hammerlab/guacamole — pull request #168 by ryan-williams (2014-09-11 04:42:45+00:00)
Title: refactor PileupElement, elementAtGreaterLocus

- elementAtGreaterLocus was mimicking the vals in PileupElement;
cleaner to advance through loci by making new PileupElements
at each CigarElement
- keep all CigarElements around in PileupElement; track current
idx into that array
- used especially in indel code downstream
- correctly handle insertions at the start of a contig (include
trailing reference base)
- correctly handle insertions at the start of a read (skip them;
they don't count for reference locus that lands at the first
read-base after them)