Bug when processing indels

[mattiyeh]

SigProfilerMatrixGenerator/SigProfilerMatrixGenerator/scripts/convert_input_to_simple_files.py

Line 1306 in 8360cbe

start -= str(int(start) - 1)

this line should be start = str(int(start) - 1) without the -=

[mdbarnesUCSD]

Hi @mattiyeh,

Thanks for reaching out about this issue with processing ICGC files. Could you please provide an example file to showcase the behavior? Thanks!

[mattiyeh]

Hi Mark,
I'm happy to provide a sample ICGC file with indels but the error is related to a commit from 3/7/2023. The full edit back then should have also removed the - from -= in order to correctly update the value of the string start.

stomach_indel_mutations.txt

You can test the code with this sample input file.

Thanks,
Marc

[mdbarnesUCSD]

Hi Marc,

Apologies that we haven't been able to get to this issue yet. Were you able to find a solution for processing ICGC input files? If you have tested your changes and found a solution (also for #159), it would be great if you could open a pull request with the fix. Please let us know, thanks!