Merge pull request #32 from cancerit/dev

Fix error in limit based indicies, bumped version for immediate release
cancerit · Mar 12, 2015 · 6bba104 · 6bba104
2 parents 5c2ac36 + 75ea98a
commit 6bba104
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Showing 5 changed files with 22 additions and 20 deletions.
diff --git a/perl/MYMETA.json b/perl/MYMETA.json
@@ -4,7 +4,7 @@
       "unknown"
    ],
    "dynamic_config" : 0,
-   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560",
+   "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690",
    "license" : [
       "agpl_3"
    ],
@@ -44,5 +44,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.3.1"
+   "version" : "v1.3.2"
 }
diff --git a/perl/MYMETA.yml b/perl/MYMETA.yml
@@ -3,27 +3,27 @@ abstract: unknown
 author:
   - unknown
 build_requires:
-  ExtUtils::MakeMaker: 0
+  ExtUtils::MakeMaker: '0'
 configure_requires:
-  ExtUtils::MakeMaker: 0
+  ExtUtils::MakeMaker: '0'
 dynamic_config: 0
-generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560'
+generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.142690'
 license: open_source
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: 1.4
+  version: '1.4'
 name: cgpPindel
 no_index:
   directory:
     - t
     - inc
 requires:
-  Const::Fast: 0.014
-  Devel::Cover: 1.09
-  File::Which: 0.05
-  List::MoreUtils: 0.33
-  List::Util: 1.38
-  Pod::Coverage: 0.23
-  Test::Fatal: 0.013
-  Try::Tiny: 0.19
-version: v1.3.1
+  Const::Fast: '0.014'
+  Devel::Cover: '1.09'
+  File::Which: '0.05'
+  List::MoreUtils: '0.33'
+  List::Util: '1.38'
+  Pod::Coverage: '0.23'
+  Test::Fatal: '0.013'
+  Try::Tiny: '0.19'
+version: v1.3.2
diff --git a/perl/bin/pindel.pl b/perl/bin/pindel.pl
@@ -65,10 +65,12 @@ BEGIN
   $threads->run(2, 'input', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'input');
 
   # count the valid input files, gives constant job count for downstream
-  my $jobs = Sanger::CGP::Pindel::Implement::determine_jobs($options) if(!exists $options->{'process'} || first { $options->{'process'} eq $_ } ('pindel', 'pin2vcf'));
-
-  $threads->run($jobs, 'pindel', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'pindel');
-  $threads->run($jobs, 'pin2vcf', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'pin2vcf');
+  if(!exists $options->{'process'} || first { $options->{'process'} eq $_ } ('pindel', 'pin2vcf')) {
+    my $jobs = Sanger::CGP::Pindel::Implement::determine_jobs($options); # method still needed to populate info
+    $jobs = $options->{'limit'} if(exists $options->{'limit'} && defined $options->{'limit'});
+    $threads->run($jobs, 'pindel', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'pindel');
+    $threads->run($jobs, 'pin2vcf', $options) if(!exists $options->{'process'} || $options->{'process'} eq 'pin2vcf');
+  }
 
   Sanger::CGP::Pindel::Implement::merge_and_bam($options) if(!exists $options->{'process'} || $options->{'process'} eq 'merge');
 

diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/lib/Sanger/CGP/Pindel.pm b/perl/lib/Sanger/CGP/Pindel.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '1.3.1';
+our $VERSION = '1.3.2';
 our @EXPORT = qw($VERSION);
 
 1;