Alistair Miles

Log last variant position with progress.

Put docs on rtfd.

Fix for pysam 0.16

2

Some fixes are needed for compatibility with pysam 0.16.

v1.1 release plan

4

Release plan: * [x] implement #78 (expose stepper) * [x] implement #79 (data fixture) * [x] update README.md with new command line help text, and also release notes and contributors...

output stats against given intervals

2

Add option to provide a list of intervals against which stats should be generated (e.g., so can provide a VCF at the command line with positions to generate stats for).

Add support for combining multiple stats types into a single record iterator. Should also be possible to support from the command line too, e.g., `--type coverage,mapq`, as long as only...

add counts of secondary alignments

2

Optionally include secondary alignments in all pileup-based statistics types. Optionally include secondary alignments in all binned statistics types. Add reads_secondary to coverage stats types as counts of reads where the...

Add sum_baseq, sum_baseq_matches, etc., to baseq stats.

binned variation stats

2

Would be useful to have binned variation stats, e.g., number of mismatches per bin, etc.

Output a field with number of reads where the qc failed flag is set.