Modkit BED file impropperly formatted.

[KloostermanJoukje]

Hello,

Another issue (#97) had the same issue as i had. And It was written that the issue would be fixed by relase 0.2.4 however when using this release, still the bed file is impropperly formatted:

improperly formatted BED line chr22 18890487 18890487
improperly formatted BED line chr22 38110048 38110048
improperly formatted BED line chrX 153909598 153909598

any idea when this will be implemented? Or how to fix it?

[KloostermanJoukje]

To create the bed file I perform the following:

local args=()
args+=("view")
args+=("--no-header")
args+=("--no-version")
args+=("--threads" "!{task.cpus}")
args+=("!{vcf}")

# -1 because positions in .bed are 0-based and 1-based in .vcf
${CMD_BCFTOOLS} "${args[@]}" | awk -v FS='\t' -v OFS='\t' '{print $1 "\t" $2-1 "\t" $2-1 "\t"}' > "!{vcf.simpleName}.bed"

[ArtRand]

Hello @JoukjeKloosterman,

In the latest release modkit still requires the strand information in the --include-bed files. I wanted to remove this requirement in 0.2.4, but it didn't make it. If you add . as the strand for all of your BED lines, that should fix the problem (as suggested in #97). The plan is to remove this requirement (default to both strands) in the next release.