hap = hapString.getBytes();
this.expected = expected;
}
public Map<Integer,VariantContext> calcAlignment() {
final SWPairwiseAlignment alignment = new SWPairwiseAlignment(ref, hap, new Parameters(3,-1,-4, -1));
final Haplotype h = new Haplotype(hap, false, alignment.getAlignmentStart2wrt1(), alignment.getCigar());
return HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(h, ref, genomeLocParser.createGenomeLoc("4", 1, 1 + ref.length), "name");
}