So Ketil ... if I understand your response(perhaps naively) why is there no SFF functions exported from Sequence.hs ?? Maybe I missed something.
Vasya On Thu, Apr 24, 2014 at 12:35 AM, Vasili I. Galchin <vigalc...@gmail.com> wrote: > Ketil, > > > I was suspicious of that ... not a pejorative comment BTW. Thx. > > Vasya > > On Thu, Apr 24, 2014 at 12:15 AM, Ketil Malde <ke...@malde.org> wrote: >> >> Vasili I. Galchin <vigalc...@gmail.com> writes: >> >>> Why are there three Fasta representation-dependent functions (toFasta, >>> toFastaQual, toFastQ) doing in Sequence.hs which presumably is meant >>> to be Sequence representation-free code? >> >> Because they are the standard formats, least common denominators, so to >> speak? Also the most common inputs to tools and algorithms. If you >> have a data structure that cannot easilty be converted into these, it >> should probably not be an instance BioSeq (or BioSeqQual). >> >> IIRC, TwoBit contains sequence information (and thus should be a BioSeq >> instance), but no quality information (and thus no BioSeqQual instance). >> >> Another example is Roche (and Ion Torrent)'s SFF format, which contains >> sequence and quality data in addition to flowgram data. >> >> -k >> -- >> If I haven't seen further, it is by standing in the footprints of giants
