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Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.

This commit is contained in:
Ryan Poplin 2013-01-09 15:30:46 -05:00
parent 6787f86803
commit 487fb2afb4
2 changed files with 3 additions and 3 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -92,6 +92,7 @@ public class GenotypingEngine {
cleanUpSymbolicUnassembledEvents( haplotypes );
if( !in_GGA_mode && samples.size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
mergeConsecutiveEventsBasedOnLD( haplotypes, samples, haplotypeReadMap, startPosKeySet, ref, refLoc );
cleanUpSymbolicUnassembledEvents( haplotypes ); // the newly created merged events could be overlapping the unassembled events
}
if( in_GGA_mode ) {
for( final VariantContext compVC : activeAllelesToGenotype ) {
@ -261,7 +262,6 @@ public class GenotypingEngine {
return returnMap;
}
protected static void cleanUpSymbolicUnassembledEvents( final List<Haplotype> haplotypes ) {
final ArrayList<Haplotype> haplotypesToRemove = new ArrayList<Haplotype>();
for( final Haplotype h : haplotypes ) {
@ -269,7 +269,7 @@ public class GenotypingEngine {
if( vc.isSymbolic() ) {
for( final Haplotype h2 : haplotypes ) {
for( final VariantContext vc2 : h2.getEventMap().values() ) {
if( vc.getStart() == vc2.getStart() && vc2.isIndel() ) {
if( vc.getStart() == vc2.getStart() && (vc2.isIndel() || vc2.isMNP()) ) { // unfortunately symbolic alleles can't currently be combined with non-point events
haplotypesToRemove.add(h);
break;
}

2
public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
View File

@ -710,7 +710,7 @@ public class VariantContextUtils {
for ( VariantContext vc : VCs ) {
// look at previous variant contexts of different type. If:
// a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
// a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
// b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list)
// c) neither: do nothing, just add vc to its own list
boolean addtoOwnList = true;