[Bioperl-l] fastq splitter

Scott Markel Scott.Markel at accelrys.com
Wed Feb 29 13:25:05 EST 2012


The leading character ('+') of the optional descriptor line is still written, just not the rest of the line.  The line count shouldn't change.

Scott


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Sean O'Keeffe
Sent: Wednesday, 29 February 29 2012 8:57 AM
To: Peter Cock
Cc: Chris Fields; <Bioperl-l at lists.open-bio.org>
Subject: Re: [Bioperl-l] fastq splitter

But wouldn't that result in a 3 line fastq output line which would screw up
other programs expecting 4 fastq lines? - e.g. bowtie.

On 29 February 2012 11:39, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Feb 29, 2012 at 4:30 PM, Sean O'Keeffe <limericksean at gmail.com>
> wrote:
> > Hi Chris,
> > Here's the perldoc for fastq - it does seem to indicate that the optional
> > descriptor (+) must match the first header. (See DESCRIPTION).
>
> i.e. If present, it must match. But the repeated descriptor can
> (and for space efficiency should) be omitted.
>
> As Chris mentioned earlier, there are sample files in the test suite
> which omit the repeated descriptor so this should be working OK.
>
> Peter
>
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