[emboss-dev] EMBOSS seqret FASTQ support

Peter biopython at maubp.freeserve.co.uk
Fri Jul 24 11:33:33 UTC 2009

On Fri, Jul 24, 2009 at 12:20 PM, Peter Rice<pmr at ebi.ac.uk> wrote:
> Peter C. wrote:
>> I was shocked to find using EMBOSS to convert "FASTQ to FASTQ" like
>> this threw away the quality scores - and I'm sure other people will also
>> make this mistake.
> Hmmm ... good point, but hard to avoid unless we simply delete "fastq"
> from the list of output formats.
> On balance, I prefer to keep it available.
> On input there is simply no way to guarantee reading quality scores
> without being told which type they are.
> On output it is reasonable to default to fastq-sanger ... otherwise what
> else could "fastq" output format write?

Well quite. In our chat in Sweden, I never expected you to offer "fastq"
as an output format in the first place, so didn't raise the issue.

> We can consider, as I say, dropping the fastq output format name from a
> future release. Let's see how users get on with it first.

As you suggest, let's see if anyone else is concerned about this.

Peter C.

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