From 80bbf5e7ad7761373a2a8d281bb2d3ad2e1286b6 Mon Sep 17 00:00:00 2001
From: David Jones <drj@sanger.ac.uk>
Date: Fri, 21 Nov 2014 10:08:59 +0000
Subject: [PATCH] Added default tumour and normal cn options to estep method

---
 lib/Sanger/CGP/Caveman/Implement.pm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/lib/Sanger/CGP/Caveman/Implement.pm b/lib/Sanger/CGP/Caveman/Implement.pm
index 40491bb..1a4bae8 100644
--- a/lib/Sanger/CGP/Caveman/Implement.pm
+++ b/lib/Sanger/CGP/Caveman/Implement.pm
@@ -120,8 +120,6 @@ sub caveman_split {
 	my $command = _which('caveman') || die "Unable to find 'caveman' in path";
 	$command .= sprintf($CAVEMAN_SPLIT,$index,$config);
 
-#$command .= ' --max-read-count 1.5 --increment 1000000';
-
 	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, $index);
   	return PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), $index);
 }
@@ -199,11 +197,11 @@ sub caveman_estep{
                     $config,
                     $normprot,
                     $tumprot);
-    if(exists() && defined()){ #Add default normal cn
+    if(exists($options->{'normdefcn'}) && defined($options->{'normdefcn'})){ #Add default normal cn
       $command .= ' -n '.$options->{'normdefcn'};
     }
 
-    if(exists() && defined()){ #Add default tumour cn
+    if(exists($options->{'tumdefcn'}) && defined($options->{'tumdefcn'})){ #Add default tumour cn
       $command .= ' -t '.$options->{'tumdefcn'};
     }
 
@@ -338,8 +336,7 @@ 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);
-	my $count = "wc -l $out";
-	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), [$command, $count], 0);
+	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
 
 	return PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);