Clones with reads less than nei_read_thres have their neighbors counted; however, since they are already excluded in the bool (df$Read.count>nei_read_thres), the subtraction by 1 undercounts their neighbors. I'm not super familiar with R, but I imagine filling the diagonal of the Hamming distance matrix with some arbitrarily high number would resolve this problem instead of subtracting by 1.
Hi Misha,
There's a bug in the following lines of code for the
filter_data_thres_df
function which counts the neighbors (specifically this function here):Clones with reads less than
nei_read_thres
have their neighbors counted; however, since they are already excluded in the bool (df$Read.count>nei_read_thres
), the subtraction by 1 undercounts their neighbors. I'm not super familiar with R, but I imagine filling the diagonal of the Hamming distance matrix with some arbitrarily high number would resolve this problem instead of subtracting by 1.Let me know your thoughts.
Thanks and take good care, Zach