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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.

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