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
