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No need to consider haplotypes which Smith-Waterman aligns off the end of the large padded reference.

This commit is contained in:
Ryan Poplin 2013-02-14 11:18:10 -05:00
parent 5cc5aedcd1
commit 871c8b3866
1 changed files with 6 additions and 4 deletions
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10
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
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@ -404,12 +404,13 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( ref, haplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND ); final SWPairwiseAlignment swConsensus = new SWPairwiseAlignment( ref, haplotype.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
haplotype.setAlignmentStartHapwrtRef( swConsensus.getAlignmentStart2wrt1() ); haplotype.setAlignmentStartHapwrtRef( swConsensus.getAlignmentStart2wrt1() );
haplotype.setCigar( AlignmentUtils.leftAlignIndel(swConsensus.getCigar(), ref, haplotype.getBases(), swConsensus.getAlignmentStart2wrt1(), 0, true) );
if( swConsensus.getCigar().toString().contains("S") || swConsensus.getCigar().getReferenceLength() < 60 ) { // protect against SW failures if( swConsensus.getCigar().toString().contains("S") || swConsensus.getCigar().getReferenceLength() < 60 || swConsensus.getAlignmentStart2wrt1() < 0 ) { // protect against unhelpful haplotype alignments
return false; return false;
} }
haplotype.setCigar( AlignmentUtils.leftAlignIndel(swConsensus.getCigar(), ref, haplotype.getBases(), swConsensus.getAlignmentStart2wrt1(), 0, true) );
final int hapStart = ReadUtils.getReadCoordinateForReferenceCoordinate( haplotype.getAlignmentStartHapwrtRef(), haplotype.getCigar(), activeRegionStart, ReadUtils.ClippingTail.LEFT_TAIL, true ); final int hapStart = ReadUtils.getReadCoordinateForReferenceCoordinate( haplotype.getAlignmentStartHapwrtRef(), haplotype.getCigar(), activeRegionStart, ReadUtils.ClippingTail.LEFT_TAIL, true );
int hapStop = ReadUtils.getReadCoordinateForReferenceCoordinate( haplotype.getAlignmentStartHapwrtRef(), haplotype.getCigar(), activeRegionStop, ReadUtils.ClippingTail.RIGHT_TAIL, true ); int hapStop = ReadUtils.getReadCoordinateForReferenceCoordinate( haplotype.getAlignmentStartHapwrtRef(), haplotype.getCigar(), activeRegionStop, ReadUtils.ClippingTail.RIGHT_TAIL, true );
if( hapStop == ReadUtils.CLIPPING_GOAL_NOT_REACHED && activeRegionStop == haplotype.getAlignmentStartHapwrtRef() + haplotype.getCigar().getReferenceLength() ) { if( hapStop == ReadUtils.CLIPPING_GOAL_NOT_REACHED && activeRegionStop == haplotype.getAlignmentStartHapwrtRef() + haplotype.getCigar().getReferenceLength() ) {
@ -445,16 +446,17 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
final SWPairwiseAlignment swConsensus2 = new SWPairwiseAlignment( ref, h.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND ); final SWPairwiseAlignment swConsensus2 = new SWPairwiseAlignment( ref, h.getBases(), SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
h.setAlignmentStartHapwrtRef( swConsensus2.getAlignmentStart2wrt1() ); h.setAlignmentStartHapwrtRef( swConsensus2.getAlignmentStart2wrt1() );
h.setCigar( AlignmentUtils.leftAlignIndel(swConsensus2.getCigar(), ref, h.getBases(), swConsensus2.getAlignmentStart2wrt1(), 0, true) );
if ( haplotype.isArtificialHaplotype() ) { if ( haplotype.isArtificialHaplotype() ) {
h.setArtificialEvent(haplotype.getArtificialEvent()); h.setArtificialEvent(haplotype.getArtificialEvent());
} }
h.leftBreakPoint = leftBreakPoint; h.leftBreakPoint = leftBreakPoint;
h.rightBreakPoint = rightBreakPoint; h.rightBreakPoint = rightBreakPoint;
if( swConsensus2.getCigar().toString().contains("S") || swConsensus2.getCigar().getReferenceLength() != activeRegionStop - activeRegionStart ) { // protect against SW failures if( swConsensus2.getCigar().toString().contains("S") || swConsensus2.getCigar().getReferenceLength() != activeRegionStop - activeRegionStart || swConsensus2.getAlignmentStart2wrt1() < 0 ) { // protect against unhelpful haplotype alignments
return false; return false;
} }
h.setCigar( AlignmentUtils.leftAlignIndel(swConsensus2.getCigar(), ref, h.getBases(), swConsensus2.getAlignmentStart2wrt1(), 0, true) );
if( FORCE_INCLUSION_FOR_GGA_MODE || !haplotypeList.contains(h) ) { if( FORCE_INCLUSION_FOR_GGA_MODE || !haplotypeList.contains(h) ) {
haplotypeList.add(h); haplotypeList.add(h);
return true; return true;