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Bug fix in HC GenotypingEngine to ensure that all the merged complex events get properly added to the priority list used by VariantContextUtils when combining multiallelic events.

This commit is contained in:
Ryan Poplin 2012-09-09 13:47:54 -04:00
parent 688fc9fb56
commit 36913706c0
1 changed files with 4 additions and 2 deletions
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6
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -188,6 +188,7 @@ public class GenotypingEngine {
return returnCalls;
}
// BUGBUG: Create a class to hold this complicated return type
@Requires({"refLoc.containsP(activeRegionWindow)", "haplotypes.size() > 0"})
public List<Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>>> assignGenotypeLikelihoodsAndCallIndependentEvents( final UnifiedGenotyperEngine UG_engine,
final ArrayList<Haplotype> haplotypes,
@ -214,7 +215,6 @@ public class GenotypingEngine {
System.out.println( ">> Events = " + h.getEventMap());
}
}
final ArrayList<String> priorityList = new ArrayList<String>(); // filled in later, used to merge overlapping events into common reference view
cleanUpSymbolicUnassembledEvents( haplotypes );
if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 3 ) { // if not in GGA mode and have at least 3 samples try to create MNP and complex events by looking at LD structure
@ -229,7 +229,9 @@ public class GenotypingEngine {
// Walk along each position in the key set and create each event to be outputted
for( final int loc : startPosKeySet ) {
if( loc >= activeRegionWindow.getStart() && loc <= activeRegionWindow.getStop() ) {
final ArrayList<VariantContext> eventsAtThisLoc = new ArrayList<VariantContext>();
final ArrayList<VariantContext> eventsAtThisLoc = new ArrayList<VariantContext>(); // the overlapping events to merge into a common reference view
final ArrayList<String> priorityList = new ArrayList<String>(); // used to merge overlapping events into common reference view
if( activeAllelesToGenotype.isEmpty() ) {
for( final Haplotype h : haplotypes ) {
final HashMap<Integer,VariantContext> eventMap = h.getEventMap();