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Bug fix in HC gga mode. 

-- Don't try to test alleles which haven't had haplotypes assigned to them
This commit is contained in:
Ryan Poplin 2013-03-21 10:59:34 -04:00
parent 1a95ce5dcf
commit b9c331c2fa
1 changed files with 4 additions and 0 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -631,6 +631,10 @@ public class GenotypingEngine {
if( eventToTest.getKey().equals(new Event(null)) ) if( eventToTest.getKey().equals(new Event(null)) )
continue; continue;
// only try to disambiguate for alleles that have had haplotypes previously assigned above
if( eventToTest.getValue().isEmpty() )
continue;
final Haplotype artificialHaplotype = eventToTest.getValue().get(0); final Haplotype artificialHaplotype = eventToTest.getValue().get(0);
if( isSubSetOf(artificialHaplotype.getEventMap(), h.getEventMap(), true) ) { if( isSubSetOf(artificialHaplotype.getEventMap(), h.getEventMap(), true) ) {
matchingEvent = eventToTest.getKey(); matchingEvent = eventToTest.getKey();