zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Adding read position rank sum test to the list of annotations that get produced with the HaplotypeCaller

This commit is contained in:
Ryan Poplin 2012-04-17 17:00:00 -04:00
parent 08a1ef2681
commit cf705f6c62
6 changed files with 27 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
View File

@ -30,7 +30,7 @@ public class BaseQualityRankSumTest extends RankSumTest {
} }
} }
} }
protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) { protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
// TODO -- implement me; how do we pull out the correct offset from the read? // TODO -- implement me; how do we pull out the correct offset from the read?
return; return;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
View File

@ -34,7 +34,7 @@ public class MappingQualityRankSumTest extends RankSumTest {
} }
} }
protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) { protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) { for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
final boolean matchesRef = ref.equals(alleleBin.getKey()); final boolean matchesRef = ref.equals(alleleBin.getKey());
final boolean matchesAlt = alts.contains(alleleBin.getKey()); final boolean matchesAlt = alts.contains(alleleBin.getKey());

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
View File

@ -123,7 +123,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
if ( context == null ) if ( context == null )
continue; continue;
fillQualsFromPileup(vc.getReference(), vc.getAlternateAlleles(), context, refQuals, altQuals); fillQualsFromPileup(vc.getReference(), vc.getAlternateAlleles(), vc.getStart(), context, refQuals, altQuals);
} }
if ( refQuals.size() == 0 || altQuals.size() == 0 ) if ( refQuals.size() == 0 || altQuals.size() == 0 )
@ -146,7 +146,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
return map; return map;
} }
protected abstract void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals); protected abstract void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals);
protected abstract void fillQualsFromPileup(final byte ref, final List<Byte> alts, final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals); protected abstract void fillQualsFromPileup(final byte ref, final List<Byte> alts, final ReadBackedPileup pileup, final List<Double> refQuals, final List<Double> altQuals);

21
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
View File

@ -12,6 +12,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele; import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.*; import java.util.*;
@ -47,11 +48,7 @@ public class ReadPosRankSumTest extends RankSumTest {
} }
} }
protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, List<Double> altQuals) { protected void fillQualsFromPileup(final Allele ref, final List<Allele> alts, final int refLoc, final Map<Allele, List<GATKSAMRecord>> stratifiedContext, final List<Double> refQuals, final List<Double> altQuals) {
// TODO -- implement me; how do we pull out the correct offset from the read?
return;
/*
for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) { for ( final Map.Entry<Allele, List<GATKSAMRecord>> alleleBin : stratifiedContext.entrySet() ) {
final boolean matchesRef = ref.equals(alleleBin.getKey()); final boolean matchesRef = ref.equals(alleleBin.getKey());
final boolean matchesAlt = alts.contains(alleleBin.getKey()); final boolean matchesAlt = alts.contains(alleleBin.getKey());
@ -59,13 +56,21 @@ public class ReadPosRankSumTest extends RankSumTest {
continue; continue;
for ( final GATKSAMRecord read : alleleBin.getValue() ) { for ( final GATKSAMRecord read : alleleBin.getValue() ) {
final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getUnclippedStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
continue;
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 );
final int numAlignedBases = AlignmentUtils.getNumAlignedBases( read );
if (readPos > numAlignedBases / 2)
readPos = numAlignedBases - (readPos + 1);
if ( matchesRef ) if ( matchesRef )
refQuals.add((double)read.getMappingQuality()); refQuals.add((double) readPos);
else else
altQuals.add((double)read.getMappingQuality()); altQuals.add((double) readPos);
} }
} }
*/
} }
protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) { protected void fillIndelQualsFromPileup(ReadBackedPileup pileup, List<Double> refQuals, List<Double> altQuals) {

2
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -73,7 +73,7 @@ public class PileupElement implements Comparable<PileupElement> {
} }
public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isAfterDeletion, final boolean isBeforeInsertion, final boolean isAfterInsertion, final boolean isNextToSoftClip) { public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeDeletion, final boolean isAfterDeletion, final boolean isBeforeInsertion, final boolean isAfterInsertion, final boolean isNextToSoftClip) {
this(read,offset, isDeletion, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, -1); this(read, offset, isDeletion, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, -1);
} }
public boolean isDeletion() { public boolean isDeletion() {
return isDeletion; return isDeletion;

14
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -381,15 +381,19 @@ public class AlignmentUtils {
return alignment; return alignment;
} }
public static int calcAlignmentByteArrayOffset(final Cigar cigar, PileupElement pileup, final int alignmentStart, final int refLocus) { public static int calcAlignmentByteArrayOffset(final Cigar cigar, final PileupElement pileupElement, final int alignmentStart, final int refLocus) {
int pileupOffset = pileup.getOffset(); return calcAlignmentByteArrayOffset( cigar, pileupElement.getOffset(), pileupElement.isInsertionAtBeginningOfRead(), pileupElement.isDeletion(), alignmentStart, refLocus );
}
public static int calcAlignmentByteArrayOffset(final Cigar cigar, final int offset, final boolean isInsertionAtBeginningOfRead, final boolean isDeletion, final int alignmentStart, final int refLocus) {
int pileupOffset = offset;
// Special case for reads starting with insertion // Special case for reads starting with insertion
if (pileup.isInsertionAtBeginningOfRead()) if (isInsertionAtBeginningOfRead)
return 0; return 0;
// Reassign the offset if we are in the middle of a deletion because of the modified representation of the read bases // Reassign the offset if we are in the middle of a deletion because of the modified representation of the read bases
if (pileup.isDeletion()) { if (isDeletion) {
pileupOffset = refLocus - alignmentStart; pileupOffset = refLocus - alignmentStart;
final CigarElement ce = cigar.getCigarElement(0); final CigarElement ce = cigar.getCigarElement(0);
if (ce.getOperator() == CigarOperator.S) { if (ce.getOperator() == CigarOperator.S) {
@ -414,7 +418,7 @@ public class AlignmentUtils {
break; break;
case D: case D:
case N: case N:
if (!pileup.isDeletion()) { if (!isDeletion) {
alignmentPos += elementLength; alignmentPos += elementLength;
} else { } else {
if (pos + elementLength - 1 >= pileupOffset) { if (pos + elementLength - 1 >= pileupOffset) {