1.1.1

• Improved variant calling multi-threaded performance
• Improved variant annotation performance
• Improved evidence allocation performance
• Improved multi-mapping read handling
  • Much lower variant and assembly allocation memory overhead
  • Now using off-heap memory for lookup tables.
• Added ReportThresholdCoverage to write BED file containing regions above a given threshold coverage
  -- Re-added coverage blacklist for excluding extremely high coverage regions
• Improved variant calling error recovery
• Ignoring indels smaller than the minimum soft clip length (default 5bp)
• Added custom "mm" SAM tag (enabling improved multi-mapping read performance)
• Indels now using same scoring model as soft clips and split reads
• Added throttling to some log messages that could result in extremely large log files
• Corrected off-by-one error in ReadsToBedpe
• Added configuration settings to allow turning off unique allocation of multi-mapping reads to assemblies and/or variant calls