Merge branch 'hotfix/v1.5.2'

cancerit · Jun 22, 2015 · 7eadb6a · 7eadb6a
2 parents 708775f + 1bb2998
commit 7eadb6a
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Showing 5 changed files with 32 additions and 24 deletions.
diff --git a/MYMETA.json b/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 2.143240",
    "license" : [
       "agpl_3"
    ],

diff --git a/MYMETA.yml b/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 2.143240'
 license: open_source
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
-  version: 1.4
+  version: '1.4'
 name: cgpCaVEManWrapper
 no_index:
   directory:
     - t
     - inc
 requires:
-  Attribute::Abstract: 1.02
-  Const::Fast: 0.014
-  Devel::Cover: 1.09
-  File::Which: 0.05
-  List::Util: 1.38
-  Pod::Coverage: 0.23
-  Test::Fatal: 0.013
-  Try::Tiny: 0.19
+  Attribute::Abstract: '1.02'
+  Const::Fast: '0.014'
+  Devel::Cover: '1.09'
+  File::Which: '0.05'
+  List::Util: '1.38'
+  Pod::Coverage: '0.23'
+  Test::Fatal: '0.013'
+  Try::Tiny: '0.19'
 version: v1.5.1
diff --git a/bin/caveman.pl b/bin/caveman.pl
@@ -260,6 +260,7 @@ sub setup {
 					'nd|norm-cn-default=i' => \$opts{'normdefcn'},
 					'c|flagConfig=s' => \$opts{'flagConfig'},
 					'f|flagToVcfConfig=s' => \$opts{'flagToVcfConfig'},
+					'a|apid=i' => \$opts{'apid'},
 					'st|seqType=s' => \$opts{'seqType'},
   ) or pod2usage(2);
 
@@ -451,6 +452,7 @@ =head1 SYNOPSIS
     -tum-cn-default        -td  Default tumour CN to use with gaps or no file provided
     -norm-cn-default       -nd  Default normal CN to use with gaps or no file provided
     -annot-bed-files       -ab  Annotation BED files - required for pulldown/WXS
+    -apid                  -a   Analysis process ID
 
   Optional flagging parameters: [default to those found in cgpCaVEManPostProcessing]
     -flagConfig            -c   Config ini file to use for flag list and settings
@@ -500,6 +502,10 @@ =head1 OPTIONS
 
 Path to ignore file. 1-based first coordinate bed style format of regions for caveman not to analyse.
 
+=item B<-apid>
+
+Analysis process ID (CGP)
+
 =item B<-tumour-cn>
 
 Path to tumour copy number file (1-based first coordinate bed style format). All analysed bases must have a CN assigned.

diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/Sanger/CGP/Caveman/Implement.pm b/lib/Sanger/CGP/Caveman/Implement.pm
@@ -266,19 +266,21 @@ sub caveman_flag{
 	my $script = _which($FLAG_SCRIPT) || die "Unable to find '$FLAG_SCRIPT' in path";
 	my $flag = $^X.' '.$script;
 	$flag .= sprintf($CAVEMAN_FLAG,
-							$for_flagging,
-							$flagged,
-							$options->{'species'},
-							$tumbam,
-							$normbam,
-							$options->{'flag-bed'},
-							$options->{'germindel'},
-							$options->{'unmatchedvcf'},
-							$ref,
-							$options->{'seqType'},
-							);
+            $for_flagging,
+            $flagged,
+            $options->{'species'},
+            $tumbam,
+            $normbam,
+            $options->{'flag-bed'},
+            $options->{'germindel'},
+            $options->{'unmatchedvcf'},
+            $ref,
+            $options->{'seqType'}
+            );
+
 	$flag .= ' -c '.$options->{'flagConfig'} if(defined $options->{'flagConfig'});
 	$flag .= ' -v '.$options->{'flagToVcfConfig'} if(defined $options->{'flagToVcfConfig'});
+	$flag .= ' -p '.$options->{'apid'} if(defined $options->{'apid'});
 	if($options->{'seqType'} eq 'pulldown') {
 	  die "ERROR: Pulldown flagging requires annotation BED files" unless(defined $options->{'annot-bed'});
 	  $flag .= ' -ab '.$options->{'annot-bed'};