v0.6.7

• Adding ability to provide bed file for sambamba slice (#307) by Brett T. Hannigan
• Adding ability to slice multiple regions at once by Brett T. Hannigan
• markdup: use uint type for read scores; fixes #137

v0.6.6

• view tool --num-filter option (#264), the syntax is x/y (x, /y), meaning samtools -f x -F y
• filtering bug fix: enable [mate_]ref_name =~ /regex/ matching (#265)

v0.6.5

• mpileup:
  • fix hanging issues (#247, thanks @nosepy)
  • queue length based on total data size (#253)
• A few more warnings are printed (#251, #254)
• Sort is more robust when memory can't be allocated (#254 by @sambrightman)

v0.6.4

• mpileup:
  • Parallellization improvements by @sambrightman (#238)
  • Fixed a bug with splitting at chromosome ends (#244)
• view adds a 'PG' record to the header (#206)
• Tool awareness of the new AH ('alternate haplotype') SAM header tag (thanks @indraniel)
• Binary builds on Linux are now done with LLVM 3.8 and LDC 0.17.1 which should improve both performance and stability
• Added YAML file generator for updating the bioconda package

v0.6.3

• Fixed handling zero-coverage bases in depth base (#225)
• Option -z/--report-zero-coverageis now deprecated, use -c 0/--min-coverage=0 instead

v0.6.2

• Updated lz4 library to fix occasional mpileup/markdup failures (#214, #224)
• Fixed a minor bug in depth window (c228c63)

v0.6.1

• depth tool:
  • new option -m (--fix-mate-overlaps) for proper counting of overlapping read pairs (#204)
  • fixed a rare bug occurring when two consecutive records have same position but different reference (#193)
• filtering (all tools):
  • empty string is now accepted (#191)
  • new string fields are recognized: strand (+/-), ref_name, and mate_ref_name (#203)

v0.6.0

• Fixed segfaults with PacBio reads (#182, #190)
• Implemented external sort in markdup command, its memory usage should be much lower now (#123)
• Added chimeric flag to filtering (#185), which selects paired reads mapped to different reference sequences

v0.5.9

• important depth base bugfixes (#167, #172)
• sort, view: support for - output file parameter
• automatic fixing of 'bin' field in BAM records whenever possible (#163)

v0.5.8

Important bug fix in depth tool: overlapping BED files are now handled correctly (#159)