specify list of scaffolds for wgsCoveragePlotter

[PAMorin]

Verify

• if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
• the version of java

Subject of the issue

specify list of scaffolds for wgsCoveragePlotter

Your environment

• version of jvarkit (unclear; installed 6/16/22 from "https://github.com/lindenb/jvarkit.git"
• which OS: Linux 8.2.2004

Steps to reproduce

I want to plot coverage of only a specific subset of scaffolds, but all scaffolds are named sequentially (e.g., scaffold_1, scaffold_2, etc.). Is there a way to substitute a list variable or array for the --include-contig-regex regular expression:

e.g., chr=("scaffold_1" "scaffold_2" "scaffold_3" "scaffold_4" "scaffold_5" "scaffold_10") java -jar ${covplot}/dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R ${REFDIR}/${REF} ${BAMDIR}/${BAMFILE} --include-contig-regex ${chr} --percentile median > ${OUTDIR}/${BAMFILE}_covplot_allChrom.svg

Expected behaviour

WGS coverage plot with only the specified scaffolds

Actual behaviour

WGS coverage plot of only the first scaffold in the list $chr

[lindenb]

@PAMorin I'm sorry I think I don't really understand the problem.

How about using a regular expression like

(scaffold_1|scaffold_2|scaffold_3|scaffold_4|scaffold_5|scaffold_10)

?

[PAMorin]

Thanks for the quick response!

It looks like you understood my problem (not understanding how to construct a multiple object expression) perfectly. This works:

chr="scaffold_4|scaffold_5|scaffold_10"

java -jar ${covplot}/dist/wgscoverageplotter.jar --dimension 1500x500 -C -1 --clip -R ${REFDIR}/${REF} ${BAMDIR}/${BAMFILE} --include-contig-regex ${chr} --percentile median  > ${OUTDIR}/${BAMFILE}_covplot_allChrom.svg

The output is attached. My genome assembly has a few hundred scaffolds, but the first 22 are chromosome-length, and I only want to plot coverage of those scaffolds. This approach allows me to specify which ones to plot, and I can further refine it to omit or include a few specific scaffolds of interest in a single plot.

Thanks,

Phil

On 6/17/22 3:17 PM, Pierre Lindenbaum wrote:

@PAMorin https://github.com/PAMorin I'm sorry I think I don't really understand the problem.

How about using a regular expression like

|(scaffold_1|scaffold_2|scaffold_3|scaffold_4|scaffold_5|scaffold_10)|

?

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