Merge pull request #17 from cancerit/dev

Correct @ in regex problem.

MANIFEST

@@ -1,7 +1,6 @@
 bin/caveman.pl
 bin/caveman_merge_results.pl
 bin/cpanm
-caveman.setup
 docs.tar.gz
 lib/Sanger/CGP/Caveman.pm
 lib/Sanger/CGP/Caveman/Implement.pm

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"
    ],

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: 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: v1.2.0

bin/caveman.pl

@@ -204,14 +204,12 @@ sub cleanup{
 
 sub getSpeciesAssemblyFromBam{
   my ($opts) = @_;
-  $opts->{'species'};
-  $opts->{'species-assembly'};
   my ($species,$assembly) = undef;
   my $bam = Bio::DB::Sam->new(-bam  =>$opts->{'tumbam'});
   my $head = $bam->header->text;
   my @split_head = split(/\n/,$head);
   foreach my $line(@split_head){
-    if($line =~ m/^@SQ/){
+    if($line =~ m/^\@SQ/){
       $assembly = $line =~ /AS:([^\t]+)/;
       $species = $line =~ /SP:([^\t]+)/;
       last;