[Bioperl-l] [Gmod-gbrowse] bp_seqfeature_delete.PL - where should I submit a patch?

Scott Cain scott at scottcain.net
Fri Oct 1 11:45:35 EDT 2010

Hi Keiran,

Well, I've been told that it is easy for non-bioperl developers to use
git to commit patches, and as if to prove it, there is a very long
wiki page on the bioperl wiki describing how to use git:


I'm not sure what the right thing is to do; I'm cc'ing the bioperl
list to get their input.


On Fri, Oct 1, 2010 at 8:46 AM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> Hi all,
> Does anyone know how I should best get push a patch (new functionality) out
> for this script which is part of the BioPerl package.
> I've added a 'fast' option which is useful for when you want to delete a
> whole dataset.  The problem I was having is I loaded a large set of data
> which had errors.  To delete it I tried to use the '-t' option but this
> continually fails after several hours (eventually runs out of memory).  To
> get round this I've added the '-f' flag which tells the script to perform
> the delete/commit on each individual feature (and associated sub-features)
> rather than attempt to do them all in a single commit.
> I've attached the modified version (unfortunately the formatting was kind of
> knackered so a patch file will be a bit iffy).
> --
> The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a
> charity registered in England with number 1021457 and acompany registered in
> England with number 2742969, whose registeredoffice is 215 Euston Road,
> London, NW1 2BE.
> Keiran Raine
> Senior Computer Biologist
> The Cancer Genome Project
> Ext: 7703
> kr2 at sanger.ac.uk
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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