[Biojava-l] Is a modification of the FASTA parser for my needs easy or should I implement something else?

[Hannes Brandstätter-Müller]

Hi!

I have 2 files as output of my sequencer: one is a standard fasta,
which is no problem, the other is a fasta file with the same headers,
but instead of simple letters, there are integer values from 0 to 40
denoting the quality of the sequencing at this position. Is it easy to
adapt the biojava fasta parser to read such files (by feeding
different classes to the parser), or should I write a specialized
parser from scratch?

Hannes