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 {