Merge branch 'release/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

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.

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);

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;