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This queue is for tickets about the Bio-SamTools CPAN distribution.

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The Basics
Id: 88172
Status: resolved
Priority: 0/
Queue: Bio-SamTools
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Owner: Nobody in particular
Requestors: keiranmraine [...] gmail.com
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AdminCc:
Bug Information
Severity: (no value)
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Fixed in: (no value)

History Show all quoted text
  Tue Aug 27 06:42:27 2013 https://www.google.com/accounts/o8/id?id=AItOawnUQUm9oQafaaMf5OlKCWjRF1zV69fbnrA - Ticket created
Subject: add qstring routine to Alignment.pm
Hi Lincoln, There are many instances where generating the standard quality string is necessary (e.g. generation of selected fastq records). It would be great if function used in the AlignWrapper->tam_line method was provided as a sub for use in Alignment: sub qstring { return join('',map{chr($_+33)} shift->qscore); } Thanks, Keiran (P.S. any plans to move Bio::DB::Sam to GitHub?)
  Thu Aug 29 13:30:18 2013 LDS [...] cpan.org - Correspondence added
I'm queueing this up for release 1.40. I'm also going to update the distribution to indicate that the library IS under GitHub, at the slightly non-obvious location of https://github.com/GMOD/GBrowse-Adaptors L On Tue Aug 27 06:42:27 2013, https://www.google.com/accounts/o8/id?id=AItOawnUQUm9oQafaaMf5OlKCWjRF1zV69fbnrA wrote: Show quoted text
> Hi Lincoln, > > There are many instances where generating the standard quality string > is necessary (e.g. generation of selected fastq records). It would be > great if function used in the AlignWrapper->tam_line method was > provided as a sub for use in Alignment: > > sub qstring { > return join('',map{chr($_+33)} shift->qscore); > } > > Thanks, > Keiran > > (P.S. any plans to move Bio::DB::Sam to GitHub?)
  Thu Aug 29 13:30:18 2013 The RT System itself - Status changed from 'new' to 'open'
  Thu Aug 29 13:30:19 2013 LDS [...] cpan.org - Status changed from 'open' to 'resolved'