[Biojava-l] FASTQ in biojava

[Michael Heuer]

On Tue, 11 May 2010, Wang, Han wrote:

> I am new to biojava. I faced some problems on the numrica values of the
> fastq file. I read the biojava API and found how to read in the fastq
> file and get the quality from each fastq reads. Unfortunately, it just
> reads the sequence of the original quality sequence rather numeric
> quality values. Can someone give me some help on this problem? I will
> really appreciate.

On Wed, 12 May 2010, Iddo Friedberg wrote:

> We're trying to get the numeric values from the biojava fastq reader. As we
> understand the API, getQuality only supplies the ASCII value of the quality
> string. How do we get the actual Q numeric values?


That is correct, the current fastq package just handles IO to/from the
Fastq memento class and conversion between different variants of the FASTQ
format.

The next step would be to go from a Fastq record to a Sequence with
quality scores.  I haven't written that part yet, guess I should get on
it.  :)

   michael