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CHANGELOG.rst

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Changelog

version 2.0.0-dev

Numerous backwards incompatible changes have been made to the vtools-gcoverage script.

  • Multiple refflat files can now be used as input if they are provided in a zip file with the -Z or --refflat-zip flag. This is useful for for instance when assessing multiple gene panels for exon coverage.
  • vtools-coverage's --per-transcript flag now exhibits different behavior. It now gets the coverage for the entire transcript as supplied by the refflat file. The old behavior was to only take the exons in the coding region and average them. This behavior is still available with the --per-transcript-cds-exons flag.
  • A -s / --short-column-names flag was added to the CLI of vtools-gcoverage. It sets shorter column names which may enhance readability in less or other terminal readers.
  • The column order of the vtools-coverage output is no longer in alphabetic order but in a more human-readable order: means, medians, at least percentages depth, at least percentages genome quality.
  • The percentage decimals in the output of vtools-gcoverage are rounded to the nearest two digits for better readability.
  • vtools-gcoverage no longer requires a -I flag to denote the input GVCF(s).
  • Multiple single sample GVCFs can now be used as input for vtools-gcoverage. The output statistics will be the average over the input GVCFs.
  • Fixed a bug in vtools-gcoverage where all bases from all GVCF records in a certain region were considered for coverage statistics, while the first and last record could have bases extruding from the region of interest. This means that results processed with this newer version of vtools-gcoverage will be slightly different for most of the data.