igv 2.15.5 → 2.15.7

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/2.15.5/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.15.7/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.15.5/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.15.7/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.15.5/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.15.7/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.15.5/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.15.7/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.5/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.7/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.15.5/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.15.7/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.15.5/examples/)***
+***[More](https://igv.org/web/release/2.15.7/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@2.15.5/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.15.7/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.7/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.7/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.15.5/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.15.7/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -18578,7 +18578,6 @@ class IGVXhr {
         });
         this.RANGE_WARNING_GIVEN = false;
         this.oauth = new Oauth();
-        this.contentLengthMap = new Map();
     }
 
     setApiKey(key) {
@@ -18656,18 +18655,6 @@ 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;
@@ -18682,11 +18669,6 @@ 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
@@ -18727,13 +18709,7 @@ class IGVXhr {
             }
 
             if (range) {
-                let rangeEnd = "";
-                if (range.size) {
-                    rangeEnd = range.start + range.size - 1;
-                    if (contentLength > 0) {
-                        rangeEnd = Math.min(rangeEnd, contentLength - 1);
-                    }
-                }
+                var rangeEnd = range.size ? range.start + range.size - 1 : "";
                 xhr.setRequestHeader("Range", "bytes=" + range.start + "-" + rangeEnd);
                 //      xhr.setRequestHeader("Cache-Control", "no-cache");    <= This can cause CORS issues, disabled for now
             }
@@ -18759,11 +18735,6 @@ 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) {
@@ -19086,10 +19057,6 @@ function getGlobalObject() {
     }
 }
 
-function isAmazonV4Signed(url) {
-    return url.indexOf("X-Amz-Signature") > -1
-}
-
 
 const igvxhr = new IGVXhr();
 
@@ -23971,7 +23938,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.15.5";
+const _version = "2.15.7";
 function version() {
     return _version
 }
@@ -32196,30 +32163,45 @@ class BufferedReader {
      * @param fulfill - function to receive result
      * @param asUint8 - optional flag to return result as an UInt8Array
      */
-    async dataViewForRange(requestedRange, asUint8) {
-
-        const hasData = (this.data && (this.range.start <= requestedRange.start) &&
-            ((this.range.start + this.range.size) >= (requestedRange.start + requestedRange.size)));
+    async dataViewForRange(requestedRange, asUint8, retries = 0) {
+        try {
+            console.log(`buffered reader ${requestedRange}`);
+            const hasData = (this.data && (this.range.start <= requestedRange.start) &&
+                ((this.range.start + this.range.size) >= (requestedRange.start + requestedRange.size)));
+
+            if (!hasData) {
+                let bufferSize;
+                // If requested range size is specified, potentially expand buffer size
+                if (requestedRange.size) {
+                    bufferSize = Math.max(this.bufferSize, requestedRange.size);
+                } else {
+                    bufferSize = this.bufferSize;
+                }
+                if (this.contentLength) {
+                    bufferSize = Math.min(bufferSize, this.contentLength - requestedRange.start);
+                }
+                const loadRange = {start: requestedRange.start, size: bufferSize};
+                const arrayBuffer = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, {range: loadRange}));
+                this.data = arrayBuffer;
+                this.range = loadRange;
+            }
 
-        if (!hasData) {
-            let bufferSize;
-            // If requested range size is specified, potentially expand buffer size
-            if (requestedRange.size) {
-                bufferSize = Math.max(this.bufferSize, requestedRange.size);
-            } else {
-                bufferSize = this.bufferSize;
+            const len = this.data.byteLength;
+            const bufferStart = requestedRange.start - this.range.start;
+            return asUint8 ?
+                new Uint8Array(this.data, bufferStart, len - bufferStart) :
+                new DataView(this.data, bufferStart, len - bufferStart)
+        } catch (e) {
+            if (retries === 0 && e.message && e.message.startsWith("416")) {
+                try {
+                    this.contentLength = await igvxhr.getContentLength(this.path, buildOptions(this.config));
+                    return this.dataViewForRange(requestedRange, asUint8, ++retries)
+                } catch (e1) {
+                    console.error(e1);
+                }
+                throw e
             }
-            const loadRange = {start: requestedRange.start, size: bufferSize};
-            const arrayBuffer = await igvxhr.loadArrayBuffer(this.path, buildOptions(this.config, {range: loadRange}));
-            this.data = arrayBuffer;
-            this.range = loadRange;
         }
-
-        const len = this.data.byteLength;
-        const bufferStart = requestedRange.start - this.range.start;
-        return asUint8 ?
-            new Uint8Array(this.data, bufferStart, len - bufferStart) :
-            new DataView(this.data, bufferStart, len - bufferStart)
     }
 }