igv 2.15.11 → 2.15.13

package/dist/igv.js

@@ -19246,7 +19246,7 @@
      */
 
     function _random(min, max) {
-        return Math.random() * (max - min) + min;
+        return Math.random() * (max - min) + min
     }
 
     const IGVColor = {
@@ -19266,7 +19266,7 @@
             accumulation.pop();
             accumulation.push(IGVColor.rgbColor(16, 16, 16));
 
-            return accumulation;
+            return accumulation
         },
 
         rgbToHex: function (rgb) {
@@ -19274,7 +19274,7 @@
             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) {
@@ -19282,10 +19282,10 @@
             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) + ")"
         },
 
         /**
@@ -19313,25 +19313,25 @@
             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)]
         },
 
         /**
@@ -19363,16 +19363,16 @@
                 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) {
@@ -19382,7 +19382,7 @@
             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) {
@@ -19391,14 +19391,14 @@
             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) {
@@ -19408,7 +19408,7 @@
 
             var g = Math.round(_random(min, max)).toString(10);
 
-            return "rgb(" + g + "," + g + "," + g + ")";
+            return "rgb(" + g + "," + g + "," + g + ")"
         },
 
         randomRGB: function (min, max) {
@@ -19420,7 +19420,7 @@
             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) {
@@ -19432,12 +19432,12 @@
             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);
@@ -19450,7 +19450,7 @@
 
             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) {
@@ -19458,38 +19458,37 @@
             }
 
             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")
             }
         },
 
@@ -19506,19 +19505,46 @@
                 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})`
             }
         },
 
@@ -19526,8 +19552,8 @@
 
             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);
             }
@@ -19538,7 +19564,7 @@
             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() + ')'
 
         },
 
@@ -19697,10 +19723,15 @@
                 "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.
     //
@@ -19927,7 +19958,7 @@
 
         // 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) => {
@@ -20007,7 +20038,7 @@
 
     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 {
@@ -20243,6 +20274,24 @@
             }
         }
 
+        /**
+         * 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");
@@ -20413,7 +20462,7 @@
                         }
                     } 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) {
@@ -25622,7 +25671,7 @@
         }
     };
 
-    const _version = "2.15.11";
+    const _version = "2.15.13";
     function version() {
         return _version
     }
@@ -41916,11 +41965,7 @@
             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") {
@@ -51296,6 +51341,13 @@
         }
     }
 
+    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();
@@ -51412,7 +51464,7 @@
         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;
@@ -51439,7 +51491,7 @@
         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;
@@ -51477,7 +51529,7 @@
         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;
@@ -51489,7 +51541,7 @@
           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);
@@ -53942,14 +53994,17 @@
       }
     };
     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) {
@@ -53961,9 +54016,9 @@
       }
     };
     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) {
@@ -53995,9 +54050,9 @@
       }
     };
     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();
       }
@@ -54036,7 +54091,7 @@
             if (size != 8) {
               throw "NotImplementedError('Unsupported Reference type')";
             }
-            var dtype = "<u8";
+            dtype = "<u8";
             item_getter = "getUint64";
             item_big_endian = false;
             item_size = 8;
@@ -54143,26 +54198,26 @@
       }
     };
     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() {
@@ -54288,7 +54343,10 @@
       }
     };
     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;
@@ -54297,7 +54355,10 @@
       }
     };
     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;
@@ -55731,8 +55792,11 @@
       }
       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;
         }