Error during parse_sam() #387
Description
Hi, I'm having trouble solving an error during sam parsing that occurs for all of the different sam files I have tried. The error is as follows:
Traceback (most recent call last):
File "/home/dnygard/projects/rrg-mlaval/dnygard/Gothic/TestPlayground2022/TADbitTest/TADbitTestScript.py", line 31, in
pytadbit.parsers.sam_parser.parse_sam(f_names1=fname1, f_names2=fname2, out_file1=out1, out_file2=out2, genome_seq=parsedGenome, re_name="HindIII", verbose=True, clean=True, mapper="BOWTIE2")
File "/usr/local/anaconda/lib/python3.9/site-packages/pytadbit/parsers/sam_parser.py", line 192, in parse_sam
tmp_name = tmp_files[0]
IndexError: list index out of range
I am running in Python 3.9 on Linux, and have been using the attached script for testing. The script gets past the genome parsing step just fine, but then halts during invocation of parse_sam(). I only provide one pair of sam files, rather than lists of files, so I don't know if that might be part of the issue. Please let me know if I can provide any additional information or if you have any questions. Thank you for your help.