2.8.1

• Better assembly handling of libraries with fragment size shorter than read length
  • #299, #300 Fixed assembly streaming loading window size to handle PE libraries with fragment size shorter than read length
  • Not considering read pair mate positions in which the mate fully overlaps the anchoring read
• #286 Explicitly logging assembly error stack trace to assist in debugging potential assembly errors.
• #306 replacing :| in BEALN reference names with _ to prevent downstream parsing errors.
• #301 Using QualityScoreDistribution instead of CollectAlignmentSummaryMetrics as placeholder picard metric gathering assembly metrics
• Driver script improvements
  • #310 fixed driver script crash on single-ended sequencing data
  • Improved error message with input argument is missing.
  • Fixed error on multisample VCF with --plotdir specified
  • #307 Added --useproperpair and --concordantreadpairdistribution driver script command line arguments
  • Driver script no longer defaults to extracting RP based on SAM flag
    • Fixes issue in which either too many or too few RP were extracted