"Vasili I. Galchin" <[email protected]> writes: >> Vis-a-vis biocore, is there already a checked in module that >> instantiates BioSeq and BioSeqQual?
> biosff and biopsl?? Yes, biosff defines an SFF data structure, basically a glorified list of records each of which is an instance of both classes. I think (a revised) TwoBit should work similarly, have an internal format (storing the sequence two bits per nucleotide), and using BioSeq and -Qual instances to extract the data to ordinary strings. IIUC, BAM files also store the sequence as two bits per nucleotide, so perahps it's worthwhile to look at Nick's SamTools package to see if there's some common ground there? -k -- If I haven't seen further, it is by standing in the footprints of giants _______________________________________________ Biohaskell mailing list [email protected] http://malde.org/cgi-bin/mailman/listinfo/biohaskell
