Version 0.9.9 ------------- 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)](https://doi.org/10.1186/1755-8794-5-54). 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)