From e34912871a0c51b928e24855f2ddc85676c2f160 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Thu, 21 Feb 2019 13:04:42 +0000
Subject: [PATCH 1/2] Fix regression - ability handle chr with no pindel mapped
 reads, introduced in 3.x tree

Also samtools can read the header from a gz sam file modified to make this more
normalised so that no issues would occur if the first file is the only one with reads.
---
 perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm b/perl/lib/Sanger/CGP/Pindel/OutputGen/BamUtil.pm
index 78030cd..25a2d3d 100644
--- 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');

From 6eacd04d08f08ffb9e348eadef30003fa63c4018 Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Thu, 21 Feb 2019 13:08:05 +0000
Subject: [PATCH 2/2] Version and details in change log

---
 CHANGES.md                    | 4 ++++
 perl/lib/Sanger/CGP/Pindel.pm | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGES.md b/CHANGES.md
index 6169f5a..b51b2a3 100644
--- 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
index b90e36d..664c4c0 100644
--- 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;