igv 2.15.4 → 2.15.5

package/README.md

@@ -18,19 +18,19 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/2.15.4/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.15.5/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.15.4/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.15.5/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.15.4/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.15.5/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.15.4/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.15.5/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.4/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.5/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.15.4/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.15.5/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.15.4/examples/)***
+***[More](https://igv.org/web/release/2.15.5/examples/)***
 
  
 # Quickstart
@@ -39,18 +39,18 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.15.4/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.4/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.4/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.15.4/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -18578,6 +18578,7 @@ class IGVXhr {
         });
         this.RANGE_WARNING_GIVEN = false;
         this.oauth = new Oauth();
+        this.contentLengthMap = new Map();
     }
 
     setApiKey(key) {
@@ -18655,6 +18656,18 @@ class IGVXhr {
         }
     }
 
+    async getContentLength(url, options) {
+        if (!this.contentLengthMap.has(url)) {
+            options = options || {};
+            options.method = 'HEAD';
+            options.GET_CONTENT_LENGTH = true;
+            const contentLengthString = await this._loadURL(url, options);
+            const contentLength = contentLengthString ? Number.parseInt(contentLengthString) : -1;
+            this.contentLengthMap.set(url, contentLength);
+        }
+        return this.contentLengthMap.get(url)
+    }
+
     async _loadURL(url, options) {
 
         const self = this;
@@ -18669,6 +18682,11 @@ class IGVXhr {
             oauthToken = await (typeof oauthToken === 'function' ? oauthToken() : oauthToken);
         }
 
+        let contentLength = -1;
+        if (options.range && !isAmazonV4Signed(url) && !isGoogleStorageSigned(url)) {
+            contentLength = await this.getContentLength(url);
+        }
+
         return new Promise(function (resolve, reject) {
 
             // Various Google tansformations
@@ -18694,13 +18712,6 @@ class IGVXhr {
             }
             const range = options.range;
 
-            // const isChrome = navigator.userAgent.indexOf('Chrome') > -1
-            // const isSafari = navigator.vendor.indexOf("Apple") === 0 && /\sSafari\//.test(navigator.userAgent)
-            // if (range && isChrome && !isAmazonV4Signed(url) && !isGoogleStorageSigned(url)) {
-            //     // Hack to prevent caching for byte-ranges. Attempt to fix net:err-cache errors in Chrome
-            //     url += url.includes("?") ? "&" : "?"
-            //     url += "someRandomSeed=" + Math.random().toString(36)
-            // }
 
             const xhr = new XMLHttpRequest();
             const sendData = options.sendData || options.body;
@@ -18716,7 +18727,13 @@ class IGVXhr {
             }
 
             if (range) {
-                var rangeEnd = range.size ? range.start + range.size - 1 : "";
+                let rangeEnd = "";
+                if (range.size) {
+                    rangeEnd = range.start + range.size - 1;
+                    if (contentLength > 0) {
+                        rangeEnd = Math.min(rangeEnd, contentLength - 1);
+                    }
+                }
                 xhr.setRequestHeader("Range", "bytes=" + range.start + "-" + rangeEnd);
                 //      xhr.setRequestHeader("Cache-Control", "no-cache");    <= This can cause CORS issues, disabled for now
             }
@@ -18742,6 +18759,11 @@ class IGVXhr {
             }
 
             xhr.onload = async function (event) {
+
+                if (options.GET_CONTENT_LENGTH) {
+                    resolve(xhr.getResponseHeader('content-length'));
+                }
+
                 // when the url points to a local file, the status is 0 but that is not an error
                 if (xhr.status === 0 || (xhr.status >= 200 && xhr.status <= 300)) {
                     if (range && xhr.status !== 206 && range.start !== 0) {
@@ -18774,6 +18796,7 @@ class IGVXhr {
                 }
             };
 
+
             xhr.onerror = function (event) {
                 if (isGoogleURL(url) && !options.retries) {
                     tryGoogleAuth();
@@ -18905,7 +18928,6 @@ function isGoogleStorageSigned(url) {
 }
 
 
-
 /**
  * Return a Google oAuth token, triggering a sign in if required.   This method should not be called until we know
  * a token is required, that is until we've tried the url and received a 401, 403, or 404.
@@ -19064,6 +19086,11 @@ function getGlobalObject() {
     }
 }
 
+function isAmazonV4Signed(url) {
+    return url.indexOf("X-Amz-Signature") > -1
+}
+
+
 const igvxhr = new IGVXhr();
 
 /*
@@ -23944,7 +23971,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.15.4";
+const _version = "2.15.5";
 function version() {
     return _version
 }
@@ -30279,7 +30306,8 @@ class FeatureFileReader {
         this.config = config || {};
         this.genome = genome;
         this.indexURL = config.indexURL;
-        this.indexed = config.indexed;
+        this.indexed = config.indexed || this.indexURL !== undefined;
+        this.queryable = this.indexed;
 
         if (isFile(this.config.url)) {
             this.filename = this.config.url.name;
@@ -31939,7 +31967,7 @@ class TextFeatureSource {
 
         const queryableFormats = new Set(["bigwig", "bw", "bigbed", "bb", "biginteract", "biggenepred", "bignarrowpeak", "tdf"]);
 
-        this.queryable = config.queryable === true;   // False by default, unless explicitly set
+        this.queryable = config.indexURL || config.queryable === true;   // False by default, unless explicitly set
         if (config.reader) {
             // Explicit reader implementation
             this.reader = config.reader;
@@ -32037,6 +32065,7 @@ class TextFeatureSource {
         //   * view is "whole genome" but no features are loaded
         //   * cache is disabled
         //   * cache does not contain requested range
+       // const containsRange = this.featureCache.containsRange(new GenomicInterval(queryChr, start, end))
         if ((isWholeGenome && !this.wgFeatures && this.supportsWholeGenome()) ||
             this.config.disableCache ||
             !this.featureCache ||
@@ -40877,7 +40906,7 @@ function monitorTrackDrag(track) {
 
     function onDragEnd() {
         if (track.trackView && track.displayMode !== "SQUISHED") {
-            track.trackView.repaintViews();      // TODO -- refine this to the viewport that was dragged after DOM refactor
+            track.trackView.updateViews();      // TODO -- refine this to the viewport that was dragged after DOM refactor
         }
     }