Merge branch 'hotfix/v3.1.2'

Author: keiranmraine

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.1.2
+
+* 3.0.5 introduced species parsing bug causing single word species names to be invalid.
+
 ## 3.1.1
 
 * Fix regression - ability to cope with chromosomes with no events.

perl/bin/pindel.pl

@@ -110,7 +110,7 @@ sub setup {
               'i|index=i' => \$opts{'index'},
               'v|version' => \$opts{'version'},
               # these are specifically for pin2vcf
-              'sp|species=s{0,}' => \@{$opts{'sp'}},
+              'sp|species=s{0,}' => \@{$opts{'species'}},
               'as|assembly=s' => \$opts{'assembly'},
               'st|seqtype=s' => \$opts{'seqtype'},
               'sg|skipgerm' => \$opts{'skipgerm'},
@@ -205,8 +205,11 @@ sub setup {
 
   $opts{'tmp'} = $tmpdir;
 
-  if(scalar @{$opts{'sp'}} > 0 ){
-     $opts{'sp'}="@{$opts{'sp'}}";
+  if(scalar @{$opts{'species'}} > 0 ){
+    $opts{'species'}="@{$opts{'species'}}";
+  }
+  else {
+    delete $opts{'species'};
   }
 
   return \%opts;

perl/bin/pindel_2_combined_vcf.pl

@@ -272,7 +272,10 @@ sub setup{
   pod2usage(-message  => "\nERROR: r|ref |".$opts{'r'}."| must be a valid file.\n", -verbose => 1,  -output => \*STDERR) unless(-f $opts{'r'});
 
   if(scalar @{$opts{'sp'}} > 0 ){
-     $opts{'sp'}="@{$opts{'sp'}}";
+    $opts{'sp'}="@{$opts{'sp'}}";
+  }
+  else {
+    delete $opts{'sp'};
   }
 
   return \%opts;

perl/lib/Sanger/CGP/Pindel.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.1.1';
+our $VERSION = '3.1.2';
 our @EXPORT = qw($VERSION);
 
 1;