2.9.1

• Reimplemented gridss_annotate_insertions_repeatmaster.R into gridss.InsertedSequenceAnnotator
  • Added --repeatmaskerbed command line option to gridss.sh to do RepeatMasker annotating of inserted sequences
  • gridss_annotate_insertions_repeatmaster.R is no longer included in GRIDSS releases
• Fixed potential memory leak when using in-process bwa alignment
• Improved performance of steps using in-process bwa alignment
• Improved performance of variant calling steps
• Limited some spammy log messages
• Improved assembly stability
  • Fixes issues some users have encountered when processing hg38 alt contigs when using bwa-aligned input files