Add test case for tabix indexed gff file without file extensions

igvteam · Aug 9, 2024 · a9dafc3 · a9dafc3
1 parent 25c83c2
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Showing 4 changed files with 49 additions and 1 deletion.
diff --git a/dev/annotation/noextensions/bgzipped_gff b/dev/annotation/noextensions/bgzipped_gff
diff --git a/dev/annotation/noextensions/bgzipped_gff_index b/dev/annotation/noextensions/bgzipped_gff_index
diff --git a/dev/annotation/noextensions/no_extensions.html b/dev/annotation/noextensions/no_extensions.html
@@ -0,0 +1,48 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta name="author" content="Jim Robinson">
+    <link rel="shortcut icon" href="https://igv.org/web/https://igv.org/web/img/favicon.ico">
+    <title>igv.js</title>
+</head>
+
+<body>
+
+<p>
+
+<h1>Test a tabix indexed GFF file with no extension</h1>
+
+<div id="igvDiv" style="padding-top: 10px;padding-bottom: 10px; border:1px solid lightgray"></div>
+
+<script type="module">
+
+    import igv from "https://cdn.jsdelivr.net/npm/[email protected]/dist/igv.esm.min.js";
+
+    var options =
+        {
+            genome: "hg38",
+            locus: "myc",
+            tracks:
+                [
+                    {
+                        name: "Genes",
+                        format: "gff3",
+                        url: `bgzipped_gff`,
+                        indexURL: `bgzipped_gff_index`
+                    }
+                ]
+        };
+
+    var igvDiv = document.getElementById("igvDiv");
+
+    igv.createBrowser(igvDiv, options)
+        .then(function (browser) {
+            console.log("Created IGV browser");
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/genome/chromAliasBB.js b/js/genome/chromAliasBB.js
@@ -20,7 +20,7 @@ class ChromAliasBB {
     }
 
     /**
-     * Return the canonical chromosome name for the alias.  If none found return the alias.
+     * Return the cached canonical chromosome name for the alias.  If none found return the alias.
      *
      * Note this will only work if a "search" for ths chromosome has been performed previously.
      *
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,7 +20,7 @@ class ChromAliasBB { @@
         }
         /**
-         * Return the canonical chromosome name for the alias.  If none found return the alias.
+         * Return the cached canonical chromosome name for the alias.  If none found return the alias.
          *
          * Note this will only work if a "search" for ths chromosome has been performed previously.
          *
@@ Expand Down @@