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

Further related bug fixes to GGA mode in the HC: some variants (especially MNPs) were causing problems because they don't have to start at the current location to match the allele being genotyped. Fixed.

This commit is contained in:
Ryan Poplin 2012-12-12 14:53:02 -05:00
parent 5632c13bf2
commit 211a6e78ea
1 changed files with 5 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
View File

@ -282,10 +282,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
for( final VariantContext compVC : activeAllelesToGenotype ) { for( final VariantContext compVC : activeAllelesToGenotype ) {
for( final Allele compAltAllele : compVC.getAlternateAlleles() ) { for( final Allele compAltAllele : compVC.getAlternateAlleles() ) {
final Haplotype insertedRefHaplotype = refHaplotype.insertAllele(compVC.getReference(), compAltAllele, activeRegionStart + compVC.getStart() - activeRegionWindow.getStart(), compVC.getStart()); final Haplotype insertedRefHaplotype = refHaplotype.insertAllele(compVC.getReference(), compAltAllele, activeRegionStart + compVC.getStart() - activeRegionWindow.getStart(), compVC.getStart());
if( !addHaplotype( insertedRefHaplotype, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop ) ) { addHaplotype( insertedRefHaplotype, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop, true );
return returnHaplotypes;
//throw new ReviewedStingException("Unable to add reference+allele haplotype during GGA-enabled assembly: " + insertedRefHaplotype);
}
} }
} }
@ -293,7 +290,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
for ( final KBestPaths.Path path : KBestPaths.getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) { for ( final KBestPaths.Path path : KBestPaths.getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) {
final Haplotype h = new Haplotype( path.getBases( graph ), path.getScore() ); final Haplotype h = new Haplotype( path.getBases( graph ), path.getScore() );
if( addHaplotype( h, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop ) ) { if( addHaplotype( h, fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop, false ) ) {
// for GGA mode, add the desired allele into the haplotype if it isn't already present // for GGA mode, add the desired allele into the haplotype if it isn't already present
if( !activeAllelesToGenotype.isEmpty() ) { if( !activeAllelesToGenotype.isEmpty() ) {
@ -308,7 +305,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
// falls into the bin for the 1bp deletion because we keep track of the artificial alleles). // falls into the bin for the 1bp deletion because we keep track of the artificial alleles).
if( vcOnHaplotype == null ) { if( vcOnHaplotype == null ) {
for( final Allele compAltAllele : compVC.getAlternateAlleles() ) { for( final Allele compAltAllele : compVC.getAlternateAlleles() ) {
addHaplotype( h.insertAllele(compVC.getReference(), compAltAllele, activeRegionStart + compVC.getStart() - activeRegionWindow.getStart(), compVC.getStart()), fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop ); addHaplotype( h.insertAllele(compVC.getReference(), compAltAllele, activeRegionStart + compVC.getStart() - activeRegionWindow.getStart(), compVC.getStart()), fullReferenceWithPadding, returnHaplotypes, activeRegionStart, activeRegionStop, false );
} }
} }
} }
@ -332,7 +329,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
return returnHaplotypes; return returnHaplotypes;
} }
private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final ArrayList<Haplotype> haplotypeList, final int activeRegionStart, final int activeRegionStop ) { private boolean addHaplotype( final Haplotype haplotype, final byte[] ref, final ArrayList<Haplotype> haplotypeList, final int activeRegionStart, final int activeRegionStop, final boolean FORCE_INCLUSION_FOR_GGA_MODE ) {
if( haplotype == null ) { return false; } if( haplotype == null ) { return false; }
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 );
@ -387,7 +384,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
return false; return false;
} }
if( !haplotypeList.contains(h) ) { if( FORCE_INCLUSION_FOR_GGA_MODE || !haplotypeList.contains(h) ) {
haplotypeList.add(h); haplotypeList.add(h);
return true; return true;
} else { } else {