Merge pull request #9 from cancerit/dev

changes all previously tested on seqware

bin/caveman.pl

@@ -255,7 +255,7 @@ sub setup {
   if(exists($opts{'normcn'}) && defined($opts{'normcn'})){
   	PCAP::Cli::file_for_reading('norm-cn-file',$opts{'normcn'});
   }
-  PCAP::Cli::file_for_reading('germline-indel-bed',$opts{'germindel'}) if(exists $opts{'process'} && $opts{'process'} eq 'flag');
+  PCAP::Cli::file_for_reading('germline-indel-bed',$opts{'germindel'}) if(!exists $opts{'process'} || (exists $opts{'process'} && $opts{'process'} eq 'flag'));
   PCAP::Cli::out_dir_check('outdir', $opts{'outdir'});
 
   PCAP::Cli::file_for_reading('flagConfig',$opts{'flagConfig'}) if(defined $opts{'flagConfig'});

lib/Sanger/CGP/Caveman/Implement.pm

@@ -331,7 +331,8 @@ sub concat {
 	my $target = $options->{'target_files'};
 	return 1 if PCAP::Threaded::success_exists(File::Spec->catdir($tmp, 'progress'), 0);
 	my $command = sprintf('cat %s > %s',$target,$out);
-	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
+	my $count = "wc -l $out";
+	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), [$command, $count], 0);
 
 	return PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
 

setup.sh

@@ -21,7 +21,7 @@
 #  along with this program. If not, see <http://www.gnu.org/licenses/>.
 ##########LICENCE##########
 
-CAVEMAN_CORE="https://github.com/cancerit/CaVEMan/archive/v1.4.2.tar.gz"
+CAVEMAN_CORE="https://github.com/cancerit/CaVEMan/archive/1.4.3.tar.gz"
 SOURCE_SAMTOOLS="https://github.com/samtools/samtools/archive/0.1.20.tar.gz"