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allow bedmethyl files with a header for bw generation#535

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ArtRand merged 2 commits intonanoporetech:masterfrom
WardDeb:master
Jan 18, 2026
Merged

allow bedmethyl files with a header for bw generation#535
ArtRand merged 2 commits intonanoporetech:masterfrom
WardDeb:master

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@WardDeb
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@WardDeb WardDeb commented Nov 7, 2025

Hello,

Thanks for the software !

The header needs to be stripped from bedmethyl files generated with modkit pileup --header, which results in quite a complicated command when one wants to generate bw files simultaneously during the pileup command. This tiny change ignores the header. Tested with both:

modkit bm tobigwig --mod-code m -g ${sizes} --negative-strand-values ${bedmethyl} pileup.bw
modkit pileup ${bam} - -t 40 --motif CG 0 -r ${fna} --combine-strands --header | tee >(modkit bedmethyl tobigwig - pileup.bw --mod-code m -g ${sizes} --suppress-progress) > pileup_header.bed

I also changed the README for the source install, as

cargo install --path .

Didn't work for me.

@ArtRand
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ArtRand commented Dec 2, 2025

@WardDeb thanks for this. Let me do a quick test on my side but looks good.

@ArtRand ArtRand merged commit a0ad253 into nanoporetech:master Jan 18, 2026
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