On Aug 27, 2013, at 9:51 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Tue, Aug 27, 2013 at 3:08 PM, Fields, Christopher J > <cjfie...@illinois.edu> wrote: >> Is there a name for the FASTQ analog? Maybe 'unwrapped'? :) > > No, EMBOSS always write unwrapped FASTQ on output, > but accepts line wrapped FASTQ on input. > >> Neils: Re: 'Most genome packages use it': can you specify? >> Most genome packages I know allow the flexibility to use >> standard line-wrapped FASTA as well, so coding an indexing >> scheme for a non-standard FASTA alone seems… tricky. >> Unless you intend on allowing both, and 'unwrapped' is just >> for optimization. >> >> chris f. > > e.g. faidx by Heng Li allows line wrapped FASTA, with the > proviso that each record uses the same line wrapping length > (so it can't cope with arbitrary FASTA files). > > Peter Yes, this is the same reasoning for Lincoln's Bio::DB::Fasta in bioperl. chris _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss