Softening the dependency on PySAM

[ilykos]

My environment is Microsoft Windows and air-gapped. Even that there exist solutions to have linux virtualization, it is unfortunate that cnvkit cannot be installed only because of PySAM. After I removed pysam imports, I was capable of doing simple segmentation with cnvlib. Please consider making PySAM optional as it is a heavy-weight package not always necessary for many useful features of cnvlib.

[etal]

That may be possible. Do you have another method for calculating the coverage depths in each bin, e.g. samtools/bedtools/mosdepth on the command line?

[LukaP-BB]

That may be possible. Do you have another method for calculating the coverage depths in each bin, e.g. samtools/bedtools/mosdepth on the command line?

I've implemented a replacement for cnvkit.py coverage in one of my workflows with the following snippet

bedtools sort -i $panel_bed | bedtools coverage -a stdin -b $bam_file -mean -sorted -g $chrom_file

$chrom_file is a tsv of the form chrN size_of_chromosome

This gives an output that is similar to cnvkit.py coverage to the rounding error, and I pipe this into a python script to add the log2 as last column.

[etal]

Done in PR #990. Hope this helps!