equals (line 407) | @Override
    method equals (line 420) | public boolean equals(final GenotypeAlleleCounts o) {
    method index (line 435) | public int index() {
    method compareTo (line 452) | @Override
    method hashCode (line 464) | @Override
    method alleleIndexToRank (line 477) | private int alleleIndexToRank(final int index,final int from, final in...
    method alleleCountAt (line 504) | public int alleleCountAt(final int rank) {
    method containsAllele (line 519) | public boolean containsAllele(final int index) {
    method alleleCountFor (line 528) | public int alleleCountFor(final int index) {
    method alleleCountsByIndex (line 540) | public int[] alleleCountsByIndex(final int maximumAlleleIndex) {
    method copyAlleleCountsByIndex (line 549) | private void copyAlleleCountsByIndex(final int[] dest, final int offse...
    method copyAlleleCounts (line 610) | public void copyAlleleCounts(final int[] dest, final int offset) {
    method first (line 629) | protected static GenotypeAlleleCounts first(final int ploidy) {
    method makeNextGenotype (line 647) | public static GenotypeAlleleCounts makeNextGenotype(final GenotypeAlle...
    method maximumAlleleIndex (line 658) | public int maximumAlleleIndex() {
    method minimumAlleleIndex (line 670) | public int minimumAlleleIndex() {
    method clone (line 681) | @Override
    method asAlleleList (line 703) | public <T extends Allele> List<T> asAlleleList(final List<T> allelesTo...
    method toAlleleIndicesArray (line 747) | public int[] toAlleleIndicesArray(final int[] dest) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypeLikelihoodCalculator.java
  class GenotypeLikelihoodCalculator (line 33) | public class GenotypeLikelihoodCalculator {
    method GenotypeLikelihoodCalculator (line 168) | protected GenotypeLikelihoodCalculator(final int ploidy, final int all...
    method ensureReadCapacity (line 193) | public void ensureReadCapacity(final int requestedCapacity) {
    method allelesToIndex (line 224) | public int allelesToIndex(final int... alleleIndices) {
    method genotypeCount (line 237) | public int genotypeCount()  {
    method genotypeAlleleCountsAt (line 255) | public GenotypeAlleleCounts genotypeAlleleCountsAt(final int index) {
    method genotypeLikelihoods (line 285) | public <A extends Allele> GenotypeLikelihoods genotypeLikelihoods(fina...
    method genotypeLikelihoods (line 314) | private double[] genotypeLikelihoods(final double[][] readLikelihoodsB...
    method genotypeLikelihoodByRead (line 336) | private double[][] genotypeLikelihoodByRead(final double[] readLikelih...
    method nextGenotypeAlleleCounts (line 361) | private GenotypeAlleleCounts nextGenotypeAlleleCounts(final GenotypeAl...
    method manyComponentGenotypeLikelihoodByRead (line 381) | private void manyComponentGenotypeLikelihoodByRead(final GenotypeAllel...
    method twoComponentGenotypeLikelihoodByRead (line 409) | private void twoComponentGenotypeLikelihoodByRead(final GenotypeAllele...
    method singleComponentGenotypeLikelihoodByRead (line 430) | private void singleComponentGenotypeLikelihoodByRead(final GenotypeAll...
    method readLikelihoodComponentsByAlleleCount (line 449) | private <A extends Allele> double[] readLikelihoodComponentsByAlleleCo...
    method ploidy (line 473) | public int ploidy() {
    method alleleCount (line 481) | public int alleleCount() {
    method alleleCountsToIndex (line 502) | public int alleleCountsToIndex(final int ... alleleCountArray) {
    method alleleHeapToIndex (line 528) | private int alleleHeapToIndex() {
    method genotypeIndexMap (line 555) | public int[] genotypeIndexMap(final int[] oldToNewAlleleIndexMap) {
    method genotypeIndexMapPerGenotypeIndex (line 587) | private void genotypeIndexMapPerGenotypeIndex(final int newGenotypeInd...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypeLikelihoodCalculators.java
  class GenotypeLikelihoodCalculators (line 29) | public class GenotypeLikelihoodCalculators {
    method buildAlleleFirstGenotypeOffsetTable (line 153) | private static int[][] buildAlleleFirstGenotypeOffsetTable(final int m...
    method buildGenotypeAlleleCountsTable (line 195) | private static GenotypeAlleleCounts[][] buildGenotypeAlleleCountsTable...
    method buildGenotypeAlleleCountsArray (line 237) | private static GenotypeAlleleCounts[] buildGenotypeAlleleCountsArray(f...
    method getInstance (line 274) | public static GenotypeLikelihoodCalculator getInstance(final int ploidy,
    method ensureCapacity (line 297) | private synchronized static void ensureCapacity(final int requestedMax...
    method ploidyLog10Extension (line 334) | private static double[] ploidyLog10Extension(final int newMaximumPloid...
    method checkPloidyAndMaximumAllele (line 353) | private static void checkPloidyAndMaximumAllele(final int ploidy, fina...
    method checkOffsetTableCapacity (line 360) | private static void checkOffsetTableCapacity(final int[][] offsetTable...
    method genotypeCount (line 381) | public final static int genotypeCount(final int ploidy, final int alle...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypingData.java
  class GenotypingData (line 31) | public class GenotypingData<A extends Allele> implements SampleList, All...
    method GenotypingData (line 48) | public GenotypingData(final PloidyModel ploidyModel, final ReadLikelih...
    method ploidyModel (line 63) | public PloidyModel ploidyModel() {
    method sampleCount (line 67) | @Override
    method sampleIndex (line 72) | @Override
    method sampleAt (line 77) | @Override
    method readLikelihoods (line 86) | public ReadLikelihoods<A> readLikelihoods() {
    method alleleCount (line 90) | @Override
    method alleleIndex (line 95) | @Override
    method alleleAt (line 100) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypingLikelihoods.java
  class GenotypingLikelihoods (line 32) | public class GenotypingLikelihoods<A extends Allele> implements SampleLi...
    method GenotypingLikelihoods (line 55) | public GenotypingLikelihoods(final AlleleList<A> alleles, final Ploidy...
    method sampleCount (line 75) | @Override
    method sampleIndex (line 80) | @Override
    method sampleAt (line 85) | @Override
    method samplePloidy (line 100) | public int samplePloidy(final int sampleIndex) {
    method sampleLikelihoods (line 114) | public GenotypeLikelihoods sampleLikelihoods(final int sampleIndex) {
    method alleleCount (line 118) | @Override
    method alleleIndex (line 123) | @Override
    method alleleAt (line 128) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/GenotypingOutputMode.java
  type GenotypingOutputMode (line 27) | public enum GenotypingOutputMode {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/HaplotypeCaller.java
  class HaplotypeCaller (line 82) | public class HaplotypeCaller implements AnnotatorCompatible {
    method getDbsnpRodBinding (line 114) | public RodBinding<VariantContext> getDbsnpRodBinding() {
    method getCompRodBindings (line 125) | public List<RodBinding<VariantContext>> getCompRodBindings() {
    method getSnpEffRodBinding (line 130) | public RodBinding<VariantContext> getSnpEffRodBinding() {
    method getResourceRodBindings (line 134) | public List<RodBinding<VariantContext>> getResourceRodBindings() {
    method alwaysAppendDbsnpId (line 138) | public boolean alwaysAppendDbsnpId() {
    method HaplotypeCaller (line 402) | public HaplotypeCaller(GenomeLocParser genomeLocParser,
    method initialize (line 412) | protected void initialize() {
    method createLikelihoodCalculationEngine (line 480) | private ReadLikelihoodCalculationEngine createLikelihoodCalculationEng...
    method setGVCFArg (line 491) | private void setGVCFArg(boolean useGVCF) {
    method map (line 497) | public List<VariantContext> map(ActiveRegionMapData activeRegionMapDat...
    method getTrimedRefBases (line 638) | private byte[] getTrimedRefBases(ActiveRegion originalRegion, ActiveRe...
    method realignReadsToTheirBestHaplotype (line 657) | private Map<GATKSAMRecord, GATKSAMRecord> realignReadsToTheirBestHaplo...
    method containsCalls (line 672) | private boolean containsCalls(final HaplotypeCallerGenotypingEngine.Ca...
    method referenceModelForNoVariation (line 690) | private List<VariantContext> referenceModelForNoVariation(final Active...
    method assembleReads (line 717) | protected AssemblyResultSet assembleReads(final ActiveRegion activeReg...
    method createReferenceHaplotype (line 744) | private Haplotype createReferenceHaplotype(final ActiveRegion activeRe...
    method createDummyStratifiedReadMap (line 756) | public static ReadLikelihoods<Haplotype> createDummyStratifiedReadMap(...
    method finalizeActiveRegion (line 764) | private void finalizeActiveRegion(final ActiveRegion activeRegion) {
    method filterNonPassingReads (line 810) | private Set<GATKSAMRecord> filterNonPassingReads(final ActiveRegion ac...
    method getPaddedLoc (line 821) | private GenomeLoc getPaddedLoc(final ActiveRegion activeRegion) {
    method splitReadsBySample (line 828) | private Map<String, List<GATKSAMRecord>> splitReadsBySample(final Coll...
    method splitReadsBySample (line 832) | private static Map<String, List<GATKSAMRecord>> splitReadsBySample(fin...
    method emitReferenceConfidence (line 849) | private boolean emitReferenceConfidence() {
    method cleanOverlappingReadPairs (line 858) | private void cleanOverlappingReadPairs(final List<GATKSAMRecord> reads) {
    method addAllIntoWriter (line 866) | private void addAllIntoWriter(List<VariantContext> variantContexts,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/HaplotypeSizeAndBaseComparator.java
  class HaplotypeSizeAndBaseComparator (line 31) | public class HaplotypeSizeAndBaseComparator implements Comparator<Haplot...
    method compare (line 32) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/HeterogeneousKmerSizeResolution.java
  type HeterogeneousKmerSizeResolution (line 27) | public enum HeterogeneousKmerSizeResolution {
    method useMaximum (line 55) | public boolean useMaximum() {
    method useMinimum (line 68) | @SuppressWarnings("unused")
    method combinesKmerSizes (line 77) | public boolean combinesKmerSizes() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/IndexedAlleleList.java
  class IndexedAlleleList (line 35) | public class IndexedAlleleList<A extends Allele> implements AlleleList<A> {
    method IndexedAlleleList (line 42) | public IndexedAlleleList() {
    method IndexedAlleleList (line 58) | public IndexedAlleleList(final A ... alleles) {
    method IndexedAlleleList (line 74) | public IndexedAlleleList(final Collection<A> alleles) {
    method alleleCount (line 78) | @Override
    method alleleIndex (line 83) | @Override
    method alleleAt (line 88) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/IndexedSampleList.java
  class IndexedSampleList (line 31) | public class IndexedSampleList implements SampleList {
    method IndexedSampleList (line 38) | public IndexedSampleList() {
    method IndexedSampleList (line 55) | public IndexedSampleList(final Collection<String> samples) {
    method IndexedSampleList (line 72) | public IndexedSampleList(final String ... samples) {
    method sampleCount (line 76) | @Override
    method sampleIndex (line 81) | @Override
    method sampleAt (line 86) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/MostLikelyAllele.java
  class MostLikelyAllele (line 30) | public final class MostLikelyAllele {
    method MostLikelyAllele (line 49) | public MostLikelyAllele(final Allele mostLikely, final Allele secondMo...
    method getMostLikelyAllele (line 64) | public Allele getMostLikelyAllele() {
    method getSecondMostLikelyAllele (line 68) | public Allele getSecondMostLikelyAllele() {
    method getLog10LikelihoodOfMostLikely (line 72) | public double getLog10LikelihoodOfMostLikely() {
    method getLog10LikelihoodOfSecondBest (line 76) | public double getLog10LikelihoodOfSecondBest() {
    method isInformative (line 83) | public boolean isInformative() {
    method isInformative (line 95) | public boolean isInformative(final double log10ThresholdForInformative) {
    method getAlleleIfInformative (line 102) | public Allele getAlleleIfInformative() {
    method getAlleleIfInformative (line 112) | public Allele getAlleleIfInformative(final double log10ThresholdForInf...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/OutputMode.java
  type OutputMode (line 27) | public enum OutputMode {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/PerReadAlleleLikelihoodMap.java
  class PerReadAlleleLikelihoodMap (line 48) | public class PerReadAlleleLikelihoodMap {
    method PerReadAlleleLikelihoodMap (line 56) | public PerReadAlleleLikelihoodMap() { }
    method add (line 64) | public void add(final GATKSAMRecord read, final Allele a, final Double...
    method getAlleleStratifiedReadMap (line 91) | protected Map<Allele,List<GATKSAMRecord>> getAlleleStratifiedReadMap() {
    method size (line 105) | public int size() {
    method add (line 115) | public void add(PileupElement p, Allele a, Double likelihood) {
    method containsPileupElement (line 131) | public boolean containsPileupElement(final PileupElement p) {
    method isEmpty (line 135) | public boolean isEmpty() {
    method getLikelihoodReadMap (line 139) | public Map<GATKSAMRecord,Map<Allele,Double>> getLikelihoodReadMap() {
    method clear (line 143) | public void clear() {
    method getStoredElements (line 149) | public Set<GATKSAMRecord> getStoredElements() {
    method getNumberOfStoredElements (line 157) | public int getNumberOfStoredElements() {
    method getLikelihoodsAssociatedWithPileupElement (line 161) | public Map<Allele,Double> getLikelihoodsAssociatedWithPileupElement(fi...
    method getLikelihoodAssociatedWithReadAndAllele (line 176) | public double getLikelihoodAssociatedWithReadAndAllele(final GATKSAMRe...
    method getMostLikelyDiploidAlleles (line 195) | public MostLikelyAllele getMostLikelyDiploidAlleles() {
    method getMostLikelyAllele (line 238) | public static MostLikelyAllele getMostLikelyAllele( final Map<Allele,D...
    method getMostLikelyAllele (line 251) | public static MostLikelyAllele getMostLikelyAllele( final Map<Allele,D...
    method toString (line 279) | public String toString() {
    method filterPoorlyModelledReads (line 306) | public List<GATKSAMRecord> filterPoorlyModelledReads(final double maxE...
    method readIsPoorlyModelled (line 341) | protected boolean readIsPoorlyModelled(final GATKSAMRecord read, final...
    method getAllelesSet (line 357) | public Set<Allele> getAllelesSet() {
    method realignReadsToMostLikelyHaplotype (line 366) | public void realignReadsToMostLikelyHaplotype(final Collection<Haploty...
    method performPerAlleleDownsampling (line 389) | public void performPerAlleleDownsampling(final double downsamplingFrac...
    method createPerAlleleDownsampledBasePileup (line 407) | public ReadBackedPileup createPerAlleleDownsampledBasePileup(final Rea...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/PloidyModel.java
  type PloidyModel (line 27) | public interface PloidyModel extends SampleList {
    method samplePloidy (line 35) | public int samplePloidy(final int sampleIndex);
    method isHomogeneous (line 42) | public boolean isHomogeneous();
    method totalPloidy (line 52) | public int totalPloidy();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/ReadErrorCorrector.java
  class ReadErrorCorrector (line 42) | public class ReadErrorCorrector {
    method ReadErrorCorrector (line 80) | public ReadErrorCorrector(final int kmerLength,
    method ReadErrorCorrector (line 118) | public ReadErrorCorrector(final int kmerLength, final byte minTailQual...
    method addReadKmers (line 127) | protected void addReadKmers(final GATKSAMRecord read) {
    method correctReads (line 143) | public final List<GATKSAMRecord> correctReads(final Collection<GATKSAM...
    method correctRead (line 178) | private GATKSAMRecord correctRead(final GATKSAMRecord inputRead) {
    method buildCorrectionMap (line 232) | private CorrectionSet buildCorrectionMap(final byte[] correctedBases) {
    method addReadsToKmers (line 261) | public void addReadsToKmers(final Collection<GATKSAMRecord> reads) {
    method computeKmerCorrectionMap (line 278) | private void computeKmerCorrectionMap() {
    method findNearestNeighbor (line 313) | private Pair<Kmer, Pair<int[], byte[]>> findNearestNeighbor(final Kmer...
    method computeMaxHLen (line 351) | private static int computeMaxHLen(final byte[] fullReferenceWithPaddin...
    class ReadErrorCorrectionStats (line 368) | private static final class ReadErrorCorrectionStats {
    class CorrectionSet (line 389) | protected static class CorrectionSet {
      method CorrectionSet (line 398) | public CorrectionSet(final int size) {
      method add (line 411) | public void add(final int offset, final byte base) {
      method get (line 427) | public List<Byte> get(final int offset) {
      method getConsensusCorrection (line 440) | public Byte getConsensusCorrection(final int offset) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/SampleList.java
  type SampleList (line 27) | public interface SampleList  {
    method sampleCount (line 29) | public int sampleCount();
    method sampleIndex (line 31) | public int sampleIndex(final String sample);
    method sampleAt (line 33) | public String sampleAt(final int sampleIndex);

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/AFCalculationResult.java
  class AFCalculationResult (line 37) | public class AFCalculationResult {
    method AFCalculationResult (line 63) | public AFCalculationResult(final int[] alleleCountsOfMLE,
    method withNewPriors (line 97) | public AFCalculationResult withNewPriors(final double[] log10PriorsOfA...
    method getAlleleCountsOfMLE (line 111) | public int[] getAlleleCountsOfMLE() {
    method getAlleleCountAtMLE (line 122) | public int getAlleleCountAtMLE(final Allele allele) {
    method getnEvaluations (line 131) | public int getnEvaluations() {
    method getAllelesUsedInGenotyping (line 143) | public List<Allele> getAllelesUsedInGenotyping() {
    method getLog10PosteriorOfAFEq0 (line 152) | public double getLog10PosteriorOfAFEq0() {
    method getLog10PosteriorOfAFGT0 (line 161) | public double getLog10PosteriorOfAFGT0() {
    method getLog10LikelihoodOfAFEq0 (line 170) | public double getLog10LikelihoodOfAFEq0() {
    method getLog10LikelihoodOfAFGT0 (line 179) | public double getLog10LikelihoodOfAFGT0() {
    method getLog10PriorOfAFEq0 (line 188) | public double getLog10PriorOfAFEq0() {
    method getLog10PriorOfAFGT0 (line 197) | public double getLog10PriorOfAFGT0() {
    method toString (line 201) | @Override
    method isPolymorphic (line 224) | public boolean isPolymorphic(final Allele allele, final double log10mi...
    method isPolymorphicPhredScaledQual (line 231) | public boolean isPolymorphicPhredScaledQual(final Allele allele, final...
    method anyPolymorphic (line 243) | public boolean anyPolymorphic(final double log10minPNonRef) {
    method getLog10PosteriorOfAFEq0ForAllele (line 271) | public double getLog10PosteriorOfAFEq0ForAllele(final Allele allele) {
    method computePosteriors (line 285) | private static double[] computePosteriors(final double[] log10Likeliho...
    method altAlleleIndex (line 303) | private int altAlleleIndex(final Allele allele) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/AFCalculator.java
  class AFCalculator (line 34) | public abstract class AFCalculator implements Cloneable {
    method AFCalculator (line 51) | protected AFCalculator() {
    method setLogger (line 59) | public void setLogger(Logger logger) {
    method getLog10PNonRef (line 71) | public AFCalculationResult getLog10PNonRef(final VariantContext vc, fi...
    method getResultFromFinalState (line 94) | protected AFCalculationResult getResultFromFinalState(final VariantCon...
    method reduceScope (line 116) | protected abstract VariantContext reduceScope(final VariantContext vc,...
    method computeLog10PNonRef (line 126) | protected abstract AFCalculationResult computeLog10PNonRef(final Varia...
    method subsetAlleles (line 140) | public abstract GenotypesContext subsetAlleles(final VariantContext vc,
    method getStateTracker (line 166) | protected StateTracker getStateTracker(final boolean reset, final int ...
    method getAltAlleleCountOfMAP (line 183) | @Deprecated

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/AFCalculatorImplementation.java
  type AFCalculatorImplementation (line 32) | public enum AFCalculatorImplementation {
    method AFCalculatorImplementation (line 92) | AFCalculatorImplementation(final Class<? extends AFCalculator> clazz, ...
    method AFCalculatorImplementation (line 103) | AFCalculatorImplementation(final Class<? extends AFCalculator> clazz) {
    method AFCalculatorImplementation (line 111) | AFCalculatorImplementation(final Class<? extends AFCalculator> clazz, ...
    method usableForParams (line 121) | public boolean usableForParams(final int requestedPloidy, final int re...
    method findInstantiationConstructor (line 131) | private Constructor<? extends AFCalculator> findInstantiationConstruct...
    method newInstance (line 154) | public AFCalculator newInstance() {
    method bestValue (line 170) | public static AFCalculatorImplementation bestValue(final int requiredP...
    method fromCalculatorClass (line 191) | public static AFCalculatorImplementation fromCalculatorClass(final Cla...
    method buildCalculatorClassToValueMap (line 201) | private static Map<Class<? extends AFCalculator>, AFCalculatorImplemen...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/AFCalculatorProvider.java
  class AFCalculatorProvider (line 36) | public abstract class AFCalculatorProvider {
    method getInstance (line 44) | public AFCalculator getInstance(final VariantContext variantContext, f...
    method getInstance (line 75) | public abstract AFCalculator getInstance(final int ploidy, final int m...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/DiploidExactAFCalculator.java
  class DiploidExactAFCalculator (line 41) | public abstract class DiploidExactAFCalculator extends ExactAFCalculator {
    method DiploidExactAFCalculator (line 45) | public DiploidExactAFCalculator() {
    method computeLog10PNonRef (line 48) | @Override
    method reduceScopeGenotypes (line 88) | @Override
    method reduceScopeCalculateLikelihoodSums (line 93) | @Override
    class DependentSet (line 111) | private static final class DependentSet {
      method DependentSet (line 115) | public DependentSet(final int[] ACcounts, final int PLindex) {
    method calculateAlleleCountConformation (line 121) | private double calculateAlleleCountConformation(final ExactACset set,
    method updateACset (line 192) | private void updateACset(final int[] newSetCounts,
    method computeLofK (line 212) | private void computeLofK(final ExactACset set,
    method pushData (line 259) | private void pushData(final ExactACset targetSet,
    method determineCoefficient (line 276) | private double determineCoefficient(int PLindex, final int j, final in...
    method subsetAlleles (line 311) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/ExactACset.java
  class ExactACset (line 32) | public final class ExactACset {
    method ExactACset (line 41) | public ExactACset(final int size, final ExactACcounts ACcounts) {
    method getACsum (line 50) | public int getACsum() {
    method equals (line 56) | public boolean equals(Object obj) {
    method getACcounts (line 60) | public ExactACcounts getACcounts() {
    method getLog10Likelihoods (line 64) | public double[] getLog10Likelihoods() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/ExactAFCalculator.java
  class ExactAFCalculator (line 42) | abstract class ExactAFCalculator extends AFCalculator {
    method compare (line 50) | @Override
    method compare (line 60) | @Override
    method compare (line 75) | @Override
    method ExactAFCalculator (line 81) | protected ExactAFCalculator() {
    class LikelihoodSum (line 88) | protected static final class LikelihoodSum implements Comparable<Likel...
      method LikelihoodSum (line 93) | public LikelihoodSum(final Allele allele, final int index) { this.al...
      method compareTo (line 95) | public int compareTo(LikelihoodSum other) {
    method getGLs (line 106) | protected static ArrayList<double[]> getGLs(final GenotypesContext GLs...
    method reduceScope (line 122) | @Override
    method reduceScopeAlleles (line 158) | protected List<Allele> reduceScopeAlleles(final VariantContext vc, fin...
    method reduceScopeCalculateLikelihoodSums (line 215) | protected abstract void reduceScopeCalculateLikelihoodSums(final Varia...
    method reduceScopeGenotypes (line 224) | protected abstract GenotypesContext reduceScopeGenotypes(final Variant...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/FixedAFCalculatorProvider.java
  class FixedAFCalculatorProvider (line 32) | public class FixedAFCalculatorProvider extends AFCalculatorProvider {
    method FixedAFCalculatorProvider (line 53) | public FixedAFCalculatorProvider(final StandardCallerArgumentCollectio...
    method FixedAFCalculatorProvider (line 71) | public FixedAFCalculatorProvider(final GenotypeCalculationArgumentColl...
    method FixedAFCalculatorProvider (line 88) | public FixedAFCalculatorProvider(final AFCalculatorImplementation pref...
    method getInstance (line 107) | @Override
    method getInstance (line 115) | @Override
    method createThreadSafeProvider (line 135) | public static AFCalculatorProvider createThreadSafeProvider(final Stan...
    method createThreadSafeProvider (line 152) | @SuppressWarnings("unused")

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/GeneralPloidyExactAFCalculator.java
  class GeneralPloidyExactAFCalculator (line 47) | public class GeneralPloidyExactAFCalculator extends ExactAFCalculator {
    method GeneralPloidyExactAFCalculator (line 54) | protected GeneralPloidyExactAFCalculator() {
    method reduceScopeGenotypes (line 57) | @Override
    method computeLog10PNonRef (line 62) | @Override
    class CombinedPoolLikelihoods (line 72) | static class CombinedPoolLikelihoods {
      method CombinedPoolLikelihoods (line 78) | public CombinedPoolLikelihoods() {
      method add (line 85) | public void add(ExactACset set) {
      method hasConformation (line 95) | public boolean hasConformation(int[] ac) {
      method getLikelihoodOfConformation (line 100) | public double getLikelihoodOfConformation(int[] ac) {
      method getGLOfACZero (line 104) | public double getGLOfACZero() {
      method getLength (line 108) | public int getLength() {
    method reduceScopeCalculateLikelihoodSums (line 114) | @Override
    method combineSinglePools (line 146) | protected void combineSinglePools(final GenotypesContext GLs,
    method fastCombineMultiallelicPool (line 182) | private CombinedPoolLikelihoods fastCombineMultiallelicPool(final Comb...
    method calculateACConformationAndUpdateQueue (line 235) | private double calculateACConformationAndUpdateQueue(final ExactACset ...
    method computeLofK (line 295) | private double computeLofK(final ExactACset set,
    method isValidConformation (line 381) | private static boolean isValidConformation(final int[] set, final int ...
    method subsetAlleles (line 404) | public GenotypesContext subsetAlleles(final VariantContext vc, final i...
    method assignGenotype (line 477) | private void assignGenotype(final GenotypeBuilder gb,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/GeneralPloidyFailOverAFCalculatorProvider.java
  class GeneralPloidyFailOverAFCalculatorProvider (line 30) | public class GeneralPloidyFailOverAFCalculatorProvider extends AFCalcula...
    method GeneralPloidyFailOverAFCalculatorProvider (line 43) | public GeneralPloidyFailOverAFCalculatorProvider(final GenotypeCalcula...
    method getInstance (line 59) | @Override
    method createThreadSafeProvider (line 76) | public static AFCalculatorProvider createThreadSafeProvider(final Geno...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/IndependentAllelesDiploidExactAFCalculator.java
  class IndependentAllelesDiploidExactAFCalculator (line 96) | public class IndependentAllelesDiploidExactAFCalculator extends DiploidE...
    class CompareAFCalculatorResultsByPNonRef (line 111) | private final static class CompareAFCalculatorResultsByPNonRef impleme...
      method compare (line 112) | @Override
    method IndependentAllelesDiploidExactAFCalculator (line 125) | protected IndependentAllelesDiploidExactAFCalculator() {
    class MyAFCalculationResult (line 133) | private static class MyAFCalculationResult extends AFCalculationResult {
      method MyAFCalculationResult (line 139) | private MyAFCalculationResult(int[] alleleCountsOfMLE, int nEvaluati...
    method computeLog10PNonRef (line 145) | @Override
    method combineAltAlleleIndependentExact (line 164) | private AFCalculationResult combineAltAlleleIndependentExact(final Var...
    method makeCombinedAltAllelesVariantContext (line 170) | private VariantContext makeCombinedAltAllelesVariantContext(final Vari...
    method computeAlleleIndependentExact (line 216) | protected final List<AFCalculationResult> computeAlleleIndependentExac...
    method goodIndependentResult (line 231) | private static boolean goodIndependentResult(final VariantContext vc, ...
    method makeAlleleConditionalContexts (line 249) | protected final List<VariantContext> makeAlleleConditionalContexts(fin...
    method biallelicCombinedGLs (line 274) | protected final VariantContext biallelicCombinedGLs(final VariantConte...
    method combineGLs (line 311) | @Deprecated
    method combineGLsPrecise (line 376) | protected Genotype combineGLsPrecise(final Genotype original, final in...
    method applyMultiAllelicPriors (line 414) | protected final List<AFCalculationResult> applyMultiAllelicPriors(fina...
    method combineIndependentPNonRefs (line 451) | protected AFCalculationResult combineIndependentPNonRefs(final Variant...
    method combineAltAlleleLikelihoods (line 485) | private boolean combineAltAlleleLikelihoods(final Genotype g, final in...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/OriginalDiploidExactAFCalculator.java
  class OriginalDiploidExactAFCalculator (line 36) | class OriginalDiploidExactAFCalculator extends DiploidExactAFCalculator {
    method OriginalDiploidExactAFCalculator (line 37) | protected OriginalDiploidExactAFCalculator() {
    method computeLog10PNonRef (line 40) | @Override
    class ExactACCache (line 70) | private final static class ExactACCache {
      method create (line 73) | private static double[] create(int n) {
      method ExactACCache (line 77) | public ExactACCache(int n) {
      method rotate (line 83) | final public void rotate() {
      method getkMinus2 (line 90) | final public double[] getkMinus2() {
      method getkMinus1 (line 94) | final public double[] getkMinus1() {
      method getkMinus0 (line 98) | final public double[] getkMinus0() {
    method linearExact (line 103) | private Pair<Integer, Integer> linearExact(final VariantContext vc,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/ReferenceDiploidExactAFCalculator.java
  class ReferenceDiploidExactAFCalculator (line 27) | public class ReferenceDiploidExactAFCalculator extends DiploidExactAFCal...
    method ReferenceDiploidExactAFCalculator (line 28) | protected ReferenceDiploidExactAFCalculator() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/afcalculate/StateTracker.java
  class StateTracker (line 48) | final class StateTracker {
    method StateTracker (line 104) | public StateTracker(final int maxAltAlleles) {
    method tooLowLikelihood (line 120) | private boolean tooLowLikelihood(final double log10LofK) {
    method isLowerAC (line 127) | private boolean isLowerAC(final ExactACcounts otherACs, final boolean ...
    method abort (line 148) | protected boolean abort(final double log10LofK, final ExactACcounts AC...
    method getAlleleCountsOfMAP (line 152) | protected int[] getAlleleCountsOfMAP() {
    method getNEvaluations (line 156) | protected int getNEvaluations() {
    method getLog10LikelihoodOfAFNotZero (line 163) | private double getLog10LikelihoodOfAFNotZero() {
    method getLog10LikelihoodOfAFzero (line 176) | private double getLog10LikelihoodOfAFzero() {
    method toAFCalculationResult (line 191) | protected AFCalculationResult toAFCalculationResult(final double[] log...
    method reset (line 220) | protected void reset(final int ensureAltAlleleCapacity) {
    method reset (line 242) | protected void reset() {
    method incNEvaluations (line 257) | protected void incNEvaluations() {
    method updateMLEifNeeded (line 267) | protected void updateMLEifNeeded(final double log10LofK, final int[] a...
    method updateMAPifNeeded (line 282) | protected void updateMAPifNeeded(final double log10PofK, final int[] a...
    method addToLikelihoodsCache (line 289) | private void addToLikelihoodsCache(final double log10LofK) {
    method setLog10LikelihoodOfAFzero (line 302) | protected void setLog10LikelihoodOfAFzero(final double log10Likelihood...
    method setLog10PosteriorOfAFzero (line 310) | protected void setLog10PosteriorOfAFzero(final double log10PosteriorOf...
    method setAllelesUsedInGenotyping (line 322) | protected void setAllelesUsedInGenotyping(List<Allele> allelesUsedInGe...
    method ensureMaximumAlleleCapacity (line 331) | public void ensureMaximumAlleleCapacity(final int capacity) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/AlleleBalance.java
  class AlleleBalance (line 70) | public class AlleleBalance extends InfoFieldAnnotation {
    method annotate (line 72) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getCounts (line 169) | private int[] getCounts(final Genotype genotype,
    method getKeyNames (line 209) | public List<String> getKeyNames() { return Arrays.asList("ABHet","ABHo...
    method getDescriptions (line 211) | public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asLis...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/AlleleBalanceBySample.java
  class AlleleBalanceBySample (line 71) | public class AlleleBalanceBySample extends GenotypeAnnotation implements...
    method annotate (line 73) | public void annotate(final RefMetaDataTracker tracker,
    method annotateWithPileup (line 119) | private Double annotateWithPileup(final AlignmentContext stratifiedCon...
    method annotateWithLikelihoods (line 144) | private Double annotateWithLikelihoods(final PerReadAlleleLikelihoodMa...
    method getKeyNames (line 176) | public List<String> getKeyNames() {
    method getDescriptions (line 180) | public List<VCFFormatHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/AnnotationInterfaceManager.java
  class AnnotationInterfaceManager (line 40) | public class AnnotationInterfaceManager {
    method createInfoFieldAnnotations (line 45) | public static List<InfoFieldAnnotation> createInfoFieldAnnotations(Lis...
    method createGenotypeAnnotations (line 57) | public static List<GenotypeAnnotation> createGenotypeAnnotations(List<...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/BaseCounts.java
  class BaseCounts (line 61) | public class BaseCounts extends InfoFieldAnnotation {
    method annotate (line 63) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 86) | public List<String> getKeyNames() { return Arrays.asList("BaseCounts"); }
    method getDescriptions (line 88) | public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asLis...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/BaseQualityRankSumTest.java
  class BaseQualityRankSumTest (line 47) | public class BaseQualityRankSumTest extends RankSumTest implements Stand...
    method getKeyNames (line 48) | @Override
    method getDescriptions (line 51) | @Override
    method getElementForRead (line 54) | @Override
    method getElementForPileupElement (line 59) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/ChromosomeCountConstants.java
  class ChromosomeCountConstants (line 33) | public class ChromosomeCountConstants {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/ChromosomeCounts.java
  class ChromosomeCounts (line 58) | public class ChromosomeCounts extends InfoFieldAnnotation implements Sta...
    method annotate (line 62) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method initialize (line 74) | public void initialize(AnnotatorCompatible walker, GenomeLocParser too...
    method getKeyNames (line 80) | public List<String> getKeyNames() {
    method getDescriptions (line 84) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/ClippingRankSumTest.java
  class ClippingRankSumTest (line 44) | public class ClippingRankSumTest extends RankSumTest {
    method getKeyNames (line 45) | @Override
    method getDescriptions (line 48) | @Override
    method getElementForRead (line 51) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/Coverage.java
  class Coverage (line 62) | public class Coverage extends InfoFieldAnnotation implements StandardAnn...
    method annotate (line 64) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 95) | public List<String> getKeyNames() { return Arrays.asList(VCFConstants....
    method getDescriptions (line 97) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/DepthPerAlleleBySample.java
  class DepthPerAlleleBySample (line 68) | public class DepthPerAlleleBySample extends GenotypeAnnotation implement...
    method annotate (line 70) | public void annotate(final RefMetaDataTracker tracker,
    method annotateWithPileup (line 87) | private void annotateWithPileup(final AlignmentContext stratifiedConte...
    method annotateWithLikelihoods (line 108) | private void annotateWithLikelihoods(final PerReadAlleleLikelihoodMap ...
    method getKeyNames (line 134) | public List<String> getKeyNames() { return Arrays.asList(VCFConstants....
    method getDescriptions (line 136) | public List<VCFFormatHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/DepthPerSampleHC.java
  class DepthPerSampleHC (line 61) | public class DepthPerSampleHC extends GenotypeAnnotation {
    method annotate (line 62) | public void annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 101) | public List<String> getKeyNames() {
    method getDescriptions (line 105) | public List<VCFFormatHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/FisherStrand.java
  class FisherStrand (line 60) | public class FisherStrand extends StrandBiasTest implements StandardAnno...
    method calculateAnnotationFromGTfield (line 69) | @Override
    method calculateAnnotationFromStratifiedContexts (line 75) | @Override
    method calculateAnnotationFromLikelihoodMap (line 85) | @Override
    method pValueForBestTable (line 103) | private Map<String, Object> pValueForBestTable(final int[][] table1, f...
    method annotationForOneTable (line 121) | protected Map<String, Object> annotationForOneTable(final double pValu...
    method getKeyNames (line 126) | public List<String> getKeyNames() {
    method getDescriptions (line 130) | public List<VCFInfoHeaderLine> getDescriptions() {
    method getContingencyArray (line 140) | public static List<Integer> getContingencyArray(final int[][] table) {
    method pValueForContingencyTable (line 155) | private Double pValueForContingencyTable(int[][] originalTable) {
    method normalizeContingencyTable (line 202) | private static int[][] normalizeContingencyTable(final int[][] table) {
    method copyContingencyTable (line 218) | private static int[][] copyContingencyTable(int[][] t) {
    method printTable (line 229) | private static void printTable(int[][] table, double pValue) {
    method printTable (line 239) | private void printTable(final String name, final int[][] table) {
    method rotateTable (line 247) | private static boolean rotateTable(int[][] table) {
    method unrotateTable (line 257) | private static boolean unrotateTable(int[][] table) {
    method computePValue (line 267) | private static double computePValue(int[][] table) {
    method sumRow (line 286) | private static int sumRow(int[][] table, int column) {
    method sumColumn (line 295) | private static int sumColumn(int[][] table, int row) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/GenotypeSummaries.java
  class GenotypeSummaries (line 45) | public class GenotypeSummaries extends InfoFieldAnnotation implements Ac...
    method annotate (line 53) | @Override
    method getKeyNames (line 82) | @Override
    method getDescriptions (line 87) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/HaplotypeScore.java
  class HaplotypeScore (line 59) | public class HaplotypeScore extends InfoFieldAnnotation implements Stand...
    method annotate (line 65) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method annotatePileup (line 77) | private Map<String, Object> annotatePileup(final ReferenceContext ref,
    class HaplotypeComparator (line 113) | private static class HaplotypeComparator implements Comparator<Haploty...
      method compare (line 115) | public int compare(Haplotype a, Haplotype b) {
    method computeHaplotypes (line 125) | private List<Haplotype> computeHaplotypes(final ReadBackedPileup pileu...
    method getHaplotypeFromRead (line 194) | private Haplotype getHaplotypeFromRead(final PileupElement p, final in...
    method getConsensusHaplotype (line 238) | private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, fi...
    method scoreReadsAgainstHaplotypes (line 282) | private double scoreReadsAgainstHaplotypes(final List<Haplotype> haplo...
    method scoreReadAgainstHaplotype (line 309) | private double scoreReadAgainstHaplotype(final PileupElement p, final ...
    method getKeyNames (line 367) | public List<String> getKeyNames() {
    method getDescriptions (line 371) | public List<VCFInfoHeaderLine> getDescriptions() {
    class Haplotype (line 375) | private static class Haplotype  {
      method Haplotype (line 380) | public Haplotype( final byte[] bases, final int[] quals ) {
      method Haplotype (line 385) | public Haplotype( final byte[] bases, final int qual ) {
      method Haplotype (line 391) | public Haplotype( final byte[] bases, final byte[] quals ) {
      method getQualitySum (line 398) | public double getQualitySum() {
      method getQuals (line 408) | public int[] getQuals() {
      method getBases (line 412) | public byte[] getBases() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/InbreedingCoeff.java
  class InbreedingCoeff (line 57) | public class InbreedingCoeff extends InfoFieldAnnotation implements Stan...
    method annotate (line 64) | @Override
    method calculateIC (line 79) | protected double calculateIC(final VariantContext vc, final GenotypesC...
    method makeCoeffAnnotation (line 133) | protected Map<String, Object> makeCoeffAnnotation(final VariantContext...
    method getKeyNames (line 143) | @Override
    method getDescriptions (line 148) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/LowMQ.java
  class LowMQ (line 55) | public class LowMQ extends InfoFieldAnnotation {
    method annotate (line 57) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 83) | public List<String> getKeyNames() { return Arrays.asList("LowMQ"); }
    method getDescriptions (line 85) | public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asLis...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/MappingQualityRankSumTest.java
  class MappingQualityRankSumTest (line 51) | public class MappingQualityRankSumTest extends RankSumTest implements St...
    method getKeyNames (line 52) | @Override
    method getDescriptions (line 55) | @Override
    method getElementForRead (line 58) | @Override
    method getElementForPileupElement (line 63) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/MappingQualityZero.java
  class MappingQualityZero (line 57) | public class MappingQualityZero extends InfoFieldAnnotation implements S...
    method annotate (line 59) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method annotatePileup (line 73) | private Map<String, Object> annotatePileup(final ReferenceContext ref,
    method annotateWithLikelihoods (line 93) | private Map<String, Object> annotateWithLikelihoods(final Map<String, ...
    method getKeyNames (line 112) | public List<String> getKeyNames() {
    method getDescriptions (line 116) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/MappingQualityZeroBySample.java
  class MappingQualityZeroBySample (line 53) | public class MappingQualityZeroBySample extends GenotypeAnnotation {
    method annotate (line 54) | public void annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 75) | public List<String> getKeyNames() { return Arrays.asList(VCFConstants....
    method getDescriptions (line 77) | public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asL...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/NBaseCount.java
  class NBaseCount (line 53) | public class NBaseCount extends InfoFieldAnnotation {
    method annotate (line 54) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 81) | public List<String> getKeyNames() {
    method getDescriptions (line 85) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/QualByDepth.java
  class QualByDepth (line 60) | public class QualByDepth extends InfoFieldAnnotation implements Standard...
    method annotate (line 63) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method indelNormalizationFactor (line 143) | private double indelNormalizationFactor(final double altAlleleLength, ...
    method fixTooHighQD (line 158) | private double fixTooHighQD(final double QD) {
    method getKeyNames (line 170) | public List<String> getKeyNames() { return Arrays.asList("QD"); }
    method getDescriptions (line 172) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/RMSMappingQuality.java
  class RMSMappingQuality (line 57) | public class RMSMappingQuality extends InfoFieldAnnotation implements St...
    method annotate (line 59) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method fillMappingQualitiesFromPileup (line 93) | private static void fillMappingQualitiesFromPileup(final int mq, final...
    method getKeyNames (line 99) | public List<String> getKeyNames() { return Arrays.asList(VCFConstants....
    method getDescriptions (line 101) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/RankSumTest.java
  class RankSumTest (line 54) | public abstract class RankSumTest extends InfoFieldAnnotation implements...
    method annotate (line 58) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method fillQualsFromPileup (line 127) | private void fillQualsFromPileup(final List<Allele> alleles,
    method fillQualsFromLikelihoodMap (line 145) | private void fillQualsFromLikelihoodMap(final List<Allele> alleles,
    method getElementForRead (line 177) | protected Double getElementForRead(final GATKSAMRecord read, final int...
    method getElementForRead (line 188) | protected abstract Double getElementForRead(final GATKSAMRecord read, ...
    method getElementForPileupElement (line 200) | protected Double getElementForPileupElement(final PileupElement p) {
    method isUsableBase (line 213) | protected boolean isUsableBase(final PileupElement p) {
    method isUsableRead (line 227) | protected boolean isUsableRead(final GATKSAMRecord read, final int ref...
    method initialize (line 239) | public void initialize (AnnotatorCompatible walker, GenomeLocParser to...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/ReadPosRankSumTest.java
  class ReadPosRankSumTest (line 55) | public class ReadPosRankSumTest extends RankSumTest implements StandardA...
    method getKeyNames (line 57) | @Override
    method getDescriptions (line 60) | @Override
    method getElementForRead (line 65) | @Override
    method getElementForPileupElement (line 78) | @Override
    method isUsableBase (line 84) | @Override
    method isUsableRead (line 89) | @Override
    method getFinalReadPosition (line 94) | private int getFinalReadPosition(final GATKSAMRecord read, final int i...
    method getNumClippedBasesAtStart (line 105) | private int getNumClippedBasesAtStart(final SAMRecord read) {
    method getNumAlignedBases (line 131) | private int getNumAlignedBases(final GATKSAMRecord read) {
    method getNumClippedBasesAtEnd (line 135) | private int getNumClippedBasesAtEnd(final GATKSAMRecord read) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/SpanningDeletions.java
  class SpanningDeletions (line 53) | public class SpanningDeletions extends InfoFieldAnnotation implements St...
    method annotate (line 55) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 83) | public List<String> getKeyNames() {
    method getDescriptions (line 87) | public List<VCFInfoHeaderLine> getDescriptions() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/StrandBiasBySample.java
  class StrandBiasBySample (line 42) | public class StrandBiasBySample extends GenotypeAnnotation {
    method annotate (line 46) | @Override
    method getKeyNames (line 63) | @Override
    method getDescriptions (line 66) | @Override
    method isAppropriateInput (line 69) | private boolean isAppropriateInput(final PerReadAlleleLikelihoodMap ma...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/StrandBiasTest.java
  class StrandBiasTest (line 52) | public abstract class StrandBiasTest extends InfoFieldAnnotation {
    method initialize (line 55) | @Override
    method annotate (line 76) | @Override
    method calculateAnnotationFromGTfield (line 113) | protected abstract Map<String, Object> calculateAnnotationFromGTfield(...
    method calculateAnnotationFromStratifiedContexts (line 115) | protected abstract Map<String, Object> calculateAnnotationFromStratifi...
    method calculateAnnotationFromLikelihoodMap (line 118) | protected abstract Map<String, Object> calculateAnnotationFromLikeliho...
    method getTableFromSamples (line 129) | protected int[][] getTableFromSamples(final GenotypesContext genotypes...
    method getSNPContingencyTable (line 162) | protected static int[][] getSNPContingencyTable(final Map<String, Alig...
    method getContingencyTable (line 197) | public static int[][] getContingencyTable(final Map<String, PerReadAll...
    method copyToMainTable (line 231) | private static void copyToMainTable(final int[] perSampleTable, final ...
    method isUsableBase (line 245) | private static boolean isUsableBase(final PileupElement p) {
    method updateTable (line 252) | private static void updateTable(final int[] table, final Allele allele...
    method passesMinimumThreshold (line 281) | protected static boolean passesMinimumThreshold(final int[] data, fina...
    method encodeSBBS (line 292) | private static int[] encodeSBBS(final String string) {
    method decodeSBBS (line 307) | private static int[][] decodeSBBS(final int[] array) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/StrandOddsRatio.java
  class StrandOddsRatio (line 68) | public class StrandOddsRatio extends StrandBiasTest implements StandardA...
    method calculateAnnotationFromGTfield (line 74) | @Override
    method calculateAnnotationFromStratifiedContexts (line 84) | @Override
    method calculateAnnotationFromLikelihoodMap (line 92) | @Override
    method calculateSOR (line 111) | final protected double calculateSOR(final int[][] originalTable) {
    method augmentContingencyTable (line 134) | private static double[][] augmentContingencyTable(final int[][] table) {
    method annotationForOneTable (line 150) | protected Map<String, Object> annotationForOneTable(final double ratio) {
    method getDescriptions (line 155) | @Override
    method getKeyNames (line 160) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/TandemRepeatAnnotator.java
  class TandemRepeatAnnotator (line 56) | public class TandemRepeatAnnotator extends InfoFieldAnnotation implement...
    method annotate (line 60) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method getKeyNames (line 90) | public List<String> getKeyNames() {
    method getDescriptions (line 94) | public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asLis...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/VariantAnnotatorEngine.java
  class VariantAnnotatorEngine (line 62) | public class VariantAnnotatorEngine {
    class VAExpression (line 72) | protected static class VAExpression {
      method VAExpression (line 77) | public VAExpression(String fullExpression, List<RodBinding<VariantCo...
    method VariantAnnotatorEngine (line 96) | public VariantAnnotatorEngine(List<String> infoFieldAnnotations, List<...
    method initializeExpressions (line 105) | public void initializeExpressions(Set<String> expressionsToUse) {
    method getRequestedExpressions (line 111) | protected List<VAExpression> getRequestedExpressions() {
    method initializeAnnotations (line 115) | private void initializeAnnotations(List<String> infoFieldAnnotations, ...
    method excludeAnnotations (line 121) | private void excludeAnnotations(List<String> annotationsToExclude) {
    method initializeDBs (line 140) | private void initializeDBs(final GenomeLocParser parser) {
    method invokeAnnotationInitializationMethods (line 155) | public void invokeAnnotationInitializationMethods(final Set<VCFHeaderL...
    method getVCFAnnotationDescriptions (line 165) | public Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
    method annotateContext (line 182) | public VariantContext annotateContext(final RefMetaDataTracker tracker,
    method annotateContext (line 189) | public VariantContext annotateContext(final RefMetaDataTracker tracker,
    method annotateContextForActiveRegion (line 216) | public VariantContext annotateContextForActiveRegion(final RefMetaData...
    method annotateContextForActiveRegion (line 225) | public VariantContext annotateContextForActiveRegion(final RefMetaData...
    method annotateDBs (line 258) | private VariantContext annotateDBs(final RefMetaDataTracker tracker, V...
    method annotateExpressions (line 262) | private void annotateExpressions(final RefMetaDataTracker tracker, fin...
    method annotateGenotypes (line 284) | private GenotypesContext annotateGenotypes(final RefMetaDataTracker tr...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/VariantOverlapAnnotator.java
  class VariantOverlapAnnotator (line 44) | public final class VariantOverlapAnnotator {
    method VariantOverlapAnnotator (line 52) | public VariantOverlapAnnotator(RodBinding<VariantContext> dbSNPBinding...
    method VariantOverlapAnnotator (line 65) | public VariantOverlapAnnotator(RodBinding<VariantContext> dbSNPBinding...
    method getVCInTrackerInLocus (line 74) | protected List<VariantContext> getVCInTrackerInLocus(final RefMetaData...
    method annotateRsID (line 94) | public VariantContext annotateRsID(final RefMetaDataTracker tracker, f...
    method annotateRsID (line 111) | public VariantContext annotateRsID(final List<VariantContext> vcsAtLoc...
    method getLoc (line 129) | private GenomeLoc getLoc(final VariantContext vc) {
    method annotateOverlaps (line 144) | public VariantContext annotateOverlaps(final RefMetaDataTracker tracke...
    method annotateOverlap (line 169) | public VariantContext annotateOverlap(final List<VariantContext> overl...
    method getRsID (line 197) | private String getRsID(final List<VariantContext> rsIDSourceVCs, final...
    method overlaps (line 225) | private boolean overlaps(final List<VariantContext> potentialOverlaps,...
    method getOverlapNames (line 233) | public Collection<String> getOverlapNames() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/ActiveRegionBasedAnnotation.java
  type ActiveRegionBasedAnnotation (line 32) | public interface ActiveRegionBasedAnnotation extends AnnotationType {
    method annotate (line 34) | public abstract Map<String, Object> annotate(final Map<String, PerRead...
    method getDescriptions (line 37) | public abstract List<VCFInfoHeaderLine> getDescriptions();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/AnnotationType.java
  type AnnotationType (line 24) | public interface AnnotationType {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/AnnotatorCompatible.java
  type AnnotatorCompatible (line 29) | public interface AnnotatorCompatible {
    method getSnpEffRodBinding (line 32) | public abstract RodBinding<VariantContext> getSnpEffRodBinding();
    method getDbsnpRodBinding (line 33) | public abstract RodBinding<VariantContext> getDbsnpRodBinding();
    method getCompRodBindings (line 34) | public abstract List<RodBinding<VariantContext>> getCompRodBindings();
    method getResourceRodBindings (line 35) | public abstract List<RodBinding<VariantContext>> getResourceRodBinding...
    method alwaysAppendDbsnpId (line 36) | public abstract boolean alwaysAppendDbsnpId();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/ExperimentalAnnotation.java
  type ExperimentalAnnotation (line 24) | public interface ExperimentalAnnotation extends AnnotationType {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/GenotypeAnnotation.java
  class GenotypeAnnotation (line 35) | public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotat...
    method annotate (line 38) | public abstract void annotate(final RefMetaDataTracker tracker,
    method getDescriptions (line 48) | public abstract List<VCFFormatHeaderLine> getDescriptions();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/InfoFieldAnnotation.java
  class InfoFieldAnnotation (line 34) | public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnota...
    method annotate (line 36) | public Map<String, Object> annotate(final RefMetaDataTracker tracker,
    method annotate (line 44) | public Map<String, Object> annotate(Map<String, PerReadAlleleLikelihoo...
    method annotate (line 49) | public abstract Map<String, Object> annotate(final RefMetaDataTracker ...
    method getDescriptions (line 57) | public abstract List<VCFInfoHeaderLine> getDescriptions();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/RodRequiringAnnotation.java
  type RodRequiringAnnotation (line 24) | public interface RodRequiringAnnotation extends AnnotationType {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/StandardAnnotation.java
  type StandardAnnotation (line 24) | public interface StandardAnnotation extends AnnotationType {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/VariantAnnotatorAnnotation.java
  class VariantAnnotatorAnnotation (line 34) | public abstract class VariantAnnotatorAnnotation {
    method getKeyNames (line 36) | public abstract List<String> getKeyNames();
    method initialize (line 39) | public void initialize (AnnotatorCompatible walker, GenomeLocParser pa...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/annotator/interfaces/WorkInProgressAnnotation.java
  type WorkInProgressAnnotation (line 24) | public interface WorkInProgressAnnotation extends AnnotationType {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/argcollection/DbsnpArgumentCollection.java
  class DbsnpArgumentCollection (line 32) | public class DbsnpArgumentCollection {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/argcollection/GenotypeCalculationArgumentCollection.java
  class GenotypeCalculationArgumentCollection (line 32) | public class GenotypeCalculationArgumentCollection implements Cloneable {
    method clone (line 128) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/argcollection/HaplotypeCallerArgumentCollection.java
  class HaplotypeCallerArgumentCollection (line 29) | public class HaplotypeCallerArgumentCollection extends StandardCallerArg...
    method clone (line 43) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/argcollection/StandardCallerArgumentCollection.java
  class StandardCallerArgumentCollection (line 41) | public class StandardCallerArgumentCollection implements Cloneable {
    method getSampleContamination (line 74) | public Map<String, Double> getSampleContamination() {
    method setSampleContamination (line 82) | public void setSampleContamination(DefaultHashMap<String, Double> samp...
    method isSampleContaminationPresent (line 100) | public boolean isSampleContaminationPresent() {
    method StandardCallerArgumentCollection (line 129) | public StandardCallerArgumentCollection() {
    method cloneTo (line 141) | public <T extends StandardCallerArgumentCollection> T cloneTo(final Cl...
    method clone (line 171) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/argcollection/UnifiedArgumentCollection.java
  class UnifiedArgumentCollection (line 33) | public class UnifiedArgumentCollection extends StandardCallerArgumentCol...
    method UnifiedArgumentCollection (line 131) | public UnifiedArgumentCollection() {
    method clone (line 135) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/AFPriorProvider.java
  class AFPriorProvider (line 29) | public abstract class AFPriorProvider {
    method AFPriorProvider (line 33) | protected AFPriorProvider() {
    method forTotalPloidy (line 51) | public double[] forTotalPloidy(final int totalPloidy) {
    method ensureCapacity (line 66) | protected void ensureCapacity(final int totalPloidy) {
    method buildPriors (line 80) | protected abstract double[] buildPriors(final int totalPloidy);

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/AlleleLikelihoodMatrixMapper.java
  class AlleleLikelihoodMatrixMapper (line 34) | public abstract class AlleleLikelihoodMatrixMapper<A extends Allele> {
    method map (line 36) | public abstract ReadLikelihoods.Matrix<A> map(final ReadLikelihoods.Ma...
    method newInstance (line 47) | public static <A extends Allele> AlleleLikelihoodMatrixMapper<A> newIn...
    method asIs (line 62) | @SuppressWarnings("unchecked")
    method map (line 69) | @Override
    method general (line 81) | private static <A extends Allele> AlleleLikelihoodMatrixMapper<A> gene...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/CustomAFPriorProvider.java
  class CustomAFPriorProvider (line 29) | public class CustomAFPriorProvider extends AFPriorProvider {
    method CustomAFPriorProvider (line 37) | public CustomAFPriorProvider(final List<Double> priorValues) {
    method buildPriors (line 57) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/GenotypingEngine.java
  class GenotypingEngine (line 65) | public abstract class GenotypingEngine<Config extends StandardCallerArgu...
    method GenotypingEngine (line 100) | protected GenotypingEngine(final Config configuration, final SampleLis...
    method setLogger (line 130) | public void setLogger(final Logger logger) {
    method getAppropriateVCFInfoHeaders (line 136) | public Set<VCFInfoHeaderLine> getAppropriateVCFInfoHeaders() {
    method getConfiguration (line 148) | public Config getConfiguration() {
    method calculateGenotypes (line 163) | public VariantCallContext calculateGenotypes(final VariantContext vc, ...
    method calculateGenotypes (line 183) | protected VariantCallContext calculateGenotypes(final RefMetaDataTrack...
    method callSourceString (line 269) | protected abstract String callSourceString();
    class OutputAlleleSubset (line 275) | private static class OutputAlleleSubset {
      method OutputAlleleSubset (line 281) | private OutputAlleleSubset(final int count, final Allele[] alleles, ...
      method outputAlleles (line 288) | private List<Allele> outputAlleles(final Allele referenceAllele) {
      method alternativeAlleleMLECounts (line 296) | public List<Integer> alternativeAlleleMLECounts() {
    method calculateOutputAlleleSubset (line 310) | private OutputAlleleSubset calculateOutputAlleleSubset(final AFCalcula...
    method forceKeepAllele (line 339) | protected abstract boolean forceKeepAllele(final Allele allele);
    method confidentlyCalled (line 349) | protected final boolean confidentlyCalled(final double conf, final dou...
    method getModelTheta (line 361) | private double getModelTheta(final GenotypeLikelihoodsCalculationModel...
    method hasTooManyAlternativeAlleles (line 388) | protected final boolean hasTooManyAlternativeAlleles(final VariantCont...
    method emptyCallContext (line 406) | protected final VariantCallContext emptyCallContext(final RefMetaDataT...
    method forceSiteEmission (line 451) | protected abstract boolean forceSiteEmission();
    method estimateReferenceConfidence (line 453) | protected final VariantCallContext estimateReferenceConfidence(Variant...
    method getAlleleFrequencyPriors (line 483) | protected final double[] getAlleleFrequencyPriors( final VariantContex...
    method estimateLog10ReferenceConfidenceForOneSample (line 509) | protected final double estimateLog10ReferenceConfidenceForOneSample(fi...
    method getRefBinomialProbLog10 (line 524) | protected final double getRefBinomialProbLog10(final int depth) {
    method composeAlleleFrequencyPriorProvider (line 539) | private static AFPriorProvider composeAlleleFrequencyPriorProvider(fin...
    method computeAlleleFrequencyPriors (line 563) | public static void computeAlleleFrequencyPriors(final int N, final dou...
    method passesEmitThreshold (line 599) | protected final boolean passesEmitThreshold(double conf, boolean bestG...
    method passesCallThreshold (line 605) | protected final boolean passesCallThreshold(double conf) {
    method composeCallAttributes (line 613) | protected Map<String,Object> composeCallAttributes(final boolean inher...
    method calculateMLEAlleleFrequencies (line 642) | private ArrayList<Double> calculateMLEAlleleFrequencies(List<Integer> ...
    method setAnnotationEngine (line 660) | public void setAnnotationEngine(final VariantAnnotatorEngine annotatio...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/HaplotypeCallerGenotypingEngine.java
  class HaplotypeCallerGenotypingEngine (line 71) | public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<Ha...
    method HaplotypeCallerGenotypingEngine (line 92) | public HaplotypeCallerGenotypingEngine(final HaplotypeCallerArgumentCo...
    method setCrossHaplotypeEventMerger (line 106) | public void setCrossHaplotypeEventMerger(final MergeVariantsAcrossHapl...
    method callSourceString (line 110) | @Override
    method forceKeepAllele (line 115) | @Override
    method forceSiteEmission (line 122) | @Override
    class CalledHaplotypes (line 130) | public static class CalledHaplotypes {
      method CalledHaplotypes (line 134) | protected CalledHaplotypes(final List<VariantContext> calls, final S...
      method getCalls (line 147) | public List<VariantContext> getCalls() {
      method getCalledHaplotypes (line 155) | public Set<Haplotype> getCalledHaplotypes() {
    method assignGenotypeLikelihoods (line 180) | public CalledHaplotypes assignGenotypeLikelihoods( final List<Haplotyp...
    method phaseCalls (line 292) | protected List<VariantContext> phaseCalls(final List<VariantContext> c...
    method constructHaplotypeMapping (line 312) | protected static Map<VariantContext, Set<Haplotype>> constructHaplotyp...
    method constructPhaseSetMapping (line 349) | protected static int constructPhaseSetMapping(final List<VariantContex...
    method constructPhaseGroups (line 444) | protected static List<VariantContext> constructPhaseGroups(final List<...
    method isBiallelic (line 481) | private static boolean isBiallelic(final VariantContext vc) {
    method createUniqueID (line 491) | private static String createUniqueID(final VariantContext vc) {
    method phaseVC (line 504) | private static VariantContext phaseVC(final VariantContext vc, final S...
    method addNonRefSymbolicAllele (line 511) | private VariantContext addNonRefSymbolicAllele(final VariantContext me...
    method prepareReadAlleleLikelihoodsForAnnotation (line 523) | private ReadLikelihoods<Allele> prepareReadAlleleLikelihoodsForAnnotat...
    method overlappingFilteredReads (line 558) | private Map<String, List<GATKSAMRecord>> overlappingFilteredReads(fina...
    method decomposeHaplotypesIntoVariantContexts (line 588) | private TreeSet<Integer> decomposeHaplotypesIntoVariantContexts(final ...
    method makePriorityList (line 620) | private List<String> makePriorityList(final List<VariantContext> vcs) {
    method getVCsAtThisLocation (line 626) | private List<VariantContext> getVCsAtThisLocation(final List<Haplotype...
    method calculateGLsForThisEvent (line 677) | private GenotypesContext calculateGLsForThisEvent( final ReadLikelihoo...
    method cleanUpSymbolicUnassembledEvents (line 693) | protected static void cleanUpSymbolicUnassembledEvents( final List<Hap...
    method createAlleleMapper (line 712) | protected static Map<Allele, List<Haplotype>> createAlleleMapper( fina...
    method createEventMapper (line 720) | protected static Map<Event, List<Haplotype>> createEventMapper( final ...
    method generateVCsFromAlignment (line 745) | @Deprecated
    method containsVCWithMatchingAlleles (line 750) | protected static boolean containsVCWithMatchingAlleles( final List<Var...
    class Event (line 759) | protected static class Event {
      method Event (line 762) | public Event( final VariantContext vc ) {
      method equals (line 766) | @Override
      method hashCode (line 771) | @Override
    method getPloidyModel (line 782) | public PloidyModel getPloidyModel() {
    method getGenotypingModel (line 791) | public GenotypingModel getGenotypingModel() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/HaplotypeLDCalculator.java
  class HaplotypeLDCalculator (line 45) | public class HaplotypeLDCalculator {
    method HaplotypeLDCalculator (line 53) | public HaplotypeLDCalculator(final List<Haplotype> haplotypes, final R...
    method buildHaplotypeLikelihoodsPerSampleIfNecessary (line 64) | private void buildHaplotypeLikelihoodsPerSampleIfNecessary() {
    method computeProbOfBeingPhased (line 92) | protected double computeProbOfBeingPhased(final VariantContext first, ...
    method pPhased (line 141) | protected double pPhased(double[] table) {
    method pPhasedTest (line 162) | protected double pPhasedTest(final double x11, final double x12, final...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/HeterozygosityAFPriorProvider.java
  class HeterozygosityAFPriorProvider (line 31) | public class HeterozygosityAFPriorProvider extends AFPriorProvider {
    method HeterozygosityAFPriorProvider (line 41) | public HeterozygosityAFPriorProvider(final double heterozygosity) {
    method buildPriors (line 52) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/InfiniteRandomMatingPopulationModel.java
  class InfiniteRandomMatingPopulationModel (line 44) | public class InfiniteRandomMatingPopulationModel implements GenotypingMo...
    method InfiniteRandomMatingPopulationModel (line 53) | public InfiniteRandomMatingPopulationModel() {
    method InfiniteRandomMatingPopulationModel (line 57) | public InfiniteRandomMatingPopulationModel(final int calculatorCachePl...
    method calculateLikelihoods (line 68) | @Override
    method noSampleLikelihoods (line 90) | private <A extends Allele> GenotypingLikelihoods<A> noSampleLikelihood...
    method singleSampleLikelihoods (line 98) | private <A extends Allele> GenotypingLikelihoods<A> singleSampleLikeli...
    method getLikelihoodsCalculator (line 110) | private GenotypeLikelihoodCalculator getLikelihoodsCalculator(final in...
    method multiSampleHeterogeneousPloidyModelLikelihoods (line 120) | private <A extends Allele> GenotypingLikelihoods<A> multiSampleHeterog...
    method multiSampleHomogeneousPloidyModelLikelihoods (line 136) | private <A extends Allele> GenotypingLikelihoods<A> multiSampleHomogen...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/LDMerger.java
  class LDMerger (line 41) | public class LDMerger extends MergeVariantsAcrossHaplotypes {
    method LDMerger (line 48) | public LDMerger(boolean DEBUG, int minSamplesToMergeSNPs, int minSampl...
    method LDMerger (line 55) | protected LDMerger() {
    method merge (line 77) | @Override
    method mergeConsecutiveEventsBasedOnLDOnce (line 113) | protected boolean mergeConsecutiveEventsBasedOnLDOnce( final List<Hapl...
    class LDMergeData (line 152) | private class LDMergeData {
      method cantBeMerged (line 157) | public LDMergeData cantBeMerged() {
      method canBeMerged (line 167) | public boolean canBeMerged(final int nSamples) {
    method getPairOfEventsToMerge (line 187) | private LDMergeData getPairOfEventsToMerge(final List<Haplotype> haplo...
    method createMergedVariantContext (line 218) | protected VariantContext createMergedVariantContext( final VariantCont...
    method replaceVariantContextsInMap (line 259) | private void replaceVariantContextsInMap(final List<Haplotype> haploty...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/MergeVariantsAcrossHaplotypes.java
  class MergeVariantsAcrossHaplotypes (line 34) | public class MergeVariantsAcrossHaplotypes {
    method merge (line 45) | public boolean merge( final List<Haplotype> haplotypes,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/UnifiedGenotypingEngine.java
  class UnifiedGenotypingEngine (line 63) | public class UnifiedGenotypingEngine extends GenotypingEngine<UnifiedArg...
    method UnifiedGenotypingEngine (line 93) | public UnifiedGenotypingEngine(final UnifiedArgumentCollection configu...
    method UnifiedGenotypingEngine (line 112) | public UnifiedGenotypingEngine(final UnifiedArgumentCollection configu...
    method setVerboseWriter (line 133) | public void setVerboseWriter(final PrintStream writer) {
    method initializeGenotypeLikelihoodsCalculationModels (line 140) | private void initializeGenotypeLikelihoodsCalculationModels() {
    method calculateLikelihoodsAndGenotypes (line 158) | public List<VariantCallContext> calculateLikelihoodsAndGenotypes(final...
    method getGenotypeLikelihoodsCalculationObject (line 194) | private static Map<String, GenotypeLikelihoodsCalculationModel> getGen...
    method calculateLikelihoods (line 225) | public VariantContext calculateLikelihoods(final RefMetaDataTracker tr...
    method calculateGenotypes (line 254) | public VariantCallContext calculateGenotypes(final RefMetaDataTracker ...
    method calculateGenotypes (line 275) | public VariantCallContext calculateGenotypes(VariantContext vc) {
    method calculateLikelihoods (line 287) | private VariantContext calculateLikelihoods(final RefMetaDataTracker t...
    method calculateGenotypes (line 301) | public VariantCallContext calculateGenotypes(final VariantContext vc, ...
    method calculateGenotypes (line 305) | public VariantCallContext calculateGenotypes(final RefMetaDataTracker ...
    method forceKeepAllele (line 315) | @Override
    method calculateGenotypes (line 320) | @Override
    method callSourceString (line 333) | @Override
    method forceSiteEmission (line 338) | @Override
    method composeCallAttributes (line 344) | @Override
    method calculateSLOD (line 362) | private double calculateSLOD(final Map<String, AlignmentContext> strat...
    method getDirectionalAfCalcResult (line 397) | private AFCalculationResult getDirectionalAfCalcResult(final Alignment...
    method getFilteredAndStratifiedContexts (line 410) | private Map<String, AlignmentContext> getFilteredAndStratifiedContexts...
    method printVerboseData (line 449) | protected void printVerboseData(final String pos, final VariantContext...
    method determineGLModelsToUse (line 497) | private void determineGLModelsToUse() {
    method getGLModelsToUse (line 548) | private List<GenotypeLikelihoodsCalculationModel.Model> getGLModelsToU...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/genotyper/VariantCallContext.java
  class VariantCallContext (line 29) | public class VariantCallContext extends VariantContext {
    method VariantCallContext (line 37) | VariantCallContext(VariantContext vc, boolean confidentlyCalledP) {
    method VariantCallContext (line 42) | VariantCallContext(VariantContext vc, boolean confidentlyCalledP, bool...
    method isCalledRef (line 56) | public boolean isCalledRef(double callConfidenceThreshold) {
    method isCalledAlt (line 65) | public boolean isCalledAlt(double callConfidenceThreshold) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java
  class AggregatedSubHaplotypeFinder (line 33) | class AggregatedSubHaplotypeFinder<F extends KBestSubHaplotypeFinder> im...
    method AggregatedSubHaplotypeFinder (line 68) | public AggregatedSubHaplotypeFinder(final Collection<F> finders) {
    method id (line 73) | @Override
    method label (line 81) | @Override
    method subFinderLabels (line 86) | @Override
    method getCount (line 96) | @Override
    method score (line 102) | @Override
    method processSubFindersIfNeeded (line 115) | private void processSubFindersIfNeeded() {
    method getKBest (line 133) | @Override
    method isReference (line 159) | @Override
    class MyKBestHaplotypeResult (line 167) | private class MyKBestHaplotypeResult extends KBestHaplotype {
      method MyKBestHaplotypeResult (line 175) | private MyKBestHaplotypeResult(final KBestSubHaplotypeFinder finder,...
      method graph (line 181) | @Override
      method score (line 186) | @Override
      method isReference (line 191) | @Override
      method rank (line 196) | @Override
      method head (line 201) | @Override
      method tail (line 206) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/BaseEdge.java
  class BaseEdge (line 35) | public class BaseEdge {
    method BaseEdge (line 45) | public BaseEdge(final boolean isRef, final int multiplicity) {
    method copy (line 55) | public BaseEdge copy() {
    method getMultiplicity (line 63) | public int getMultiplicity() {
    method getDotLabel (line 71) | public String getDotLabel() {
    method incMultiplicity (line 79) | public void incMultiplicity(final int incr) {
    method getPruningMultiplicity (line 91) | public int getPruningMultiplicity() {
    method setMultiplicity (line 99) | public void setMultiplicity( final int value ) {
    method isRef (line 108) | public boolean isRef() {
    method setIsRef (line 116) | public void setIsRef( final boolean isRef ) {
    class EdgeWeightComparator (line 124) | public static class EdgeWeightComparator implements Comparator<BaseEdg...
      method compare (line 125) | @Override
    method add (line 140) | public BaseEdge add(final BaseEdge edge) {
    method orRef (line 154) | public static BaseEdge orRef(final Collection<BaseEdge> edges, final i...
    method max (line 169) | public BaseEdge max(final BaseEdge edge) {
    method toString (line 174) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/BaseGraph.java
  class BaseGraph (line 41) | public class BaseGraph<V extends BaseVertex, E extends BaseEdge> extends...
    method BaseGraph (line 49) | public BaseGraph(final int kmerSize, final EdgeFactory<V,E> edgeFactor...
    method getKmerSize (line 60) | public int getKmerSize() {
    method isReferenceNode (line 68) | public boolean isReferenceNode( final V v ) {
    method isSource (line 83) | public boolean isSource( final V v ) {
    method isSink (line 92) | public boolean isSink( final V v ) {
    method getSources (line 101) | public Set<V> getSources() {
    method getSinks (line 113) | public Set<V> getSinks() {
    method convertToSequenceGraph (line 129) | public SeqGraph convertToSequenceGraph() {
    method getAdditionalSequence (line 159) | public byte[] getAdditionalSequence( final V v ) {
    method isRefSource (line 168) | public boolean isRefSource( final V v ) {
    method isRefSink (line 189) | public boolean isRefSink( final V v ) {
    method getReferenceSourceVertex (line 209) | public V getReferenceSourceVertex( ) {
    method getReferenceSinkVertex (line 221) | public V getReferenceSinkVertex( ) {
    method getNextReferenceVertex (line 235) | public V getNextReferenceVertex( final V v ) {
    method getNextReferenceVertex (line 246) | public V getNextReferenceVertex( final V v, final boolean allowNonRefP...
    method getPrevReferenceVertex (line 274) | public V getPrevReferenceVertex( final V v ) {
    method referencePathExists (line 290) | public boolean referencePathExists(final V fromVertex, final V toVerte...
    method getReferenceBytes (line 316) | public byte[] getReferenceBytes( final V fromVertex, final V toVertex,...
    method addVertices (line 340) | public void addVertices(final V... vertices) {
    method addVertices (line 349) | public void addVertices(final Collection<V> vertices) {
    method addEdges (line 359) | public void addEdges(final V start, final V... remaining) {
    method addEdges (line 372) | public void addEdges(final E template, final V start, final V... remai...
    method outgoingVerticesOf (line 385) | public Set<V> outgoingVerticesOf(final V v) {
    method incomingVerticesOf (line 398) | public Set<V> incomingVerticesOf(final V v) {
    method neighboringVerticesOf (line 411) | public Set<V> neighboringVerticesOf(final V v) {
    method printGraph (line 421) | public void printGraph(final File destination, final int pruneFactor) {
    method printGraph (line 434) | public void printGraph(final PrintStream graphWriter, final boolean wr...
    method cleanNonRefPaths (line 459) | public void cleanNonRefPaths() {
    method pruneLowWeightChains (line 496) | public void pruneLowWeightChains( final int pruneFactor ) {
    method removeSingletonOrphanVertices (line 504) | public void removeSingletonOrphanVertices() {
    method removeVerticesNotConnectedToRefRegardlessOfEdgeDirection (line 519) | public void removeVerticesNotConnectedToRefRegardlessOfEdgeDirection() {
    method removePathsNotConnectedToRef (line 539) | public void removePathsNotConnectedToRef() {
    method graphEquals (line 585) | public static <T extends BaseVertex, E extends BaseEdge> boolean graph...
    method seqEquals (line 619) | private boolean seqEquals( final E edge1, final E edge2, final BaseGra...
    method incomingEdgeOf (line 629) | public E incomingEdgeOf(final V v) {
    method outgoingEdgeOf (line 638) | public E outgoingEdgeOf(final V v) {
    method getSingletonEdge (line 648) | private E getSingletonEdge(final Collection<E> edges) {
    method addOrUpdateEdge (line 660) | public void addOrUpdateEdge(final V source, final V target, final E e) {
    method toString (line 669) | @Override
    method verticesWithinDistance (line 683) | protected Set<V> verticesWithinDistance(final V source, final int dist...
    method subsetToNeighbors (line 702) | public BaseGraph<V,E> subsetToNeighbors(final V target, final int dist...
    method subsetToRefSource (line 722) | public BaseGraph<V,E> subsetToRefSource() {
    method containsAllVertices (line 736) | public boolean containsAllVertices(final Collection<? extends V> verti...
    method hasCycles (line 748) | public boolean hasCycles() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/BaseGraphIterator.java
  class BaseGraphIterator (line 38) | public class BaseGraphIterator<T extends BaseVertex, E extends BaseEdge>...
    method BaseGraphIterator (line 56) | public BaseGraphIterator(final BaseGraph<T,E> graph, final T start,
    method iterator (line 68) | @Override
    method hasNext (line 73) | @Override
    method next (line 78) | @Override
    method remove (line 91) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/BaseVertex.java
  class BaseVertex (line 32) | public class BaseVertex {
    method BaseVertex (line 47) | public BaseVertex(final byte[] sequence) {
    method isEmpty (line 60) | public boolean isEmpty() {
    method length (line 68) | public int length() {
    method BaseVertex (line 76) | protected BaseVertex(final String sequence) {
    method equals (line 80) | @Override
    method seqEquals (line 98) | public boolean seqEquals(final BaseVertex b) {
    method hashCode (line 106) | @Override
    method toString (line 114) | @Override
    method getSequence (line 126) | public byte[] getSequence() {
    method getSequenceString (line 134) | public String getSequenceString() {
    method getAdditionalSequence (line 149) | public byte[] getAdditionalSequence(final boolean source) {
    method setAdditionalInfo (line 157) | public void setAdditionalInfo(final String info) {
    method additionalInfo (line 165) | public String additionalInfo() { return additionalInfo; }
    method hasAmbiguousSequence (line 181) | public boolean hasAmbiguousSequence() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/CommonSuffixSplitter.java
  class CommonSuffixSplitter (line 46) | public class CommonSuffixSplitter {
    method CommonSuffixSplitter (line 52) | public CommonSuffixSplitter() {}
    method split (line 61) | public boolean split(final SeqGraph graph, final SeqVertex v) {
    method wouldEliminateRefSource (line 126) | private boolean wouldEliminateRefSource(final SeqGraph graph, final Se...
    method allVerticesAreTheCommonSuffix (line 146) | private boolean allVerticesAreTheCommonSuffix(final SeqVertex commonSu...
    method safeToSplit (line 163) | private boolean safeToSplit(final SeqGraph graph, final SeqVertex bot,...
    method commonSuffix (line 188) | protected static SeqVertex commonSuffix(final Collection<SeqVertex> mi...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/DeBruijnVertex.java
  class DeBruijnVertex (line 30) | public class DeBruijnVertex extends BaseVertex {
    method DeBruijnVertex (line 37) | public DeBruijnVertex( final byte[] sequence ) {
    method getKmerSize (line 45) | public int getKmerSize() {
    method getSuffixString (line 53) | public String getSuffixString() {
    method getSuffix (line 65) | public byte getSuffix() {
    method getSuffixAsArray (line 76) | private byte[] getSuffixAsArray() {
    method getAdditionalSequence (line 83) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java
  class DeadEndKBestSubHaplotypeFinder (line 36) | final class DeadEndKBestSubHaplotypeFinder implements KBestSubHaplotypeF...
    method DeadEndKBestSubHaplotypeFinder (line 46) | protected DeadEndKBestSubHaplotypeFinder() {
    method id (line 49) | @Override
    method label (line 54) | @Override
    method subFinderLabels (line 59) | @Override
    method getCount (line 64) | @Override
    method getKBest (line 69) | @Override
    method isReference (line 77) | @Override
    method score (line 82) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java
  class EmptyPathHaplotypeFinderNode (line 35) | class EmptyPathHaplotypeFinderNode implements KBestSubHaplotypeFinder {
    method EmptyPathHaplotypeFinderNode (line 48) | public EmptyPathHaplotypeFinderNode(final SeqGraph graph, final SeqVer...
    method id (line 52) | @Override
    method label (line 57) | @Override
    method subFinderLabels (line 62) | @Override
    method getCount (line 67) | @Override
    method getKBest (line 72) | @Override
    method isReference (line 81) | @Override
    method score (line 86) | @Override
    class MyBestHaplotypePath (line 102) | private class MyBestHaplotypePath extends KBestHaplotype {
      method MyBestHaplotypePath (line 127) | public MyBestHaplotypePath(final SeqGraph graph, final SeqVertex ver...
      method graph (line 132) | @Override
      method score (line 137) | @Override
      method rank (line 142) | @Override
      method head (line 147) | @Override
      method tail (line 152) | @Override
      method isReference (line 157) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/GraphUtils.java
  class GraphUtils (line 37) | final public class GraphUtils {
    method GraphUtils (line 38) | private GraphUtils() {}
    method compPrefixLen (line 47) | protected static int compPrefixLen(final List<byte[]> listOfBytes, fin...
    method compSuffixLen (line 66) | protected static int compSuffixLen(final List<byte[]> listOfBytes, fin...
    method getKmers (line 83) | protected static List<byte[]> getKmers(final Collection<SeqVertex> ver...
    method minKmerLength (line 97) | protected static int minKmerLength(final Collection<byte[]> kmers) {
    method findLongestUniqueSuffixMatch (line 124) | public static PrimitivePair.Int findLongestUniqueSuffixMatch(final byt...
    method longestSuffixMatch (line 151) | public static int longestSuffixMatch(final byte[] seq, final byte[] km...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KBestHaplotype.java
  class KBestHaplotype (line 31) | public abstract class KBestHaplotype implements Comparable<KBestHaplotyp...
    method graph (line 38) | public abstract SeqGraph graph();
    method score (line 47) | public abstract double score();
    method isReference (line 54) | public abstract boolean isReference();
    method rank (line 63) | public abstract int rank();
    method bases (line 76) | public byte[] bases() {
    method haplotype (line 98) | public Haplotype haplotype() {
    method path (line 112) | public Path<SeqVertex,BaseEdge> path() {
    method compareTo (line 131) | public int compareTo(final KBestHaplotype other) {
    method hashCode (line 136) | @Override
    method equals (line 141) | @Override
    method toString (line 146) | @Override
    method equals (line 160) | protected boolean equals(final KBestHaplotype other) {
    method head (line 169) | protected abstract SeqVertex head();
    method tail (line 176) | protected abstract KBestHaplotype tail();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KBestHaplotypeFinder.java
  class KBestHaplotypeFinder (line 38) | public class KBestHaplotypeFinder extends AbstractList<KBestHaplotype> i...
    method KBestHaplotypeFinder (line 81) | public KBestHaplotypeFinder(final SeqGraph graph, final SeqVertex sour...
    method KBestHaplotypeFinder (line 97) | public KBestHaplotypeFinder(final SeqGraph graph, final Set<SeqVertex>...
    method KBestHaplotypeFinder (line 129) | public KBestHaplotypeFinder(SeqGraph graph) {
    method createAggregatedFinder (line 138) | private KBestSubHaplotypeFinder createAggregatedFinder() {
    method removeCycles (line 153) | private static SeqGraph removeCycles(final SeqGraph original, final Se...
    method findGuiltyVerticesAndEdgesToRemoveCycles (line 189) | private static boolean findGuiltyVerticesAndEdgesToRemoveCycles(final ...
    method get (line 216) | @Override
    method iterator (line 223) | @Override
    method size (line 248) | @Override
    method iterator (line 262) | public Iterator<KBestHaplotype> iterator(final int k) {
    method createVertexFinder (line 293) | protected KBestSubHaplotypeFinder createVertexFinder(final SeqVertex v...
    method createChildrenFinders (line 324) | private Map<BaseEdge, KBestSubHaplotypeFinder> createChildrenFinders(f...
    method printDOT (line 341) | public void printDOT(final PrintWriter out) {
    method printDOT (line 382) | public void printDOT(final File file) throws FileNotFoundException {
    method printDOTFile (line 402) | @SuppressWarnings("unused") // Available for debugging purposes.
    method score (line 415) | public double score(final byte[] bases) {
    method score (line 427) | public double score(final Haplotype haplotype) {
    method unique (line 451) | public List<KBestHaplotype> unique(final int maxSize) {
    method unique (line 482) | public List<KBestHaplotype> unique() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KBestSubHaplotypeFinder.java
  type KBestSubHaplotypeFinder (line 33) | interface KBestSubHaplotypeFinder {
    method id (line 40) | public String id();
    method label (line 49) | public String label();
    method subFinderLabels (line 56) | public Set<Pair<? extends KBestSubHaplotypeFinder,String>> subFinderLa...
    method getCount (line 62) | public abstract int getCount();
    method getKBest (line 73) | public KBestHaplotype getKBest(int k);
    method isReference (line 80) | public boolean isReference();
    method score (line 90) | public double score(byte[] bases, int offset, int length);

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KMerCounter.java
  class KMerCounter (line 35) | public class KMerCounter {
    method KMerCounter (line 49) | public KMerCounter(final int kmerLength) {
    method getKmerCount (line 59) | public int getKmerCount(final Kmer kmer) {
    method getCountedKmers (line 69) | public Collection<CountedKmer> getCountedKmers() {
    method getKmersWithCountsAtLeast (line 78) | public Collection<Kmer> getKmersWithCountsAtLeast(final int minCount) {
    method clear (line 90) | public void clear() {
    method addKmer (line 100) | public void addKmer(final Kmer kmer, final int kmerCount) {
    method toString (line 112) | @Override
    class CountedKmer (line 120) | public static class CountedKmer implements Comparable<CountedKmer> {
      method CountedKmer (line 124) | private CountedKmer(final Kmer kmer) {
      method getKmer (line 128) | public Kmer getKmer() {
      method getCount (line 132) | public int getCount() {
      method toString (line 136) | @Override
      method compareTo (line 144) | @Override
    method addKmer (line 157) | protected void addKmer(final String rawKmer, final int kmerCount) {
    method addKmers (line 166) | protected void addKmers(final String ... kmers) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/Kmer.java
  class Kmer (line 29) | public class Kmer {
    method Kmer (line 42) | public Kmer(byte[] kmer) {
    method Kmer (line 53) | public Kmer(final String kmer) {
    method Kmer (line 67) | public Kmer(final byte[] bases, final int start, final int length) {
    method Kmer (line 82) | public Kmer(final Kmer kmer) {
    method Kmer (line 89) | public Kmer(final Kmer kmer, final byte nextChar) {
    method subKmer (line 105) | public Kmer subKmer(final int newStart, final int newLength) {
    method bases (line 116) | public byte[] bases() {
    method copyTo (line 141) | public void copyTo(final int start, final byte[] dest, final int offse...
    method copyTo (line 161) | public void copyTo(final byte[] dest, final int offset) {
    method unsafePeekAtBases (line 171) | private byte[] unsafePeekAtBases() {
    method baseString (line 178) | public String baseString() {
    method length (line 186) | public int length() {
    method getDifferingPositions (line 206) | public int getDifferingPositions(final Kmer other,
    method toString (line 227) | @Override
    method equals (line 232) | @Override
    method hashCode (line 250) | @Override
    method myHashCode (line 264) | private static int myHashCode(final byte a[], final int start, final i...
    method base (line 275) | public byte base(final int i) {
    method shift (line 279) | public Kmer shift(final byte nextChar) {
    method lastBase (line 290) | public byte lastBase() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KmerSearchableGraph.java
  type KmerSearchableGraph (line 29) | public interface KmerSearchableGraph<V extends BaseVertex, E extends Bas...
    method findKmer (line 38) | V findKmer(Kmer k);
    method getKmerSize (line 45) | int getKmerSize();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/KmerSequence.java
  class KmerSequence (line 37) | public class KmerSequence implements List<Kmer> {
    method KmerSequence (line 50) | public KmerSequence(final SAMRecord read, final int kmerSize) {
    method KmerSequence (line 60) | @SuppressWarnings("unused")
    method KmerSequence (line 71) | public KmerSequence(final byte[] sequence, final int kmerSize) {
    method KmerSequence (line 84) | protected KmerSequence(final byte[] sequence, final int start, final i...
    method kmerSize (line 108) | public int kmerSize() {
    method subsequence (line 112) | public KmerSequence subsequence(final int from, final int to) {
    method size (line 123) | @Override
    method isEmpty (line 128) | @Override
    method contains (line 133) | @Override
    method iterator (line 163) | @Override
    method toArray (line 186) | @Override
    method toArray (line 191) | @Override
    method add (line 212) | @Override
    method remove (line 217) | @Override
    method containsAll (line 222) | @Override
    method addAll (line 230) | @Override
    method addAll (line 235) | @Override
    method removeAll (line 240) | @Override
    method retainAll (line 245) | @Override
    method clear (line 250) | @Override
    method get (line 255) | @Override
    method set (line 263) | @Override
    method add (line 268) | @Override
    method remove (line 273) | @Override
    method indexOf (line 278) | @Override
    method lastIndexOf (line 302) | @Override
    method listIterator (line 326) | @Override
    method listIterator (line 331) | @Override
    method subList (line 336) | @Override
    method getBytes (line 345) | public byte[] getBytes() {
    class MyKmer (line 356) | protected class MyKmer extends Kmer {
      method MyKmer (line 362) | public MyKmer(final int start) {
    class MyListIterator (line 370) | private class MyListIterator implements ListIterator<Kmer> {
      method MyListIterator (line 378) | private MyListIterator(final int idx) {
      method hasNext (line 382) | @Override
      method next (line 387) | @Override
      method hasPrevious (line 392) | @Override
      method previous (line 397) | @Override
      method nextIndex (line 402) | @Override
      method previousIndex (line 407) | @Override
      method remove (line 412) | @Override
      method set (line 417) | @Override
      method add (line 422) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/LowWeightChainPruner.java
  class LowWeightChainPruner (line 39) | public class LowWeightChainPruner<V extends BaseVertex, E extends BaseEd...
    method LowWeightChainPruner (line 42) | public LowWeightChainPruner(int pruneFactor) {
    method pruneLowWeightChains (line 51) | public void pruneLowWeightChains(final BaseGraph<V,E> graph) {
    method mustBeKept (line 81) | private boolean mustBeKept(final Path<V, E> path, final int pruneFacto...
    method getLinearChains (line 99) | protected final Collection<Path<V,E>> getLinearChains(final BaseGraph<...
    method extendLinearChain (line 128) | protected final Path<V,E> extendLinearChain(final Path<V, E> path) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/MultiSampleEdge.java
  class MultiSampleEdge (line 46) | public class MultiSampleEdge extends BaseEdge {
    method MultiSampleEdge (line 58) | public MultiSampleEdge(final boolean isRef, final int multiplicity, fi...
    method copy (line 68) | @Override
    method flushSingleSampleMultiplicity (line 77) | public void flushSingleSampleMultiplicity() {
    method incMultiplicity (line 87) | @Override
    method getPruningMultiplicity (line 93) | @Override
    method getDotLabel (line 98) | @Override
    method getCurrentSingleSampleMultiplicity (line 104) | protected int getCurrentSingleSampleMultiplicity() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/Path.java
  class Path (line 40) | public class Path<T extends BaseVertex, E extends BaseEdge> {
    method Path (line 60) | public Path(final T initialVertex, final BaseGraph<T, E> graph) {
    method makePath (line 74) | protected static <T extends BaseVertex, E extends BaseEdge> Path<T,E> ...
    method Path (line 88) | protected Path(final Path<T,E> p) {
    method Path (line 105) | public Path(final Path<T,E> p, final E edge) {
    method length (line 124) | public int length() {
    method Path (line 137) | public Path(final E edge, final Path<T,E> p) {
    method getOutgoingEdgesOfLastVertex (line 154) | public Collection<E> getOutgoingEdgesOfLastVertex() {
    method containsEdge (line 163) | public boolean containsEdge( final E edge ) {
    method containsVertex (line 178) | public boolean containsVertex(final T v) {
    method isSuffix (line 193) | public boolean isSuffix(final Path<T, E> other) {
    method pathsAreTheSame (line 211) | protected boolean pathsAreTheSame(Path<T,E> path) {
    method toString (line 215) | @Override
    method getGraph (line 234) | public BaseGraph<T, E> getGraph() {
    method getEdges (line 242) | public List<E> getEdges() { return edgesInOrder; }
    method getVertices (line 248) | public List<T> getVertices() {
    method getScore (line 269) | public int getScore() { return totalScore; }
    method getLastVertex (line 275) | public T getLastVertex() { return lastVertex; }
    method getFirstVertex (line 281) | public T getFirstVertex() {
    method getBases (line 293) | public byte[] getBases() {
    method calculateCigar (line 309) | public  Cigar calculateCigar(final byte[] refSeq) {
    method equalScoreAndSequence (line 318) | public boolean equalScoreAndSequence(final Path<T,E> other) {
    method equalSequence (line 328) | public boolean equalSequence(final Path<T,E> other) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/RecursiveSubHaplotypeFinder.java
  class RecursiveSubHaplotypeFinder (line 47) | class RecursiveSubHaplotypeFinder extends AggregatedSubHaplotypeFinder<R...
    method RecursiveSubHaplotypeFinder (line 64) | public RecursiveSubHaplotypeFinder(final SeqGraph graph, final SeqVert...
    method createChildFinderCollection (line 83) | private static Collection<EdgeSubHaplotypeFinder> createChildFinderCol...
    method isReference (line 107) | @Override
    method label (line 112) | @Override
    method subFinderLabels (line 117) | @Override
    method simplifyZeros (line 131) | private String simplifyZeros(final String edgeLabel) {
    class EdgeSubHaplotypeFinder (line 140) | protected static class EdgeSubHaplotypeFinder implements KBestSubHaplo...
      method EdgeSubHaplotypeFinder (line 150) | private EdgeSubHaplotypeFinder(final SeqVertex vertex, final BaseEdg...
      method calibrateEdgeScore (line 157) | private void calibrateEdgeScore(final double log10TotalMultiplicityA...
      method id (line 161) | @Override
      method label (line 166) | @Override
      method subFinderLabels (line 171) | @Override
      method getCount (line 176) | @Override
      method getKBest (line 181) | @Override
      method isReference (line 186) | @Override
      method score (line 191) | @Override
    method id (line 205) | @Override
    class ChildKBestSubHaplotype (line 219) | private static class ChildKBestSubHaplotype extends KBestHaplotype {
      method ChildKBestSubHaplotype (line 227) | public ChildKBestSubHaplotype(final SeqVertex vertex, final BaseEdge...
      method graph (line 234) | @Override
      method score (line 239) | @Override
      method rank (line 244) | @Override
      method head (line 249) | @Override
      method tail (line 254) | @Override
      method isReference (line 259) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/Route.java
  class Route (line 37) | public class Route<V extends BaseVertex, E extends BaseEdge> extends Pat...
    method Route (line 51) | public Route(final V initialVertex, final BaseGraph<V, E> graph) {
    method equals (line 57) | @Override
    method Route (line 77) | public Route(final Route<V,E> prefix, final V nextVertex) {
    method Route (line 92) | public Route(final V prevVertex, final Route<V,E> suffix) {
    method resolvePrefixEdge (line 99) | private static <V extends BaseVertex,E extends BaseEdge>  E resolvePre...
    method resolveSuffixEdge (line 111) | private static <V extends BaseVertex,E extends BaseEdge>  E resolveSuf...
    method Route (line 129) | public Route(final E initialEdge, final Route<V,E> suffix) {
    method Route (line 152) | protected Route(final Route<V, E> route) {
    method Route (line 167) | public Route(final Route<V, E> route, final E edge) {
    method isSuffix (line 173) | @Override
    method toString (line 187) | @Override
    method isRouteSuffix (line 195) | protected boolean isRouteSuffix(final Route<V,E> other) {
    method lastVertexIsForkOrJoin (line 222) | public boolean lastVertexIsForkOrJoin() {
    method getPrefixRouteWithLastVertexThatIsForkOrJoin (line 231) | public Route<V,E> getPrefixRouteWithLastVertexThatIsForkOrJoin() {
    method splicePrefix (line 246) | public Route<V,E> splicePrefix(final int length) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/RouteFinder.java
  class RouteFinder (line 33) | public class RouteFinder {
    method extendRouteBackwards (line 47) | private static <V extends BaseVertex, E extends BaseEdge> Route<V,E> e...
    method extendRouteForwards (line 106) | private static  <V extends BaseVertex, E extends BaseEdge> Route<V,E> ...
    method findRoute (line 141) | @SuppressWarnings("unchecked")

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/SeqGraph.java
  class SeqGraph (line 39) | public class SeqGraph extends BaseGraph<SeqVertex, BaseEdge> {
    class MyEdgeFactory (line 43) | private static class MyEdgeFactory implements EdgeFactory<SeqVertex, B...
      method createEdge (line 44) | @Override
    method SeqGraph (line 74) | public SeqGraph(final int kmer) {
    method simplifyGraph (line 83) | public void simplifyGraph() {
    method simplifyGraph (line 87) | protected void simplifyGraph(final int maxCycles) {
    method simplifyGraphOnce (line 121) | private boolean simplifyGraphOnce(final int iteration) {
    method printGraphSimplification (line 143) | private void printGraphSimplification(final File file) {
    method zipLinearChains (line 159) | public boolean zipLinearChains() {
    method isLinearChainStart (line 195) | private boolean isLinearChainStart(final SeqVertex source) {
    method traceLinearChain (line 211) | private LinkedList<SeqVertex> traceLinearChain(final SeqVertex zipStar...
    method mergeLinearChain (line 251) | protected boolean mergeLinearChain(final LinkedList<SeqVertex> linearC...
    method mergeLinearChainVertices (line 273) | protected SeqVertex mergeLinearChainVertices(final List<SeqVertex> ver...
    class VertexBasedTransformer (line 290) | private abstract class VertexBasedTransformer {
      method dontModifyGraphEvenIfPossible (line 296) | public boolean dontModifyGraphEvenIfPossible() { return dontModifyGr...
      method setDontModifyGraphEvenIfPossible (line 297) | public void setDontModifyGraphEvenIfPossible() { this.dontModifyGrap...
      method transformUntilComplete (line 302) | public boolean transformUntilComplete() {
      method tryToTransform (line 325) | abstract boolean tryToTransform(final SeqVertex v);
    class MergeDiamonds (line 341) | protected class MergeDiamonds extends VertexBasedTransformer {
      method tryToTransform (line 342) | @Override
    class MergeTails (line 398) | protected class MergeTails extends VertexBasedTransformer {
      method tryToTransform (line 399) | @Override
    class MergeCommonSuffices (line 433) | protected class MergeCommonSuffices extends VertexBasedTransformer {
      method tryToTransform (line 434) | @Override
    class SplitCommonSuffices (line 453) | protected class SplitCommonSuffices extends VertexBasedTransformer {
      method tryToTransform (line 456) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/SeqVertex.java
  class SeqVertex (line 47) | public final class SeqVertex extends BaseVertex {
    method SeqVertex (line 56) | public SeqVertex(final byte[] sequence) {
    method SeqVertex (line 64) | public SeqVertex(final String sequence) {
    method SeqVertex (line 72) | public SeqVertex(final SeqVertex toCopy) {
    method getId (line 81) | public int getId() {
    method toString (line 85) | @Override
    method equals (line 95) | @Override
    method hashCode (line 109) | @Override
    method withoutSuffix (line 120) | public SeqVertex withoutSuffix(final byte[] suffix) {
    method withoutPrefixAndSuffix (line 132) | public SeqVertex withoutPrefixAndSuffix(final byte[] prefix, final byt...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/SharedSequenceMerger.java
  class SharedSequenceMerger (line 39) | public class SharedSequenceMerger {
    method SharedSequenceMerger (line 40) | public SharedSequenceMerger() { }
    method merge (line 49) | public boolean merge(final SeqGraph graph, final SeqVertex v) {
    method canMerge (line 95) | private boolean canMerge(final SeqGraph graph, final SeqVertex v, fina...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
  class SharedVertexSequenceSplitter (line 76) | public class SharedVertexSequenceSplitter {
    method SharedVertexSequenceSplitter (line 94) | public SharedVertexSequenceSplitter(final SeqGraph graph, final Collec...
    method prefersPrefixMerging (line 113) | protected static boolean prefersPrefixMerging() {
    method splitAndUpdate (line 126) | public boolean splitAndUpdate(final SeqVertex top, final SeqVertex bot...
    method meetsMinMergableSequenceForEitherPrefixOrSuffix (line 137) | public boolean meetsMinMergableSequenceForEitherPrefixOrSuffix(final i...
    method meetsMinMergableSequenceForPrefix (line 146) | public boolean meetsMinMergableSequenceForPrefix(final int minCommonSe...
    method meetsMinMergableSequenceForSuffix (line 155) | public boolean meetsMinMergableSequenceForSuffix(final int minCommonSe...
    method split (line 164) | public void split() {
    method updateGraph (line 200) | public void updateGraph(final SeqVertex top, final SeqVertex bot) {
    method commonPrefixAndSuffixOfVertices (line 261) | protected static Pair<SeqVertex, SeqVertex> commonPrefixAndSuffixOfVer...
    method processEdgeToRemove (line 288) | private BaseEdge processEdgeToRemove(final SeqVertex v, final BaseEdge...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/TestGraph.java
  class TestGraph (line 35) | public final class TestGraph extends BaseGraph<DeBruijnVertex, BaseEdge> {
    class MyEdgeFactory (line 39) | private static class MyEdgeFactory implements EdgeFactory<DeBruijnVert...
      method createEdge (line 40) | @Override
    method TestGraph (line 49) | public TestGraph() {
    method TestGraph (line 57) | public TestGraph(int kmerSize) {
    method addKmersToGraph (line 68) | public void addKmersToGraph( final byte[] kmer1, final byte[] kmer2, f...
    method convertToSequenceGraph (line 89) | public SeqGraph convertToSequenceGraph() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/graphs/VertexOrder.java
  type VertexOrder (line 27) | public enum VertexOrder {
    method inverse (line 30) | public VertexOrder inverse() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/ErrorModel.java
  class ErrorModel (line 43) | public class ErrorModel {
    method ErrorModel (line 63) | public ErrorModel(final UnifiedArgumentCollection UAC,
    method isInformativeElement (line 156) | private boolean isInformativeElement(double[] likelihoods) {
    method ErrorModel (line 173) | public ErrorModel(double[] pvector) {
    method pileupElementMatches (line 181) | public static boolean pileupElementMatches(PileupElement pileupElement...
    method log10PoissonProbabilitySiteGivenQual (line 233) | private double log10PoissonProbabilitySiteGivenQual(byte q, int covera...
    method getSiteLogErrorProbabilityGivenQual (line 240) | public double getSiteLogErrorProbabilityGivenQual(int qual) {
    method getMaxQualityScore (line 244) | public byte getMaxQualityScore() {
    method getMinQualityScore (line 248) | public byte getMinQualityScore() {
    method getMinSignificantQualityScore (line 252) | public int getMinSignificantQualityScore() {
    method getMaxSignificantQualityScore (line 256) | public int getMaxSignificantQualityScore() {
    method getReferenceDepth (line 260) | public int getReferenceDepth() {
    method hasData (line 264) | public boolean hasData() {
    method getErrorModelVector (line 268) | public ProbabilityVector getErrorModelVector() {
    method toString (line 272) | public String toString() {
    method getTotalReferenceDepth (line 287) | public static int getTotalReferenceDepth(HashMap<String, ErrorModel> p...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
  class GeneralPloidyGenotypeLikelihoodsCalculationModel (line 59) | public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel e...
    method GeneralPloidyGenotypeLikelihoodsCalculationModel (line 63) | protected GeneralPloidyGenotypeLikelihoodsCalculationModel(UnifiedArgu...
    method getTrueAlleles (line 73) | protected VariantContext getTrueAlleles(final RefMetaDataTracker tracker,
    method parseLaneIDs (line 116) | public static Set<String> parseLaneIDs(Collection<String> readGroups) {
    method getLaneIDFromReadGroupString (line 132) | public static String getLaneIDFromReadGroupString(String readGroupID) {
    class PoolGenotypeData (line 145) | protected static class PoolGenotypeData {
      method PoolGenotypeData (line 152) | public PoolGenotypeData(final String name, final GeneralPloidyGenoty...
    method determineAlternateAlleles (line 161) | protected List<Allele> determineAlternateAlleles(final List<PoolGenoty...
    method getLikelihoods (line 209) | public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
    method getPerLaneErrorModels (line 303) | protected HashMap<String, ErrorModel> getPerLaneErrorModels(final RefM...
    method getPoolGenotypeLikelihoodObject (line 347) | protected abstract GeneralPloidyGenotypeLikelihoods getPoolGenotypeLik...
    method getInitialAllelesToUse (line 356) | protected abstract List<Allele> getInitialAllelesToUse(final RefMetaDa...
    method getFinalAllelesToUse (line 363) | protected abstract List<Allele> getFinalAllelesToUse(final RefMetaData...
    method getEndLocation (line 368) | protected abstract int getEndLocation(final RefMetaDataTracker tracker,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/GeneralPloidyIndelGenotypeLikelihoods.java
  class GeneralPloidyIndelGenotypeLikelihoods (line 46) | public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidy...
    method GeneralPloidyIndelGenotypeLikelihoods (line 56) | public GeneralPloidyIndelGenotypeLikelihoods(final List<Allele> alleles,
    method add (line 92) | public int add(ReadBackedPileup pileup, UnifiedArgumentCollection UAC) {
    method add (line 166) | private int add(ReadBackedPileup pileup, ErrorModel errorModel) {
    method getLikelihoodOfConformation (line 215) | public void getLikelihoodOfConformation(final ExactACset ACset,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
  class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel (line 46) | public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel exten...
    method GeneralPloidyIndelGenotypeLikelihoodsCalculationModel (line 67) | protected GeneralPloidyIndelGenotypeLikelihoodsCalculationModel(final ...
    method getPoolGenotypeLikelihoodObject (line 77) | protected GeneralPloidyGenotypeLikelihoods getPoolGenotypeLikelihoodOb...
    method getInitialAllelesToUse (line 88) | protected List<Allele> getInitialAllelesToUse(final RefMetaDataTracker...
    method getFinalAllelesToUse (line 112) | protected List<Allele> getFinalAllelesToUse(final RefMetaDataTracker t...
    method getEndLocation (line 127) | protected int getEndLocation(final RefMetaDataTracker tracker,

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/GenotypeLikelihoodsCalculationModel.java
  class GenotypeLikelihoodsCalculationModel (line 45) | public abstract class GenotypeLikelihoodsCalculationModel {
    type Model (line 50) | public enum Model {
    method GenotypeLikelihoodsCalculationModel (line 66) | protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollectio...
    method getLikelihoods (line 84) | public abstract VariantContext getLikelihoods(final RefMetaDataTracker...
    method getFilteredDepth (line 94) | protected int getFilteredDepth(ReadBackedPileup pileup) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/GenotypingModel.java
  type GenotypingModel (line 32) | public interface GenotypingModel {
    method calculateLikelihoods (line 47) | public <A extends Allele> GenotypingLikelihoods<A> calculateLikelihood...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/HomogeneousPloidyModel.java
  class HomogeneousPloidyModel (line 30) | public class HomogeneousPloidyModel implements PloidyModel, SampleList {
    method HomogeneousPloidyModel (line 45) | public HomogeneousPloidyModel(final SampleList samples, final int ploi...
    method sampleCount (line 53) | @Override
    method sampleAt (line 58) | @Override
    method sampleIndex (line 63) | @Override
    method samplePloidy (line 68) | @Override
    method checkSampleIndex (line 74) | private void checkSampleIndex(final int sampleIndex) {
    method isHomogeneous (line 81) | @Override
    method totalPloidy (line 86) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/IndelGenotypeLikelihoodsCalculationModel.java
  class IndelGenotypeLikelihoodsCalculationModel (line 56) | public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLi...
    method IndelGenotypeLikelihoodsCalculationModel (line 69) | protected IndelGenotypeLikelihoodsCalculationModel(final UnifiedArgume...
    method computeConsensusAlleles (line 79) | protected static List<Allele> computeConsensusAlleles(final ReferenceC...
    method getLikelihoods (line 90) | public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
    method getHaplotypeMapFromAlleles (line 157) | public static void getHaplotypeMapFromAlleles(final List<Allele> allel...
    method getEventLength (line 182) | public static int getEventLength(List<Allele> alleleList) {
    method getInitialAlleleList (line 201) | public static List<Allele> getInitialAlleleList(final RefMetaDataTrack...
    method getFilteredDepth (line 243) | protected int getFilteredDepth(ReadBackedPileup pileup) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/ProbabilityVector.java
  class ProbabilityVector (line 32) | public class ProbabilityVector {
    method ProbabilityVector (line 44) | public ProbabilityVector(double[] vec, boolean compressRange) {
    method ProbabilityVector (line 64) | public ProbabilityVector(double[] vec) {
    method ProbabilityVector (line 68) | public ProbabilityVector(ProbabilityVector other, boolean compressRang...
    method getMinVal (line 73) | public int getMinVal() { return minVal;}
    method getMaxVal (line 74) | public int getMaxVal() { return maxVal;}
    method getProbabilityVector (line 75) | public double[] getProbabilityVector() { return probabilityArray;}
    method getProbabilityVector (line 77) | public double[] getProbabilityVector(int minVal, int maxVal) {
    method getUncompressedProbabilityVector (line 88) | public double[] getUncompressedProbabilityVector() {
    method getLogProbabilityForIndex (line 103) | public double getLogProbabilityForIndex(int idx) {
    method compressVector (line 111) | public static ProbabilityVector compressVector(double[] vec ) {
    method getMinIdx (line 121) | private static int getMinIdx(double[] vec, int maxValIdx) {
    method getMaxIdx (line 139) | private static int getMaxIdx(double[] vec, int maxValIdx) {
    method logDotProduct (line 156) | public double logDotProduct(ProbabilityVector other) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/RefVsAnyResult.java
  class RefVsAnyResult (line 29) | public final class RefVsAnyResult {
    method getDP (line 43) | protected int getDP() { return AD_Ref_Any[0] + AD_Ref_Any[1]; }
    method capByHomRefLikelihood (line 48) | protected void capByHomRefLikelihood() {
    method RefVsAnyResult (line 57) | @Deprecated
    method RefVsAnyResult (line 70) | public RefVsAnyResult(final int likelihoodCapacity) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/ReferenceConfidenceMode.java
  type ReferenceConfidenceMode (line 27) | public enum ReferenceConfidenceMode {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/ReferenceConfidenceModel.java
  class ReferenceConfidenceModel (line 70) | public class ReferenceConfidenceModel {
    method ReferenceConfidenceModel (line 89) | public ReferenceConfidenceModel(final GenomeLocParser genomeLocParser,
    method getVCFHeaderLines (line 106) | public Set<VCFHeaderLine> getVCFHeaderLines() {
    method close (line 117) | public void close() {
    method calculateRefConfidence (line 143) | public List<VariantContext> calculateRefConfidence(final Haplotype ref...
    method getGLwithWorstGQ (line 223) | protected final GenotypeLikelihoods getGLwithWorstGQ(final GenotypeLik...
    method getIndelPLs (line 234) | protected final GenotypeLikelihoods getIndelPLs(final int ploidy, fina...
    method indelPLCache (line 245) | private final GenotypeLikelihoods indelPLCache(final int ploidy, final...
    method initializeIndelPLCache (line 253) | private synchronized GenotypeLikelihoods[] initializeIndelPLCache(fina...
    method calcGenotypeLikelihoodsOfRefVsAny (line 287) | @Deprecated
    method calcGenotypeLikelihoodsOfRefVsAny (line 326) | public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final String s...
    method getPileupsOverReference (line 384) | private List<ReadBackedPileup> getPileupsOverReference(final Haplotype...
    method getOverlappingVariantContext (line 419) | protected final VariantContext getOverlappingVariantContext(final Geno...
    method sumMismatchingQualities (line 443) | protected final int sumMismatchingQualities(final byte[] readBases,
    method isReadInformativeAboutIndelsOfSize (line 476) | protected boolean isReadInformativeAboutIndelsOfSize(final byte[] read...
    method calcNIndelInformativeReads (line 520) | protected final int calcNIndelInformativeReads(final ReadBackedPileup ...
    method createReferenceHaplotype (line 549) | public static Haplotype createReferenceHaplotype(final ActiveRegion ac...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/model/SNPGenotypeLikelihoodsCalculationModel.java
  class SNPGenotypeLikelihoodsCalculationModel (line 61) | public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLike...
    method SNPGenotypeLikelihoodsCalculationModel (line 69) | protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollec...
    method getLikelihoods (line 75) | public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
    method determineAlternateAlleles (line 198) | protected List<Allele> determineAlternateAlleles(final byte ref, final...
    method createBAQedPileup (line 228) | public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pile...
    class BAQedPileupElement (line 237) | public static class BAQedPileupElement extends PileupElement {
      method BAQedPileupElement (line 238) | public BAQedPileupElement( final PileupElement PE ) {
      method getQual (line 242) | @Override
    class SampleGenotypeData (line 251) | private static class SampleGenotypeData {
      method SampleGenotypeData (line 257) | public SampleGenotypeData(final String name, final DiploidSNPGenotyp...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readlikelihood/PairHMMLikelihoodCalculationEngine.java
  class PairHMMLikelihoodCalculationEngine (line 59) | public class PairHMMLikelihoodCalculationEngine implements ReadLikelihoo...
    method initialValue (line 72) | @Override
    type PCR_ERROR_MODEL (line 100) | public enum PCR_ERROR_MODEL {
    method PairHMMLikelihoodCalculationEngine (line 139) | public PairHMMLikelihoodCalculationEngine(final byte constantGCP, fina...
    method close (line 159) | @Override
    method capMinimumReadQualities (line 165) | private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQu...
    method modifyReadQualities (line 182) | private List<GATKSAMRecord> modifyReadQualities(final List<GATKSAMReco...
    method initializePairHMM (line 212) | private void initializePairHMM(final List<Haplotype> haplotypes, final...
    method finalizePairHMM (line 234) | private void finalizePairHMM() {
    method computeReadLikelihoods (line 238) | @Override
    method computeReadLikelihoods (line 261) | private void computeReadLikelihoods(final ReadLikelihoods.Matrix<Haplo...
    method buildGapContinuationPenalties (line 274) | private Map<GATKSAMRecord, byte[]> buildGapContinuationPenalties(final...
    method writeDebugLikelihoods (line 284) | private void writeDebugLikelihoods(final ReadLikelihoods.Matrix<Haplot...
    method writeDebugLikelihoods (line 295) | private void writeDebugLikelihoods(final GATKSAMRecord processedRead, ...
    method computeDiploidHaplotypeLikelihoods (line 306) | @Deprecated
    method computeDiploidHaplotypeLikelihoods (line 314) | @Deprecated
    method normalizeDiploidLikelihoodMatrixFromLog10 (line 356) | @Deprecated
    method initializePCRErrorModel (line 390) | private void initializePCRErrorModel() {
    method getErrorModelAdjustedQual (line 404) | protected static byte getErrorModelAdjustedQual(final int repeatLength...
    method applyPCRErrorModel (line 408) | protected void applyPCRErrorModel(final byte[] readBases, final byte[]...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readlikelihood/ReadLikelihoodCalculationEngine.java
  type ReadLikelihoodCalculationEngine (line 35) | public interface ReadLikelihoodCalculationEngine {
    type Implementation (line 37) | enum Implementation {
    method computeReadLikelihoods (line 68) | public ReadLikelihoods<Haplotype> computeReadLikelihoods(AssemblyResul...
    method close (line 71) | public void close();

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readlikelihood/ReadLikelihoods.java
  class ReadLikelihoods (line 55) | public class ReadLikelihoods<A extends Allele> implements SampleList, Al...
    method ReadLikelihoods (line 128) | @SuppressWarnings("unchecked")
    method setupIndexes (line 157) | private void setupIndexes(final Map<String, List<GATKSAMRecord>> reads...
    method setupSampleData (line 164) | private void setupSampleData(final int sampleIndex, final Map<String, ...
    method clone (line 186) | public ReadLikelihoods<A> clone() {
    method ReadLikelihoods (line 210) | @SuppressWarnings("unchecked")
    method findReferenceAllele (line 227) | private int findReferenceAllele(final AlleleList<A> alleles) {
    method sampleIndex (line 242) | public int sampleIndex(final String sample) {
    method sampleCount (line 251) | public int sampleCount() {
    method sampleAt (line 262) | public String sampleAt(final int sampleIndex) {
    method alleleIndex (line 273) | public int alleleIndex(final A allele) {
    method alleleCount (line 282) | @SuppressWarnings("unused")
    method alleleAt (line 294) | public A alleleAt(final int alleleIndex) {
    method sampleReads (line 305) | public List<GATKSAMRecord> sampleReads(final int sampleIndex) {
    method sampleMatrix (line 321) | public Matrix<A> sampleMatrix(final int sampleIndex) {
    method normalizeLikelihoods (line 339) | public void normalizeLikelihoods(final boolean bestToZero, final doubl...
    method normalizeLikelihoodsPerRead (line 361) | private void normalizeLikelihoodsPerRead(final boolean bestToZero, fin...
    method samples (line 404) | public List<String> samples() {
    method alleles (line 422) | public List<A> alleles() {
    method searchBestAllele (line 435) | private BestAllele searchBestAllele(final int sampleIndex, final int r...
    method changeReads (line 460) | public void changeReads(final Map<GATKSAMRecord, GATKSAMRecord> readRe...
    type Matrix (line 485) | public interface Matrix<A extends Allele> extends AlleleList<A> {
      method reads (line 492) | public List<GATKSAMRecord> reads();
      method alleles (line 499) | public List<A> alleles();
      method set (line 510) | public void set(final int alleleIndex, final int readIndex, final do...
      method get (line 522) | public double get(final int alleleIndex, final int readIndex);
      method alleleIndex (line 531) | @SuppressWarnings("unused")
      method readIndex (line 542) | @SuppressWarnings("unused")
      method alleleCount (line 550) | public int alleleCount();
      method readCount (line 557) | public int readCount();
      method alleleAt (line 566) | public A alleleAt(final int alleleIndex);
      method readAt (line 575) | public GATKSAMRecord readAt(final int readIndex);
      method copyAlleleLikelihoods (line 585) | public void copyAlleleLikelihoods(final int alleleIndex, final doubl...
    method marginalize (line 600) | public <B extends Allele> ReadLikelihoods<B> marginalize(final Map<B, ...
    method marginalize (line 649) | public <B extends Allele> ReadLikelihoods<B> marginalize(final Map<B, ...
    method overlappingReadIndicesBySampleIndex (line 697) | private int[][] overlappingReadIndicesBySampleIndex(final GenomeLoc ov...
    method unclippedReadOverlapsRegion (line 719) | public static boolean unclippedReadOverlapsRegion(final GATKSAMRecord ...
    method unclippedReadOverlapsRegion (line 723) | private static boolean unclippedReadOverlapsRegion(final GATKSAMRecord...
    method marginalLikelihoods (line 738) | private double[][][] marginalLikelihoods(final int oldAlleleCount, fin...
    method oldToNewAlleleIndexMap (line 769) | private <B extends Allele> int[] oldToNewAlleleIndexMap(final Map<B, L...
    method filterToOnlyOverlappingUnclippedReads (line 806) | @SuppressWarnings("unused")
    method filterPoorlyModeledReads (line 845) | public void filterPoorlyModeledReads(final double maximumErrorPerBase) {
    method readIsPoorlyModelled (line 868) | protected boolean readIsPoorlyModelled(final int sampleIndex, final in...
    method addReads (line 890) | public void addReads(final Map<String, List<GATKSAMRecord>> readsBySam...
    method extendsLikelihoodArrays (line 914) | private void extendsLikelihoodArrays(double initialLikelihood, int sam...
    method appendReads (line 925) | private void appendReads(final List<GATKSAMRecord> newSampleReads, fin...
    method addNonReferenceAllele (line 957) | public void addNonReferenceAllele(final A nonRefAllele) {
    method addNonReferenceAlleleLikelihoodsPerSample (line 983) | private void addNonReferenceAlleleLikelihoodsPerSample(final int allel...
    method contaminationDownsampling (line 997) | public void contaminationDownsampling(final Map<String, Double> perSam...
    method bestAlleles (line 1030) | public Collection<BestAllele> bestAlleles() {
    method readsByBestAlleleMap (line 1048) | public Map<A, List<GATKSAMRecord>> readsByBestAlleleMap(final int samp...
    method readsByBestAlleleMap (line 1064) | @SuppressWarnings("unused")
    method readsByBestAlleleMap (line 1077) | private void readsByBestAlleleMap(final int sampleIndex, final Map<A, ...
    method readIndex (line 1096) | @SuppressWarnings("unused")
    method readCount (line 1110) | public int readCount() {
    method sampleReadCount (line 1125) | public int sampleReadCount(int sampleIndex) {
    class BestAllele (line 1133) | public class BestAllele {
      method BestAllele (line 1162) | private BestAllele(final int sampleIndex, final int readIndex, final...
      method isInformative (line 1171) | public boolean isInformative() {
    method removeSampleReads (line 1176) | private void removeSampleReads(final int sampleIndex, final IntArrayLi...
    method removeSampleReads (line 1216) | private void removeSampleReads(final int sampleIndex, final Collection...
    method readIndexBySampleIndex (line 1270) | private Object2IntMap<GATKSAMRecord> readIndexBySampleIndex(final int ...
    method toPerReadAlleleLikelihoodMap (line 1287) | @Deprecated
    method toPerReadAlleleLikelihoodMap (line 1300) | @Deprecated
    class SampleMatrix (line 1319) | private class SampleMatrix implements Matrix<A> {
      method SampleMatrix (line 1323) | private SampleMatrix(final int sampleIndex) {
      method reads (line 1327) | @Override
      method alleles (line 1332) | @Override
      method set (line 1337) | @Override
      method get (line 1342) | @Override
      method alleleIndex (line 1347) | @Override
      method readIndex (line 1352) | @Override
      method alleleCount (line 1357) | @Override
      method readCount (line 1362) | @Override
      method alleleAt (line 1367) | @Override
      method readAt (line 1372) | @Override
      method copyAlleleLikelihoods (line 1382) | @Override
    method checkSampleIndex (line 1397) | private void checkSampleIndex(final int sampleIndex) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readlikelihood/ReadLikelihoodsArrayCache.java
  class ReadLikelihoodsArrayCache (line 29) | public class ReadLikelihoodsArrayCache {
    method getDoubleArray (line 32) | public double[][] getDoubleArray(int alleleCount, int sampleReadCount) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/DanglingChainMergingGraph.java
  class DanglingChainMergingGraph (line 38) | public abstract class DanglingChainMergingGraph extends BaseGraph<MultiD...
    method DanglingChainMergingGraph (line 49) | protected DanglingChainMergingGraph(final int kmerSize, final EdgeFact...
    method setMaxMismatchesInDanglingHead (line 53) | protected void setMaxMismatchesInDanglingHead(final int maxMismatchesI...
    class MyEdgeFactory (line 60) | protected static class MyEdgeFactory implements EdgeFactory<MultiDeBru...
      method MyEdgeFactory (line 63) | public MyEdgeFactory(int numPruningSamples) {
      method createEdge (line 67) | @Override
      method createEdge (line 72) | public MultiSampleEdge createEdge(final boolean isRef, final int mul...
    class DanglingChainMergeHelper (line 81) | protected static final class DanglingChainMergeHelper {
      method DanglingChainMergeHelper (line 86) | public DanglingChainMergeHelper(final List<MultiDeBruijnVertex> dang...
    method recoverDanglingTails (line 105) | public void recoverDanglingTails(final int pruneFactor, final int minD...
    method recoverDanglingHeads (line 126) | public void recoverDanglingHeads(final int pruneFactor, final int minD...
    method recoverDanglingTail (line 157) | protected int recoverDanglingTail(final MultiDeBruijnVertex vertex, fi...
    method recoverDanglingHead (line 179) | protected int recoverDanglingHead(final MultiDeBruijnVertex vertex, fi...
    method cigarIsOkayToMerge (line 201) | protected boolean cigarIsOkayToMerge(final Cigar cigar, final boolean ...
    method mergeDanglingTail (line 229) | protected int mergeDanglingTail(final DanglingChainMergeHelper danglin...
    method mergeDanglingHead (line 268) | protected int mergeDanglingHead(final DanglingChainMergeHelper danglin...
    method generateCigarAgainstDownwardsReferencePath (line 301) | protected DanglingChainMergeHelper generateCigarAgainstDownwardsRefere...
    method generateCigarAgainstUpwardsReferencePath (line 329) | protected DanglingChainMergeHelper generateCigarAgainstUpwardsReferenc...
    method findPathUpwardsToLowestCommonAncestor (line 357) | protected List<MultiDeBruijnVertex> findPathUpwardsToLowestCommonAnces...
    method findPathDownwardsToHighestCommonDescendantOfReference (line 386) | protected List<MultiDeBruijnVertex> findPathDownwardsToHighestCommonDe...
    type TraversalDirection (line 405) | private enum TraversalDirection {
    method getReferencePath (line 418) | protected List<MultiDeBruijnVertex> getReferencePath(final MultiDeBrui...
    method getBasesForPath (line 440) | public byte[] getBasesForPath(final List<MultiDeBruijnVertex> path, fi...
    method bestPrefixMatch (line 465) | protected int bestPrefixMatch(final byte[] path1, final byte[] path2, ...
    method getMaxMismatches (line 489) | private int getMaxMismatches(final int lengthOfDanglingBranch) {
    method extendDanglingPathAgainstReference (line 493) | protected boolean extendDanglingPathAgainstReference(final DanglingCha...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/HaplotypeGraph.java
  class HaplotypeGraph (line 51) | public class HaplotypeGraph extends ReadThreadingGraph {
    method HaplotypeGraph (line 128) | public HaplotypeGraph(final String string) {
    method HaplotypeGraph (line 141) | public HaplotypeGraph(final int kmerSize) {
    method getReferenceVertices (line 153) | public Set<MultiDeBruijnVertex> getReferenceVertices() {
    method getHaplotypeRoute (line 165) | public HaplotypeRoute getHaplotypeRoute(final Haplotype haplotype) {
    method buildHaplotypeRoute (line 180) | private HaplotypeRoute buildHaplotypeRoute(final Haplotype haplotype) {
    method getReferenceBases (line 193) | @SuppressWarnings("unused")
    method getReferenceHaplotype (line 203) | public Haplotype getReferenceHaplotype() {
    method HaplotypeGraph (line 216) | public HaplotypeGraph(final int kmerSize, final List<Haplotype> haplot...
    method findReferenceHaplotypeOrFail (line 241) | private Haplotype findReferenceHaplotypeOrFail(final List<Haplotype> h...
    method HaplotypeGraph (line 254) | public HaplotypeGraph(final ReadThreadingGraph template, final List<Ha...
    method updateHaplotypeStructures (line 278) | private void updateHaplotypeStructures() {
    method buildHaplotypesByVertex (line 315) | private Map<MultiDeBruijnVertex, Set<HaplotypeRoute>> buildHaplotypesB...
    method printGraph (line 345) | public void printGraph(final String fileName) {
    method printGraph (line 352) | @Override
    method findStart (line 372) | @Override
    method hasNonReferenceEnds (line 382) | public boolean hasNonReferenceEnds() {
    method mergeCommonChains (line 414) | public void mergeCommonChains() {
    method mergeCommonChainsComposeMergeSet (line 446) | private MultiDeBruijnVertex mergeCommonChainsComposeMergeSet(final Set...
    method mergeCommonChainsInitialize (line 499) | private void mergeCommonChainsInitialize(final Set<MultiDeBruijnVertex...
    method mergeVertices (line 515) | private void mergeVertices(final MultiDeBruijnVertex refVertex, final ...
    method uniqueKmerMap (line 568) | public Map<Kmer,MultiDeBruijnVertex> uniqueKmerMap() {
    method equals (line 572) | @Override
    method toString (line 582) | @Override
    method getHaplotypes (line 591) | public Set<Haplotype> getHaplotypes() {
    method getHaplotypeRouteMap (line 600) | public Map<Haplotype,HaplotypeRoute> getHaplotypeRouteMap() {
    method getEnclosingHaplotypeRoutes (line 610) | public Set<HaplotypeRoute> getEnclosingHaplotypeRoutes(final MultiDeBr...
    method getReferenceRoute (line 626) | public HaplotypeRoute getReferenceRoute() {
    method equals (line 650) | public boolean equals(HaplotypeGraph other) {
    method equals$ReferencePaths (line 690) | private boolean equals$ReferencePaths(final HaplotypeGraph g1, final H...
    method equalsBuildChildrenBySuffixMap (line 711) | private static Map<String, MultiDeBruijnVertex> equalsBuildChildrenByS...
    method equals$matchVertexBySequenceMaps (line 720) | private static List<Pair<MultiDeBruijnVertex, MultiDeBruijnVertex>> eq...
    method equalsBuildSourceBySequenceMap (line 736) | private static Map<String, MultiDeBruijnVertex> equalsBuildSourceBySeq...
    method equalsCollisionResolverExtendedSequence (line 776) | private static String equalsCollisionResolverExtendedSequence(final Ha...
    method calculateAnchorableVertexSet (line 850) | private Set<MultiDeBruijnVertex> calculateAnchorableVertexSet() {
    method getAnchorableVertices (line 915) | public Set<MultiDeBruijnVertex> getAnchorableVertices() {
    method calculateRejoins (line 953) | @Deprecated

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/HaplotypeRoute.java
  class HaplotypeRoute (line 36) | public class HaplotypeRoute extends Route<MultiDeBruijnVertex,MultiSampl...
    method HaplotypeRoute (line 49) | public HaplotypeRoute(final Route<MultiDeBruijnVertex, MultiSampleEdge...
    method subRoute (line 68) | @SuppressWarnings("unused")
    method vertexSet (line 88) | public Set<MultiDeBruijnVertex> vertexSet() {
    method getVertexPosition (line 102) | public int getVertexPosition(final MultiDeBruijnVertex vertex) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/LocalAssemblyEngine.java
  class LocalAssemblyEngine (line 61) | public abstract class LocalAssemblyEngine {
    method LocalAssemblyEngine (line 90) | protected LocalAssemblyEngine(final int numBestHaplotypesPerGraph) {
    method assemble (line 104) | protected abstract List<AssemblyResult> assemble(List<GATKSAMRecord> r...
    method runLocalAssembly (line 117) | public AssemblyResultSet runLocalAssembly(final ActiveRegion activeReg...
    method findBestPaths (line 185) | protected List<Haplotype> findBestPaths(final List<SeqGraph> graphs, f...
    method pathIsTooDivergentFromReference (line 275) | private boolean pathIsTooDivergentFromReference(final Cigar c) {
    method printDebugGraphTransform (line 290) | protected void printDebugGraphTransform(final BaseGraph graph, final F...
    method cleanupSeqGraph (line 299) | protected AssemblyResult cleanupSeqGraph(final SeqGraph seqGraph) {
    method sanityCheckGraph (line 341) | private <T extends BaseVertex, E extends BaseEdge> void sanityCheckGra...
    method sanityCheckReferenceGraph (line 351) | private <T extends BaseVertex, E extends BaseEdge> void sanityCheckRef...
    method printGraphs (line 371) | private void printGraphs(final List<SeqGraph> graphs) {
    method getPruneFactor (line 396) | public int getPruneFactor() {
    method setPruneFactor (line 400) | public void setPruneFactor(int pruneFactor) {
    method shouldErrorCorrectKmers (line 404) | public boolean shouldErrorCorrectKmers() {
    method setErrorCorrectKmers (line 408) | public void setErrorCorrectKmers(boolean errorCorrectKmers) {
    method setGraphWriter (line 412) | public void setGraphWriter(PrintStream graphWriter) {
    method getMinBaseQualityToUseInAssembly (line 416) | public byte getMinBaseQualityToUseInAssembly() {
    method setMinBaseQualityToUseInAssembly (line 420) | public void setMinBaseQualityToUseInAssembly(byte minBaseQualityToUseI...
    method isDebug (line 424) | public boolean isDebug() {
    method setDebug (line 428) | public void setDebug(boolean debug) {
    method isAllowCyclesInKmerGraphToGeneratePaths (line 432) | public boolean isAllowCyclesInKmerGraphToGeneratePaths() {
    method setAllowCyclesInKmerGraphToGeneratePaths (line 436) | public void setAllowCyclesInKmerGraphToGeneratePaths(boolean allowCycl...
    method isDebugGraphTransformations (line 440) | public boolean isDebugGraphTransformations() {
    method setDebugGraphTransformations (line 444) | public void setDebugGraphTransformations(boolean debugGraphTransformat...
    method isRecoverDanglingBranches (line 448) | public boolean isRecoverDanglingBranches() {
    method setRecoverDanglingBranches (line 452) | public void setRecoverDanglingBranches(final boolean recoverDanglingBr...
    method setMinDanglingBranchLength (line 456) | public void setMinDanglingBranchLength(final int minDanglingBranchLeng...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/MultiDeBruijnVertex.java
  class MultiDeBruijnVertex (line 36) | public final class MultiDeBruijnVertex extends DeBruijnVertex {
    method MultiDeBruijnVertex (line 49) | MultiDeBruijnVertex(byte[] sequence) {
    method equals (line 53) | @Override
    method toString (line 63) | @Override
    method addRead (line 78) | protected void addRead(final String name) {
    method hashCode (line 83) | @Override
    method additionalInfo (line 86) | @Override
    method getId (line 91) | int getId() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/ReadThreadingAssembler.java
  class ReadThreadingAssembler (line 39) | public class ReadThreadingAssembler extends LocalAssemblyEngine {
    method ReadThreadingAssembler (line 61) | public ReadThreadingAssembler() {
    method ReadThreadingAssembler (line 65) | public ReadThreadingAssembler(final int maxAllowedPathsForReadThreadin...
    method ReadThreadingAssembler (line 73) | protected ReadThreadingAssembler(final int maxAllowedPathsForReadThrea...
    method setJustReturnRawGraph (line 80) | protected void setJustReturnRawGraph(boolean justReturnRawGraph) {
    method addResult (line 84) | private void addResult(final List<AssemblyResult> results, final Assem...
    method assemble (line 89) | @Override
    method createGraph (line 125) | protected AssemblyResult createGraph(final List<GATKSAMRecord> reads,
    method toString (line 216) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/ReadThreadingGraph.java
  class ReadThreadingGraph (line 41) | public class ReadThreadingGraph extends DanglingChainMergingGraph
    method ReadThreadingGraph (line 92) | public ReadThreadingGraph(final int kmerSize) {
    method getNextVertices (line 104) | protected Set<MultiDeBruijnVertex> getNextVertices(final MultiDeBruijn...
    method ReadThreadingGraph (line 128) | protected ReadThreadingGraph(final int kmerSize, final boolean debugGr...
    method resetToInitialState (line 141) | private void resetToInitialState() {
    method addSequence (line 155) | protected void addSequence(final byte[] sequence, final boolean isRef) {
    method addSequence (line 164) | public void addSequence(final String seqName, final byte[] sequence, f...
    method addSequence (line 173) | public void addSequence(final String seqName, final byte[] sequence, f...
    method addSequence (line 187) | public void addSequence(final String seqName, final String sampleName,...
    method threadSequence (line 207) | private void threadSequence(final SequenceForKmers seqForKmers) {
    method findStart (line 241) | protected int findStart(final SequenceForKmers seqForKmers) {
    method isThreadingStart (line 262) | protected boolean isThreadingStart(final Kmer kmer) {
    method setThreadingStartOnlyAtExistingVertex (line 274) | public void setThreadingStartOnlyAtExistingVertex(final boolean value) {
    method getThreadingStartOnlyAtExistingVertex (line 284) | public boolean getThreadingStartOnlyAtExistingVertex() {
    method buildGraphIfNecessary (line 292) | public void buildGraphIfNecessary() {
    method removeVertex (line 323) | @Override
    method removeSingletonOrphanVertices (line 335) | public void removeSingletonOrphanVertices() {
    method isLowComplexity (line 353) | public boolean isLowComplexity() {
    class NonUniqueResult (line 360) | private static class NonUniqueResult {
      method NonUniqueResult (line 364) | private NonUniqueResult(Set<Kmer> nonUniques, int kmerSize) {
    method determineKmerSizeAndNonUniques (line 379) | protected NonUniqueResult determineKmerSizeAndNonUniques(final int min...
    method getAllPendingSequences (line 419) | private Collection<SequenceForKmers> getAllPendingSequences() {
    method determineNonUniqueKmers (line 433) | static protected Collection<Kmer> determineNonUniqueKmers(final Sequen...
    method convertToSequenceGraph (line 445) | @Override
    method increaseCountsInMatchedKmers (line 451) | private void increaseCountsInMatchedKmers(final SequenceForKmers seqFo...
    method getOrCreateKmerVertex (line 477) | private MultiDeBruijnVertex getOrCreateKmerVertex(final byte[] sequenc...
    method getUniqueKmerVertex (line 489) | private MultiDeBruijnVertex getUniqueKmerVertex(final Kmer kmer, final...
    method createVertex (line 504) | private MultiDeBruijnVertex createVertex(final Kmer kmer) {
    method extendChainByOne (line 531) | private MultiDeBruijnVertex extendChainByOne(final MultiDeBruijnVertex...
    method addRead (line 563) | protected void addRead(final GATKSAMRecord read) {
    method baseIsUsableForAssembly (line 596) | protected boolean baseIsUsableForAssembly(final byte base, final byte ...
    method getNonUniqueKmers (line 605) | protected Set<Kmer> getNonUniqueKmers() {
    method toString (line 609) | @Override
    method findKmer (line 617) | @Override
    method ReadThreadingGraph (line 641) | public ReadThreadingGraph(final String s) {
    method kmerSizeFromString (line 656) | private static int kmerSizeFromString(final String str) {
    method applyString (line 674) | private void applyString(final String str) {
    method pathElementId (line 751) | private static String pathElementId(final String element) {
    method pathElementSeq (line 772) | private static String pathElementSeq(final String element) {
    method extendSequence (line 788) | private static byte[] extendSequence(final byte[] sequence, final byte...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/haplotypecaller/readthreading/SequenceForKmers.java
  class SequenceForKmers (line 29) | final class SequenceForKmers {
    method SequenceForKmers (line 39) | SequenceForKmers(final String name, byte[] sequence, int start, int st...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/indelrealigner/ConsensusDeterminationModel.java
  type ConsensusDeterminationModel (line 27) | public enum ConsensusDeterminationModel {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/indelrealigner/ConstrainedMateFixingManager.java
  class ConstrainedMateFixingManager (line 44) | public class ConstrainedMateFixingManager {
    method remove (line 92) | private SAMRecord remove(PriorityQueue<SAMRecord> queue) {
    class SAMRecordHashObject (line 99) | private static class SAMRecordHashObject {
      method SAMRecordHashObject (line 103) | public SAMRecordHashObject(SAMRecord record, boolean wasModified) {
    method ConstrainedMateFixingManager (line 115) | public ConstrainedMateFixingManager(final GenomeLocParser genomeLocPar...
    method getNReadsInQueue (line 128) | public int getNReadsInQueue() {
    method getReadsInQueueForTesting (line 137) | protected List<SAMRecord> getReadsInQueueForTesting() {
    method canMoveReads (line 141) | public boolean canMoveReads(GenomeLoc earliestPosition) {
    method noReadCanMoveBefore (line 150) | private boolean noReadCanMoveBefore(int pos, SAMRecord addedRead) {
    method addRead (line 154) | public void addRead(SAMRecord newRead, boolean readWasModified) {
    method addReads (line 158) | public void addReads(List<GATKSAMRecord> newReads, Set<GATKSAMRecord> ...
    method addRead (line 163) | protected void addRead(SAMRecord newRead, boolean readWasModified, boo...
    method writeRead (line 274) | private void writeRead(SAMRecord read) {
    method iSizeTooBigToMove (line 282) | public boolean iSizeTooBigToMove(SAMRecord read) {
    method iSizeTooBigToMove (line 286) | public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertS...
    method purgeUnmodifiedMates (line 291) | private void purgeUnmodifiedMates() {
    method pairedReadIsMovable (line 302) | private boolean pairedReadIsMovable(SAMRecord read) {
    method close (line 309) | public void close() {
    method getResultRecords (line 316) | public List<SAMRecord> getResultRecords() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/indelrealigner/IndelRealigner.java
  class IndelRealigner (line 65) | public class IndelRealigner extends ReadWalker {
    method IndelRealigner (line 106) | public IndelRealigner(GenomeLocParser genomeLocParser,
    method initialize (line 115) | @Override
    method getFilter (line 125) | @Override
    method map (line 131) | @Override
    method emit (line 180) | private void emit(final GATKSAMRecord read) {
    method emitReadLists (line 192) | private void emitReadLists() {
    method doNotTryToClean (line 202) | private boolean doNotTryToClean(GATKSAMRecord read) {
    method populateKnownIndels (line 214) | private void populateKnownIndels(RefMetaDataTracker metaDataTracker) {
    method abortCleanForCurrentInterval (line 223) | private void abortCleanForCurrentInterval() {
    method cleanAndCallMap (line 229) | private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read,...
    method mismatchQualitySumIgnoreCigar (line 250) | private static int mismatchQualitySumIgnoreCigar(final AlignedRead aRe...
    method clean (line 276) | private void clean(ReadBin readsToClean) {
    method generateAlternateConsensesFromKnownIndels (line 404) | private void generateAlternateConsensesFromKnownIndels(final Set<Conse...
    method determineReadsThatNeedCleaning (line 422) | private long determineReadsThatNeedCleaning(final List<GATKSAMRecord> ...
    method generateAlternateConsensesFromReads (line 480) | private void generateAlternateConsensesFromReads(final LinkedList<Alig...
    method createAndAddAlternateConsensus (line 503) | private void createAndAddAlternateConsensus(final byte[] read, final S...
    method createAlternateConsensus (line 513) | private Consensus createAlternateConsensus(final int indexOnRef, final...
    method createAlternateConsensus (line 583) | private Consensus createAlternateConsensus(final int indexOnRef, final...
    method findBestOffset (line 617) | private Pair<Integer, Integer> findBestOffset(final byte[] ref, final ...
    method updateRead (line 656) | private boolean updateRead(final Cigar altCigar, final int altPosOnRef...
    method alternateReducesEntropy (line 760) | private boolean alternateReducesEntropy(final List<AlignedRead> reads,...
    method unclipCigar (line 844) | protected static Cigar unclipCigar(Cigar cigar) {
    method isClipOperator (line 853) | private static boolean isClipOperator(CigarOperator op) {
    method reclipCigar (line 857) | protected static Cigar reclipCigar(Cigar cigar, SAMRecord read) {
    class AlignedRead (line 877) | private class AlignedRead {
      method AlignedRead (line 886) | public AlignedRead(GATKSAMRecord read) {
      method getRead (line 891) | public GATKSAMRecord getRead() {
      method getReadLength (line 895) | public int getReadLength() {
      method getReadBases (line 899) | public byte[] getReadBases() {
      method getBaseQualities (line 905) | public byte[] getBaseQualities() {
      method getUnclippedBases (line 912) | private void getUnclippedBases() {
      method getCigar (line 951) | public Cigar getCigar() {
      method setCigar (line 955) | public void setCigar(Cigar cigar) {
      method setCigar (line 960) | public void setCigar(Cigar cigar, boolean fixClippedCigar) {
      method reclipCigar (line 985) | private Cigar reclipCigar(Cigar cigar) {
      method setAlignmentStart (line 990) | public void setAlignmentStart(int start) {
      method getAlignmentStart (line 994) | public int getAlignmentStart() {
      method getOriginalAlignmentStart (line 998) | public int getOriginalAlignmentStart() {
      method finalizeUpdate (line 1004) | public boolean finalizeUpdate() {
      method setMismatchScoreToReference (line 1039) | public void setMismatchScoreToReference(int score) {
      method getMismatchScoreToReference (line 1043) | public int getMismatchScoreToReference() {
      method setAlignerMismatchScore (line 1047) | public void setAlignerMismatchScore(long score) {
      method getAlignerMismatchScore (line 1051) | public long getAlignerMismatchScore() {
    method realignmentProducesBadAlignment (line 1062) | private boolean realignmentProducesBadAlignment(final GATKSAMRecord re...
    method realignmentProducesBadAlignment (line 1075) | protected static boolean realignmentProducesBadAlignment(final GATKSAM...
    method onTraversalDone (line 1079) | @Override
    method getResultSam (line 1096) | public List<SAMRecord> getResultSam() {
    class Consensus (line 1100) | private static class Consensus {
      method Consensus (line 1107) | public Consensus(byte[] str, Cigar cigar, int positionOnReference) {
      method equals (line 1115) | @Override
      method equals (line 1120) | public boolean equals(Consensus c) {
      method hashCode (line 1124) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/indelrealigner/ReadBin.java
  class ReadBin (line 37) | class ReadBin implements HasGenomeLocation {
    method ReadBin (line 45) | public ReadBin(final GenomeLocParser parser, final int referencePaddin...
    method add (line 52) | public void add(GATKSAMRecord read) {
    method getReads (line 64) | public List<GATKSAMRecord> getReads() {
    method getReference (line 68) | public byte[] getReference(RefContentProvider refContentProvider) {
    method getLocation (line 79) | public GenomeLoc getLocation() {
    method size (line 83) | public int size() {
    method clear (line 87) | public void clear() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/AbstractPowerCalculator.java
  class AbstractPowerCalculator (line 29) | public class AbstractPowerCalculator {
    class PowerCacheKey (line 34) | protected static class PowerCacheKey {
      method PowerCacheKey (line 38) | public PowerCacheKey(int n, double delta) {
      method equals (line 43) | @Override
      method hashCode (line 56) | @Override
    method calculateLogLikelihood (line 67) | protected static double calculateLogLikelihood(int depth, int alts, do...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/CallStatsGenerator.java
  class CallStatsGenerator (line 34) | public class CallStatsGenerator {
    method CallStatsGenerator (line 40) | public CallStatsGenerator(boolean enableQscoreOutput) {
    method setupOutputColumns (line 45) | private List<String> setupOutputColumns(boolean enableQscoreOutput) {
    method generateHeader (line 110) | public String generateHeader() {
    method generateCallStats (line 114) | public String generateCallStats(CandidateMutation candidate) {
    method generate (line 187) | private String generate(HashMap<String, String> d) {
    method format (line 198) | private String format(String s) { return s; }
    method format (line 199) | private String format(Integer i) { return fmt.format(i); }
    method format (line 200) | private String format(Double d) {
    method format (line 207) | private String format(List<Integer> ints) {
    method getSiteInfoString (line 215) | private String getSiteInfoString(boolean isDbsnpSite, boolean isCosmic...
    method getStrandTableString (line 229) | private String getStrandTableString(int[] ci) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/CandidateMutation.java
  class CandidateMutation (line 35) | public class CandidateMutation {
    method CandidateMutation (line 115) | public CandidateMutation(GenomeLoc location, char refAllele) {
    method getScore (line 120) | public int getScore() {
    method isGermlineAtRisk (line 124) | public boolean isGermlineAtRisk() {
    method getCountOfNormalsObservedIn (line 128) | public int getCountOfNormalsObservedIn() {
    method setRejectionReasons (line 145) | public void setRejectionReasons(List<String> rejectionReasons) {
    method addRejectionReason (line 152) | public void addRejectionReason(String reason) {
    method getStrandContingencyTable (line 164) | public int[] getStrandContingencyTable() {
    method setStrandContingencyTable (line 168) | public void setStrandContingencyTable(int[] strandContingencyTable) {
    method getLocation (line 172) | public GenomeLoc getLocation() {
    method isDbsnpSite (line 176) | public boolean isDbsnpSite() {
    method setDbsnpSite (line 180) | public void setDbsnpSite(boolean dbsnpSite) {
    method getDbsnpVC (line 184) | public VariantContext getDbsnpVC() {
    method setDbsnpVC (line 188) | public void setDbsnpVC(VariantContext dbsnpVC) {
    method isCovered (line 192) | public boolean isCovered() {
    method setCovered (line 196) | public void setCovered(boolean covered) {
    method getSequenceContext (line 200) | public String getSequenceContext() {
    method setSequenceContext (line 204) | public void setSequenceContext(String sequenceContext) {
    method getRefAllele (line 208) | public char getRefAllele() {
    method getAltAllele (line 212) | public char getAltAllele() {
    method setAltAllele (line 216) | public void setAltAllele(char altAllele) {
    method isRejected (line 220) | public boolean isRejected() {
    method setRejected (line 224) | public void setRejected(boolean rejected) {
    method getInitialTumorLod (line 228) | public double getInitialTumorLod() {
    method setInitialTumorLod (line 232) | public void setInitialTumorLod(double initialTumorLod) {
    method getInitialNormalLod (line 236) | public double getInitialNormalLod() {
    method setInitialNormalLod (line 240) | public void setInitialNormalLod(double initialNormalLod) {
    method getTumorLodFStar (line 244) | public double getTumorLodFStar() {
    method setTumorLodFStar (line 248) | public void setTumorLodFStar(double tumorLodFStar) {
    method getTumorLodFStarForward (line 253) | public double getTumorLodFStarForward() {
    method setTumorLodFStarForward (line 257) | public void setTumorLodFStarForward(double tumorLodFStarForward) {
    method getTumorLodFStarReverse (line 261) | public double getTumorLodFStarReverse() {
    method setTumorLodFStarReverse (line 265) | public void setTumorLodFStarReverse(double tumorLodFStarReverse) {
    method getTumorF (line 269) | public double getTumorF() {
    method setTumorF (line 273) | public void setTumorF(double tumorF) {
    method getNormalF (line 277) | public double getNormalF() {
    method setNormalF (line 281) | public void setNormalF(double normalF) {
    method getInitialTumorRefQualitySum (line 285) | public int getInitialTumorRefQualitySum() {
    method setInitialTumorRefQualitySum (line 289) | public void setInitialTumorRefQualitySum(int initialTumorRefQualitySum) {
    method getInitialTumorAltQualitySum (line 293) | public int getInitialTumorAltQualitySum() {
    method setInitialTumorAltQualitySum (line 297) | public void setInitialTumorAltQualitySum(int initialTumorAltQualitySum) {
    method getInitialTumorNonRefQualitySum (line 301) | public int getInitialTumorNonRefQualitySum() {
    method setInitialTumorNonRefQualitySum (line 305) | public void setInitialTumorNonRefQualitySum(int initialTumorNonRefQual...
    method getInitialNormalRefQualitySum (line 309) | public int getInitialNormalRefQualitySum() {
    method setInitialNormalRefQualitySum (line 313) | public void setInitialNormalRefQualitySum(int initialNormalRefQualityS...
    method getInitialNormalAltQualitySum (line 317) | public int getInitialNormalAltQualitySum() {
    method setInitialNormalAltQualitySum (line 321) | public void setInitialNormalAltQualitySum(int initialNormalAltQualityS...
    method getInitialNormalBestGenotype (line 325) | public DiploidGenotype getInitialNormalBestGenotype() {
    method setInitialNormalBestGenotype (line 329) | public void setInitialNormalBestGenotype(DiploidGenotype initialNormal...
    method getInitialTumorReadDepth (line 333) | public int getInitialTumorReadDepth() {
    method setInitialTumorReadDepth (line 337) | public void setInitialTumorReadDepth(int initialTumorReadDepth) {
    method getInitialNormalReadDepth (line 341) | public int getInitialNormalReadDepth() {
    method setInitialNormalReadDepth (line 345) | public void setInitialNormalReadDepth(int initialNormalReadDepth) {
    method getTumorSampleName (line 349) | public String getTumorSampleName() {
    method setTumorSampleName (line 353) | public void setTumorSampleName(String tumorSampleName) {
    method getNormalSampleName (line 357) | public String getNormalSampleName() {
    method setNormalSampleName (line 361) | public void setNormalSampleName(String normalSampleName) {
    method getRejectionReasons (line 365) | public List<String> getRejectionReasons() {
    method getInitialTumorRefCounts (line 369) | public int getInitialTumorRefCounts() {
    method setInitialTumorRefCounts (line 373) | public void setInitialTumorRefCounts(int initialTumorRefCounts) {
    method getInitialTumorAltCounts (line 377) | public int getInitialTumorAltCounts() {
    method setInitialTumorAltCounts (line 381) | public void setInitialTumorAltCounts(int initialTumorAltCounts) {
    method getInitialNormalRefCounts (line 385) | public int getInitialNormalRefCounts() {
    method setInitialNormalRefCounts (line 389) | public void setInitialNormalRefCounts(int initialNormalRefCounts) {
    method getInitialNormalAltCounts (line 393) | public int getInitialNormalAltCounts() {
    method setInitialNormalAltCounts (line 397) | public void setInitialNormalAltCounts(int initialNormalAltCounts) {
    method getTumorQ20Count (line 401) | public int getTumorQ20Count() {
    method setTumorQ20Count (line 405) | public void setTumorQ20Count(int tumorQ20Count) {
    method getNormalQ20Count (line 409) | public int getNormalQ20Count() {
    method setNormalQ20Count (line 413) | public void setNormalQ20Count(int normalQ20Count) {
    method getTumorInsertionCount (line 417) | public int getTumorInsertionCount() {
    method setTumorInsertionCount (line 421) | public void setTumorInsertionCount(int tumorInsertionCount) {
    method getTumorDeletionCount (line 425) | public int getTumorDeletionCount() {
    method setTumorDeletionCount (line 429) | public void setTumorDeletionCount(int tumorDeletionCount) {
    method getTotalReads (line 433) | public int getTotalReads() {
    method setTotalReads (line 437) | public void setTotalReads(int totalReads) {
    method getMapQ0Reads (line 441) | public int getMapQ0Reads() {
    method setMapQ0Reads (line 445) | public void setMapQ0Reads(int mapQ0Reads) {
    method getContaminationFraction (line 449) | public double getContaminationFraction() {
    method setContaminationFraction (line 453) | public void setContaminationFraction(double contaminationFraction) {
    method getContaminantLod (line 457) | public double getContaminantLod() {
    method setContaminantLod (line 461) | public void setContaminantLod(double contaminantLod) {
    method getTumorAltForwardOffsetsInRead (line 465) | public List<Integer> getTumorAltForwardOffsetsInRead() {
    method setTumorAltForwardOffsetsInRead (line 469) | public void setTumorAltForwardOffsetsInRead(List<Integer> tumorAltForw...
    method getTumorAltReverseOffsetsInRead (line 473) | public List<Integer> getTumorAltReverseOffsetsInRead() {
    method setTumorAltReverseOffsetsInRead (line 477) | public void setTumorAltReverseOffsetsInRead(List<Integer> tumorAltReve...
    method getTumorForwardOffsetsInReadMedian (line 481) | public Double getTumorForwardOffsetsInReadMedian() {
    method setTumorForwardOffsetsInReadMedian (line 485) | public void setTumorForwardOffsetsInReadMedian(Double tumorForwardOffs...
    method getTumorForwardOffsetsInReadMad (line 489) | public Double getTumorForwardOffsetsInReadMad() {
    method setTumorForwardOffsetsInReadMad (line 493) | public void setTumorForwardOffsetsInReadMad(Double tumorForwardOffsets...
    method getTumorReverseOffsetsInReadMedian (line 497) | public Double getTumorReverseOffsetsInReadMedian() {
    method setTumorReverseOffsetsInReadMedian (line 501) | public void setTumorReverseOffsetsInReadMedian(Double tumorReverseOffs...
    method getTumorReverseOffsetsInReadMad (line 505) | public Double getTumorReverseOffsetsInReadMad() {
    method setTumorReverseOffsetsInReadMad (line 509) | public void setTumorReverseOffsetsInReadMad(Double tumorReverseOffsets...
    method getPower (line 513) | public double getPower() {
    method setPower (line 517) | public void setPower(double power) {
    method getTumorPower (line 521) | public double getTumorPower() {
    method setTumorPower (line 525) | public void setTumorPower(double tumorPower) {
    method getNormalPower (line 529) | public double getNormalPower() {
    method setNormalPower (line 533) | public void setNormalPower(double normalPower) {
    method isCosmicSite (line 537) | public boolean isCosmicSite() {
    method setCosmicSite (line 541) | public void setCosmicSite(boolean cosmicSite) {
    method isSeenInPanelOfNormals (line 545) | public boolean isSeenInPanelOfNormals() {
    method getPanelOfNormalsVC (line 549) | public VariantContext getPanelOfNormalsVC() {
    method setPanelOfNormalsVC (line 553) | public void setPanelOfNormalsVC(VariantContext panelOfNormalsVC) {
    method getPowerToDetectPositiveStrandArtifact (line 557) | public double getPowerToDetectPositiveStrandArtifact() {
    method setPowerToDetectPositiveStrandArtifact (line 561) | public void setPowerToDetectPositiveStrandArtifact(double powerToDetec...
    method getPowerToDetectNegativeStrandArtifact (line 565) | public double getPowerToDetectNegativeStrandArtifact() {
    method setPowerToDetectNegativeStrandArtifact (line 569) | public void setPowerToDetectNegativeStrandArtifact(double powerToDetec...
    method getNormalPowerWithSNPPrior (line 573) | public double getNormalPowerWithSNPPrior() {
    method setNormalPowerWithSNPPrior (line 577) | public void setNormalPowerWithSNPPrior(double normalPowerWithSNPPrior) {
    method getNormalPowerNoSNPPrior (line 581) | public double getNormalPowerNoSNPPrior() {
    method setNormalPowerNoSNPPrior (line 585) | public void setNormalPowerNoSNPPrior(double normalPowerNoSNPPrior) {
    method getTumorAltMaxMapQ (line 589) | public int getTumorAltMaxMapQ() {
    method setTumorAltMaxMapQ (line 593) | public void setTumorAltMaxMapQ(int tumorAltMaxMapQ) {
    method getTumorRefMaxMapQ (line 597) | public int getTumorRefMaxMapQ() {
    method setTumorRefMaxMapQ (line 601) | public void setTumorRefMaxMapQ(int tumorRefMaxMapQ) {
    method getTumorRefQualityScores (line 605) | public List<Integer> getTumorRefQualityScores() {
    method setTumorRefQualityScores (line 609) | public void setTumorRefQualityScores(List<Integer> tumorRefQualityScor...
    method getTumorAltQualityScores (line 613) | public List<Integer> getTumorAltQualityScores() {
    method setTumorAltQualityScores (line 617) | public void setTumorAltQualityScores(List<Integer> tumorAltQualityScor...
    method getNormalRefQualityScores (line 621) | public List<Integer> getNormalRefQualityScores() {
    method setNormalRefQualityScores (line 625) | public void setNormalRefQualityScores(List<Integer> normalRefQualitySc...
    method getNormalAltQualityScores (line 629) | public List<Integer> getNormalAltQualityScores() {
    method setNormalAltQualityScores (line 633) | public void setNormalAltQualityScores(List<Integer> normalAltQualitySc...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/LocusReadPile.java
  class LocusReadPile (line 43) | public class LocusReadPile {
    method LocusReadPile (line 65) | public LocusReadPile(ReadBackedPileup pileup, char refBase, int minQua...
    method LocusReadPile (line 69) | public LocusReadPile(ReadBackedPileup pileup, char refBase, int minQua...
    method getOverlappingFragmentFilteredPileupButPreferMismatches (line 130) | public static ReadBackedPileup getOverlappingFragmentFilteredPileupBut...
    method getOverlappingFragmentFilteredPileup (line 134) | public static ReadBackedPileup getOverlappingFragmentFilteredPileup(Re...
    method getOverlappingFragmentFilteredPileup (line 138) | public static ReadBackedPileup getOverlappingFragmentFilteredPileup(Re...
    method estimateAlleleFraction (line 192) | public double estimateAlleleFraction(char ref, char alt) {
    method estimateAlleleFraction (line 196) | public static double estimateAlleleFraction(ReadBackedPileup pileup, c...
    method calculateLogLikelihood (line 204) | public double calculateLogLikelihood(byte alt, double f) {
    method calculateAltVsRefLOD (line 208) | public double calculateAltVsRefLOD(ReadBackedPileup pileup, byte alt, ...
    method calculateAltVsRefLOD (line 212) | public static double calculateAltVsRefLOD(ReadBackedPileup pileup, byt...
    method calculateAltVsRefLOD (line 218) | public double calculateAltVsRefLOD(byte alt, double fAlternate, double...
    method calculateRefVsAltLOD (line 222) | public double calculateRefVsAltLOD(ReadBackedPileup pileup, byte alt, ...
    method calculateLogLikelihood (line 226) | static public double calculateLogLikelihood(ReadBackedPileup pileup, b...
    method calculateLikelihoods (line 246) | public VariableAllelicRatioGenotypeLikelihoods calculateLikelihoods(Re...
    method calculateLikelihoods (line 250) | public VariableAllelicRatioGenotypeLikelihoods calculateLikelihoods(do...
    method getFilteredBaseCount (line 264) | public int getFilteredBaseCount(int minBaseQualityScore) {
    method getBestGenotype (line 268) | public DiploidGenotype getBestGenotype(VariableAllelicRatioGenotypeLik...
    method getHetVsRef (line 283) | public double getHetVsRef(VariableAllelicRatioGenotypeLikelihoods like...
    method getAltVsRef (line 288) | public double getAltVsRef(VariableAllelicRatioGenotypeLikelihoods like...
    method getRefVsAlt (line 295) | public static double getRefVsAlt(VariableAllelicRatioGenotypeLikelihoo...
    method extractRefHetHom (line 304) | protected static double[] extractRefHetHom(VariableAllelicRatioGenotyp...
    method logAddSafe (line 349) | private static double logAddSafe(double inOne, double inTwo) {
    method getDeletionsCount (line 357) | public int getDeletionsCount() {
    method getInsertionsCount (line 361) | public int getInsertionsCount() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/MuTectArgumentCollection.java
  class MuTectArgumentCollection (line 27) | public class MuTectArgumentCollection {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/MuTectStats.java
  class MuTectStats (line 30) | public class MuTectStats {
    method calculateMAD (line 32) | public static double calculateMAD(double[] dd, double median) {
    method getMedian (line 41) | public static double getMedian(double[] data) {
    method convertIntegersToDoubles (line 65) | public static double[] convertIntegersToDoubles(List<Integer> integers)

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/Mutect.java
  class Mutect (line 62) | public class Mutect extends IntervalLocusWalker {
    method Mutect (line 87) | public Mutect(GenomeLocParser genomeLocParser,
    method getNormalLocusSamTraverser (line 105) | private IntervalLocusSamTraverser getNormalLocusSamTraverser(
    method initialize (line 121) | @Override
    method getFilter (line 143) | @Override
    method getVCInTrackerInLocus (line 149) | private List<VariantContext> getVCInTrackerInLocus(String rodName, fin...
    method cleanNoneRefPileupElement (line 158) | private ReadBackedPileup cleanNoneRefPileupElement(ReadBackedPileup ra...
    method map (line 170) | @Override
    method filterReads (line 484) | private LocusReadPile filterReads(final ReferenceContext ref, final Re...
    method performRejection (line 519) | private void performRejection(CandidateMutation candidate) {
    method onTraversalDone (line 584) | @Override
    method getResultVCFRecords (line 589) | public List<VariantContext> getResultVCFRecords() {
    method getResultVCFOutInfos (line 593) | public List<String> getResultVCFOutInfos() {
    class PileupComparatorByAltRefQual (line 597) | public static class PileupComparatorByAltRefQual implements Comparator...
      method PileupComparatorByAltRefQual (line 600) | public PileupComparatorByAltRefQual(byte alt) {
      method compare (line 604) | public int compare(PileupElement o1, PileupElement o2) {
      method internalCompare (line 608) | public int internalCompare(byte base1, byte qual1, byte base2, byte ...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/NormalPowerCalculator.java
  class NormalPowerCalculator (line 31) | public class NormalPowerCalculator extends AbstractPowerCalculator {
    method NormalPowerCalculator (line 34) | public NormalPowerCalculator(double constantEps, double constantLodThr...
    method NormalPowerCalculator (line 40) | public NormalPowerCalculator(double constantEps, double constantLodThr...
    method cachingPowerCalculation (line 46) | public double cachingPowerCalculation(int n) throws MathException {
    method calculateNormalLod (line 56) | protected static double calculateNormalLod(int depth, int alts, double...
    method calculatePower (line 60) | protected static double calculatePower(int depth, double eps, double l...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/QualitySums.java
  class QualitySums (line 30) | public class QualitySums {
    method QualitySums (line 47) | public QualitySums(boolean enableQualityScoreTracking) {
    method getQualitySum (line 51) | public int getQualitySum(final char base) {
    method getCounts (line 59) | public int getCounts(final char base) {
    method incrementSum (line 67) | public void incrementSum(final char base, final int count, final int q...
    method getOtherQualities (line 77) | public int getOtherQualities(final char base) {
    method getBaseQualityScores (line 86) | public List<Integer> getBaseQualityScores(final char base) {
    method reset (line 94) | public void reset() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/SequenceUtils.java
  class SequenceUtils (line 41) | public class SequenceUtils {
    method createSequenceContext (line 43) | public static String createSequenceContext(RefContentProvider refConte...
    method getStrandContingencyTable (line 63) | public static int[] getStrandContingencyTable(ReadBackedPileup forward...
    method getForwardOffsetsInRead (line 81) | public static List<Integer> getForwardOffsetsInRead(ReadBackedPileup p) {
    method getReverseOffsetsInRead (line 85) | public static List<Integer> getReverseOffsetsInRead(ReadBackedPileup p) {
    method getOffsetsInRead (line 89) | public static List<Integer> getOffsetsInRead(ReadBackedPileup p, boole...
    method isReadHeavilySoftClipped (line 102) | public static boolean isReadHeavilySoftClipped(SAMRecord rec, float th...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/TumorPowerCalculator.java
  class TumorPowerCalculator (line 31) | public class TumorPowerCalculator extends AbstractPowerCalculator{
    method TumorPowerCalculator (line 35) | public TumorPowerCalculator(double constantEps, double constantLodThre...
    method TumorPowerCalculator (line 39) | public TumorPowerCalculator(double constantEps, double constantLodThre...
    method cachingPowerCalculation (line 46) | public double cachingPowerCalculation(int n, double delta) throws Math...
    method calculateTumorLod (line 59) | protected static double calculateTumorLod(int depth, int alts, double ...
    method calculatePower (line 64) | protected static double calculatePower(int depth, double eps, double l...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/VCFGenerator.java
  class VCFGenerator (line 46) | public class VCFGenerator {
    method getVCFHeaderInfo (line 47) | public static Set<VCFHeaderLine> getVCFHeaderInfo() {
    method generateVC (line 80) | public static VariantContext generateVC(CandidateMutation m) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/mutect/VariableAllelicRatioGenotypeLikelihoods.java
  class VariableAllelicRatioGenotypeLikelihoods (line 34) | public class VariableAllelicRatioGenotypeLikelihoods extends DiploidSNPG...
    method VariableAllelicRatioGenotypeLikelihoods (line 47) | public VariableAllelicRatioGenotypeLikelihoods(char ref, double f) {
    method getLikelihood (line 56) | public double getLikelihood(DiploidGenotype g) {
    method calculateGenotypeLikelihoods (line 60) | protected DiploidSNPGenotypeLikelihoods calculateGenotypeLikelihoods(b...
    method add (line 110) | public int add(byte observedBase1, byte qualityScore1) {
    method inCache (line 139) | @Override
    method setCache (line 144) | @Override

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/printreads/BaseRecalibration.java
  class BaseRecalibration (line 47) | public class BaseRecalibration {
    method BaseRecalibration (line 68) | public BaseRecalibration(final GATKReport report, final int quantizati...
    method recalibrateRead (line 104) | public void recalibrateRead(final GATKSAMRecord read) {
    method hierarchicalBayesianQualityEstimate (line 168) | protected static double hierarchicalBayesianQualityEstimate(final doub...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/printreads/PrintReads.java
  class PrintReads (line 55) | public class PrintReads extends ReadWalker {
    method PrintReads (line 99) | public PrintReads(GenomeLocParser genomeLocParser,
    method initialize (line 108) | @Override
    method setReadTransformers (line 128) | protected void setReadTransformers(final List<ReadTransformer> readTra...
    method checkActiveReadTransformers (line 141) | protected void checkActiveReadTransformers(final List<ReadTransformer>...
    method buildBQSRTransformerArgsMap (line 161) | private Map<String, Object> buildBQSRTransformerArgsMap() {
    method buildMisencodedBaseQualityReadTransformerArgsMap (line 171) | private Map<String, Object> buildMisencodedBaseQualityReadTransformerA...
    method getFilter (line 178) | @Override
    method filter (line 184) | public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
    method map (line 202) | @Override
    method onTraversalDone (line 220) | @Override
    method getResultRecords (line 225) | public List<GATKSAMRecord> getResultRecords() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/printreads/RecalibrationReport.java
  class RecalibrationReport (line 48) | public class RecalibrationReport {
    method RecalibrationReport (line 61) | public RecalibrationReport(final GATKReport report) {
    method RecalibrationReport (line 65) | public RecalibrationReport(final GATKReport report, final SortedSet<St...
    method getReadGroups (line 109) | private static SortedSet<String> getReadGroups(final GATKReport report) {
    method combine (line 130) | public void combine(final RecalibrationReport other) {
    method getQuantizationInfo (line 138) | public QuantizationInfo getQuantizationInfo() {
    method getRecalibrationTables (line 142) | public RecalibrationTables getRecalibrationTables() {
    method getRequestedCovariates (line 146) | public Covariate[] getRequestedCovariates() {
    method initializeReadGroupCovariates (line 158) | private void initializeReadGroupCovariates(final SortedSet<String> all...
    method parseAllCovariatesTable (line 170) | private void parseAllCovariatesTable(final GATKReportTable reportTable...
    method parseQualityScoreTable (line 195) | private void parseQualityScoreTable(final GATKReportTable reportTable,...
    method parseReadGroupTable (line 214) | private void parseReadGroupTable(final GATKReportTable reportTable, fi...
    method asDouble (line 225) | private double asDouble(final Object o) {
    method asLong (line 236) | private long asLong(final Object o) {
    method getRecalDatum (line 247) | private RecalDatum getRecalDatum(final GATKReportTable reportTable, fi...
    method initializeQuantizationTable (line 269) | private QuantizationInfo initializeQuantizationTable(GATKReportTable t...
    method initializeArgumentCollectionTable (line 290) | private RecalibrationArgumentCollection initializeArgumentCollectionTa...
    method calculateQuantizedQualities (line 355) | public void calculateQuantizedQualities() {
    method createGATKReport (line 359) | public GATKReport createGATKReport() {
    method getRAC (line 363) | public RecalibrationArgumentCollection getRAC() {
    method getCovariates (line 371) | @Deprecated
    method isEmpty (line 379) | public boolean isEmpty() {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/realignertargetcreator/Event.java
  class Event (line 32) | public class Event {
    method Event (line 41) | public Event(GenomeLoc loc, int furthestStopPos, EventType type) {
    method merge (line 59) | public void merge(Event e) {
    method isReportableEvent (line 91) | public boolean isReportableEvent(GenomeLocParser genomeLocParser) {
    method getLoc (line 98) | public GenomeLoc getLoc(GenomeLocParser genomeLocParser) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/realignertargetcreator/EventPair.java
  class EventPair (line 31) | public class EventPair {
    method EventPair (line 35) | public EventPair(Event left, Event right) {
    method EventPair (line 40) | public EventPair(Event left, Event right, TreeSet<GenomeLoc> set1, Tre...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/realignertargetcreator/EventType.java
  type EventType (line 27) | public enum EventType {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/algorithms/walker/realignertargetcreator/RealignerTargetCreator.java
  class RealignerTargetCreator (line 48) | public class RealignerTargetCreator extends LocusWalker {
    method RealignerTargetCreator (line 57) | public RealignerTargetCreator(GenomeLocParser genomeLocParser,
    method initialize (line 65) | @Override
    method getFilter (line 70) | @Override
    method map (line 80) | protected void map(RefMetaDataTracker tracker,
    method reduce (line 149) | private EventPair reduce(Event value, EventPair sum) {
    method onTraversalDone (line 172) | @Override
    method getTargetIntervals (line 184) | public List<GenomeLoc> getTargetIntervals() {
    method canBeMerged (line 188) | private boolean canBeMerged(Event left, Event right) {
    method mergeEvents (line 192) | static private Event mergeEvents(Event left, Event right) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/BaseCompressTools.java
  class BaseCompressTools (line 29) | public class BaseCompressTools {
    method compressBase (line 36) | public static byte[] compressBase(byte[] base, byte[] qual) {
    method decompressBase (line 87) | public static byte[] decompressBase(byte[] compressedBases, byte[] qua...
    method setBase (line 111) | private static void setBase(byte baseVal, byte[] qual, byte[] result, ...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/QualityCompressTools.java
  class QualityCompressTools (line 41) | public class QualityCompressTools {
    method getCode (line 45) | private static final CodeTree getCode() {
    method compressQual (line 66) | public static byte[] compressQual(byte[] qual) {
    method deCompressQual (line 95) | public static byte[] deCompressQual(byte[] compressedQual) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/AdaptiveHuffmanCompress.java
  class AdaptiveHuffmanCompress (line 43) | public final class AdaptiveHuffmanCompress {
    method main (line 46) | public static void main(String[] args) throws IOException {
    method compress (line 69) | public static void compress(InputStream in, BitOutputStream out) throw...
    method isPowerOf2 (line 96) | private static boolean isPowerOf2(int x) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/AdaptiveHuffmanDecompress.java
  class AdaptiveHuffmanDecompress (line 39) | public final class AdaptiveHuffmanDecompress {
    method main (line 42) | public static void main(String[] args) throws IOException {
    method decompress (line 65) | public static void decompress(BitInputStream in, OutputStream out) thr...
    method isPowerOf2 (line 91) | private static boolean isPowerOf2(int x) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/BitInputStream.java
  class BitInputStream (line 35) | public final class BitInputStream {
    method BitInputStream (line 57) | public BitInputStream(InputStream in) {
    method read (line 74) | public int read() throws IOException {
    method readNoEof (line 97) | public int readNoEof() throws IOException {
    method close (line 110) | public void close() throws IOException {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/BitOutputStream.java
  class BitOutputStream (line 34) | public final class BitOutputStream {
    method BitOutputStream (line 55) | public BitOutputStream(OutputStream out) {
    method write (line 71) | public void write(int b) throws IOException {
    method close (line 90) | public void close() throws IOException {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/CanonicalCode.java
  class CanonicalCode (line 64) | public final class CanonicalCode {
    method CanonicalCode (line 98) | public CanonicalCode(int[] codeLens) {
    method CanonicalCode (line 147) | public CanonicalCode(CodeTree tree, int symbolLimit) {
    method buildCodeLengths (line 157) | private void buildCodeLengths(Node node, int depth) {
    method getSymbolLimit (line 184) | public int getSymbolLimit() {
    method getCodeLength (line 196) | public int getCodeLength(int symbol) {
    method toCodeTree (line 207) | public CodeTree toCodeTree() {
    method max (line 235) | private static int max(int[] array) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/CodeTree.java
  class CodeTree (line 60) | public final class CodeTree {
    method CodeTree (line 84) | public CodeTree(InternalNode root, int symbolLimit) {
    method buildCodeList (line 98) | private void buildCodeList(Node node, List<Integer> prefix) {
    method getCode (line 134) | public List<Integer> getCode(int symbol) {
    method toString (line 149) | public String toString() {
    method toString (line 157) | private static void toString(String prefix, Node node, StringBuilder s...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/FrequencyTable.java
  class FrequencyTable (line 40) | public final class FrequencyTable {
    method FrequencyTable (line 55) | public FrequencyTable(int[] freqs) {
    method getSymbolLimit (line 74) | public int getSymbolLimit() {
    method get (line 85) | public int get(int symbol) {
    method set (line 97) | public void set(int symbol, int freq) {
    method increment (line 112) | public void increment(int symbol) {
    method checkSymbol (line 121) | private void checkSymbol(int symbol) {
    method toString (line 132) | public String toString() {
    method buildCodeTree (line 149) | public CodeTree buildCodeTree() {
    class NodeWithFrequency (line 185) | private static class NodeWithFrequency implements Comparable<NodeWithF...
      method NodeWithFrequency (line 192) | public NodeWithFrequency(Node nd, int lowSym, long freq) {
      method compareTo (line 200) | public int compareTo(NodeWithFrequency other) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/HuffmanCompress.java
  class HuffmanCompress (line 40) | public final class HuffmanCompress {
    method main (line 43) | public static void main(String[] args) throws IOException {
    method getFrequencies (line 78) | private static FrequencyTable getFrequencies(File file) throws IOExcep...
    method writeCodeLengthTable (line 96) | public static void writeCodeLengthTable(BitOutputStream out, Canonical...
    method compress (line 111) | public static void compress(CodeTree code, InputStream in, BitOutputSt...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/HuffmanDecoder.java
  class HuffmanDecoder (line 31) | public final class HuffmanDecoder {
    method HuffmanDecoder (line 50) | public HuffmanDecoder(BitInputStream in) {
    method read (line 63) | public int read() throws IOException {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/HuffmanDecompress.java
  class HuffmanDecompress (line 37) | public final class HuffmanDecompress {
    method main (line 40) | public static void main(String[] args) throws IOException {
    method readCodeLengthTable (line 65) | public static CanonicalCode readCodeLengthTable(BitInputStream in) thr...
    method decompress (line 79) | public static void decompress(CodeTree code, BitInputStream in, Output...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/HuffmanEncoder.java
  class HuffmanEncoder (line 32) | public final class HuffmanEncoder {
    method HuffmanEncoder (line 51) | public HuffmanEncoder(BitOutputStream out) {
    method write (line 65) | public void write(int symbol) throws IOException {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/InternalNode.java
  class InternalNode (line 30) | public final class InternalNode extends Node {
    method InternalNode (line 38) | public InternalNode(Node left, Node right) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/Leaf.java
  class Leaf (line 28) | public final class Leaf extends Node {
    method Leaf (line 34) | public Leaf(int sym) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/compress/huffman/Node.java
  class Node (line 28) | public abstract class Node {
    method Node (line 31) | Node() {}

FILE: src/main/java/org/ncic/bioinfo/sparkseq/debug/DebugWriter.java
  class DebugWriter (line 31) | public class DebugWriter {
    method DebugWriter (line 35) | public DebugWriter(String filePath) {
    method write (line 43) | public void write(byte content) {
    method write (line 52) | public void write(String content) {
    method newline (line 61) | public void newline(){

FILE: src/main/java/org/ncic/bioinfo/sparkseq/exceptions/CompressException.java
  class CompressException (line 27) | public class CompressException extends GATKException {
    method CompressException (line 28) | public CompressException() {
    method CompressException (line 32) | public CompressException(String info) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/exceptions/GATKException.java
  class GATKException (line 27) | public class GATKException extends RuntimeException {
    method GATKException (line 28) | public GATKException(String msg) {
    method GATKException (line 32) | public GATKException(String message, Throwable throwable) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/exceptions/ReviewedGATKException.java
  class ReviewedGATKException (line 27) | public class ReviewedGATKException extends GATKException {
    method ReviewedGATKException (line 29) | public ReviewedGATKException(String msg) {
    method ReviewedGATKException (line 33) | public ReviewedGATKException(String message, Throwable throwable) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/exceptions/UserException.java
  class UserException (line 34) | @DocumentedGATKFeature(
    method UserException (line 39) | public UserException(String msg) {
    method UserException (line 43) | public UserException(String msg, Throwable e) {
    method UserException (line 47) | private UserException(Throwable e) {
    method getMessage (line 51) | protected static String getMessage(Throwable t) {
    class BadInput (line 56) | public static class BadInput extends UserException {
      method BadInput (line 57) | public BadInput(String message) {
    class CommandLineException (line 62) | public static class CommandLineException extends UserException {
      method CommandLineException (line 63) | public CommandLineException(String message) {
    class MalformedGenomeLoc (line 68) | public static class MalformedGenomeLoc extends UserException {
      method MalformedGenomeLoc (line 69) | public MalformedGenomeLoc(String message, GenomeLoc loc) {
      method MalformedGenomeLoc (line 73) | public MalformedGenomeLoc(String message) {
    class ErrorWritingBamFile (line 78) | public static class ErrorWritingBamFile extends UserException {
      method ErrorWritingBamFile (line 79) | public ErrorWritingBamFile(String message) {
    class MalformedBAM (line 84) | public static class MalformedBAM extends UserException {
      method MalformedBAM (line 85) | public MalformedBAM(SAMRecord read, String message) {
      method MalformedBAM (line 89) | public MalformedBAM(File file, String message) {
      method MalformedBAM (line 93) | public MalformedBAM(String source, String message) {
    class MisencodedBAM (line 98) | public static class MisencodedBAM extends UserException {
      method MisencodedBAM (line 99) | public MisencodedBAM(SAMRecord read, String message) {
      method MisencodedBAM (line 103) | public MisencodedBAM(String source, String message) {
    class BadArgumentValue (line 108) | public static class BadArgumentValue extends CommandLineException {
      method BadArgumentValue (line 109) | public BadArgumentValue(String arg, String message) {
    class CouldNotReadInputFile (line 114) | public static class CouldNotReadInputFile extends UserException {
      method CouldNotReadInputFile (line 115) | public CouldNotReadInputFile(String message, Exception e) {
      method CouldNotReadInputFile (line 119) | public CouldNotReadInputFile(File file) {
      method CouldNotReadInputFile (line 123) | public CouldNotReadInputFile(File file, String message) {
      method CouldNotReadInputFile (line 127) | public CouldNotReadInputFile(String file, String message) {
      method CouldNotReadInputFile (line 131) | public CouldNotReadInputFile(File file, String message, Exception e) {
      method CouldNotReadInputFile (line 135) | public CouldNotReadInputFile(File file, Exception e) {
      method CouldNotReadInputFile (line 139) | public CouldNotReadInputFile(String message) {
    class IncompatibleReadFiltersException (line 144) | public static class IncompatibleReadFiltersException extends CommandLi...
      method IncompatibleReadFiltersException (line 145) | public IncompatibleReadFiltersException(final String filter1, final ...
    class ReadMissingReadGroup (line 150) | public static class ReadMissingReadGroup extends MalformedBAM {
      method ReadMissingReadGroup (line 151) | public ReadMissingReadGroup(final SAMRecord read) {
    class MalformedFile (line 156) | public static class MalformedFile extends UserException {
      method MalformedFile (line 157) | public MalformedFile(String message) {
      method MalformedFile (line 161) | public MalformedFile(String message, Exception e) {
      method MalformedFile (line 165) | public MalformedFile(File f, String message) {
      method MalformedFile (line 169) | public MalformedFile(File f, String message, Exception e) {
      method MalformedFile (line 173) | public MalformedFile(String name, String message) {
      method MalformedFile (line 177) | public MalformedFile(String name, String message, Exception e) {
    class DeprecatedAnnotation (line 182) | public static class DeprecatedAnnotation extends UserException {
      method DeprecatedAnnotation (line 183) | public DeprecatedAnnotation(String annotationName, String version) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/fileio/format/SingleFastqInputFormat.java
  class SingleFastqInputFormat (line 51) | public class SingleFastqInputFormat extends FileInputFormat<Void,Text> {
    class SingleFastqRecordReader (line 53) | public static class SingleFastqRecordReader extends RecordReader<Void,...
      method SingleFastqRecordReader (line 88) | public SingleFastqRecordReader(Configuration conf, FileSplit split) ...
      method positionAtFirstRecord (line 118) | private void positionAtFirstRecord(FSDataInputStream stream) throws ...
      method initialize (line 163) | public void initialize(InputSplit split, TaskAttemptContext context)...
      method getCurrentKey (line 168) | public Void getCurrentKey() {
      method getCurrentValue (line 175) | public Text getCurrentValue() {
      method nextKeyValue (line 182) | public boolean nextKeyValue() throws IOException, InterruptedExcepti...
      method close (line 191) | public void close() throws IOException {
      method createKey (line 198) | public Text createKey() {
      method createValue (line 205) | public Text createValue() {
      method getPos (line 212) | public long getPos() {
      method getProgress (line 219) | public float getProgress() {
      method makePositionMessage (line 226) | public String makePositionMessage() {
      method lowLevelFastqRead (line 230) | protected boolean lowLevelFastqRead(Text readName, Text value) throw...
      method next (line 257) | public boolean next(Text value) throws IOException {
      method appendLineInto (line 275) | private int appendLineInto(Text dest, boolean eofOk) throws EOFExcep...
    method createRecordReader (line 290) | public RecordReader<Void, Text> createRecordReader(

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/Basic2SAMRecordTransfer.java
  class Basic2SAMRecordTransfer (line 45) | public class Basic2SAMRecordTransfer {
    method Basic2SAMRecordTransfer (line 54) | public Basic2SAMRecordTransfer(SAMFileHeader header) {
    method transfer (line 60) | public SAMRecord transfer(final BasicSamRecord basicSamRecord) {
    method parseTag (line 111) | private void parseTag(final SAMRecord samRecord, final String tag) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/CollectionConverter.java
  class CollectionConverter (line 32) | public class CollectionConverter {
    method asJavaList (line 34) | public static <T> List<T> asJavaList(scala.collection.Iterable<T> raw) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/FastqRecord2ShortReadTransfer.java
  class FastqRecord2ShortReadTransfer (line 33) | public class FastqRecord2ShortReadTransfer {
    method transfer (line 35) | public static ShortRead transfer(FastqRecord record) {
    method transferRead1 (line 46) | public static ShortRead transferRead1(FastqPairRecord record) {
    method transferRead2 (line 57) | public static ShortRead transferRead2(FastqPairRecord record) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/GATKReportTransfer.java
  class GATKReportTransfer (line 35) | public class GATKReportTransfer {
    method lines2Report (line 37) | public static GATKReport lines2Report(List<String> lines) {
    method report2Lines (line 56) | public static List<String> report2Lines(GATKReport report) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/SAMHeaderTransfer.java
  class SAMHeaderTransfer (line 37) | public class SAMHeaderTransfer {
    method transfer (line 39) | public static SAMFileHeader transfer(SamHeaderInfo samHeaderInfo){

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/SAMReadGroupRecordTransfer.java
  class SAMReadGroupRecordTransfer (line 30) | public class SAMReadGroupRecordTransfer {
    method transfer (line 32) | public static SAMReadGroupRecord transfer(ReadGroupInfo readGroupInfo) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/SAMRecord2BasicTransfer.java
  class SAMRecord2BasicTransfer (line 35) | public class SAMRecord2BasicTransfer {
    method transfer (line 46) | public BasicSamRecord transfer(final SAMRecord alignment) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/SAMSequenceDictTransfer.java
  class SAMSequenceDictTransfer (line 34) | public class SAMSequenceDictTransfer {
    method transfer (line 36) | public static SAMSequenceDictionary transfer(RefContigInfo refContigIn...

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/VC2VcfRecordTransfer.java
  class VC2VcfRecordTransfer (line 50) | public class VC2VcfRecordTransfer {
    method VC2VcfRecordTransfer (line 59) | public VC2VcfRecordTransfer(VCFHeader header, RefContigInfo refContigI...
    method transfer (line 64) | public VcfRecord transfer(VariantContext variantContext) {
    method transfer (line 68) | public VcfRecord transfer(VariantContext variantContext, boolean withG...
    method getFilterString (line 128) | private String getFilterString(final VariantContext vc) {
    method formatVCFField (line 135) | String formatVCFField(final Object val) {
    method formatVCFDouble (line 161) | public static String formatVCFDouble(final double d) {
    method writeInfoString (line 181) | private void writeInfoString(final Map<String, String> infoFields, fin...
    method buildAlleleStrings (line 204) | public Map<Allele, String> buildAlleleStrings(final VariantContext vc) {
    method addGenotypeData (line 216) | public void addGenotypeData(final VariantContext vc, final Map<Allele,...
    method writeAllele (line 303) | private void writeAllele(final Allele allele, final Map<Allele, String...
    method countOccurrences (line 310) | static int countOccurrences(final char c, final String s) {
    method isMissingValue (line 318) | static boolean isMissingValue(final String s) {

FILE: src/main/java/org/ncic/bioinfo/sparkseq/transfer/VcfRecord2VCTransfer.java
  class VcfRecord2VCTransfer (line 53) | public class VcfRecord2VCTransfer {
    method VcfRecord2VCTransfer (line 63) | public VcfRecord2VCTransfer(VcfHeaderInfo vcfHeaderInfo) {
    method transfer (line 69) | public VariantContext transfer(VcfRecord vcfRecord) {
    method parseQual (line 123) | protected static Double parseQual(double qual) {
    method parseFilters (line 138) | protected List<String> parseFilters(final String filterString) {
    method parseInfo (line 169) | private Map<String, Object> parseInfo(String infoField) {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/TestDebug.java
  class TestDebug (line 43) | public class TestDebug extends AbstractTestCase {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/adapters/TestBQSRGather.java
  class TestBQSRGather (line 36) | public class TestBQSRGather extends TestCase {
    method testBQSRGather (line 38) | public void testBQSRGather() {
    method testParallelBQSRGather (line 54) | public void testParallelBQSRGather() {
    method getRecalTableLines (line 70) | private static List<String> getRecalTableLines(String filePath) {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/TestIntervalLocusSamTraverser.java
  class TestIntervalLocusSamTraverser (line 55) | public class TestIntervalLocusSamTraverser extends AbstractTestCase {
    method testIntervalLocusSamTraverser (line 57) | public void testIntervalLocusSamTraverser() {
    method getNormalReads (line 103) | protected static java.util.List<SAMRecord> getNormalReads(SamHeaderInf...
    method getTumorReads (line 107) | protected static java.util.List<SAMRecord> getTumorReads(SamHeaderInfo...
    method getMutectRefContentProvider (line 111) | protected static RefContentProvider getMutectRefContentProvider(SAMSeq...
    method getLocusWalkerFilterUtils (line 117) | protected static FilterUtils getLocusWalkerFilterUtils() {
    method getLocusInfo (line 126) | private static List<LocusInfo> getLocusInfo() {
    class LocusInfo (line 143) | static class LocusInfo {
      method LocusInfo (line 147) | LocusInfo(String line) {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/TestLocusSamTraverser.java
  class TestLocusSamTraverser (line 38) | public class TestLocusSamTraverser extends TestCase {
    method testLocusSamTraverser (line 39) | public void testLocusSamTraverser() {
    method testLocusSamTraverser2 (line 72) | public void testLocusSamTraverser2() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/TestReadSamTraverser.java
  class TestReadSamTraverser (line 36) | public class TestReadSamTraverser extends TestCase {
    method testReadSamTraverser (line 38) | public void testReadSamTraverser() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/TestRegionSamTraverser.java
  class TestRegionSamTraverser (line 38) | public class TestRegionSamTraverser extends TestCase {
    method testRegionSamTraverser (line 40) | public void testRegionSamTraverser() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/TestSamContentProvider.java
  class TestSamContentProvider (line 38) | public class TestSamContentProvider extends TestCase {
    method testReadTraverser (line 40) | public void testReadTraverser() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/data/sam/filter/TestFilterUtils.java
  class TestFilterUtils (line 39) | public class TestFilterUtils extends TestCase {
    method testCreate (line 41) | public void testCreate() {
    method testFilterWhenReadTraverse (line 53) | public void testFilterWhenReadTraverse() {
    method testFilterWhenLocusTraverse (line 72) | public void testFilterWhenLocusTraverse() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/AbstractTestCase.java
  class AbstractTestCase (line 53) | public abstract class AbstractTestCase extends TestCase {
    method readRefContentValue (line 55) | protected static String readRefContentValue(String filePath) {
    method readRefContent (line 70) | protected static String readRefContent() {
    method readLargeRefContent (line 74) | protected static String readLargeRefContent() {
    method getRefContentProvider (line 78) | protected static RefContentProvider getRefContentProvider(SAMSequenceD...
    method getLargeRefContentProvider (line 84) | protected static RefContentProvider getLargeRefContentProvider(SAMSequ...
    method loadVcfPartition (line 90) | protected static VcfRecordPartition loadVcfPartition(String filePath, ...
    method getRealignerTargetIntervalValue (line 97) | protected static java.util.List<GenomeLoc> getRealignerTargetIntervalV...
    method getRealignerTargetInterval (line 121) | protected static java.util.List<GenomeLoc> getRealignerTargetInterval(...
    method getLargeRealignerTargetInterval (line 125) | protected static java.util.List<GenomeLoc> getLargeRealignerTargetInte...
    method getOriginReads (line 129) | protected static java.util.List<SAMRecord> getOriginReads(SamHeaderInf...
    method getRealignedReads (line 133) | protected static java.util.List<SAMRecord> getRealignedReads(SamHeader...
    method getRecaledReads (line 137) | protected static java.util.List<SAMRecord> getRecaledReads(SamHeaderIn...
    method getLargeOriginReads (line 141) | protected static java.util.List<SAMRecord> getLargeOriginReads(SamHead...
    method getLargeRealignedReads (line 145) | protected static java.util.List<SAMRecord> getLargeRealignedReads(SamH...
    method getLargeRecaledReads (line 149) | protected static java.util.List<SAMRecord> getLargeRecaledReads(SamHea...
    method getReads (line 153) | protected static java.util.List<SAMRecord> getReads(String filePath, S...
    method readList2Map (line 181) | protected static Map<String, SAMRecord> readList2Map(java.util.List<SA...
    method getRecalTableLinesValue (line 187) | private static java.util.List<String> getRecalTableLinesValue(String f...
    method getRecalTableLines (line 203) | protected static java.util.List<String> getRecalTableLines() {
    method getLargeRecalTableLines (line 207) | protected static java.util.List<String> getLargeRecalTableLines() {
    method getGvcfValue (line 211) | protected static java.util.List<VcfRecord> getGvcfValue(String filePat...
    method getGvcf (line 217) | protected static java.util.List<VcfRecord> getGvcf(RefContigInfo refCo...
    method getLargeGvcf (line 221) | protected static java.util.List<VcfRecord> getLargeGvcf(RefContigInfo ...
    method getVcf (line 225) | protected static java.util.List<VcfRecord> getVcf(RefContigInfo refCon...
    method getLargeVcf (line 229) | protected static java.util.List<VcfRecord> getLargeVcf(RefContigInfo r...
    method getIntervals (line 233) | protected static java.util.List<GenomeLoc> getIntervals(RefContigInfo ...

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestActiveRegionFinder.java
  class TestActiveRegionFinder (line 48) | public class TestActiveRegionFinder extends AbstractTestCase {
    method testActiveRegionFinder (line 50) | public void testActiveRegionFinder() {
    method getStandardActiveRegionInfo (line 86) | public static List<ActiveRegionInfo> getStandardActiveRegionInfo() {
    class ActiveRegionInfo (line 106) | static class ActiveRegionInfo {
      method ActiveRegionInfo (line 111) | ActiveRegionInfo(int start, int end, int readCount) {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestBaseRecalibrator.java
  class TestBaseRecalibrator (line 49) | public class TestBaseRecalibrator extends AbstractTestCase {
    method testBaseRecalibrator (line 51) | public void testBaseRecalibrator() {
    method getRecalRefContentProvider (line 88) | protected static RefContentProvider getRecalRefContentProvider(SAMSequ...

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestGenotypeGVCFs.java
  class TestGenotypeGVCFs (line 53) | public class TestGenotypeGVCFs extends AbstractTestCase {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestHaplotypeCaller.java
  class TestHaplotypeCaller (line 50) | public class TestHaplotypeCaller extends AbstractTestCase {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestIndelRealigner.java
  class TestIndelRealigner (line 48) | public class TestIndelRealigner extends AbstractTestCase {
    method testIndelRealigner (line 50) | public void testIndelRealigner() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestMapDataSerialization.java
  class TestMapDataSerialization (line 61) | public class TestMapDataSerialization extends AbstractTestCase {
    method testHaplotypeCallerWithDbsnp (line 63) | public void testHaplotypeCallerWithDbsnp() {
    method serializationObject (line 115) | private <T extends Serializable> byte[] serializationObject(T obj) {
    method deserializationObject (line 137) | @SuppressWarnings("unchecked")

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestMutect.java
  class TestMutect (line 57) | public class TestMutect extends AbstractTestCase {
    method testMutect (line 59) | public void testMutect() {
    method getNormalReads (line 120) | protected static java.util.List<SAMRecord> getNormalReads(SamHeaderInf...
    method getTumorReads (line 124) | private static java.util.List<SAMRecord> getTumorReads(SamHeaderInfo h...
    method getMutectRefContentProvider (line 128) | private static RefContentProvider getMutectRefContentProvider(SAMSeque...
    method getMutectVcf (line 134) | private static java.util.List<VcfRecord> getMutectVcf(RefContigInfo re...
    method getMutectOutTxt (line 138) | private static java.util.List<String> getMutectOutTxt() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestPrintReads.java
  class TestPrintReads (line 49) | public class TestPrintReads extends AbstractTestCase {
    method testPrintReads (line 50) | public void testPrintReads() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/algorithms/walker/TestRealignerTargetCreator.java
  class TestRealignerTargetCreator (line 45) | public class TestRealignerTargetCreator extends AbstractTestCase {
    method testTargetCreator (line 47) | public void testTargetCreator() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/compress/TestBaseCompress.java
  class TestBaseCompress (line 29) | public class TestBaseCompress extends AbstractTestCase {
    method testFastqCompress (line 30) | public void testFastqCompress() {
    method testFastqCompressWithN (line 38) | public void testFastqCompressWithN() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/compress/TestCompressRate.java
  class TestCompressRate (line 38) | public class TestCompressRate extends AbstractTestCase {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/compress/TestFastqCompress.java
  class TestFastqCompress (line 29) | public class TestFastqCompress extends TestCase {
    method testFastqCompress (line 31) | public void testFastqCompress() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/compress/TestKryo.java
  class TestKryo (line 36) | public class TestKryo extends TestCase {
    method testKyro (line 38) | public void testKyro() {
    method serializationObject (line 53) | private byte[] serializationObject(Kryo kryo, byte[] obj) {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/compress/TestQualCompress.java
  class TestQualCompress (line 41) | public class TestQualCompress extends AbstractTestCase {
    method testBuild (line 43) | public void testBuild() throws IOException {
    method testQualityCompress (line 79) | public void testQualityCompress() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/transfer/TestRecalTableTransfer.java
  class TestRecalTableTransfer (line 32) | public class TestRecalTableTransfer extends AbstractTestCase {
    method testRecalTableTransfer (line 34) | public void testRecalTableTransfer() {

FILE: src/test/java/org/ncic/bioinfo/sparkseq/transfer/TestSAMRecordTransfer.java
  class TestSAMRecordTransfer (line 42) | public class TestSAMRecordTransfer extends AbstractTestCase {
    method testSAMRecordTransfer (line 44) | public void testSAMRecordTransfer() {