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@d-cameron d-cameron released this 11 Feb 10:05
· 942 commits to master since this release
v2.1.0
1243674

This release adds additional command-line utilities and arguments that enables GRIDSS to be run in a targeted manner.

As usual, this release also contains bug fixes and performance enhancements.

  • Added ExtractFullReads utility to extract all fragments overlapping a set of regions of interest. Unlike simpler utilities such as samtools view, both reads in a read pairs are extracted if either of them overlap a ROI, and all chimeric alignment records are extracted if a split read overlaps a ROI.
  • AllocateEvidence can now recalculate the read and assembly support independently.
  • Fixed a bug causing breakpoints with 1 base of untemplated inserted sequence were being reported as clean breakpoints with 1bp more of reference sequence sequence (i.e. the untemplated inserted sequence is treated as being aligned to one side of the breakpoint even though the base is mismatched).
  • Improved multi-threading including a direct patch of samtools/htsjdk#1249
  • Added gridss_separate.sh example script which splits out the pipeline steps performed by CallVariants into separate command line invocations.
  • Updated htsjdk and picard versions.

Note that since GRIDSS uses the picard command line parser, the picard syntax transition period also applies to GRIDSS.

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