SigProfilerMatrixGenerator icon indicating copy to clipboard operation
SigProfilerMatrixGenerator copied to clipboard

Published 20 hours ago • verified publisher icon AlexandrovLab

Bug when processing indels

Open mattiyeh opened this issue 1 year ago • 3 comments

https://github.com/AlexandrovLab/SigProfilerMatrixGenerator/blob/8360cbe3c0e3e0392a9addba9639ceb18a2dd7f6/SigProfilerMatrixGenerator/scripts/convert_input_to_simple_files.py#L1306

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

mattiyeh avatar Oct 08 '23 18:10 mattiyeh

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!

mdbarnesUCSD avatar Nov 10 '23 20:11 mdbarnesUCSD

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

mattiyeh avatar Nov 10 '23 21:11 mattiyeh

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!

mdbarnesUCSD avatar Dec 04 '23 19:12 mdbarnesUCSD