int hi = i % unrolledCivars.size();
final Civar c = unrolledCivars.get(hi);
final String h = haplotypes.get(hi);
int offset = h.length() <= readLength ? 0 : i % (h.length() - readLength);
int to = Math.min(h.length(),offset + readLength);
result.add(c.eventOffsets(reference,offset,to));
}
return result;
}
private static final Pattern cigarPattern = Pattern.compile("(\\d+)([=A-Z])");