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Releases: biod/sambamba

v0.5.7

05 Aug 11:32
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  • 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

16 Jul 14:05
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  • 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

28 Jun 19:56
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  • 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

14 Apr 21:09
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bugfix: CRAM support was broken in v0.5.3 due to outdated htslib interface file

v0.5.3

13 Apr 19:49
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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

07 Apr 08:26
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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

08 Jan 09:50
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  • Bug fixes in depth tool (#110)
  • Bug fix in SAM parser (#111)
  • Filtering by supplementary flag (#113)

v0.5.0

11 Dec 20:34
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  • 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

12 Nov 22:42
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v0.5.0-alpha Pre-release
Pre-release

see v0.5.0

binaries with latest updates

22 Jul 16:40
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Pre-release

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