[emboss-dev] EMBOSS seqret FASTQ support

[Peter Rice]

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?

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.

regards,

Peter Rice