v0.5.5
- Multiple bug fixes in
mpileup
tool, thanks to heavy testing by @rernst (#75, #142, #143) - Updated
flagstat
andmarkdup
output to be equivalent to recent versions ofsamtools
andPicard
respectively (#141, #148 ) Fixed support for unsorted BED files in(fixed in 0.5.8)depth
tool (#147)- Added back optional output filename in
index
(it was removed in 0.5.0) - Fixed a bug in uncompressed BAM writing (#137)