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@etal etal released this 13 Apr 16:43
· 8 commits to master since this release

Version 0.9.11

New features

  • Most commands include a new option, --diploid-parx-genome, to treat the
    pseudoautosomal regions (PAR1/2) of human chromosome X as autosomal, i.e. diploid
    regardless of sample sex. The value it takes is a human reference genome ID such as
    "grch38". This feature should help reduce false calls on sex chromosomes in human
    samples. (Thanks @rollf; #789)
  • The fix command takes a new option --smoothing-window-fraction to allow manual
    tuning of the smoothing window used in GC and other automatic bias corrections.
    (Thanks @kkchau; #859)
  • hg38 refFlat and genome accessibility data files are now included in the source tree.
    (Thanks @berguner; #822, #837)

Bug fixes

  • The Docker image once again includes the additional scripts beyond cnvkit.py.
  • User-specified sample sex with -x now works properly. (Thanks @28rietd and @ccoo22;
    #843, #851)
  • User-specified smoothing window size now applies in HMM segmentation. (Thanks
    @zhuying412; #833, #835)
  • An error in export vcf has been fixed. (Thanks @pwwang; #818)

Other updates

  • Dependency versions are updated to match Ubuntu 23.04 Lunar, more or less.
  • Automated testing is done on Python version 3.8 through 3.12 -- these are the
    "supported" versions.
  • Small documentation fixes.

New Contributors

Full Changelog: v0.9.10...v0.9.11