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1. Remove explicit loop over chromosomes: "while read main_chrom"
2. Refactor to use bedops -m / bedmap --count
3. Apply same code to cluster both nearby bam1 and bam2 coordinates
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I am finding that I need to strip all headers from my starch files before piping them into bedmap in order to get the proper output, even when using the `--header` tag.
Download toy example [here]…
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John
Few more points:
1) I was just looking at files created by bamintersect. How come there are two counts.anc_info.txt files? Can ${INTERMEDIATEDIR}/${sample_name}.counts.anc_info.txt be put in…
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I have five bed files: `A.bed, B.bed, C.bed, D.bed, E.bed`.
1) I want to extract all locus in `A.bed` that have an overlaps with B.bed and E.bed BUT NOT with C.bed OR
2) Extract all locus in …
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Hi I've tried compiling with gcc 4.8.5 and 7.4.0, however I'm getting peculiar linking errors for stuff which should be already supplied with the compiler libraries.
E.g.,
```
collect2: error: …
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Hi,
I would like to remove bedops from my local because I actually wanted to download it through home-brew. I see that my `which bedops` turns `/usr/local/bin/bedops` I dont know which functions are …
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Hi, I am wondering if bedmap will consider the **strand** info from bed6 file. Or if there any options about the control of strand. And I didn't google any useful info about the questions.
Another q…
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This would be a lovely feature, and I can't find an elegant/easy way to do this inline in a bash script.
E.g. how would I modify
```
cut -f1-4,8 "$filename".bed | bedmap --indicator --echo --ec…
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