CRISPRessoPooled not always writing to .info file

[npklein]

Describe the bug

I'm not sure if this is expected behavior or not, but at

CRISPResso2/CRISPResso2/CRISPRessoPooledCORE.py

Line 1207 in 2b16392

with open(chr_output_filename, 'r') as f_in:

MAPPED_REGIONS/*.info files are expected, but they are only written if the full chromosome is run (without chunking).

In

CRISPResso2/CRISPResso2/CRISPRessoPooledCORE.py

Line 1176 in 2b16392

sub_chr_command = chr_cmd.replace("__REGION__", ":%d-%d "%(curr_pos, curr_end))

and 1177 I think (if .info files should be written for all chunks) that:

sub_chr_command = chr_cmd.replace("__REGION__", ":%d-%d "%(curr_pos, curr_end))                                
chr_output_filename = _jp('MAPPED_REGIONS/%s_%s_%s.info' % (chr_str, curr_pos, curr_end))

should be replaced by:

chr_output_filename = _jp('MAPPED_REGIONS/%s_%s_%s.info' % (chr_str, curr_pos, curr_end))
sub_chr_command = chr_cmd.replace("__REGION__", ":%d-%d "%(curr_pos, curr_end)).replace("__DEMUX_CHR_LOGFILENAME__",chr_output_filename)               

as this is also in https://github.com/pinellolab/CRISPResso2/blob/2b163927faa4ca37a1dc8294ffd1c18dd057b62e/CRISPResso2/CRISPRessoPooledCORE.py#L1184C191.

If .info files should not be written for all chunks, can resolve this issue

[kclem]

Hi @npklein are the .info files useful to you? I had avoided writing them for the chunking options because it would potentially create a lot of files.

[npklein]

I'm not sure if I am using CRISPResso wrong, but in

with open(REPORT_ALL_DEPTH, 'w') as f:
    f.write('chr_id\tstart\tend\tnumber of reads\toutput filename\n')
        for chr_output_filename in chr_output_filenames:
            with open(chr_output_filename, 'r') as f_in:
                for line in f_in:
                    f.write(line)

it is reading the info files as far as I can see, so without writing them the chunking doesn't work.

[kclem]

Hi npklein - just pushed this fix now.