A solution to core dumped and/or running too slow

[YichaoOU]

Hi,

I found the call_peaks function could cause the program to halt or fail due to empty sections in the for loop for sect in sections.

A simple solution is to exit the function before the for loop:

    if len(sections)==0:
        peak_dict['Nclusters'] = peak_number
        return peak_dict 

I also found the --plot option can make the program freeze.

By saying halt or freeze, I think the program is still running, because for my Igg bam file, which is only 15MB, The program is finished. But when I have a ~200MB bam file, the program took more than 1 day and then core dumped (not because of memory). With the simple fixed, it is running smoothly now.

Best,
Yichao

[YichaoOU]

I also added logging.basicConfig(level = logging.INFO), otherwise even with --debug, the program did not output anything.

[YichaoOU]

Update, for bam file around 100M to 200M, UMI-deduplicated, clipper took about a week to finish, single core.