bedtools jaccard segmentation fault

[Adrien-Evo]

Hi.
I had segmentation fault error using bedtools jaccard on one file in particular. I narrowed down the region where the error could be found. It's the file a. Files are sorted.

a

chr9	140514400	140514600
chr9	140773000	140773200
chr9	141044600	141045000
chr9	141054200	141054400

b

chr9	140370600	140371000
chr9	140446600	140447000
chr9	140447000	140447400
chr9	140470200	140470400
chr9	140470600	140470800
chr9	140501000	140501200
chr9	140501400	140501600
chr9	140512200	140512600
chr9	140512600	140514400
chr9	140514400	140514600

bedtools jaccard -a a -b b -f 1e-09

bedtools is v2.29.0

[kernco]

I'm experiencing this bug with one of my bed files too. It works if I just flip which file I specify as "-a" and which as "-b", so I think it's some edge case in bedtools rather than a problem with the file.

[38]

This should be fixed in the latest release already. arq5x/bedtools2#780

And dup with arq5x/bedtools2#779

Confirmed 2.29.1 doesn't have the issue. https://github.com/arq5x/bedtools2/releases/tag/v2.29.1