[Bioperl-l] Merging separate sequence and quality files to FASTQ ?

Chris Fields cjfields at illinois.edu
Thu Dec 3 09:39:35 EST 2009

On Dec 3, 2009, at 8:20 AM, Peter wrote:

> On Thu, Dec 3, 2009 at 1:47 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> FASTQ parsing had undergone a major revision prior to
>> 1.6.1 (the latest release in CPAN).  Basically, it now parses
>> all three FASTQ variants.  However, Peter indicates there
>> may still be a problem, and it's likely he's running 1.6.1.
>> Peter can you confirm that?
> I had BioPerl from SVN circa 1.6.1 (not sure if this was before
> or after the release of 1.6.1 now):
> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.0069
> $ perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION,"\n"'
> 1.0069
> If the tuples mean anything to you:
> $ perl -MBio::Root::Version -e 'printf "%vd\n", $Bio::Root::Version::VERSION'
> $ perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION'
> I just updated to revision 16435, and retested. I get the same
> BioPerl version numbers, and the same extra blank line in the
> sequence FASTQ output as Dan reported.
> Peter

Okay I will try to look into it today (it should be an easy fix).  There are two issues, correct?

1) extra blank line.
2) missing description

Dan, could you go ahead and submit this as a bug, just in case (so we don't lose track)?  Otherwise it might get lost on the mail list or wiki.


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