[Bioperl-l] Next-gen modules

[Cook, Malcolm]

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 at gmod.cvs.sourceforge.net<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: $!";
      }