Merge branch 'hotfix/v3.1.1'

cancerit · Feb 21, 2019 · 5077315 · 5077315
2 parents 9455fb8 + 6eacd04
commit 5077315
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.1.1
+
+* Fix regression - ability to cope with chromosomes with no events.
+
 ## 3.1.0
 
 * Incorporates updated pindel which improves sensitivity

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 = '3.1.0';
+our $VERSION = '3.1.1';
 our @EXPORT = qw($VERSION);
 
 1;
diff --git a/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm b/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm
@@ -64,9 +64,9 @@ sub sam_to_sorted_bam {
     $command .= sprintf ' zcat %s | ', $sam_files->[0];
   }
   else {
-    my $first_file = shift @{$sam_files};
+    my $header_from = $sam_files->[0];
     $command .= "cd $base_dir; ";
-    $command .= sprintf q{ (zcat %s ; zgrep -v '^@' %s) | }, $first_file, join q{ }, @{$sam_files};
+    $command .= sprintf q{ (samtools view -H %s ; zcat %s | grep -v '^@' ) | }, $header_from, join q{ }, @{$sam_files};
   }
 
   $command .= which('bamsort');