Re: Next-gen modules

[Cook, Malcolm-2]

Lincoln?  Scot?

Hi there!

How do I get the permissions I need if Lincoln wants me to submit the patch below which fixes this bug: http://rt.cpan.org/Public/Bug/Display.html?id=50532

% cvs -d :pserver:anonymous@...<http://lists.open-bio.org/mailman/listinfo/bioperl-l>:/cvsroot/gmod co gbrowse-adaptors/Bio-SamTools

Cheers,

--Malcolm Cook - Stowers Institute for Medical Research



*** Sam.pm.~1.18.~      Thu Sep 24 14:57:53 2009
--- Sam.pm      Fri Oct 23 11:05:14 2009
***************
*** 1219,1230 ****
      my $expand_flags  = $args{-expand_flags};
      my $split_splices = $args{-split} || $args{-split_splices};

!     -e $bam_path && -r _  or croak "$fa_path does not exist or is not readable";
      my $bam = Bio::DB::Bam->open($bam_path)      or croak "$bam_path open: $!";

      my $fai;
      if ($fa_path) {
!       -e $fa_path  && -r _  or croak "$fa_path does not exist or is not readable";
        $fai = Bio::DB::Sam::Fai->open($fa_path)  or croak "$fa_path open: $!";
      }

--- 1219,1232 ----
      my $expand_flags  = $args{-expand_flags};
      my $split_splices = $args{-split} || $args{-split_splices};

!     -e $bam_path or croak "$bam_path does not exist";
!     -r _  or croak "is not readable";
      my $bam = Bio::DB::Bam->open($bam_path)      or croak "$bam_path open: $!";

      my $fai;
      if ($fa_path) {
!       -e $fa_path or croak "$fa_path does not exist";
!       -r _  or croak "$fa_path is not readable";
        $fai = Bio::DB::Sam::Fai->open($fa_path)  or croak "$fa_path open: $!";
      }




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[Scott Cain-4]

Hi Malcolm,

You need a SourceForge user account that you'll tell me, so I can give
you developer permissions, and then get an svn checkout of the
gbrowse-adaptors repo (we switched to svn last month).

Scott


On Fri, Oct 23, 2009 at 12:16 PM, Cook, Malcolm <MEC@...> wrote:

> Lincoln?  Scot?
>
> Hi there!
>
> How do I get the permissions I need if Lincoln wants me to submit the patch
> below which fixes this bug:
> http://rt.cpan.org/Public/Bug/Display.html?id=50532
>
> % cvs -d :pserver:anonymous@...:/cvsroot/gmod co
> gbrowse-adaptors/Bio-SamTools
>
> Cheers,
>
> --Malcolm Cook - Stowers Institute for Medical Research
>
>
>
> *** Sam.pm.~1.18.~      Thu Sep 24 14:57:53 2009
> --- Sam.pm      Fri Oct 23 11:05:14 2009
> ***************
> *** 1219,1230 ****
>       my $expand_flags  = $args{-expand_flags};
>       my $split_splices = $args{-split} || $args{-split_splices};
>
> !     -e $bam_path && -r _  or croak "$fa_path does not exist or is not
> readable";
>       my $bam = Bio::DB::Bam->open($bam_path)      or croak "$bam_path open:
> $!";
>
>       my $fai;
>       if ($fa_path) {
> !        -e $fa_path  && -r _  or croak "$fa_path does not exist or is not
> readable";
>          $fai = Bio::DB::Sam::Fai->open($fa_path)  or croak "$fa_path open:
> $!";
>       }
>
> --- 1219,1232 ----
>       my $expand_flags  = $args{-expand_flags};
>       my $split_splices = $args{-split} || $args{-split_splices};
>
> !     -e $bam_path or croak "$bam_path does not exist";
> !     -r _  or croak "is not readable";
>       my $bam = Bio::DB::Bam->open($bam_path)      or croak "$bam_path open:
> $!";
>
>       my $fai;
>       if ($fa_path) {
> !        -e $fa_path or croak "$fa_path does not exist";
> !        -r _  or croak "$fa_path is not readable";
>          $fai = Bio::DB::Sam::Fai->open($fa_path)  or croak "$fa_path open:
> $!";
>       }
>
>
>
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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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