Merge branch 'hotfix/2.1.9'

David Jones · David Jones · commit 3bca8c8d2c8a · 2017-10-12T13:45:59.000+01:00
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+### 2.1.9
+* Fix missed compilation failure
+
 ### 2.1.8
 * Fix issues with empty output from tophatpost when running tophat_filter
 
diff --git a/perl/lib/Sanger/CGP/CgpRna.pm b/perl/lib/Sanger/CGP/CgpRna.pm
@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.1.8';
+our $VERSION = '2.1.9';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/perl/lib/Sanger/CGP/Tophat/Implement.pm b/perl/lib/Sanger/CGP/Tophat/Implement.pm
@@ -536,7 +536,7 @@ sub tophatfusion_post {
 	PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);
 
 	#If the output is empty, ensure that it passes further checks by adding ##EOF## to the file.
-	$output_post = $post_rundir.'/result.txt';
+	my $output_post = $post_rundir.'/result.txt';
 	if(-s $output_post == 0){
 		system("echo '##EOF##' > $output_post") && die "An error occurred: $!";
 	}

Original file line number	Diff line number	Diff line change
`@@ -536,7 +536,7 @@ sub tophatfusion_post {`
`536`	`536`	`PCAP::Threaded::external_process_handler(File::Spec->catdir($tmp, 'logs'), $command, 0);`
`537`	`537`
`538`	`538`	`#If the output is empty, ensure that it passes further checks by adding ##EOF## to the file.`
`539`		`- $output_post = $post_rundir.'/result.txt';`
	`539`	`+ my $output_post = $post_rundir.'/result.txt';`
`540`	`540`	`if(-s $output_post == 0){`
`541`	`541`	`system("echo '##EOF##' > $output_post") && die "An error occurred: $!";`
`542`	`542`	`}`