WFA2-lib for local alignment

[aa25desh]

I am currently trying to use the alignEndsFree function in the WFA2 library to perform local alignment between pairs of sequences. However, I am having trouble obtaining the required input arguments for this function.

Specifically, the alignEndsFree function requires four arguments: patternBeginFree, patternEndFree, textBeginFree, and textEndFree, which correspond to the beginning and end for the pattern and text sequences. However, I am unsure how to obtain these.

Additionally, I noticed that in the benchmark section of the WFA2, a global parameters struct is used to obtain the input arguments for the alignEndsFree function. However, I am unsure how to modify this approach to get patternBeginFree, patternEndFree, textBeginFree, and textEndFree for a given pattern and text.

[smarco]

Hi,

Perhaps this ticket can help you out HERE.

Give it a go and let me know if I can help.

Best,