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@d-cameron d-cameron released this 14 Oct 08:27
· 65 commits to master since this release
v2.12.2
28fd5fa

Critical bug fix release

DO NOT USE THE PREVIOUS GRIDSS VERSION (version 2.12.1): the previous version contained a critical bug in the preprocessing step that removes all split reads.

All results from GRIDS 2.12.1 should be rerun - the assembly.bam and gridss.working directories must be deleted before rerunning

  • #513 Fixed critical regression error
    • The #513 fix in v2.12.1 incorrectly removed the SA tag instead of the aa as intended
    • This resulted in all split read being treated as soft clipped reads. v2.12.1 outputs, assembly.bam, and gridss.working directories should be deleted and GRIDSS rerun
  • #526 limiting parallel GC threads to match --threads
  • #522 gridss: required arguments now depends on which step is being run
  • #529 gridss_somatic_filter: added error message when neither of --output and --fulloutput are specified
  • #531 GeneratePonBedpe: Fixed unnecessary imprecise call inclusion error message.
  • #530 Not outputing time version if time is not being run
  • #530 Continuing even when setting the ulimit fails
  • #523 cleaning up any old samtools sort temp files
  • Fixed VIRUSBreakend max coverage threshold not being calculated
  • fixes OutOfMemory Error
  • Increased heap size for gridss.VirusBreakendFilter
  • fixes OutOfMemory Error
  • Added gridss.DumpReadSupport to exporting all supporting evidence to BED/BEDPE
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