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Release 0.1.4
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@tfenne tfenne released this 08 May 16:14
0.1.4
e9c60af

Release 0.1.4 introduces the following changes to existing tools:

  • CallMolecularConsensusReads
    • Added the ability to filter the maximum number of reads going into a consensus read
  • CallMolecularConsensusReads and FilterConsensusReads
    • No longer have default values for their --min-reads and --min-consensus-base-quality/--min-base-quality parameters. The correct values for these parameters is highly library/coverage dependent and is best set by the user.
  • CallMolecularConsensusReads and CallDuplexConsensusReads
    • Raw reads are end-trimmed for Ns after low-quality masking, prior to consensus calling
    • Raw reads that are FR pairs with read length > insert size are trimmed to the insert size prior to consensus calling
  • ErrorRateByReadPosition
    • Fixed a bug whereby the cumulative error plot produced in the PDF incorrectly started the R2 error count at the cumulative sum of the R1 error count.
    • Added the count of errors (in addition to error rate) to the output file
  • FilterSomaticVcf
    • Now gracefully handles reads who's insert size and mapping information disagree. Warnings will be logged for all such reads, but the tool will not stop/exit upon finding such reads. Should reduce the frequency of "genomicPosition is outside of template" error messages
    • Works with VCFs that do not contain #contig lines in the header

In addition the following new tools were added:

  • DemuxFastqs: Performs sample demultiplexing on FASTQs
  • CorrectUmis: Corrects UMI sequences in BAM files when a set of fixed UMIs (not randommers) are used

Miscellaneous:

  • Added support for cross-building scala 2.11 and 2.12
  • Tools that invoke R scripts will now produce less noisy output
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