Version 0.9.9

etal released this 01 Jun 19:43

· 197 commits to master since this release

This release contains a new script and, more importantly, a volley of bug fixes by @tskir, a new CNVkit collaborator.

New script

genome_instability_index.py

For each given sample (.cnr or .cns, ideally .call.cns), this script reports two values, the number of non-neutral segments and the fraction of the total sequencing-accessible genome that they cover. Together, these values have been described as the Genome Instability Index (G2I) by Bonnet et al. (2012). These numbers are not difficult to calculate directly from .cns files, but they are frequently requested, so here you go.

Bug fixes by @tskir

Installation:

Set NetworkX minimum version to work with pomegranate on Python 3.9. (#614, #606; thanks @auberginekenobi)

genemetrics, diagram, scatter:

Fix an error in iterating over chromosomes during gene-wise operations or gene selection. (#580, #573, #576, #579; thanks @diushiguzhi @eriktoo @hrkemp @drmrgd @HYan-lei)

access:

Fix an error when all chromosomes listed in the exclusion BED file appear only once. (#581, #574; thanks @dajana17)

autobin:

Allow specifying explicit output filenames via -o/--output. If this option is not used, the behavior is the same as before. Some pipeline frameworks such as Snakemake require output filenames to be explicit in wrapped commands. (#608, #607; thanks @enes-ak)
Fix median-size file selection. (#613, #611; thanks @michaelsykes)

coverage:

Fix a potential crash with the -c option; generally make the -c option's results more stable. This changes the results you'd get with coverage -c compared to previous CNVkit versions, but in any case -c isn't recommended
for production use, only for algorithm exploration. (#598, #593; thanks @joys8998)

genemetrics:

Rename column n_bins to probes in output, for compatibility with 'call' and 'export' commands. (#586, #585; thanks @eriktoo)

scatter:

Avoid losing short segments in rasterized PNG output, depending on DPI settings. (#615, #604; thanks @jimmy200340)
Allow NCBI-style chromosome names that contain a ".", e.g. "NC_039902.1". (#603, #602; thanks @amora197)

segment:

Fix an IndexError during smoothing when the signal is shorter than a window, e.g. on chrY where the chromosome contains few bins. (#590, #587; thanks @tetedange13)

Improvements from other contributors

scripts/guess_baits.py: Fix a copy-paste error on script launch. (#588; thanks @sssimonyang)
Documentation: Link to the Debian package alongside other packages. (#562; thanks @mr-c)

Assets 2