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