Merge pull request #18 from cancerit/dev

Updated to use c implementation of alleleCounter
cancerit · Oct 6, 2014 · 0652a57 · 0652a57
2 parents dee6847 + 25bc3d4
commit 0652a57
Show file tree

Hide file tree

Showing 5 changed files with 5 additions and 6 deletions.
diff --git a/perl/MYMETA.json b/perl/MYMETA.json
@@ -37,5 +37,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.3.1"
+   "version" : "v1.4.0"
 }
diff --git a/perl/MYMETA.yml b/perl/MYMETA.yml
@@ -19,4 +19,4 @@ no_index:
     - inc
 requires:
   Const::Fast: 0.014
-version: v1.3.1
+version: v1.4.0
diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/lib/Sanger/CGP/Ascat.pm b/perl/lib/Sanger/CGP/Ascat.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.3.1';
+our $VERSION = '1.4.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

diff --git a/perl/lib/Sanger/CGP/Ascat/Implement.pm b/perl/lib/Sanger/CGP/Ascat/Implement.pm
@@ -77,11 +77,10 @@ sub allele_count {
     my $sname = sanitised_sample_from_bam($input);
     my $alleleCountOut = File::Spec->catfile($ac_out,$sname .'.allct');
 
-    my $allc_exe = _which('alleleCounter.pl');
+    my $allc_exe = _which('alleleCounter');
     my $allc_lib = dirname($allc_exe);
 
-    my $command = "$^X ";
-    $command .= $allc_exe;
+    my $command = $allc_exe;
     $command .= sprintf $ALLELE_COUNT_PARA, $input, $alleleCountOut, $options->{'snp_loci'};
     $command .= '-m '.$options->{'minbasequal'} if exists $options->{'minbasequal'};