// Using a static variable because contigs may overlap multiple regions and cause dupes
chunk.setReadName(chunk.getReadName() + "_" + chunkIdx++);
chunk.setAlignmentStart(actualPos + calcIndelOffset(startIdx, contig.getCigar()));
chunk.setCigar(cigar);
chunk.setReadString(bases);
chunk.clearAttributes();
// chunk.setAttribute("ZZ", contig.getCigarString());
chunk.setAttribute("ZZ", contig.getReferenceName() + ":" + contig.getAlignmentStart() +
":" + contig.getCigarString());