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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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Request to add a 'plot largest n contigs' for WGSCoveragePlotter #207

Open DeadlineWasYesterday opened 1 year ago

DeadlineWasYesterday commented 1 year ago

Hi Pierre, I know you hate people, but I am actually a cat. I've been using WGSCoveragePlotter a lot and I think it could benefit from having an option to only plot the first n largest contigs. Assemblies have many small, fragmented contigs that make the plot messy. I've been using the --min-contig-length parameter as a workaround. It'll be a whole lot more convenient to just specify an n.

Just a consideration if you end up updating the script later. Thanks.

lindenb commented 1 year ago

Hi, sorry I don't think I will implement this. But how about using

 --skip-contig-regex `sort -t $'\t' -k2,2nr reference.fa.fai |  tail -n +8  | cut -f 1 | paste -s -d '|'`

?