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2.3.0
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@d-cameron d-cameron released this 10 Jun 15:00
· 850 commits to master since this release
v2.3.0
66422b1

Optimisation and bug fix release. The headline feature of this release is the GRIDSS lite driver script

  • Added grids_lite.sh driver script. Lower sensitivity but twice as fast
  • gridss.sh is now a proper driver script with command line parsing
  • Default minimum called event size is now 10bp (down from 32bp)
  • Improved error messages
  • Unknown chromsomes in BLACKLIST bed will now raise an error
    • This prevents a blacklist with the wrong prefix being used ineffectively (e.g. "chr1" in black vs "1" in reference)
    • Added ENCFF001TDO.bed hg19 blacklist without chr prefixes
  • Max clique calling for each orientation (++, +-, -+, --, -, +) is now done in parallel
  • Q2 tag is optional and is no longer populated by default
    • This reduces the size of the intermediate files
    • fallback base quality score is 20
  • No longer auto-adding contigs to sequence dictionary
  • No longer allowing unknown contigs in breakpoint ALT alleles
  • Bug fix: IdentifyVariants was not writing to temp files when requested
  • Bug fix: no longer recreating sam header for every assembly contig
  • Bug fix: async BAM parsing now respects CRC flag
  • Fixed race condition in aysnc BAM reader
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