Running indexcov on small input BAMs about goleft

[brentp]

thanks for the test-case. This happens because I require at least 2 bins for each chromosome and there arent' that many in this file. I'm updating the code to output: "indexcov: no usable chromsomes in bam"
with a non-zero exit code. This will be in the next release.

[chapmanb]

Awesome, thanks for much for digging into this so quickly.

[brentp]

by the way, indexcov only needs the bam for the sequence names, so for testing, you can have a .bai that covers, e.g. 100MB and have the .bam that's only the output of samtools view -H $bam

[brentp]

@chapmanb sorry to stall you on this, but I'd recommend to wait for another release cycle. indexcov got good enough that I got a lot of feedback on improvements. so the usage will change a bit (-d/--directory) instead of (-p/--prefix). The text output should be mostly the same, I just present it the plots differently. So you could proceed, but might be best to wait for another release cycle.

[chapmanb]

Thanks Brent, glad to see all the improvements. I'll start up on this one again after the 0.1.11 release is ready. Thanks again for all your work on this.