On Thu, Sep 17, 2009 at 8:24 AM, Peter Rice <[email protected]> wrote: > >> Also, in contrary to what the documentation predicts, using the fastq >> format for the output does not ignore the quality scores. (Not that >> would be particularly useful, but…) > > This is deliberate. We have to write somethign in FASTQ format and we > default to the fastq-sanger format. On input, fastq-sanger ignores qualities > because there is no safe way to decide which format is correct.
So again, could you reconsider making "fastq" act like "fastq-sanger"? The Sanger FASTQ format allows ASCII 33 to 126 for the quality scores, a superset of the Solexa/Illumina FASTQ varaints - so even if you don't know which kind of FASTQ file you have, and you don't care about the qualities, parsing it as a Sanger FASTQ file will work. Peter C. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
