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Fixing bug from when FragmentUtils merging function moved over to the soft clipped start instead of the unclipped start

This commit is contained in:
Ryan Poplin 2012-08-30 10:10:43 -04:00
parent 81d5eca975
commit 57d997f06f
2 changed files with 4 additions and 23 deletions
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1
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -73,5 +73,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("000fd36d5cf8090386bb2ac15e3ab0b5"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
}

26
public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
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@ -128,22 +128,13 @@ public class FragmentUtils {
return create(reads, reads.size(), SamRecordGetter);
}
public final static List<GATKSAMRecord> mergeOverlappingPairedFragments( List<GATKSAMRecord> overlappingPair ) {
public final static List<GATKSAMRecord> mergeOverlappingPairedFragments( final List<GATKSAMRecord> overlappingPair ) {
final byte MIN_QUAL_BAD_OVERLAP = 16;
if( overlappingPair.size() != 2 ) { throw new ReviewedStingException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
GATKSAMRecord firstRead = overlappingPair.get(0);
GATKSAMRecord secondRead = overlappingPair.get(1);
/*
System.out.println("read 0 unclipped start:"+overlappingPair.get(0).getUnclippedStart());
System.out.println("read 0 unclipped end:"+overlappingPair.get(0).getUnclippedEnd());
System.out.println("read 1 unclipped start:"+overlappingPair.get(1).getUnclippedStart());
System.out.println("read 1 unclipped end:"+overlappingPair.get(1).getUnclippedEnd());
System.out.println("read 0 start:"+overlappingPair.get(0).getAlignmentStart());
System.out.println("read 0 end:"+overlappingPair.get(0).getAlignmentEnd());
System.out.println("read 1 start:"+overlappingPair.get(1).getAlignmentStart());
System.out.println("read 1 end:"+overlappingPair.get(1).getAlignmentEnd());
*/
if( !(secondRead.getSoftStart() <= firstRead.getSoftEnd() && secondRead.getSoftStart() >= firstRead.getSoftStart() && secondRead.getSoftEnd() >= firstRead.getSoftEnd()) ) {
firstRead = overlappingPair.get(1); // swap them
secondRead = overlappingPair.get(0);
@ -155,15 +146,6 @@ public class FragmentUtils {
return overlappingPair; // fragments contain indels so don't merge them
}
/* // check for inconsistent start positions between uncliped/soft alignment starts
if (secondRead.getAlignmentStart() >= firstRead.getAlignmentStart() && secondRead.getUnclippedStart() < firstRead.getUnclippedStart())
return overlappingPair;
if (secondRead.getAlignmentStart() <= firstRead.getAlignmentStart() && secondRead.getUnclippedStart() > firstRead.getUnclippedStart())
return overlappingPair;
if (secondRead.getUnclippedStart() < firstRead.getAlignmentEnd() && secondRead.getAlignmentStart() >= firstRead.getAlignmentEnd())
return overlappingPair;
*/
final Pair<Integer, Boolean> pair = ReadUtils.getReadCoordinateForReferenceCoordinate(firstRead, secondRead.getSoftStart());
final int firstReadStop = ( pair.getSecond() ? pair.getFirst() + 1 : pair.getFirst() );
@ -183,7 +165,7 @@ public class FragmentUtils {
}
for(int iii = firstReadStop; iii < firstRead.getReadLength(); iii++) {
if( firstReadQuals[iii] > MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] > MIN_QUAL_BAD_OVERLAP && firstReadBases[iii] != secondReadBases[iii-firstReadStop] ) {
return overlappingPair;// high qual bases don't match exactly, probably indel in only one of the fragments, so don't merge them
return overlappingPair; // high qual bases don't match exactly, probably indel in only one of the fragments, so don't merge them
}
if( firstReadQuals[iii] < MIN_QUAL_BAD_OVERLAP && secondReadQuals[iii-firstReadStop] < MIN_QUAL_BAD_OVERLAP ) {
return overlappingPair; // both reads have low qual bases in the overlap region so don't merge them because don't know what is going on
@ -197,7 +179,7 @@ public class FragmentUtils {
}
final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() );
returnRead.setAlignmentStart( firstRead.getUnclippedStart() );
returnRead.setAlignmentStart( firstRead.getSoftStart() );
returnRead.setReadBases( bases );
returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() );