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
commented
1 year ago 
I am currently trying to use the
alignEndsFreefunction 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, andtextEndFree, 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
parametersstruct is used to obtain the input arguments for thealignEndsFreefunction. However, I am unsure how to modify this approach to getpatternBeginFree,patternEndFree,textBeginFree, andtextEndFreefor a given pattern and text.