[Bioperl-l] FASTQ output
cjfields at illinois.edu
Tue Jun 30 23:48:11 EDT 2009
I am working on FASTQ output and noticed a real oddity. Apparently,
there are three write_* methods for this module, with the odd choice
of write_seq for Bio::SeqIO::fastq writing FASTA, not FASTQ.
write_qual() writes Qual format:
and write_fastq() writes FASTQ. Now, maybe it's just me, but I think
an implementation of write_seq() for a specific format should probably
output that format and not something else entirely unexpected. Also,
is there a reason for duplicating output code for qual and FASTA
output within Bio::SeqIO::fastq, i.e. should we call Bio::SeqIO::fasta/
I would consider the write_seq() issue a bug, the others are really
just maintenance issues. Anyone have problems with me changing that
up a bit?
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