samtools/samtools — pull request #299 by jkbonfield (2014-09-19 16:27:36+00:00)
Title: Cram3 updates

1. Samtools flagstat now uses the sam_open API instead of bam_open, meaning it can run on SAM, BAM and CRAM instead of BAM only.

2. Several tools have been updated to call hts_set_opt to control which SAM columns are needed by the application and whether or not the MD/NM tags should be auto-computed.