Bedtools runs infinitely with large memory usage under sorted option when there's unmapped reads

[kheber]

Hello,

Thank you for creating and maintaining bedtools: I find the various options that other tools do not offer very helpful.

In running bedtools subtract with the -sorted option and using .bam files for -a and -b, I found that when I did not remove unmapped reads that bedtools would run infinitely. Moreover, after a while the tool would grow its memory usage to around 40 GiB, and I believe this happens when it encounters the unmapped reads towards the end of the file. When I remove these reads from my .bam files, the issue is resolved. I have not tested similar behavior under bedtools intersect or other commands.

I am wondering if it would be possible to have bedtools skip these unmapped reads or at least throw a warning/error about it?