Possible issue with tinvycov covplot --whitelist

[bmsacchi]

Hi! Great tool, very convenient and easy to use! Just want to bring to your attention a potential problem. If chromosome names supplied to whitelist are not in the same order as the bam file, the labels are swapped in the plot. For example, using --whitelist X,Y the X chromosome appeared to have very low coverage, and the Y chromosome very high coverage - in a female sample that does not have a Y, so this seemed super weird! Samtools coverage showed low Y coverage and high X coverage, as anticipated. Y comes before X in my coordinate ordered bamfile, and running --whitelist Y,X recovers a plot that resembles what I'd expect based on samtools coverage output. The order of labels matches whitelist, but the order of which chromosome is plotted does not.

[cmdoret]

Hey @bmsacchi, thanks for reporting this issue! 😃
I'll take a look when possible, but if you have an idea for a fix or feel like contributing, I would gladly review and accept a PR.