2.8.0

• Reverted to MATEID instead of PARID for the VCF breakpoint record pairing.
  • MATEID is the correct field to use according to the VCF specifications.
• Added FIX_SA and FIX_MISSING_HARD_CLIP to gridss.ComputeSamTags
  • FIX_SA: rewrites split read SA tags
    • corrects GATK indel realignment SA tag data inconsistency
  • FIX_MISSING_HARD_CLIP: infers missing hard clipping if split read records have different read lengths
    • corrects for GATK indel realignment stripping hard clipping when realigning
  • GRIDSS log files should no longer be full of SA tag of read ********** refers to missing alignments warning messages!
  • There should be significantly fewer data inconsistencies when running on GATK indel realigned bams.
• #291 Updated libraries to htsjdk 2.21.1 and picard 2.21.8
  • Improved CRAM support
• #278 the nominal position breakpoint position at both breakend records is guaranteed to be the same
• #293 gridss.GeneratePonBedpe now defaults to treating the first sample as the normal
• #283 Validating steps command line argument. Fixed bug with "all"/"call" step parsing
• gridss_somatic_filter.R now writes VCF header for all filters
• #295 Added error message if using a very old samtools version
• #296 gridss_annotate_insertions_repeatmasker.R now explicitly sets repeatmasker column types
  • Fixes crash reading a repeatmasker .fa.out file when using integer chromosome numbers without a chr prefix.
• #292 gridss.SoftClipToSplitReads now soft clips alignments that align over the start or end of a chromosome
  • Fixes occasional crash during assembly realignment with older bwa versions
• #287 assembly contig per-base support treats RP anchoring with no valid kmers treated as the anchoring read was ignored
  • Fixes crash when one of two reads in a read pair is shorter than 25bp