68ce55148e01821feaa65e31d1f3c504e7b37171,java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java,IndelGenotyperV2Walker,printVCFLine,#VCFWriter#IndelPrecall#,828
Before Change
if ( event_length == 0 ) { // insertion
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,true) );
alleles.add( Allele.create(call.getVariant().getBases(), false ));
} else { //deletion:
alleles.add( Allele.create(Allele.NULL_ALLELE_STRING,false) );
alleles.add( Allele.create(call.getVariant().getBases(), true ));
After Change
List<Allele> homref_alleles = null; // when needed, will contain two identical copies of ref allele - needed to generate hom-ref genotype
if ( call.getVariant() == null ) {
// we will need to cteate genotype with two (hom) ref alleles (below).
// we can not use 'alleles' list here, since that list is supposed to contain
// only *distinct* alleles observed at the site or VCFContext will frown upon us...
alleles.add( Allele.create(refBases[(int)start-1],true) );
homref_alleles = new ArrayList<Allele>(2);
homref_alleles.add( alleles.get(0));
homref_alleles.add( alleles.get(0));
} else {