I'm finding it hard to express my problem in very few words (so I may have missed the solution to my problem while googling for it). I need to align two sequences, but as an output I want to know which base of my sequence translates to which base of the reference sequence, so I would get a sort of a map. I don't need to see two lines of letters under each other.
To explain, I want to use this map as a part of my code, to bridge some information about the sequence at the input side and some at the reference side (SNP's). I have a hunch this kind of mapping is used somewhere along while doing a classical alignment, but I wouldn't mind your advice before I start digging in the code of aligners.
Nevertheless I still need to keep this alignment 'classical' in the sense to know where the gaps and variations are.
Thanks for any hints/suggestions.