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.
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.