From e2001c6eb49f1c89b472b40e9ae4f3398931ed93 Mon Sep 17 00:00:00 2001
From: Nick-Eagles <nick.eagles@libd.org>
Date: Fri, 11 Oct 2024 13:18:00 -0400
Subject: [PATCH] Support automatically importing gzip'd GTF files, which occur
 in the recent annotation files (e.g. 2024)

---
 R/read10xVisiumWrapper.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/read10xVisiumWrapper.R b/R/read10xVisiumWrapper.R
index 430943e9..6bf42111 100644
--- a/R/read10xVisiumWrapper.R
+++ b/R/read10xVisiumWrapper.R
@@ -72,7 +72,10 @@ read10xVisiumWrapper <- function(
                 web[grep('--transcriptome=', web)]
             )
         }
-        reference_gtf <- file.path(reference_path, "genes", "genes.gtf")
+        reference_gtf <- list.files(
+            file.path(reference_path, "genes"), "^genes\\.gtf(\\.gz)?$",
+            full.names = TRUE
+        )
     }
     reference_gtf <- reference_gtf[file.exists(reference_gtf)]
     if (length(reference_gtf) > 1) {