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2.9.3
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@d-cameron d-cameron released this 08 Jun 16:57
· 482 commits to master since this release
v2.9.3
59d7733
  • #348 Fixed NPE in GeneratePonBedpe
  • Cleaning up named sorted temporary bam file when no longer required
  • Added ASSEMBLY_BIAS single breakend assembly support bias filter
    • This is a more generalised version of the ASSEMBLY_ONLY/NO_ASSEMBLY filters
  • Added NO_SR and NO_RP filters to reduce single breakend FDR
  • Fixed "Record should have been dropped" in SoftClipToSplitReads when using external alignment
  • Only writing a single realignment record for anchoring bases
    • Fixes edge case where unphased variants are sometimes phased cis
  • Removed SoftClipsToSplitReads.REALIGN_ANCHORING_BASES parameter
    • This split breakend/anchoring sequence alignment approach ends up worse than realigning the entire read. If the initial assembly was over-aligned, it will remain so. Worse, it will result in a soft clip in the anchoring bases thus inserted sequence which should be aligned to the other side.
    • The is a reversion to pre-2.9.0 GRIDSS behavour
  • Reduced lock contention when performing multi-threaded BAM reading
  • Not attempting realignment for sequences shorter than 20bp
    • Fixes issues with in-process bwa instablility when aligning very short sequences
    • Added AnnotateInsertedSequence.MIN_SEQUENCE_LENGTH parameter with default of 20
    • SoftClipsToSplitReads.MIN_CLIP_LENTH now defaults to 20
  • Added ability to dump the sequences sent for in-process realignment to a fastq file
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