[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1202

[Jason Stajich]

Scott-

Was a simple fix. I've fixed on the main trunk and the 1.0 branch and
added a test for this in our test suite.  This fix will be part of 1.01
when it is pushed out at the end of the week.  Thanks for the bug report.

-jason
On Tue, 4 Jun 2002 bioperl-bugs@bioperl.org wrote:

> JitterBug notification
>
> new message incoming/1202
>
> Message summary for PR#1202
> 	From: s.mcahren@lilly.com
> 	Subject: Bug with Bio::SeqIO::Qual.pm
> 	Date: Tue, 4 Jun 2002 17:00:18 -0400
> 	0 replies 	0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
> >From s.mcahren@lilly.com Tue Jun  4 17:00:18 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g54L0Ido011004
> 	for <bioperl-bugs@pw600a.bioperl.org>; Tue, 4 Jun 2002 17:00:18 -0400
> Date: Tue, 4 Jun 2002 17:00:18 -0400
> Message-Id: <200206042100.g54L0Ido011004@pw600a.bioperl.org>
> From: s.mcahren@lilly.com
> To: bioperl-bugs@bioperl.org
> Subject: Bug with Bio::SeqIO::Qual.pm
>
> Full_Name: Scott McAhren
> Module: SeqIO::Qual
> Version: 1.0
> PerlVer: 5.6.0
> OS: solaris
> Submission from: us_proxy_indy.xh1.lilly.com (40.0.40.10)
>
>
> The SeqIO module is improperly paring a qual file with the following
> phd2fasta/phrap format that has \n at the end of lines.  The parser seems to be
> concatinating the last entry with the first entry on the next line.
>
> ex:
> >seq1
> 14 24 29 29 29 29 25 33 25 29 27 32 28 32 23 19 9 9
> 9 19 13 20 12 13 6 6 8 16 19 29 32 30 33 28 28 28 24
> 29 30 30 30 30 30 30 29 35 30 30 28 28 28 32 29 29
>
> gets translated to:
> qual = 14 24 29 29 29 29 25 33 25 29 27 32 28 32 23 19 9 99 19 13 20 12 13 6 6 8
> 16 19 29 32 30 33 28 28 28 2429 30 30 30 30 30 30 29 35 30 30 28 28 28 32 29 29
>
>
>
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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu