zero cov output problem

[parlar]

Hi again,

sambamba_v0.5.9 depth base -L bed -z (or --report-zero-coverage) bam
does not seem to output zero-coverage bases?

cheers

Pär

[parlar]

Sorry for bumping this issue. I guess that you have your hands full - as everyone. I'm just wondering if you were planning to look at this or if if you feel that it has a lower priority. Then I'll invest the time to make a work-around.

[lomereiter]

Hi Pär, your guess is correct, but I look forward to making depth tool production-ready. A test case from your side would be very helpful.

[parlar]

Sure! Just let me know. A bam file, targets.bed, and a reference depth call output using bedtools and the same input - would that be ok?

[lomereiter]

Yes, that would be perfect.

[parlar]

I'll make it available then and send you a link.

[lomereiter]

closing as duplicate of #225