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Version 0.7.9
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@etal etal released this 14 Mar 18:15
· 1067 commits to master since this release
v0.7.9
9a069c4

Bug fixes, most importantly to work around an API change in pysam.

Installation:

  • Require pysam version earlier than 0.9 (#86)

fix, reference:

  • If the majority of target bins have no or very low coverage, warn the user
    about this, skip bias corrections, and mask out the low-coverage target bins
    during centering to ensure the output is still vaguely usable and sane.
    This issue could occur because the wrong target BED was used initially, or
    maybe hybridization failed in library prep.

reference:

  • Ensure the output table's columns are ordered correctly. In some cases it was
    possible for the output tables columns to be ordered differently, which still
    works in CNVkit, but is weird.

call, rescale, export:

  • Check specified gender more sensibly; on failure, default to female.
    Specifically, use case-insensitive string comparison to test whether the given
    argument means "male". Treating chrX as having neutral ploidy is probably a
    less surprising fallback, especially if the "-y" flag is forgotten elsewhere
    in the pipeline.
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