Is the BWAMEM method in mapping.py still being used or have people moved to BWA-MEM2?
If no one is using the method, I would upgrade it to BWAMEM2 by changing the hardcoded parameters/function call. If it's being used, I might instead add a BWA-MEM2 function.
Is the BWAMEM method in mapping.py still being used or have people moved to BWA-MEM2? If no one is using the method, I would upgrade it to BWAMEM2 by changing the hardcoded parameters/function call. If it's being used, I might instead add a BWA-MEM2 function.
Jakub