v1.2.0

New features

• Added option to plot yfrac histogram and Gaussian mixture model (#65, #24, etc)
• Added automatic CPA score (doi: 10.1186/s13073-020-00735-4) calculation (multiple requests by mail)
• Added number of reads to statistics file for auto parsing purposes
• Added new blacklist files, including acen and gvar (makes more sense than acen only)

Important changes

• now requires matplotlib
• output x_chr_statistics.txt is renamed x_statistics.txt

Fixes #59

Fixes #59 by

• Allowing NaN in .json files
• Allowing NaN during Z-score calculation, segment averaging

Omit duplicate removal now optional

• Added --normdup flag

Automated paired-end processing

• The --paired flag is removed

Implemented workaround for issue #24

• Added chromosome Y fraction cutoff parameter, as an alternative to automatic gender prediction through Gaussian mixture models.

Bugfix release: robust vs small reference

Although small references (1-20) are not recommended, WisecondorX should not generate errors from this version on.

Towards more straightforward z-score calculations

Minor changes:

• Samples in null set reference (required for z-scores) are no longer median centered. This procedure had a negligible effect, yet was inconsistent (as it was only applied to autosomes).
• Instead, actual z-scores are calculated as (X-u)/sd, instead of X/sd in previous version.
• Terminology update from monoploid/diploid/triploid to 1n/2n/3n, which is more appropriate when referring to single aberrations.

Default calling based on z-scores

Minor changes:

• Cairo bitmap (for .png writing) no longer default.
• Fixed color bug in plots.

Major change:

• Aberration calling is now dependent on the segmental z-scores (default), instead of a ratio cut-off (still optional).

Bugfix release

Gender forcing bugfix release

WiseCondorX: gonosome handling

Better handle gonosomes