For those not on the email list, htslib/samtools/bcftools version 1.1 was just released.
The most major improvements (in my opinion) are:
- Sorting BAM files with thousands of reference contigs now completes in a reasonable amount of time
- Fixed samtools calmd memory leak
- Fixed samtools idxstats when displaying statistics from indices generated by samtools 0.1.x
It should be noted that the idxstats change is actually a change to what was included in the index, which was done incorrectly in version 1.0. Other changes are included in the email I linked to above.