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Bug fix for read pos rank sum test annotation. Shouldn't be using the un-hardclipped start as the alignment start.

This commit is contained in:
Ryan Poplin 2012-06-22 14:53:29 -04:00
parent 735b59d942
commit 429ad44421
2 changed files with 14 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
View File

@ -56,12 +56,12 @@ 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 ); final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
continue; continue;
int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 ); int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, false, 0, 0 );
final int numAlignedBases = AlignmentUtils.getNumAlignedBases( read ); final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
if (readPos > numAlignedBases / 2) if (readPos > numAlignedBases / 2)
readPos = numAlignedBases - (readPos + 1); readPos = numAlignedBases - (readPos + 1);

12
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -342,6 +342,18 @@ public class AlignmentUtils {
return n; return n;
} }
public static int getNumAlignedBasesCountingSoftClips(final SAMRecord r) {
int n = 0;
final Cigar cigar = r.getCigar();
if (cigar == null) return 0;
for (final CigarElement e : cigar.getCigarElements())
if (e.getOperator() == CigarOperator.M || e.getOperator() == CigarOperator.S)
n += e.getLength();
return n;
}
public static byte[] alignmentToByteArray(final Cigar cigar, final byte[] read, final byte[] ref) { public static byte[] alignmentToByteArray(final Cigar cigar, final byte[] read, final byte[] ref) {
final byte[] alignment = new byte[read.length]; final byte[] alignment = new byte[read.length];