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Release 0.5.0
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@nh13 nh13 released this 11 Feb 15:31
0.5.0
f08a4c6

Release 0.5.0 introduces the following changes to existing tools:

  • CallDuplexConsensusReads: Fixed a rare bug where the consensus base quality could be zero or one if the two strands' base qualities differ by two or less.
  • FilterConsensusReads: Fix for bug where duplex reads formed from raw reads from a single strand only could be incorrectly filtered.
  • CorrectUmis: Now stores the original UMI sequences in the OX tag upon correction.
  • DemuxFastqs: Bug fix to correct quality scores in output BAM files
  • ClipOverlappingReads: Removed previously deprecated tool. Use ClipBam instead.
  • ClipBam:
    • Now optionally outputs metrics about clipping present in reads before and after execution.
    • New option to "upgrade" clipping, e.g. replace existing soft-clipping with hard-clipping

Changes to APIs were as follows:

  • Various deprecated methods were removed this release.
  • Metric formatting now prints smaller Doubles in scientific notation, and the formatting is generally more efficient.
  • NeedlemanWunchAligner gained a Glocal alignment mode for aligning all of a query sequence to a sub-region of a target sequence
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