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@d-cameron d-cameron released this 06 May 14:34
· 578 commits to master since this release
v2.9.0
2ea3435
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Learn about vigilant mode.

This release includes significant changes to how GRIDSS performs preprocessing and alignment. GRIDSS now uses in-process bwa alignment instead of requiring a command-line bwa. This requires an additional .img file which is generated from the bwa index. A new setupreference step has been added to GRIDSS driver script so all files related to the reference genome can be generated as a once-off operation.

  • Added setupreference step to GRIDSS driver script
    • One-off initialisation and files written to the reference genome directory are now explicitly a separate step
  • Added BWA JNI interface
    • External alignment no longer required
  • Added PreprocessForBreakendAssembly command line program
    • Combines ComputeSamTags and SoftClipsToSplitReads in a single pass over each input.sv.bam file.
    • Approximately 50% speedup in preprocessing time due to better parallelisation
  • Added SoftClipsToSplitReads REALIGN_UNANCHORED_BASES option
  • Using REALIGN_UNANCHORED_BASES instead of REALIGN_ENTIRE_READ for assembly realignment
    • Fixes an issue with GRIDSS2 having slightly sensitivity than GRIDSS1 for deletions in which the ref has a tandem duplication (e.g SINE-SINE becomes SINE)
  • Fixed bug causing the nominal position of the two sides of a breakpoint with homology to not match for both BND records
  • Better error message if aligner process is killed
  • Added max/max/mean mapq INFO fields
  • #319 Writing out all reproduction data for all assembly errors to prevent early abort truncating the file write
  • #329 Fixed crash in gridss_annotate_insertions_repeatmaster.R when processing chromomsomes containing ":" (HLA types)
  • #312 now supporting arbitrary split read alignment overlaps (fixes java.lang.OutOfMemoryError error)
  • Standardised error codes to match sysexits.h
    • More meaningful exit codes from gridss.sh
  • #334 cleaned up driver script logging
    • Full log file now include all log messages
  • #323 added --nojni command line option to disable native acceleration
  • Updated htsjdk/picard versions
  • Fixed error where split read records to be dropped were not actually dropped.
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