gmcvicker/genome — pull request #4 by funnell (2013-06-14 19:52:13+00:00)
Title: Split read load bam read depth

This looks like it works. I used the cigar information to calculate coverage. Right now reads with a deletion at a particular position are included in the calculation, but the 'N' cigar operation is skipped along with clipped bases, insertions, and padded bases.
Give this a try and if it looks okay I'll merge it into master.