* Add support for user settable window function (wig track) (igvteam#…

…1734) * Summarize wig track with "mean" by default -- this was the case for bigwig until zoomed in, then "raw" values, now mean is used consistently
arpanda · Apr 2, 2024 · a500e2d · a500e2d
1 parent 081ac2f
commit a500e2d
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diff --git a/dev/wig/encode.html b/dev/wig/encode.html
diff --git a/dev/wig/windowFunctions.html b/dev/wig/windowFunctions.html
@@ -0,0 +1,83 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>IGV-JB</title>
+    <!-- Font Awesome CSS-->
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
+
+    <!-- Juicebox CSS-->
+    <link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/juicebox.js@2.2.2/dist/css/juicebox.css">
+
+</head>
+<body>
+
+
+<div id="igvDiv" style="flex-grow:0;flex-shrink:0;flex-basis: 950px"></div>
+
+
+<script type="module">
+
+    import igv from "../../js"
+
+
+    // Start igv.js and create regions
+    const igvConfig =
+        {
+            genome: "hg19",
+            locus: "chr8:61,424,086-62,080,568",
+            "tracks": [
+                {
+                    "url": "https://www.encodeproject.org/files/ENCFF000ARZ/@@download/ENCFF000ARZ.bigWig",
+                    "name": "H3K4me1 bigwig",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url":  "../../test/data/tdf/ENCFF000ARZ.wig.tdf",
+                    "name":  "H3K4me1 tdf",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url": "../../test/data/wig/ENCFF000ARZ.wig",
+                    "name": "H3K4me1 mean",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url": "../../test/data/wig/ENCFF000ARZ.wig",
+                    "name": "H3K4me1 min",
+                    "windowFunction": "min",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url": "../../test/data/wig/ENCFF000ARZ.wig",
+                    "name": "H3K4me1 max",
+                    "windowFunction": "max",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url": "../../test/data/wig/ENCFF000ARZ.wig",
+                    "name": "H3K4me1 none",
+                    "windowFunction": "none",
+                    "autoscaleGroup": "1"
+                },
+                {
+                    "url": "../../test/data/wig/ENCFF000ARZ.wig",
+                    "name": "H3K4me1 points",
+                    "graphType": "points",
+                    "autoscaleGroup": "1"
+                }
+            ]
+        }
+
+    igv.createBrowser(document.getElementById("igvDiv"), igvConfig)
+
+        .then(async function (igvBrowser) {
+
+
+        })
+
+
+</script>
+
+</body>
+</html>
diff --git a/js/bigwig/bwReader.js b/js/bigwig/bwReader.js
@@ -30,7 +30,6 @@ import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index
 import {buildOptions, isDataURL} from "../util/igvUtils.js"
 import getDecoder from "./bbDecoders.js"
 import {parseAutoSQL} from "../util/ucscUtils.js"
-import summarizeWigData from "./summarizeWigData.js"
 import Trix from "./trix.js"
 import BPTree from "./bpTree.js"
 
@@ -131,7 +130,7 @@ class BWReader {
             }))
 
             // Parse data and return features
-            const allFeatures = []
+            const features = []
             for (let item of leafItems) {
                 const uint8Array = new Uint8Array(arrayBuffer, item.dataOffset - start, item.dataSize)
                 let plain
@@ -141,22 +140,14 @@ class BWReader {
                 } else {
                     plain = uint8Array
                 }
-                decodeFunction.call(this, new DataView(plain.buffer), chrIdx1, bpStart, chrIdx2, bpEnd, allFeatures, this.chromTree.idToName, windowFunction)
+                decodeFunction.call(this, new DataView(plain.buffer), chrIdx1, bpStart, chrIdx2, bpEnd, features, this.chromTree.idToName, windowFunction)
             }
 
-            allFeatures.sort(function (a, b) {
+            features.sort(function (a, b) {
                 return a.start - b.start
             })
 
-            // If we are reading "raw" wig data optionally summarize it with window function.
-            // Zoom level data is already summarized
-            if (decodeFunction === decodeWigData &&
-                bpPerPixel &&
-                ("mean" === windowFunction || "min" === windowFunction || "max" === windowFunction)) {
-                return summarizeWigData(allFeatures, bpPerPixel, windowFunction)
-            } else {
-                return allFeatures
-            }
+            return features
         }
     }
 

diff --git a/js/bigwig/bwSource.js b/js/bigwig/bwSource.js
@@ -28,12 +28,14 @@ import pack from "../feature/featurePacker.js"
 
 class BWSource {
 
+    queryable = true
+    wgValues = {}
+    windowFunctions = ["mean", "min", "max"]
+
     constructor(config, genome) {
         this.reader = new BWReader(config, genome)
         this.genome = genome
         this.format = config.format || "bigwig"
-        this.wgValues = {}
-        this.queryable = true
     }
 
     async getFeatures({chr, start, end, bpPerPixel, windowFunction}) {

diff --git a/js/bigwig/summarizeWigData.js b/js/bigwig/summarizeWigData.js
diff --git a/js/feature/textFeatureSource.js b/js/feature/textFeatureSource.js
@@ -151,6 +151,9 @@ class TextFeatureSource {
         const queryChr = genome ? genome.getChromosomeName(chr) : chr
         const isWholeGenome = ("all" === queryChr.toLowerCase())
 
+        start = start || 0
+        end = end || Number.MAX_SAFE_INTEGER
+
         // Various conditions that can require a feature load
         //   * view is "whole genome" but no features are loaded
         //   * cache is disabled