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@d-cameron d-cameron released this 11 May 01:11
· 1431 commits to master since this release
0.11.3
a73be49

Usability improvements:

  • Reporting MAPQ > 60 as warning. Such values are typically from aligners that do follow the SAM specifications when reporting MAPQ
  • Updated example script with java version check, and default hg19 blacklist
  • INPUT_CATEGORY (IC) command-line arguments are now 1-based to match downstream analysis using the StructuralVariantAnnotation package

Additional VCF outputs:

  • Reporting inexact homology lengths (max 300bp in either direction) in IHOMLEN field
  • Using PARID instead of MATEID when writing VCF output

Performance improvements:

  • Retaining cache of memoized paths between contig calls
  • Removing partial misassembled contigs (too long to be valid breakend) during assembly instead of as post-assembly filter
  • Not assembling when local graph complexity exceeds threshold (default threshold is 400 time median complexity of 500x coverage WGS sequencing).

Bug fixes/correctness improvements:

  • Using language-independent locale
  • Improved breakpoint positioning when inexact homology is present
  • Incorporating RP/OEA anchor reads into assembly to enable longer assembly into the reference-supporting bases
  • More conservative path collapse during assembly
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