Option to exclude contigs in the reference

[SLAment]

Hi! Thanks for a great tool. I was wondering if you could implement an option to remove a contig or a list of contigs when calculating the stats. Sometimes I have bacterial contaminations, or the mitochondrial contig has crazy coverage compared to the chromosomes, so I fear those values might inflate upwards the average depth of coverage in the report. Rather than re-map the reads to a reduced reference genome, I think it would be great if Cramino could consider it if asked.

Thanks!

[wdecoster]

Great suggestion. I will add that. Thanks!

[wdecoster]

Hi,

While I haven't added this yet, I would just like to point out that you can use samtools to filter the file and pipe that into cramino to read from stdin. That should get you what you want.

Cheers,
Wouter