igv 2.15.6 → 2.15.8

package/dist/igv.js

@@ -9681,6 +9681,7 @@
                 menuItems.push(unsetColorMenuItem({trackView, label: "Unset track color"}));
                if(trackView.track.config.type === 'wig' || trackView.track.config.type === 'annotation') {
                    menuItems.push(colorPickerMenuItem({trackView, label: "Set alt color", option: "altColor"}));
+                   menuItems.push(unsetAltColorMenuItem({trackView, label: "Unset alt color"}));
                }
             }
 
@@ -9882,6 +9883,20 @@
         }
     }
 
+    function unsetAltColorMenuItem({trackView, label}) {
+
+        const $e = $$1('<div>');
+        $e.text(label);
+
+        return {
+            object: $e,
+            click: () => {
+                trackView.track.altColor = undefined;
+                trackView.repaintViews();
+            }
+        }
+    }
+
     function trackRenameMenuItem(trackView) {
 
         const click = e => {
@@ -18665,7 +18680,6 @@
 
             const self = this;
 
-            //console.log(`${Date.now()}   ${url}`)
             url = mapUrl$1(url);
 
             options = options || {};
@@ -18715,7 +18729,10 @@
                 }
 
                 if (range) {
-                    var rangeEnd = range.size ? range.start + range.size - 1 : "";
+                    let rangeEnd = "";
+                    if (range.size) {
+                        rangeEnd = 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
                 }
@@ -18741,20 +18758,34 @@
                 }
 
                 xhr.onload = async function (event) {
-                    // when the url points to a local file, the status is 0 but that is not an error
+
+                    // when the url points to a local file, the status is 0
                     if (xhr.status === 0 || (xhr.status >= 200 && xhr.status <= 300)) {
-                        if (range && xhr.status !== 206 && range.start !== 0) {
-                            // For small files a range starting at 0 can return the whole file => 200
-                            // Provide just the slice we asked for, throw out the rest quietly
-                            // If file is large warn user
-                            if (xhr.response.length > 100000 && !self.RANGE_WARNING_GIVEN) {
-                                alert(`Warning: Range header ignored for URL: ${url}.  This can have severe performance impacts.`);
+                        if ("HEAD" === options.method) {
+                            // Support fetching specific headers.  Attempting to fetch all headers can be problematic with CORS
+                            const headers = options.requestedHeaders || ['content-length'];
+                            const headerMap = {};
+                            for (let h of headers) {
+                                headerMap[h] = xhr.getResponseHeader(h);
                             }
-                            resolve(xhr.response.slice(range.start, range.start + range.size));
-
+                            resolve(headerMap);
                         } else {
-                            resolve(xhr.response);
+                            // Assume "GET" or "POST"
+                            if (range && xhr.status !== 206 && range.start !== 0) {
+
+                                // For small files a range starting at 0 can return the whole file => 200
+                                // Provide just the slice we asked for, throw out the rest quietly
+                                // If file is large warn user
+                                if (xhr.response.length > 100000 && !self.RANGE_WARNING_GIVEN) {
+                                    alert(`Warning: Range header ignored for URL: ${url}.  This can have severe performance impacts.`);
+                                }
+                                resolve(xhr.response.slice(range.start, range.start + range.size));
+                            } else {
+                                resolve(xhr.response);
+                            }
                         }
+                    } else if (xhr.status === 416) {
+                        handleError(Error(`416 Unsatisfiable Range`));
                     } else if ((typeof gapi !== "undefined") &&
                         ((xhr.status === 404 || xhr.status === 401 || xhr.status === 403) &&
                             isGoogleURL(url)) &&
@@ -18764,9 +18795,6 @@
                     } else {
                         if (xhr.status === 403) {
                             handleError("Access forbidden: " + url);
-                        } else if (xhr.status === 416) {
-                            //  Tried to read off the end of the file.   This shouldn't happen, but if it does return an
-                            handleError("Unsatisfiable range");
                         } else {
                             handleError(xhr.status);
                         }
@@ -18898,6 +18926,24 @@
                 }
             }
         }
+
+        /**
+         * This method should only be called when it is known the server supports HEAD requests.  It is used to recover
+         * from 416 errors from out-of-spec WRT range request servers.  Notably Globus.
+         * * *
+         * @param url
+         * @param options
+         * @returns {Promise<unknown>}
+         */
+        async getContentLength(url, options) {
+            options = options || {};
+            options.method = 'HEAD';
+            options.requestedHeaders = ['content-length'];
+            const headerMap = await this._loadURL(url, options);
+            const contentLengthString = headerMap['content-length'];
+            return contentLengthString ? Number.parseInt(contentLengthString) : 0
+        }
+
     }
 
     function isGoogleStorageSigned(url) {
@@ -21107,6 +21153,10 @@
 
     }
 
+    function registerFileFormats(name, fields) {
+        FileFormats[name] = {fields: fields};
+    }
+
     var TrackUtils = /*#__PURE__*/Object.freeze({
         __proto__: null,
         knownFileExtensions: knownFileExtensions,
@@ -21114,7 +21164,8 @@
         inferFileFormat: inferFileFormat,
         inferFileFormatFromHeader: inferFileFormatFromHeader,
         inferTrackType: inferTrackType,
-        inferIndexPath: inferIndexPath
+        inferIndexPath: inferIndexPath,
+        registerFileFormats: registerFileFormats
     });
 
     const pairs =
@@ -23944,7 +23995,7 @@
         }
     };
 
-    const _version = "2.15.6";
+    const _version = "2.15.8";
     function version() {
         return _version
     }
@@ -27083,10 +27134,10 @@
 
         static defaults = {
             height: 50,
-            color: 'rgb(0, 0, 150)',
-            altColor: 'rgb(0, 0, 150)',
             autoHeight: false,
-            visibilityWindow: undefined,
+            visibilityWindow: undefined,   // Identifies property that should be copied from config
+            color: undefined,  // Identifies property that should be copied from config
+            altColor: undefined,  // Identifies property that should be copied from config
             supportHiDPI: true
         }
 
@@ -31956,6 +32007,7 @@
                 this.queryable = true;
             } else if ("htsget" === config.sourceType) {
                 this.reader = new HtsgetVariantReader(config, genome);
+                this.queryable = true;
             } else if (config.sourceType === 'ucscservice') {
                 this.reader = new UCSCServiceReader(config.source);
                 this.queryable = true;
@@ -32169,30 +32221,45 @@
          * @param fulfill - function to receive result
          * @param asUint8 - optional flag to return result as an UInt8Array
          */
-        async dataViewForRange(requestedRange, asUint8) {
+        async dataViewForRange(requestedRange, asUint8, retries = 0) {
+            try {
 
-            const hasData = (this.data && (this.range.start <= requestedRange.start) &&
-                ((this.range.start + this.range.size) >= (requestedRange.start + requestedRange.size)));
+                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 (!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;
                 }
-                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)
+                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
+                }
+            }
         }
     }
 
@@ -40401,6 +40468,9 @@
         }
     }
 
+    const DEFAULT_COLOR$2 = 'rgb(0, 0, 150)';
+
+
     class FeatureTrack extends TrackBase {
 
         static defaults = {
@@ -40832,8 +40902,11 @@
                 color = this.colorTable.getColor(value);
             } else if (feature.color) {
                 color = feature.color;   // Explicit color for feature
-            } else {
-                color = this.color;   // Track default
+            }
+
+            // If no explicit setting use the default
+            if (!color) {
+                color = DEFAULT_COLOR$2;   // Track default
             }
 
             if (feature.alpha && feature.alpha !== 1) {
@@ -41418,8 +41491,6 @@
             showAllBases: false,
             showInsertions: true,
             showMismatches: true,
-            color: DEFAULT_ALIGNMENT_COLOR,
-            coverageColor: DEFAULT_COVERAGE_COLOR,
             height: 300,
             coverageTrackHeight: 50
         }
@@ -41439,6 +41510,10 @@
 
             this.alignmentTrack.setTop(this.coverageTrack, this.showCoverage);
 
+            if(!this.showAlignments) {
+                this._height = this.coverageTrackHeight;
+            }
+
             // The sort object can be an array in the case of multi-locus view, however if multiple sort positions
             // are present for a given reference frame the last one will take precedence
             if (config.sort) {
@@ -41915,15 +41990,6 @@
             }
             const chords = makePairedAlignmentChords(inView);
             sendChords(chords, this, refFrame, 0.02);
-
-            // const chordSetColor = IGVColor.addAlpha("all" === refFrame.chr ? this.color : getChrColor(refFrame.chr), 0.02)
-            // const trackColor = IGVColor.addAlpha(this.color || 'rgb(0,0,255)', 0.02)
-            //
-            // // name the chord set to include track name and locus
-            // const encodedName = this.name.replaceAll(' ', '%20')
-            // const chordSetName = "all" === refFrame.chr ? encodedName :
-            //     `${encodedName} (${refFrame.chr}:${refFrame.start}-${refFrame.end}`
-            // this.browser.circularView.addChords(chords, {name: chordSetName, color: chordSetColor, trackColor: trackColor})
         }
 
         addSplitChordsForViewport(viewport) {
@@ -41940,15 +42006,6 @@
 
             const chords = makeSupplementalAlignmentChords(inView);
             sendChords(chords, this, refFrame, 0.02);
-
-            // const chordSetColor = IGVColor.addAlpha("all" === refFrame.chr ? this.color : getChrColor(refFrame.chr), 0.02)
-            // const trackColor = IGVColor.addAlpha(this.color || 'rgb(0,0,255)', 0.02)
-            //
-            // // name the chord set to include track name and locus
-            // const encodedName = this.name.replaceAll(' ', '%20')
-            // const chordSetName = "all" === refFrame.chr ? encodedName :
-            //     `${encodedName} (${refFrame.chr}:${refFrame.start}-${refFrame.end}`
-            // this.browser.circularView.addChords(chords, {name: chordSetName, color: chordSetColor, trackColor: trackColor})
         }
     }
 
@@ -42005,7 +42062,7 @@
             let color;
             if (this.parent.coverageColor) {
                 color = this.parent.coverageColor;
-            } else if (this.parent.color !== undefined && typeof this.parent.color !== "function") {
+            } else if (this.parent.color  && typeof this.parent.color !== "function") {
                 color = IGVColor.darkenLighten(this.parent.color, -35);
             } else {
                 color = DEFAULT_COVERAGE_COLOR;
@@ -42846,8 +42903,9 @@
                 case "tag":
                     if (this.parent.color) {
                         return (typeof this.parent.color === "function") ? this.parent.color(alignment) : this.parent.color
+                    } else {
+                        return DEFAULT_CONNECTOR_COLOR
                     }
-                    return DEFAULT_CONNECTOR_COLOR
                 default:
                     return this.getAlignmentColor(alignment)
 
@@ -42859,6 +42917,8 @@
             let color = DEFAULT_ALIGNMENT_COLOR;   // The default color if nothing else applies
             if (this.parent.color) {
                 color = (typeof this.parent.color === "function") ? this.parent.color(alignment) : this.parent.color;
+            } else {
+                color = DEFAULT_ALIGNMENT_COLOR;
             }
             const option = this.colorBy;
             switch (option) {
@@ -44670,12 +44730,12 @@
      * THE SOFTWARE.
      */
 
+    const DEFAULT_COLOR$1 = 'rgb(150, 150, 150)';
+
     class WigTrack extends TrackBase {
 
         static defaults = {
             height: 50,
-            color: 'rgb(150, 150, 150)',
-            altColor: 'rgb(150, 150, 150)',
             flipAxis: false,
             logScale: false,
             windowFunction: 'mean',
@@ -44808,7 +44868,7 @@
             const pixelWidth = options.pixelWidth;
             options.pixelHeight;
             const bpEnd = bpStart + pixelWidth * bpPerPixel + 1;
-            const posColor = this.color || WigTrack.defaults.color;
+            const posColor = this.color || DEFAULT_COLOR$1;
 
             let baselineColor;
             if (typeof posColor === "string" && posColor.startsWith("rgb(")) {
@@ -44952,7 +45012,7 @@
          */
 
         getColorForFeature(f) {
-            let c = (f.value < 0 && this.altColor) ? this.altColor : this.color || WigTrack.defaults.color;
+            let c = (f.value < 0 && this.altColor) ? this.altColor : this.color || DEFAULT_COLOR$1;
             return (typeof c === "function") ? c(f.value) : c
         }
 
@@ -46680,7 +46740,7 @@
 
     const isString = isString$2;
 
-
+    const DEFAULT_COLOR = "rgb(0,0,150)";
     const DEFAULT_VISIBILITY_WINDOW = 1000000;
     const TOP_MARGIN = 10;
     const STANDARD_FIELDS = new Map([["REF", "referenceBases"], ["ALT", "alternateBases"], ["QUAL", "quality"], ["FILTER", "filter"]]);
@@ -46730,6 +46790,7 @@
                 this.colorTables = new Map();
                 this.colorTables.set(config.colorBy, new ColorTable(config.colorTable));
             }
+            this._color = config.color;
             this._strokecolor = config.strokecolor;
             this._context_hook = config.context_hook;
 
@@ -46762,7 +46823,7 @@
         }
 
         get color() {
-            return this._color
+            return this._color || DEFAULT_COLOR
         }
 
         set color(c) {
@@ -62103,7 +62164,8 @@
         setOauthToken,
         oauth,
         version,
-        setApiKey
+        setApiKey,
+        registerFileFormats
     };
 
     return index;