From 489c887d1ea633719d7e3ca071a4b7a37c893710 Mon Sep 17 00:00:00 2001
From: Thomas Clarke <tc20@sanger.ac.uk>
Date: Thu, 10 Mar 2022 13:11:21 +0000
Subject: [PATCH 1/2] applied masking to pindel output

---
 perl/bin/pindel_2_combined_vcf.pl | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/perl/bin/pindel_2_combined_vcf.pl b/perl/bin/pindel_2_combined_vcf.pl
index 0e6a625..37ac95b 100755
--- a/perl/bin/pindel_2_combined_vcf.pl
+++ b/perl/bin/pindel_2_combined_vcf.pl
@@ -195,6 +195,11 @@ sub _process_fh{
   my ($active_sam_fh, $sample, $strand);
   while(my $record = $record_generator->next_record){
 
+    if($record->ref_seq eq $record->alt_seq) {
+      warn "SKIP: Dirty record due to issue in pindel core";
+      next;
+    }
+
     next if($opts->{'s'} && ($record->p_mt_pos + $record->p_mt_neg) < 3);
 
     $record->id($id_gen->next);

From 70c95c550ee345599c88b0791fba418563f86740 Mon Sep 17 00:00:00 2001
From: Thomas Clarke <tc20@sanger.ac.uk>
Date: Wed, 16 Mar 2022 16:09:31 +0000
Subject: [PATCH 2/2] 3.9.0 updates

---
 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 e07be09..308c594 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.9.0
+- Masking of pindel calls where ref == alt implemented to remove invalid calls from pindel output
+  - Core pindel fix required to resolve the underlying problem
+
 ## 3.8.0
 
 - Adds `-noflag` option to `pindel.pl` for use cases where flagging needs to be executed separately or not at all.
diff --git a/perl/lib/Sanger/CGP/Pindel.pm b/perl/lib/Sanger/CGP/Pindel.pm
index 74c5c5b..512a6e1 100644
--- a/perl/lib/Sanger/CGP/Pindel.pm
+++ b/perl/lib/Sanger/CGP/Pindel.pm
@@ -33,7 +33,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.8.0';
+our $VERSION = '3.9.0';
 our @EXPORT = qw($VERSION);
 
 1;