[emboss-dev] EMBOSS seqret FASTQ support

Peter Rice pmr at ebi.ac.uk
Fri Jul 24 10:14:23 UTC 2009

Peter C. wrote:
> I'd like to re-test with your fixes. I presume these things are being fixed
> in the public CVS repository, so I could try building EMBOSS from there.
> Is there a particular branch? Or are you planning an EMBOSS 6.1.1
> release shortly?

You found various things in sequence formats, but all are resolved by
changes to ajseqread.c and ajseqwrite.c

Assuming I am happy with the test I plan to make a patch which will
update those files.

The CVS code would have new things for the next release. For now, if you
are using the 6.1.0 release, patching is the way to go.

Fixes so far:

FASTQ format changes:

* sequence and quality scores on one line
* quality ID line shortened to '+'
* Solexa negative quality score output corrected
* Phred quality score rounding error fixed
* Corrected reading of quality lines starting with '@'

GenBank format changes:

* protein (genpept and refseqp) formats auto-detect fix for multiple
input sequences

Intelligenetics format:

* Sequence ID corrected for DOS format input file

Did I miss anything?


Peter Rice

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