Merge branch 'hotfix/2.3.4'

* RG tags are converted to shell safe strings before passing to Star. partially resolve #30.

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 2.3.4
+
+* RG tags are converted to shell safe strings before passing to Star. partially resolve #30.
+
 ## 2.3.3
 
 * fixed verison numbers

Dockerfile

@@ -57,7 +57,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="2.3.3" \
+      version="2.3.4" \
       description="cgpRna docker"
 
 RUN apt-get -yq update

perl/lib/Sanger/CGP/CgpRna.pm

@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.3.3';
+our $VERSION = '2.3.4';
 our @EXPORT = qw($VERSION);
 
 1;

perl/lib/Sanger/CGP/Star/Implement.pm

@@ -198,15 +198,14 @@ sub format_rg_tags {
 
 	push @rg_header, 'LB:'.$options->{'LB'} if(exists $options->{'LB'});
 	# Quotes need to be around the description (DS:) tag text
-	push @rg_header, '"DS:'.$options->{'DS'}.'"' if(exists $options->{'DS'});
+	push @rg_header, 'DS:'.$options->{'DS'} if(exists $options->{'DS'});
 	push @rg_header, 'PL:'.$options->{'PL'} if(exists $options->{'PL'});
 	push @rg_header, 'PU:'.$options->{'PU'} if(exists $options->{'PU'});
 
 	foreach my $r(@rg_tags){
 	  unless($r eq '@RG' || $r =~ /^ID/){
 	    my @tag = split ':', $r;
 	    if(!exists $options->{$tag[0]}){
-	      $r = '"'.$r.'"' if($r =~ /DS:/);
 	      push @rg_header, $r;
 	    }
 	    # Once the RG tag has been formatted correctly for the CGP mapped BAM, add any pre-existing tags to a comment line to store what was in the BAM RG tags previously
@@ -226,7 +225,9 @@ sub format_rg_tags {
 
 	$options->{'commentfile'} = $comment_file unless($first_file->fastq);
 
-	$options->{'rgline'} = join(" ",@rg_header);
+	# convert tags to shell safe tags before passing them to star in command line
+	my @shell_safe_rg_header = map { _to_commandline_safe_tag_for_star($_) } @rg_header;
+	$options->{'rgline'} = join(" ", @shell_safe_rg_header);
 
   return 1;
 }
@@ -598,6 +599,19 @@ sub _which {
 	return $path;
 }
 
+sub _to_commandline_safe_tag_for_star {
+	# according to this: https://unix.stackexchange.com/a/398649
+	# preserving tag values is complicated
+	my $tag = shift;
+	# first escape backslashes
+	$tag =~ s/\\/\\\\/g;
+	# then escape other needed-to-escape characters.
+	# this will inevitably introduce an extra backslash into the tag if there's an '!', but for now no other way to escape '!' to prevent bash history expansion.
+	$tag =~ s/([`"!\$])/\\$1/g;
+	# double quoted it
+	return sprintf q{"%s"}, $tag;
+}
+
 1;
 
 __END__