Jaccard analysis segmentation fault

[Clockris]

Hi,

I am trying to do some analysis using the command

bedtools jaccard -a $file1 -b $file2

but for some reason Bedtools crash giving me as error "Segmentation fault (core dumped)".

When I try to run

bedtools jaccard -a $file1 -b $file3

and

bedtools jaccard -a $file2 -b $file3

the command works but with

bedtools jaccard -a $file3 -b $file2

it give me segmentation fault again.

It works even if I run

bedtools jaccard -a $file2 -b $file1

The problem seems to be the file2, but it is wired that when it is in the -b position the program works fine and by the way I didn't find any problematic feature in that file that could justify a crash. Do you have any idea about this problem?

Thanks.

Attached there are the files to make the tests.

file1=H3K27ac_ENCSR763IDK_bin100_gap0_peaks.bed.txt
file2=H3K36me3_ENCSR499FXI_bin100_gap0_peaks.bed.txt
file3=H3K4me1_ENCSR155XVP_bin100_gap0_peaks.bed.txt

H3K4me1_ENCSR155XVP_bin100_gap0_peaks.bed.txt
H3K27ac_ENCSR763IDK_bin100_gap0_peaks.bed.txt
H3K36me3_ENCSR499FXI_bin100_gap0_peaks.bed.txt

PS I am working with version 2.29.0 of bedtools on a SGE server using RedHas as OS.

[38]

This is caused by access previously allocated memory.

I should make the fix in PR #780. @arq5x, would you like to have a look ?

[arq5x]

This is fixed in master and a new test has been added. Thanks for reporting it and thanks to @38 for fixing it!

[Clockris]

I tried the fixed version, it works fine, thanks.