readExtension3 are usefull for counting fixed fragments (Feature request for Rsubread::featureCounts: read length adjustment). Recently I considered one condition of counting reads based on their 5' most base, whose position was shifted. For example, the 5' most base is first shifted by a fixed number based on POS and CIGAR fields, then reads are summarized. It is useful if the middle point of fragments are considered in some IP experiments. So an added option
read2pos will be able to handle this situation well.
And, is it possible to add another option to count reads only in plus or minus strand of the genomes?
I also expect these options can be added in the linux version.