Return read counts per chromosome

[AndreasHeger]

Similar to idxstats, return for each chromosome:

1. Total read count
2. Mapped read count
3. Unmapped read count (e.g. where one of a pair is mapped and the other is not)

[bioinformed]

I agree this would be useful functionality, but perhaps better in in an application and not the core library. What will we do when users request counts based on BED file masking, on/near/off-target counts, stratification by mapping quality, etc? That said, I don't have a problem if the application is part of pysam -- just that we don't attempt to build all of this functionality into the AlignmentFile object.

[AndreasHeger]

Thanks. The gist of this feature is simply to expose the data that is contained in the BAM index anyways, i.e. there is not any algorithmic component.

[bioinformed]

Ah-- I thought you meant to build a counter function that generated data similar to idxstats. It all that is being proposed is an API to expose idxstats then I withdraw all objections.

[AndreasHeger]

Note to self: add total