bedtools jaccard segmentation fault

Adrien-Evo commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

This should be fixed in the latest release already. https://github.com/arq5x/bedtools2/pull/780

And dup with https://github.com/arq5x/bedtools2/issues/779

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

arq5x / bedtools

bedtools jaccard segmentation fault #153