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Release 0.3.0
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@nh13 nh13 released this 05 Oct 19:22
0.3.0
4db53c0

Release 0.3.0 introduces the following changes to existing tools:

  • ClipBam - The --overlapping-reads option was not being used internally and is deprecated in favor of --clip-overlapping-reads. This caused overlapping reads to always be clipped.
  • CollectDuplexSeqMetrics - Added the optional output of duplex-umi frequencies with DuplexUmiMetrics.
  • DemuxFastqs - The default output sort order is changed from Unsorted to Queryname. Add an option --illumina-standards to output file names using Illumina naming conventions. Tuned the amount of memory used, especially for a large # of samples (>96).
  • CallDuplexConsensusReads - Do not except when we find potential collisions in duplex molecules, instead, do not generate a consensus read.
  • FilterBam - adding a few more filters.
  • Added a global parameter for log-level.

In addition, the following new tools were added:

  • CollectErccMetrics - This will collect metrics for analyzing ERCC spike-ins in
    RNA-Seq experiments for dose response but not fold-change
    response.

Finally, changes to various APIs were as follows:

  • ReferenceSetBuilder - Moved to the testing packages for use in projects that extend fgbio.
  • Alignment - Added subByQuery() and subByTarget() methods to Alignment.
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