Handle VCF files with no info fields. Fixes #1868

igvteam · Aug 8, 2024 · 25c83c2 · 25c83c2
1 parent 3172d44
commit 25c83c2
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Showing 5 changed files with 97 additions and 31 deletions.
diff --git a/dev/variant/noheader.html b/dev/variant/noheader.html
@@ -0,0 +1,44 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <meta content="IE=edge" http-equiv="X-UA-Compatible">
+    <meta content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no" name="viewport">
+    <meta content="" name="description">
+    <meta content="" name="author">
+    <link href=https://igv.org/web/img/favicon.ico rel="shortcut icon">
+    <title>indel</title>
+
+</head>
+
+<body>
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js";
+
+    const options =
+        {
+            genome: "hg19",
+            locus: "chr6:63,498,615-63,498,653",
+            tracks: [
+                {
+                    "url": "../../test/data/vcf/noheader.vcf"
+                },
+
+            ]
+        };
+
+    igv.createBrowser(document.getElementById('igvDiv'), options)
+        .then(function (browser) {
+
+        })
+
+
+</script>
+
+</body>
+
+</html>
diff --git a/js/variant/variant.js b/js/variant/variant.js
@@ -46,7 +46,7 @@ class Variant {
         this.filter = tokens[6]
         this.info = {}
         const infoStr = tokens[7]
-        if (infoStr) {
+        if (infoStr && infoStr !== '.') {
             for (let elem of infoStr.split(';')) {
                 var element = elem.split('=')
                 this.info[element[0]] = element[1]
@@ -205,9 +205,10 @@ class Variant {
             }
         }
 
-        if (this.info) {
+        const infoKeys = Object.keys(this.info)
+        if (this.info && infoKeys.length > 0) {
             fields.push({html: '<hr style="border-top: dotted 1px;border-color: #c9c3ba" />'})
-            for (let key of Object.keys(this.info)) {
+            for (let key of infoKeys) {
                 fields.push({name: key, value: arrayToString(decodeURIComponent(this.info[key]))})
             }
         }
@@ -274,7 +275,7 @@ class SVComplement {
     }
 
     getAttributeValue(key) {
-       return this.mate.getAttributeValue(key)
+        return this.mate.getAttributeValue(key)
     }
 
     getInfo(tag) {
@@ -297,7 +298,7 @@ class SVComplement {
         popupData.push({name: 'Pos', value: `${StringUtils.numberFormatter(this.pos)}`})
         popupData.push({html: '<hr style="border-top: dotted 1px;border-color: #c9c3ba" />'})
         popupData.push("SV")
-        popupData.push(... this.mate.popupData(genomicLocation, genomeId))
+        popupData.push(...this.mate.popupData(genomicLocation, genomeId))
 
         return popupData
     }

diff --git a/js/variant/variantTrack.js b/js/variant/variantTrack.js
@@ -126,23 +126,26 @@ class VariantTrack extends TrackBase {
         this.header = await this.getHeader()
 
         // Set colorBy, if not explicitly set default to allele frequency, if available, otherwise default to none (undefined)
-        const infoFields = new Set(Object.keys(this.header.INFO))
-        if (this.config.colorBy) {
-            this.colorBy = this.config.colorBy
-        } else if (!this.config.color && infoFields.has('AF')) {
-            this.colorBy = 'AF'
-        }
+        if(this.header.INFO) {
+            const infoFields = new Set(Object.keys(this.header.INFO))
+            if (this.config.colorBy) {
+                this.colorBy = this.config.colorBy
+            } else if (!this.config.color && infoFields.has('AF')) {
+                this.colorBy = 'AF'
+            }
 
-        // Configure menu items based on info available
-        if (infoFields.has('AF')) {
-            this._colorByItems.set('AF', 'Allele frequency')
-        }
-        if (infoFields.has('VT')) {
-            this._colorByItems.set('VT', 'Variant Type')
-        }
-        if (infoFields.has('SVTYPE')) {
-            this._colorByItems.set('SVTYPE', 'SV Type')
+            // Configure menu items based on info available
+            if (infoFields.has('AF')) {
+                this._colorByItems.set('AF', 'Allele frequency')
+            }
+            if (infoFields.has('VT')) {
+                this._colorByItems.set('VT', 'Variant Type')
+            }
+            if (infoFields.has('SVTYPE')) {
+                this._colorByItems.set('SVTYPE', 'SV Type')
+            }
         }
+
         if (this.config.colorBy && !this._colorByItems.has(this.config.colorBy)) {
             this._colorByItems.set(this.config.colorBy, this.config.colorBy)
         }

diff --git a/test/data/vcf/noheader.vcf b/test/data/vcf/noheader.vcf
@@ -0,0 +1,5 @@
+##fileformat=VCFv4.2
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr6	63498622	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779765' target='_blank'>rs1779765</a>	T	A	.	.	.
+chr6	63498633	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779766' target='_blank'>rs1779766</a>	G	A	.	.	.
+chr6	63498639	<a href='https://www.ncbi.nlm.nih.gov/snp/rs1779767' target='_blank'>rs1779767</a>	G	A	.	.	.
diff --git a/test/testVariant.js b/test/testVariant.js
@@ -6,10 +6,11 @@ import {assert} from 'chai'
 import getDataWrapper from "../js/feature/dataWrapper.js"
 import {createGenome} from "./utils/MockGenome.js"
 import pack from "../js/feature/featurePacker.js"
-
-const genome = createGenome()
 import Browser from "../js/browser.js"
+import VariantTrack from "../js/variant/variantTrack.js"
 
+const genome = createGenome()
+const browser = {genome}
 
 suite("testVariant", function () {
 
@@ -156,9 +157,6 @@ suite("testVariant", function () {
             indexURL: "test/data/vcf/large_header.vcf.idx"
         }
 
-
-        const browser = {genome}
-
         const track = await Browser.prototype.createTrack.call(browser, config)
         assert.equal(track.type, "variant")
 
@@ -171,15 +169,13 @@ suite("testVariant", function () {
     })
 
     test("tabix indexed - large header", async function () {
+
         const config = {
             url: "test/data/vcf/large_header.vcf",
             indexURL: "test/data/vcf/large_header.vcf.idx"
 
         }
 
-
-        const browser = {genome}
-
         const track = await Browser.prototype.createTrack.call(browser, config)
         assert.equal(track.type, "variant")
 
@@ -213,9 +209,6 @@ suite("testVariant", function () {
             indexed: false
         }
 
-
-        const browser = {genome}
-
         const track = await Browser.prototype.createTrack.call(browser, config)
         assert.equal(track.type, "variant")
 
@@ -258,6 +251,26 @@ suite("testVariant", function () {
 
     })
 
+    test("Test no info fields", async function () {
+
+        const url = "test/data/vcf/noheader.vcf"
+
+        const config = {url}
+
+        const track = await Browser.prototype.createTrack.call(browser, config)
+
+        await track.postInit()
+
+        const variants = await track.getFeatures("chr6", 0, Number.MAX_SAFE_INTEGER)
+
+        assert.equal(variants.length, 3)
+
+        for (let v of variants) {
+            assert.equal(v.type, "SNP")
+        }
+
+    })
+
 
 })