Sorry if I'm missing the obvious, but after I perform a pairwise alignment between two strings, I'd like to query positions in the
pattern to learn what position it aligns to in the
subject -- is this functionality already there and I'm missing it, or do I need to rig up a utility function?
For instance, suppose we have this example:
library(Biostrings) (pw <- pairwiseAlignment('GTCA', 'GATACA')) Global PairwiseAlignmentsSingleSubject (1 of 1) pattern:  GT--CA subject:  GATACA score: -17.95402
I'd like to know that the 3rd (C) letter in pattern aligned to the 5th position in subject.
I can rig up something very basic (and probably breaks around many corner cases) that parses
GT--CA) to count the dashes or whatever to translate one index to the other, but is there something more straightforward (and better thought out) already implemented that I'm missing?