v0.5.7

• depth tool: one can now provide through the -Lparameter a region (CHR/CHR:BEG/CHR:BEG-END) instead of a filename, avoiding the need to write a single-line BED file (#114)
• markdup tool: multiple files can be provided at once, so that the output contains merged records with duplicates marked/removed (#71)

v0.5.6

• Fixed mpileup bugs (#151, #153)
• Additions to depth tool:
  • BED header is printed in window and region modes (#145)
  • --min-base-quality option now works in all modes (#154)

v0.5.5

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

v0.5.4

bugfix: CRAM support was broken in v0.5.3 due to outdated htslib interface file

v0.5.3

mpileup tool has been effectively revived (the old code was broken - #127) and is now much more feature-complete; it has still not been heavily tested, though.

• since now only samtools 1.x versions are supported
• BCF format is treated as it should be, without decompression (prior versions converted it to VCF for simplicity, but that's often slow)
• the output data from multiple processes, that are in text formats (pileup, VCF) or uncompressed BCF, are stored in memory lz4-compressed (a fast and lightweight compression algorithm); this adds some computational overhead (almost negligible in most usage scenarios) but allows to use much less RAM
• default buffer size (size of an uncompressed chunk of BAM file) is increased from 4MB to 64MB (thanks to the above mentioned internal compression)

v0.5.2

sort tool improvements:

• fixed a memory leak (#116)
• added --natural-sort/-N option for sorting by read name as done in samtools (#109/#132)
• the tool is now lenient to file deletion failures (#124) that can occur on NFS (fixed by @chapmanb)

v0.5.1

• Bug fixes in depth tool (#110)
• Bug fix in SAM parser (#111)
• Filtering by supplementary flag (#113)

v0.5.0

• filtering in merge and sort
• new tool for assessing coverage of regions: 'depth'
• merge tool: allow references to have different order in input files (indexes are required in this case), disable GC and reduce its usage
• sort tool: also get rid of most GC allocations
• automatic on-the-fly index creation when writing a coordinate-sorted *.bam file
• CRAM support in view and index; builds upon htslib, remember to set $REF_CACHE
• bugfix in markdup: don't segfault on empty files (#100)
• index tool no longer supports optional index filename argument

v0.5.0-alpha

see v0.5.0

binaries with latest updates

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