Package org.broadinstitute.gatk.utils

Examples of org.broadinstitute.gatk.utils.GenomeLoc.onSameContig()


        GenomeLoc last = null;
        List<GenomeLoc> contigLocs = null;
        for (GenomeLoc loc: sorted) {
            if (GenomeLoc.isUnmapped(loc))
                continue;
            if (last == null || !last.onSameContig(loc)) {
                contigLocs = new ArrayList<GenomeLoc>();
                splits.put(loc.getContig(), contigLocs);
            }
            contigLocs.add(loc);
            last = loc;
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