I would like to compare aligned reads back to the reference sequence. Matches, mismatches, insertions and deletions are present in my alignments but no soft/hard clipping. I aim for having an exhaustive enumeration of all occurring (mis)matches\indels per position (of the read) over all reads.
I get the position and length of indels by means of explodeCigarOps and explodeCigarOpLengths.
I also know how to get my query and reference sequence to the 'pairwise' space (using 'sequenceLayer'). What would be the best way to record per position and read if and which mismatch occurs?
Basically a kind of compareStrings followed, right?
I just wonder if I miss some fancy function..
I would appreciate any comments!