Support automatically importing gzip'd GTF files, which occur in the recent annotation files (e.g. 2024)

Nick-Eagles · Nick-Eagles · commit e2001c6eb49f · 2024-10-11T13:18:00.000-04:00
diff --git 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) {

Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,10 @@ read10xVisiumWrapper <- function(`
`72`	`72`	`web[grep('--transcriptome=', web)]`
`73`	`73`	`)`
`74`	`74`	`}`
`75`		`- reference_gtf <- file.path(reference_path, "genes", "genes.gtf")`
	`75`	`+ reference_gtf <- list.files(`
	`76`	`+ file.path(reference_path, "genes"), "^genes\\.gtf(\\.gz)?$",`
	`77`	`+ full.names = TRUE`
	`78`	`+ )`
`76`	`79`	`}`
`77`	`80`	`reference_gtf <- reference_gtf[file.exists(reference_gtf)]`
`78`	`81`	`if (length(reference_gtf) > 1) {`