WisecondorX: bugfix release

Changes

• fixed import statements

WisecondorX

changes

• Python 3.x compatible
• New visualizations: colors, weighted dots, weighted segments
• New CBS: stretches of blacklisted bins serve as certain breakpoints
• New param to force gender typed analysis
• Fixes: issue #15; issue with multithreading (now it doesn't use more cores than requested ...); index interval issue R vs python
• True between-sample z-scoring technique. Less subject to other-than-the-studied aberrations.
• No more manual fetal gender selection prior to 'newref', thanks to '--nipt' argument. '--nipt' flag clusters female and male feti in two groups. Including male feti for autosomes processing improves NIPT normalization, possibly caused by X and Y reads that wrongly map autosomes.
• Y-fraction parameter argument is removed.

Important remark

All samples should be remapped prior to using this version. There are lots of changes, even in the earliest stage (convert) that could negatively impact the performance wisecondorX when using a .npz file in v1.x.x that was created in v0.2.x.

WisecondorX: point release

• Added support for paired-end data
• Gender prediction is now Y-based, instead of X-and-Y-based. The latter technique proved problematic when large X-deletions were present.
• Changed the definition of segmental Z-scores: These used to evaluate the null hypothesis 'this segment does not contain a significant bin'. Now it checks whether a segment significantly differs from other segments, which is particularly interesting for NIPT.
• Added 'output interpretation' to readme for less experienced users.

WiseCondorX: Unified References

• Automated and updated gender prediction
• deprecated gender split references, unified genders in references
• code clean up

WARNING:

• Breaks backwards compatibility with NPZ files generated with previous versions. A conversion script will be provided to convert older NPZ files.

WisecondorX: point release

• Added z-scores
• Fixed masking issue for large bin sizes
• Made robust vs whole-chromosome blacklisting

Breaking changes

• Plot output renamed from chromosomeWide.png to genome_wide.png
• Statistics file suffix changed from _statistics.txt to _chr_statistics.txt

WisecondorX: Initial release

v0.1.0

fixed manifest (#2)