1 Jul 05:48
FASTQ output
Chris Fields <cjfields <at> illinois.edu>
2009-07-01 03:48:11 GMT
2009-07-01 03:48:11 GMT
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: http://www.bioperl.org/wiki/Qual_sequence_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/ qual instead? 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? chris
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