Merge branch 'hotfix/v3.2.2'

cancerit · Jul 16, 2019 · e142055 · e142055
2 parents 842c110 + 2b9c671
commit e142055
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Showing 4 changed files with 7 additions and 3 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.2.2
+
+* Handle Input files that may have no reads at all, specifically an issue when generating a normal panel.
+
 ## 3.2.1
 
 * Added Dockerfile and docker documentation

diff --git a/Dockerfile b/Dockerfile
@@ -37,7 +37,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="v3.2.1" \
+      version="v3.2.2" \
       description="cgpPindel docker"
 
 RUN apt-get -yq update

diff --git a/perl/lib/Sanger/CGP/Pindel.pm b/perl/lib/Sanger/CGP/Pindel.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.2.1';
+our $VERSION = '3.2.2';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm b/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm
@@ -66,7 +66,7 @@ sub sam_to_sorted_bam {
   else {
     my $header_from = $sam_files->[0];
     $command .= "cd $base_dir; ";
-    $command .= sprintf q{ (samtools view -H %s ; zcat %s | grep -v '^@' ) | }, $header_from, join q{ }, @{$sam_files};
+    $command .= sprintf q{ (samtools view -H %s ; zcat %s | grep -v '^@' || true ) | }, $header_from, join q{ }, @{$sam_files};
   }
 
   $command .= which('bamsort');