From 53136563c75357e79a038466c26657d1869acb5f Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Mon, 8 Apr 2024 22:06:59 +1200
Subject: [PATCH] Add code to fix allele in --change-gene-id

Refs pombase/canto#2677
---
 lib/Canto/Track/TrackUtil.pm | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/lib/Canto/Track/TrackUtil.pm b/lib/Canto/Track/TrackUtil.pm
index b127be4c2..6d18641b3 100644
--- a/lib/Canto/Track/TrackUtil.pm
+++ b/lib/Canto/Track/TrackUtil.pm
@@ -459,6 +459,17 @@ sub change_gene_id
         $gene->update();
       }
     }
+
+    my $allele_rs = $cursdb->resultset('Allele');
+
+    while (defined (my $allele = $allele_rs->next())) {
+      my $primary_identifier = $allele->primary_identifier();
+      if ($primary_identifier =~ /^$from_id:/) {
+        $primary_identifier =~ s/^$from_id:/$to_id:/;
+        $allele->primary_identifier($primary_identifier);
+        $allele->update();
+      }
+    }
   };
 
   Canto::Track::curs_map($self->config(), $track_schema, $proc);