Recognize #gffTags directive in bed files and treat "name" property a…

…ccordingly, consistent with IGV desktop. See #1550
igvteam · Jan 23, 2025 · 4ca37f4 · 4ca37f4
1 parent 696a29f
commit 4ca37f4
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Showing 4 changed files with 58 additions and 7 deletions.
diff --git a/dev/annotation/gffTags.html b/dev/annotation/gffTags.html
@@ -0,0 +1,47 @@
+<!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 of a CSI index with a gtf file</h1>
+
+<div id="igvDiv" style="padding-top: 10px;padding-bottom: 10px; border:1px solid lightgray"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js";
+
+    var options =
+        {
+            genome: "hg19",
+            locus: "chr1:1000-2000",
+            tracks:
+                [
+                    {
+                        name: "gff tags",
+                        format: "bed",
+                        url: `../../test/data/bed/gfftags.bed`,
+                    }
+                ]
+        };
+
+    var igvDiv = document.getElementById("igvDiv");
+
+    igv.createBrowser(igvDiv, options)
+        .then(function (browser) {
+            console.log("Created IGV browser");
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/feature/decode/ucsc.js b/js/feature/decode/ucsc.js
@@ -2,6 +2,7 @@ import {IGVColor} from "../../../node_modules/igv-utils/src/index.js"
 import DecodeError from "./decodeError.js"
 
 import {parseAttributeString} from "../gff/parseAttributeString.js"
+import GFFHelper from "../gff/gffHelper.js"
 
 
 /**
@@ -36,12 +37,16 @@ function decodeBed(tokens, header, maxColumnCount = Number.MAX_SAFE_INTEGER) {
                 feature.attributes = {}
                 for (let kv of attributeKVs) {
                     feature.attributes[kv[0]] = kv[1]
-                    if (header.nameField != undefined && kv[0] === header.nameField) {
-                        feature.name = kv[1]
+                    if(gffTags) {
+                        if (header.nameField != undefined && kv[0] === header.nameField) {
+                            feature.name = kv[1]
+                        } else if (!feature.name && GFFHelper.gffNameFields.has(kv[0])) {
+                            feature.name = kv[1];
+                        }
                     }
                 }
             }
-            if (!feature.name) {
+            if (!feature.name && !gffTags) {
                 feature.name = tokens[3] === '.' ? '' : tokens[3]
             }
         }

diff --git a/js/feature/gff/gffHelper.js b/js/feature/gff/gffHelper.js
@@ -1,10 +1,10 @@
 import {isExon, isTranscript, isTranscriptPart} from "./so.js"
 import {GFFFeature, GFFTranscript} from "./gffFeature.js"
 
-const gffNameFields = ["Name", "transcript_id", "gene_name", "gene", "gene_id", "alias", "locus", "name" ]
 
 class GFFHelper {
 
+    static gffNameFields = new Set(["Name", "transcript_id", "gene_name", "gene", "gene_id", "alias", "locus", "name" ])
     constructor(options) {
         this.format = options.format
         this.nameField = options.nameField
@@ -201,11 +201,10 @@ class GFFHelper {
         // Find name (label) property
         for (let f of features) {
             if(typeof f.getAttributeValue === 'function') {
-
                 if (this.nameField) {
                     f.name = f.getAttributeValue(this.nameField)
                 } else {
-                    for (let nameField of gffNameFields) {
+                    for (let nameField of GFFHelper.gffNameFields) {
                         const v = f.getAttributeValue(nameField)
                         if (v) {
                             f.name = v

diff --git a/test/data/bed/gfftags.bed b/test/data/bed/gfftags.bed
@@ -1,6 +1,6 @@
 #gffTags
 track name="chr1" description="chr1 Annotations" itemRgb="On"
-chr1	1088	1128	Key1=INS230;Key2=Foo	0	+	1088	1088	65,105,225
+chr1	1088	1128	Key1=INS230;Key2=Foo;Name=INS230	0	+	1088	1088	65,105,225
 chr1	133	2809	Key2=Bar;Key1=terminator	0	+	133	133	65,105,225
 chr1	1301	1746	Key1=M13 origin;Key2=Baz	0	+	1301	1301	65,105,225
 chr1	1301	1746	Key1=M13 origin;Key2=Baz	0	+	1301	1301	65,105,225