Examples of GenomeLoc


Examples of org.broadinstitute.gatk.utils.GenomeLoc

        if (indelSize == 0)
            return;

        final List<Allele> alleles = new ArrayList<Allele>();

        final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,locStart+offset,locStart+offset);
        final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,windowBases.getBytes());

        final int prefixLen = 10;
        final String prefix = refBases.substring(locStart+offset-prefixLen,locStart+offset);
        if (indelSize < 0) { // deletion
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