From 034211fb22188930161a9d79d0e52b92f7c4b948 Mon Sep 17 00:00:00 2001
From: Kez Cleal <42997789+kcleal@users.noreply.github.com>
Date: Wed, 31 Jul 2024 16:50:47 +0100
Subject: [PATCH] Updated GFF3 GTF names

---
 src/hts_funcs.cpp | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/hts_funcs.cpp b/src/hts_funcs.cpp
index 332e7f2..d1fbb8d 100644
--- a/src/hts_funcs.cpp
+++ b/src/hts_funcs.cpp
@@ -1821,6 +1821,10 @@ namespace HGW {
                         std::vector<std::string> keyval = Utils::split(item, '=');
                         if (keyval[0] == "ID") {
                             rid = keyval[1];
+                        } else if (keyval[0] == "Name") {
+                            parent = keyval[1];
+		            rid = keyval[1];
+                            break;
                         }
                         else if (keyval[0] == "Parent") {
                             parent = keyval[1];
@@ -1828,12 +1832,12 @@ namespace HGW {
                         }
                     } else {
                         std::vector<std::string> keyval = Utils::split(item, ' ');
-                        if (keyval[0] == "transcript_id") {
-                            rid = keyval[1];
-                        }
-                        else if (keyval[0] == "gene_id") {
+                        if (keyval[0] == "gene_id") {
                             parent = keyval[1];
+			    rid = keyval[1];
                             break;
+                        } else if (keyval[0] == "transcript_id") {
+                            rid = keyval[1];
                         }
                     }
                 }