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v0.7.0

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@roryk roryk released this 11 Oct 15:57
v0.7.0
6c8c8cc
  • Fix for kallisto output failing due to defaultdict not being imported. Thanks to @andreas-wilm for the fix.
  • Added tagcount option --parse_tags to use BAM tags rather than parsing read names (UM for UMI, CR for cell barcode)
  • Added tagcount option --gene_tags to use BAM tags to get ID of mapping gene (GX tag).
  • Fix tagcount with --genemap option not including a column name for the index.
  • Add sparse subcommand to turn a matrix into a sparse matrix.
  • Add fasttagcount subcommand. This assumes the input BAM/SAM file is coordinate sorted. Reduces memory usage by over
    100x and runtime by 30-40% for deep samples.
  • Warn, don't fail if transcripts are missing from the genemap.
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