[Bioperl-l] Bug in Bio::SeqIO::fastq - seq length of 1 with quality of 0 (zero)

[Nath]

It's been a while since I was involved with Perl/BioPerl.....

I installed the latest version of BioPerl (1.6.901) through CPAN and
used it to parse some fastq files. I get an exception thrown when a
sequence has length = 1 and a quality of 0 (zero).

-- start test.pl --
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $seq_io = Bio::SeqIO->new(-file => 'test.fastq', -format =>
'fastq');
while (my $seq = $seq_io->next_seq){ }
-- end test.pl --

-- start test.fastq --
@someID1.f
G
+
0
-- end test.fastq --

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Missing sequence and/or quality data; line: 4
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/
Root.pm:472
STACK: Bio::SeqIO::fastq::next_dataset /usr/lib/perl5/site_perl/5.8.8/
Bio/SeqIO/fastq.pm:97
STACK: Bio::SeqIO::fastq::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/
SeqIO/fastq.pm:29
STACK: test.pl:7
-----------------------------------------------------------

-- start test.fastq --
@someID1.f
G
+
0
@someID2
AG
+
DD
-- end test.fastq --

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Quality string [0 at someID2] of length [9]
doesn't match length of sequence G
[1], line: 6
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/
Root.pm:472
STACK: Bio::SeqIO::fastq::next_dataset /usr/lib/perl5/site_perl/5.8.8/
Bio/SeqIO/fastq.pm:102
STACK: Bio::SeqIO::fastq::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/
SeqIO/fastq.pm:29
STACK: test.pl:7
-----------------------------------------------------------

Note that the quality string parsed from the file for someID1.f also
includes the @someID2 sequence ID line. This may be related to Bug
#3068 that was apparently fixed about 1yr ago.