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2.4.0
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@d-cameron d-cameron released this 20 Jun 07:30
· 786 commits to master since this release
v2.4.0
9197c9d

Improved performance, usability, and reduced the minimum event size reported to 10bp.

  • Minimum callable event size called reduced to 10bp
    • This parameter is configurable by specifying a CONFIGURATON_FILE file containing variantcalling.minSize=10
  • Runtime of assembly step decreased by 27% by optimising data structures used
  • Runtime of variant calling (max clique) decreased by 50% by reverting back to parallel processing of all orientations
  • Added wrapper shell scripts
    • gridss.sh
      • this is a wrapper to the full GRIDSS pipeline
    • gridss_lite.sh
      • this wraps a faster but less sensitive GRIDSS pipeline.
      • Sub-clonal and hard to call variants callable by the full GRIDSS pipeline will be missed by this pipeline.
  • #74 Using CTX instead of ITX to match BreakDancer notation in simple event annotator script
  • Improved startup times by caching the in-memory 2-bit encoded representation of the reference genome.
    • A REFERENCE.gridsscache file will be created in the same directory as the reference genome.
  • gridss.
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