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1.1.2
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@d-cameron d-cameron released this 30 Jan 07:32
· 1257 commits to master since this release
v1.1.2
b03f5a0
  • Added explicit IGNORE_DUPLICATES parameters.
    • Duplicates are now ignored for assembly and variant calling purposes
  • BLACKLIST parameter removed from ExtractSVReads
    • No need to re-extract when changing blacklists
    • Fixes bug in which hard clipped chimeric records could not be rehydrated due to removal of blacklisted primary alignment records
  • WORKING_DIR parameter added to SoftClipToSplitRead
    • Fixes intermediate files being written to incorrect directory
  • Spanning assemblies now only considered local in the direction of assembly
    • Fixes asymmetry in SINGLE_ASSEMBLY VCF filter
  • Reduced memory consumption of ReportThresholdCoverage
  • SAMRecordUtil.clearMateInformation() now also clears the mate unmapped flag
    • Fixes "Mate unmapped flag should not be set for unpaired read." errors
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