v0.9.11

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

• @pwwang made their first contribution in #818
• @berguner made their first contribution in #837
• @zhuying412 made their first contribution in #835
• @kkchau made their first contribution in #844
• @28rietd made their first contribution in #851

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