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] 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);