[Bioperl-l] CommandExts and arrays

[Mark A. Jensen]

Don't think you want 'no strict'; the error's saying something about syntax to 
you.
In the snippet, I see a missing opening single quote for output_file.bam.

The asterisk means "expect an array ref", so that's ok.

----- Original Message ----- 
From: "Ben Bimber" <bbimber at gmail.com>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Friday, May 21, 2010 9:58 AM
Subject: [Bioperl-l] CommandExts and arrays


>I am getting an error when trying to pass an array as a param with
> command exts.  I hope there is something obvious i'm missing, but I
> cant seem to figure this out.
>
> I am trying to run the merge two BAM files using
> Bio::Tools::Run::Samtools using something like this:
>
> my $new_bam = Bio::Tools::Run::Samtools->new(
> -command => 'merge',
>     -program_dir => '/usr/bin/samtools/',
> )->run(
> -obm => output_file.bam',
> -ibm => ['file1.bam', 'file2.bam'],
> );
>
> When i use an array for the -ibm param, I get an error saying 'cannot
> use string 'file1' as an arrayref while strict refs in place'.  The
> error comes from this code in CommandExts.pm, around line 989.  adding
> 'no strict' right before the final line stops the error:
>
>    # expand arrayrefs
>    my $l = $#files;
>    for (0..$l) {
> if (ref($files[$_]) eq 'ARRAY') {
>     splice(@files, $_, 1, @{$files[$_]});
> #error thrown from this line
>     splice(@switches, $_, 1, ($switches[$_]) x @{$files[$_]});
> }
>
>
> Thanks for the help.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>