igv 2.15.11 → 2.15.13

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/2.15.10/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.15.13/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.15.10/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.15.13/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.15.10/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.15.13/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.15.10/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.15.13/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.10/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.15.13/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.15.10/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.15.13/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.15.10/examples/)***
+***[More](https://igv.org/web/release/2.15.13/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@2.15.10/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/](https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.15.10/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.15.13/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -19240,7 +19240,7 @@ BinaryHeap.prototype = {
  */
 
 function _random(min, max) {
-    return Math.random() * (max - min) + min;
+    return Math.random() * (max - min) + min
 }
 
 const IGVColor = {
@@ -19260,7 +19260,7 @@ const IGVColor = {
         accumulation.pop();
         accumulation.push(IGVColor.rgbColor(16, 16, 16));
 
-        return accumulation;
+        return accumulation
     },
 
     rgbToHex: function (rgb) {
@@ -19268,7 +19268,7 @@ const IGVColor = {
         return (rgb && rgb.length === 4) ? "#" +
             ("0" + parseInt(rgb[1], 10).toString(16)).slice(-2) +
             ("0" + parseInt(rgb[2], 10).toString(16)).slice(-2) +
-            ("0" + parseInt(rgb[3], 10).toString(16)).slice(-2) : '';
+            ("0" + parseInt(rgb[3], 10).toString(16)).slice(-2) : ''
     },
 
     hexToRgb: function (hex) {
@@ -19276,10 +19276,10 @@ const IGVColor = {
         var cooked = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
 
         if (null === cooked) {
-            return undefined;
+            return undefined
         }
 
-        return "rgb(" + parseInt(cooked[1], 16) + "," + parseInt(cooked[2], 16) + "," + parseInt(cooked[3], 16) + ")";
+        return "rgb(" + parseInt(cooked[1], 16) + "," + parseInt(cooked[2], 16) + "," + parseInt(cooked[3], 16) + ")"
     },
 
     /**
@@ -19307,25 +19307,25 @@ const IGVColor = {
         switch (i % 6) {
             case 0:
                 r = v, g = t, b = p;
-                break;
+                break
             case 1:
                 r = q, g = v, b = p;
-                break;
+                break
             case 2:
                 r = p, g = v, b = t;
-                break;
+                break
             case 3:
                 r = p, g = q, b = v;
-                break;
+                break
             case 4:
                 r = t, g = p, b = v;
-                break;
+                break
             case 5:
                 r = v, g = p, b = q;
-                break;
+                break
         }
 
-        return [Math.floor(r * 255), Math.floor(g * 255), Math.floor(b * 255)];
+        return [Math.floor(r * 255), Math.floor(g * 255), Math.floor(b * 255)]
     },
 
     /**
@@ -19357,16 +19357,16 @@ const IGVColor = {
             b = IGVColor.hue2rgb(p, q, h - 1 / 3);
         }
 
-        return [r * 255, g * 255, b * 255];
+        return [r * 255, g * 255, b * 255]
     },
 
     hue2rgb: (p, q, t) => {
         if (t < 0) t += 1;
         if (t > 1) t -= 1;
-        if (t < 1 / 6) return p + (q - p) * 6 * t;
-        if (t < 1 / 2) return q;
-        if (t < 2 / 3) return p + (q - p) * (2 / 3 - t) * 6;
-        return p;
+        if (t < 1 / 6) return p + (q - p) * 6 * t
+        if (t < 1 / 2) return q
+        if (t < 2 / 3) return p + (q - p) * (2 / 3 - t) * 6
+        return p
     },
 
     rgbaColor: function (r, g, b, a) {
@@ -19376,7 +19376,7 @@ const IGVColor = {
         b = IGVMath.clamp(b, 0, 255);
         a = IGVMath.clamp(a, 0.0, 1.0);
 
-        return "rgba(" + r + "," + g + "," + b + "," + a + ")";
+        return "rgba(" + r + "," + g + "," + b + "," + a + ")"
     },
 
     rgbColor: function (r, g, b) {
@@ -19385,14 +19385,14 @@ const IGVColor = {
         g = IGVMath.clamp(g, 0, 255);
         b = IGVMath.clamp(b, 0, 255);
 
-        return "rgb(" + r + "," + g + "," + b + ")";
+        return "rgb(" + r + "," + g + "," + b + ")"
     },
 
     greyScale: function (value) {
 
         var grey = IGVMath.clamp(value, 0, 255);
 
-        return "rgb(" + grey + "," + grey + "," + grey + ")";
+        return "rgb(" + grey + "," + grey + "," + grey + ")"
     },
 
     randomGrey: function (min, max) {
@@ -19402,7 +19402,7 @@ const IGVColor = {
 
         var g = Math.round(_random(min, max)).toString(10);
 
-        return "rgb(" + g + "," + g + "," + g + ")";
+        return "rgb(" + g + "," + g + "," + g + ")"
     },
 
     randomRGB: function (min, max) {
@@ -19414,7 +19414,7 @@ const IGVColor = {
         var g = Math.round(_random(min, max)).toString(10);
         var b = Math.round(_random(min, max)).toString(10);
 
-        return "rgb(" + r + "," + g + "," + b + ")";
+        return "rgb(" + r + "," + g + "," + b + ")"
     },
 
     randomRGBConstantAlpha: function (min, max, alpha) {
@@ -19426,12 +19426,12 @@ const IGVColor = {
         var g = Math.round(_random(min, max)).toString(10);
         var b = Math.round(_random(min, max)).toString(10);
 
-        return "rgba(" + r + "," + g + "," + b + "," + alpha + ")";
+        return "rgba(" + r + "," + g + "," + b + "," + alpha + ")"
     },
 
     addAlpha: function (color, alpha) {
 
-        if(color === "0" || color === ".") {
+        if (color === "0" || color === ".") {
             color = "rgb(0,0,0)";
         } else {
             const c = this.colorNameToHex(color);
@@ -19444,7 +19444,7 @@ const IGVColor = {
 
         if (color.startsWith("rgba")) {
             const idx = color.lastIndexOf(",");
-            return color.substring(0, idx+1) + alpha.toString() + ")";
+            return color.substring(0, idx + 1) + alpha.toString() + ")"
         }
 
         if (isHex) {
@@ -19452,38 +19452,37 @@ const IGVColor = {
         }
 
         if (color.startsWith("rgb")) {
-            return color.replace("rgb", "rgba").replace(")", ", " + alpha + ")");
+            return color.replace("rgb", "rgba").replace(")", ", " + alpha + ")")
         } else {
             console.log(color + " is not an rgb style string");
-            return color;
+            return color
         }
     },
 
     rgbComponents: function (color) {
 
-        if(color === "0" || color === ".") {
-            return [0,0,0];
+        if (color === "0" || color === ".") {
+            return [0, 0, 0]
         }
         const isHex = /(^#[0-9A-F]{6}$)|(^#[0-9A-F]{3}$)/i.test(color);
         if (isHex) {
             color = IGVColor.hexToRgb(color);
         } else {
-            if(!color.startsWith("rgb")) {
+            if (!color.startsWith("rgb")) {
                 const hex = this.colorNameToHex(color);
                 color = this.hexToRgb(hex);
             }
         }
 
         if (color.startsWith("rgb(")) {
-            return color.substring(4, color.length-1).split(",").map(s => Number.parseInt(s.trim()));
-         } else if (color.startsWith("rgba(")) {
-            return color.substring(5, color.length-1).split(",").map((s, i) => {
+            return color.substring(4, color.length - 1).split(",").map(s => Number.parseInt(s.trim()))
+        } else if (color.startsWith("rgba(")) {
+            return color.substring(5, color.length - 1).split(",").map((s, i) => {
                 s = s.trim();
                 return i === 3 ? Number.parseFloat(s) : Number.parseInt(s)
-            });
-        }
-        else {
-            throw Error("Unrecognized color string: color");
+            })
+        } else {
+            throw Error("Unrecognized color string: color")
         }
     },
 
@@ -19500,19 +19499,46 @@ const IGVColor = {
             g = Math.floor(alpha * src[1] + (1 - alpha) * dest[1]),
             b = Math.floor(alpha * src[2] + (1 - alpha) * dest[2]);
 
-        return "rgb(" + r + "," + g + "," + b + ")";
+        return "rgb(" + r + "," + g + "," + b + ")"
 
     },
 
-
+    /**
+     * Return a color represented by the string.  If the string is not a recognized color format return the
+     * string itself.  This function exists for backward compatibility,  createColorStringSafe is preferredz
+     * @param str
+     */
     createColorString: function (str) {
+        // Excel will quote color strings, strip all quotes
+        const color = this.createColorStringSafe(str);
+        return color ? color : str
+    },
+
+    /**
+     * If str is a recognized color format return a string encoding the color
+     * @param str
+     */
+    createColorStringSafe: function (str) {
         // Excel will quote color strings, strip all quotes
         str = stripQuotes$1(str);
 
-        if (str.includes(",")) {
-            return str.startsWith("rgb") ? str : "rgb(" + str + ")";
-        } else {
-            return str;
+        if (str.startsWith('rgb(') && str.endsWith(')')) {
+            return str
+        }
+        if (str.startsWith('#') && str.length < 8) {
+            return str
+        }
+
+        // See if string is a recognized web color
+        const hex = this.colorNameToHex(str);
+        if (hex) {
+            return hex
+        }
+
+        // UCSC format (e.g.  0,0,255)
+        const tokens = str.split(",");
+        if (tokens.length === 3 && isColorComponent(tokens[0]) && isColorComponent(tokens[1]) && isColorComponent(tokens[2])) {
+            return `rgb(${str})`
         }
     },
 
@@ -19520,8 +19546,8 @@ const IGVColor = {
 
         let src;
         let hexColor = this.colorNameToHex(color);
-        if(hexColor) {
-            src  = IGVColor.hexToRgb(hexColor);
+        if (hexColor) {
+            src = IGVColor.hexToRgb(hexColor);
         } else {
             src = color.startsWith('rgb(') ? color : IGVColor.hexToRgb(color);
         }
@@ -19532,7 +19558,7 @@ const IGVColor = {
         const g = Math.max(0, Math.min(255, Number.parseInt(components[1].trim()) + amt));
         const b = Math.max(0, Math.min(255, Number.parseInt(components[2].trim()) + amt));
 
-        return 'rgb(' + r.toString() + ',' + g.toString() + ',' + b.toString() + ')';
+        return 'rgb(' + r.toString() + ',' + g.toString() + ',' + b.toString() + ')'
 
     },
 
@@ -19691,10 +19717,15 @@ const IGVColor = {
             "lightslategrey": "#778899",
             "slategrey": "#708090"
         };
-        return definedColorNames[colorName];
+        return definedColorNames[colorName]
     }
 };
 
+function isColorComponent(str) {
+    const num = Number.parseInt(str);
+    return !Number.isNaN(num) && num >= 0 && num <= 255
+}
+
 // Support for oauth token based authorization
 // This class supports explicit setting of an oauth token either globally or for specific hosts.
 //
@@ -19921,7 +19952,7 @@ async function init$1(config) {
 
     // Note: callback is added when accessToken is requested
     const codeClientConfig = {
-        client_id: config.client_id,
+        client_id: config.client_id || config.clientId,
         scope: config.scope || 'https://www.googleapis.com/auth/userinfo.profile',
         state: config.state || 'igv',
         error: (err) => {
@@ -20001,7 +20032,7 @@ async function getAccessToken(scope) {
 
 function getScopeForURL(url) {
     if (isGoogleDriveURL(url)) {
-        return "https://www.googleapis.com/auth/drive.readonly"
+        return "https://www.googleapis.com/auth/drive.file"
     } else if (isGoogleStorageURL(url)) {
         return "https://www.googleapis.com/auth/devstorage.read_only"
     } else {
@@ -20237,6 +20268,24 @@ class IGVXhr {
         }
     }
 
+    /**
+     * A wrapper around loadArrayBuffer that inflates gzipped data
+     * @param url
+     * @param options
+     * @returns {Promise<Uint8Array>}
+     */
+     async loadByteArray(url, options) {
+        const arraybuffer = await this.loadArrayBuffer(url, options);
+        let plain;
+        if (isgzipped(arraybuffer)) {
+            plain = ungzip_blocks(arraybuffer);
+        } else {
+            plain = new Uint8Array(arraybuffer);
+        }
+        return plain
+    }
+
+
     async loadJson(url, options) {
         options = options || {};
         const method = options.method || (options.sendData ? "POST" : "GET");
@@ -20407,7 +20456,7 @@ class IGVXhr {
                     }
                 } else if (xhr.status === 416) {
                     handleError(Error(`416 Unsatisfiable Range`));
-                } else if ((typeof gapi !== "undefined") &&
+                } else if (isInitialized() &&
                     ((xhr.status === 404 || xhr.status === 401 || xhr.status === 403) &&
                         isGoogleURL(url)) &&
                     !options.retries) {
@@ -25616,7 +25665,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.15.11";
+const _version = "2.15.13";
 function version() {
     return _version
 }
@@ -41910,11 +41959,7 @@ function renderFeatureLabel(ctx, feature, featureX, featureX1, featureY, referen
         if (name === undefined) name = feature.id || feature.ID;
         if (!name || name === '.') return
 
-
-        let pixelXOffset = options.pixelXOffset || 0;
-        const t1 = Math.max(featureX, -pixelXOffset);
-        const t2 = Math.min(featureX1, -pixelXOffset + options.viewportWidth);
-        let centerX = (t1 + t2) / 2;
+        let centerX = (featureX + featureX1) / 2;
 
         let transform;
         if (this.displayMode === "COLLAPSED" && this.labelDisplayMode === "SLANT") {
@@ -51290,6 +51335,13 @@ class BlobFile {
     }
 }
 
+var __defProp = Object.defineProperty;
+var __defNormalProp = (obj, key, value) => key in obj ? __defProp(obj, key, { enumerable: true, configurable: true, writable: true, value }) : obj[key] = value;
+var __publicField = (obj, key, value) => {
+  __defNormalProp(obj, typeof key !== "symbol" ? key + "" : key, value);
+  return value;
+};
+
 // esm/core.js
 async function _unpack_struct_from_async(structure, async_buf, offset = 0) {
   var output = /* @__PURE__ */ new Map();
@@ -51406,7 +51458,7 @@ var Struct = class {
     return big_endian;
   }
   async unpack_from_async(fmt, async_buf, offset) {
-    var offset = Number(offset || 0);
+    offset = Number.parseInt(offset || 0);
     const total_size = this.calcsize(fmt);
     const local_buffer = await async_buf.slice(offset, offset + total_size);
     let local_offset = 0;
@@ -51433,7 +51485,7 @@ var Struct = class {
     return output;
   }
   unpack_from(fmt, buffer, offset) {
-    var offset = Number(offset || 0);
+    offset = Number.parseInt(offset || 0);
     const total_size = this.calcsize(fmt);
     const local_buffer = buffer.slice(offset, offset + total_size);
     let local_offset = 0;
@@ -51471,7 +51523,7 @@ var DataView64 = class extends DataView {
     const left = BigInt(this.getUint32(byteOffset, littleEndian));
     const right = BigInt(this.getUint32(byteOffset + 4, littleEndian));
     let combined = littleEndian ? left + (right << 32n) : (left << 32n) + right;
-    return Number(combined);
+    return Number.parseInt(combined);
   }
   getInt64(byteOffset, littleEndian) {
     var low, high;
@@ -51483,7 +51535,7 @@ var DataView64 = class extends DataView {
       low = this.getUint32(byteOffset + 4, false);
     }
     let combined = BigInt(low) + (BigInt(high) << 32n);
-    return Number(combined);
+    return Number.parseInt(combined);
   }
   getString(byteOffset, littleEndian, length) {
     const str_buffer = this.buffer.slice(byteOffset, byteOffset + length);
@@ -53936,14 +53988,17 @@ var AbstractBTree = class {
   }
 };
 var BTreeV1 = class extends AbstractBTree {
-  B_LINK_NODE = /* @__PURE__ */ new Map([
-    ["signature", "4s"],
-    ["node_type", "B"],
-    ["node_level", "B"],
-    ["entries_used", "H"],
-    ["left_sibling", "Q"],
-    ["right_sibling", "Q"]
-  ]);
+  constructor() {
+    super(...arguments);
+    __publicField(this, "B_LINK_NODE", /* @__PURE__ */ new Map([
+      ["signature", "4s"],
+      ["node_type", "B"],
+      ["node_level", "B"],
+      ["entries_used", "H"],
+      ["left_sibling", "Q"],
+      ["right_sibling", "Q"]
+    ]));
+  }
   async _read_node_header(offset, node_level) {
     let node = await _unpack_struct_from_async(this.B_LINK_NODE, this.fh, offset);
     if (node_level != null) {
@@ -53955,9 +54010,9 @@ var BTreeV1 = class extends AbstractBTree {
   }
 };
 var BTreeV1Groups = class extends BTreeV1 {
-  NODE_TYPE = 0;
   constructor(fh, offset) {
     super(fh, offset);
+    __publicField(this, "NODE_TYPE", 0);
     this.ready = this.init();
   }
   async _read_node(offset, node_level) {
@@ -53989,9 +54044,9 @@ var BTreeV1Groups = class extends BTreeV1 {
   }
 };
 var BTreeV1RawDataChunks = class extends BTreeV1 {
-  NODE_TYPE = 1;
   constructor(fh, offset, dims) {
     super(fh, offset);
+    __publicField(this, "NODE_TYPE", 1);
     this.dims = dims;
     this.ready = this.init();
   }
@@ -54030,7 +54085,7 @@ var BTreeV1RawDataChunks = class extends BTreeV1 {
         if (size != 8) {
           throw "NotImplementedError('Unsupported Reference type')";
         }
-        var dtype = "<u8";
+        dtype = "<u8";
         item_getter = "getUint64";
         item_big_endian = false;
         item_size = 8;
@@ -54137,26 +54192,26 @@ var BTreeV1RawDataChunks = class extends BTreeV1 {
   }
 };
 var BTreeV2 = class extends AbstractBTree {
-  B_TREE_HEADER = /* @__PURE__ */ new Map([
-    ["signature", "4s"],
-    ["version", "B"],
-    ["node_type", "B"],
-    ["node_size", "I"],
-    ["record_size", "H"],
-    ["depth", "H"],
-    ["split_percent", "B"],
-    ["merge_percent", "B"],
-    ["root_address", "Q"],
-    ["root_nrecords", "H"],
-    ["total_nrecords", "Q"]
-  ]);
-  B_LINK_NODE = /* @__PURE__ */ new Map([
-    ["signature", "4s"],
-    ["version", "B"],
-    ["node_type", "B"]
-  ]);
   constructor(fh, offset) {
     super(fh, offset);
+    __publicField(this, "B_TREE_HEADER", /* @__PURE__ */ new Map([
+      ["signature", "4s"],
+      ["version", "B"],
+      ["node_type", "B"],
+      ["node_size", "I"],
+      ["record_size", "H"],
+      ["depth", "H"],
+      ["split_percent", "B"],
+      ["merge_percent", "B"],
+      ["root_address", "Q"],
+      ["root_nrecords", "H"],
+      ["total_nrecords", "Q"]
+    ]));
+    __publicField(this, "B_LINK_NODE", /* @__PURE__ */ new Map([
+      ["signature", "4s"],
+      ["version", "B"],
+      ["node_type", "B"]
+    ]));
     this.ready = this.init();
   }
   async _read_root_node() {
@@ -54282,7 +54337,10 @@ var BTreeV2 = class extends AbstractBTree {
   }
 };
 var BTreeV2GroupNames = class extends BTreeV2 {
-  NODE_TYPE = 5;
+  constructor() {
+    super(...arguments);
+    __publicField(this, "NODE_TYPE", 5);
+  }
   async _parse_record(buf, offset, size) {
     let namehash = (await struct.unpack_from_async("<I", buf, offset))[0];
     offset += 4;
@@ -54291,7 +54349,10 @@ var BTreeV2GroupNames = class extends BTreeV2 {
   }
 };
 var BTreeV2GroupOrders = class extends BTreeV2 {
-  NODE_TYPE = 6;
+  constructor() {
+    super(...arguments);
+    __publicField(this, "NODE_TYPE", 6);
+  }
   async _parse_record(buf, offset, size) {
     let creationorder = (await struct.unpack_from_async("<Q", buf, offset))[0];
     offset += 8;
@@ -55725,8 +55786,11 @@ var Dataset = class extends Array {
   }
   async getValue(data) {
     const dtype = await this.dtype;
-    if (dtype.startsWith("S")) {
-      return (await data).map((s) => s.substr(0, s.indexOf("\0")));
+    if ((typeof dtype === "string" || dtype instanceof String) && dtype.startsWith("S")) {
+      return (await data).map((s) => {
+        let idx = s.indexOf("\0");
+        return idx >= 0 ? s.substring(0, idx) : s;
+      });
     } else {
       return data;
     }