Peter C. wrote:
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.
Yes, but it is dangerous if they could really be Solexa qualities.
What we could do is provide a utility that reads in fastq-sanger format
and checks whether the quality scores make most sense as Sanger, SOlexa
or Ilumina.
I consider reading as fastq-sanger by default to be rather dangerous.
Peter
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