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Expanded unit tests for AlignmentUtils 

-- Added JIRA entries for the remaining capabilities to be fixed up and unit tested
This commit is contained in:
Mark DePristo 2013-01-31 17:26:22 -05:00 committed by Ryan Poplin
parent 206eab80e3
commit 22f7fe0d52
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
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@ -107,7 +107,7 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), 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, 0, 0 );
final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read ); final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
if (readPos > numAlignedBases / 2) if (readPos > numAlignedBases / 2)
readPos = numAlignedBases - (readPos + 1); readPos = numAlignedBases - (readPos + 1);