igv 3.7.1 → 3.7.3

package/dist/igv.esm.js

@@ -10632,7 +10632,7 @@ function createMenuElements$1(itemList, popover) {
     return list;
 }
 
-/*! @license DOMPurify 3.3.0 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.0/LICENSE */
+/*! @license DOMPurify 3.3.1 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.1/LICENSE */
 
 const {
   entries,
@@ -10939,7 +10939,7 @@ const _createHooksMap = function _createHooksMap() {
 function createDOMPurify() {
   let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
   const DOMPurify = root => createDOMPurify(root);
-  DOMPurify.version = '3.3.0';
+  DOMPurify.version = '3.3.1';
   DOMPurify.removed = [];
   if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document || !window.Element) {
     // Not running in a browser, provide a factory function
@@ -11285,6 +11285,12 @@ function createDOMPurify() {
       }
       addToSet(FORBID_CONTENTS, cfg.FORBID_CONTENTS, transformCaseFunc);
     }
+    if (cfg.ADD_FORBID_CONTENTS) {
+      if (FORBID_CONTENTS === DEFAULT_FORBID_CONTENTS) {
+        FORBID_CONTENTS = clone(FORBID_CONTENTS);
+      }
+      addToSet(FORBID_CONTENTS, cfg.ADD_FORBID_CONTENTS, transformCaseFunc);
+    }
     /* Add #text in case KEEP_CONTENT is set to true */
     if (KEEP_CONTENT) {
       ALLOWED_TAGS['#text'] = true;
@@ -14759,13 +14765,12 @@ function stripQuotes$1(value) {
 
 const transcriptTypes = new Set(['transcript', 'primary_transcript', 'processed_transcript', 'mRNA', 'mrna',
     'lnc_RNA', 'miRNA', 'ncRNA', 'rRNA', 'scRNA', 'snRNA', 'snoRNA', 'tRNA']);
-const cdsTypes = new Set(['CDS', 'cds']);
-const codonTypes = new Set(['start_codon', 'stop_codon']);
+const cdsTypes = new Set(['CDS', 'cds', 'start_codon', 'stop_codon']);
 const utrTypes = new Set(['5UTR', '3UTR', 'UTR', 'five_prime_UTR', 'three_prime_UTR', "3'-UTR", "5'-UTR"]);
 const exonTypes = new Set(['exon', 'coding-exon']);
 
 const transcriptPartTypes = new Set();
-for (let cltn of [cdsTypes, codonTypes, utrTypes, exonTypes]) {
+for (let cltn of [cdsTypes, utrTypes, exonTypes]) {
     for (let t of cltn) {
         transcriptPartTypes.add(t);
     }
@@ -14780,7 +14785,7 @@ function isIntron(type) {
 }
 
 function isCoding(type) {
-    return cdsTypes.has(type) || codonTypes.has(type)
+    return cdsTypes.has(type)
 }
 
 function isUTR(type) {
@@ -14960,12 +14965,17 @@ class GFFTranscript extends GFFFeature {
         if (exon) {
             exon.cdStart = exon.cdStart ? Math.min(cds.start, exon.cdStart) : cds.start;
             exon.cdEnd = exon.cdEnd ? Math.max(cds.end, exon.cdEnd) : cds.end;
-            exon.readingFrame = cds.readingFrame;
-            // TODO -- merge attributes?
+            if (cds.readingFrame !== undefined) {
+                if (exon.readingFrame === undefined) {
+                    exon.readingFrame = cds.readingFrame;
+                } else {
+                    // Keep reading frame of first CDS in direction of transcription
+                    if (this.strand === '+') ; else {
+                        exon.readingFrame = cds.readingFrame;
+                    }
+                }
+            }
         } else {
-            // cds.cdStart = cds.start
-            // cds.cdEnd = cds.end
-            // exons.push(cds)
             console.error("No exon found spanning " + cds.start + "-" + cds.end);
         }
 
@@ -14977,6 +14987,11 @@ class GFFTranscript extends GFFFeature {
         this.cdEnd = this.cdEnd ? Math.max(cds.end, this.cdEnd) : cds.end;
     }
 
+    addTerminalCodon(codon) {
+        // Treat terminal codons as CDS
+        this.addCDS(codon);
+    }
+
     addUTR(utr) {
 
         let exon;
@@ -14997,7 +15012,10 @@ class GFFTranscript extends GFFFeature {
                 if (utr.end < exon.end) {
                     exon.cdStart = utr.end;
                 }
-                if (utr.start > exon.start) {
+                // Do not "backup" the cdEnd based on a UTR record.  A stop_codon might extend cdEnd into the UTR, and we
+                // don't want to quash that with the UTR. Although stop codons are not translated, visually
+                // they appear as part exonic coding sequence. This is a long established convention,
+                if (exon.cdEnd === undefined || utr.start > exon.cdEnd) {
                     exon.cdEnd = utr.start;
                 }
             }
@@ -31912,7 +31930,7 @@ class RemoteFile$1 {
         headers['Range'] = rangeString;
 
         let url = this.url.slice();    // slice => copy
-        // headers['User-Agent'] = 'straw'
+        headers['User-Agent'] = 'IGV';
         if (this.config.oauthToken) {
             const token = resolveToken(this.config.oauthToken);
             headers['Authorization'] = `Bearer ${token}`;
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 };
 
 const isNode = typeof process !== 'undefined' && process.versions != null && process.versions.node != null;
@@ -34004,6 +34181,8 @@ class HicFile {
         this.normalizationTypes = ['NONE'];
         this.matrixCache = new LRU$1(10);
         this.blockCache = new BlockCache();
+        this.normVectorIndexPosition = -1;
+        this.normVectorIndexSize = -1;
 
         // args may specify an io.File object, a local path (Node only), or a url
         if (args.file) {
@@ -34023,9 +34202,9 @@ class HicFile {
             }
         } else if (args.path) {
             // path argument, assumed local file
-            throw Error(`path property is deprecated, use NodeLocalFile`)
+            throw Error(`path property is deprecated, use NodeLocalFile`);
         } else {
-            throw Error("Arguments must include file, blob, url, or path")
+            throw Error("Arguments must include file, blob, url, or path");
         }
     }
 
@@ -34050,15 +34229,15 @@ class HicFile {
             const binaryParser = new BinaryParser(new DataView(data));
             this.magic = binaryParser.getString();
             this.version = binaryParser.getInt();
-            return this.version
+            return this.version;
         } else {
-            return this.version
+            return this.version;
         }
     }
 
     async getMetaData() {
         await this.init();
-        return this.meta
+        return this.meta;
     }
 
     async readHeaderAndFooter() {
@@ -34066,13 +34245,13 @@ class HicFile {
         // Read initial fields magic, version, and footer position
         let data = await this.file.read(0, 16);
         if (!data || data.byteLength === 0) {
-            throw Error("File content is empty")
+            throw Error("File content is empty");
         }
         let binaryParser = new BinaryParser(new DataView(data));
         this.magic = binaryParser.getString();
         this.version = binaryParser.getInt();
         if (this.version < 5) {
-            throw Error("Unsupported hic version: " + this.version)
+            throw Error("Unsupported hic version: " + this.version);
         }
         this.footerPosition = binaryParser.getLong();
 
@@ -34081,7 +34260,7 @@ class HicFile {
         await this.readFooter();
 
         const bodyPostion = Object.values(this.masterIndex).reduce((min, currentValue) => {
-            return Math.min(min, currentValue.start)
+            return Math.min(min, currentValue.start);
         }, Number.MAX_VALUE);
 
         const remainingSize = bodyPostion - 16;
@@ -34166,7 +34345,7 @@ class HicFile {
             "version": this.version,
             "genome": this.genomeId,
             "chromosomes": this.chromosomes,
-            "resolutions": this.bpResolutions,
+            "resolutions": this.bpResolutions
         };
 
 
@@ -34274,14 +34453,14 @@ class HicFile {
             chrIdx2 = tmp;
         }
 
-        const key = Matrix$2.getKey(chrIdx1 , chrIdx2);
+        const key = Matrix$2.getKey(chrIdx1, chrIdx2);
         const idx = this.masterIndex[key];
         if (!idx) {
-            return undefined
+            return undefined;
         }
         const data = await this.file.read(idx.start, idx.size);
         if (!data) {
-            return undefined
+            return undefined;
         }
 
         return Matrix$2.parseMatrix(data, this.chromosomes);
@@ -34304,7 +34483,7 @@ class HicFile {
 
         const blocks = await this.getBlocks(region1, region2, units, binsize);
         if (!blocks || blocks.length === 0) {
-            return []
+            return [];
         }
 
         const contactRecords = [];
@@ -34370,23 +34549,23 @@ class HicFile {
 
         if (idx1 === undefined) {
             console.log("No chromosome named: " + region1.chr);
-            return []
+            return [];
         }
         if (idx2 === undefined) {
             console.log("No chromosome named: " + region2.chr);
-            return []
+            return [];
         }
 
         const matrix = await this.getMatrix(idx1, idx2);
         if (!matrix) {
             console.log("No matrix for " + region1.chr + "-" + region2.chr);
-            return []
+            return [];
         }
 
         const zd = matrix.getZoomData(binSize, unit);
         if (!zd) {
-            let msg = `No data avalailble for resolution: ${binSize}  for map ${region1.chr}-${region2.chr}`;
-            throw new Error(msg)
+            let msg = `No data available for resolution: ${binSize}  for map ${region1.chr}-${region2.chr}`;
+            throw new Error(msg);
         }
 
         const blockNumbers = zd.getBlockNumbers(region1, region2, this.version);
@@ -34417,7 +34596,7 @@ class HicFile {
         const idx = await zd.blockIndex.getBlockIndexEntry(blockNumber);
 
         if (!idx) {
-            return undefined
+            return undefined;
         } else {
             let data = await this.file.read(idx.filePosition, idx.size);
             if (!data) {
@@ -34530,7 +34709,7 @@ class HicFile {
 
         const index = normVectorIndex[key];
 
-        return undefined !== index
+        return undefined !== index;
 
     }
 
@@ -34556,20 +34735,20 @@ class HicFile {
 
         if (!normVectorIndex) {
             console.log("Normalization vectors not present in this file");
-            return undefined
+            return undefined;
         }
 
         const status = await this.isNormalizationValueAvailableAtResolution(type, chr, unit, binSize);
 
         if (false === status) {
 
-            const str = `Normalization option ${ type } not available at resolution ${ binSize }. Will use NONE.`;
+            const str = `Normalization option ${type} not available at resolution ${binSize}. Will use NONE.`;
             console.log(str);
 
             if (this.alert) {
                 this.alert(str);
-            } 
-            return undefined
+            }
+            return undefined;
         }
 
         const idx = normVectorIndex[key];
@@ -34596,37 +34775,44 @@ class HicFile {
             return undefined;
         }
 
-        if (!this.normVectorIndex) {
+        if (this.normVectorIndex) {
+            return this.normVectorIndex;
+        }
 
-            // If nvi is not supplied, try reading from remote lambda service
-            if (!this.config.nvi && this.remote && this.url) {
-                const url = new URL(this.url);
-                const key = encodeURIComponent(url.hostname + url.pathname);
-                if(nvi.hasOwnProperty(key)) {
-                    this.config.nvi = nvi[key];
-                }
+
+        // If we know the position of the norm vector index, read it directly.  This is the case for hic v9 files
+        if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
+            const range = {start: this.normVectorIndexPosition, size: this.normVectorIndexSize};
+            return this.readNormVectorIndex(range);
+        }
+
+        // See if nvi (normVector position and size) is provided in config or can be inferred from url
+        if (!this.config.nvi && this.remote && this.url) {
+            const url = new URL(this.url);
+            const key = encodeURIComponent(url.hostname + url.pathname);
+            if (nvi.hasOwnProperty(key)) {
+                this.config.nvi = nvi[key];
             }
+        }
 
-            if (this.config.nvi) {
-                const nviArray = decodeURIComponent(this.config.nvi).split(",");
-                const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
-                return this.readNormVectorIndex(range)
-            } else {
-                try {
-                    await this.readNormExpectedValuesAndNormVectorIndex();
-                    return this.normVectorIndex
-                } catch (e) {
-                    if (e.code === "416" || e.code === 416) {
-                        // This is expected if file does not contain norm vectors
-                        this.normExpectedValueVectorsPosition = undefined;
-                    } else {
-                        console.error(e);
-                    }
+        if (this.config.nvi) {
+            const nviArray = decodeURIComponent(this.config.nvi).split(",");
+            const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
+            return this.readNormVectorIndex(range);
+        } else {
+            try {
+                await this.readNormExpectedValuesAndNormVectorIndex();
+                return this.normVectorIndex;
+            } catch (e) {
+                if (e.code === "416" || e.code === 416) {
+                    // This is expected if file does not contain norm vectors
+                    this.normExpectedValueVectorsPosition = undefined;
+                } else {
+                    console.error(e);
                 }
             }
         }
 
-        return this.normVectorIndex
     }
 
     async getNormalizationOptions() {
@@ -34816,9 +35002,9 @@ class HicFile {
 
     getFileChrName(chrAlias) {
         if (this.chrAliasTable.hasOwnProperty(chrAlias)) {
-            return this.chrAliasTable[chrAlias]
+            return this.chrAliasTable[chrAlias];
         } else {
-            return chrAlias
+            return chrAlias;
         }
     }
 
@@ -34847,7 +35033,7 @@ function getNormalizationVectorKey(type, chrIdx, unit, resolution) {
 }
 
 function isGoogleDrive(url) {
-    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0
+    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0;
 }
 
 class Block {
@@ -35586,6 +35772,11 @@ function getAminoAcidLetterWithExonGap(strand, phase, phaseExtentStart, phaseExt
         }
 
         if (remainder) {
+
+            if (!riteExon) {
+                return undefined
+            }
+
             stringA = sequenceInterval.getSequence(remainder.start, remainder.end);
 
             if (!stringA) {
@@ -50359,19 +50550,26 @@ class AlignmentBlock {
 
 class BamFilter {
     constructor(options) {
-        if (!options) options = {};
-        this.vendorFailed = options.vendorFailed = false !== options.vendorFailed;
-        this.duplicate = options.duplicate = false !== options.duplicate;
+        options = options || {};
+
+        // Default to true unless explicitly set to false
+        this.vendorFailed = options.vendorFailed !== false;
+
+        // Support both 'duplicate' and 'duplicates' as synonyms
+        const duplicateValue = options.duplicate !== undefined ? options.duplicate : options.duplicates;
+        this.duplicate = duplicateValue !== false;
+
         this.secondary = options.secondary || false;
         this.supplementary = options.supplementary || false;
         this.mq = options.mq || 0;
+
         if (options.readgroups) {
             this.readgroups = new Set(options.readgroups);
         }
     }
 
     pass(alignment) {
-        if(!alignment.isMapped()) return false
+        if (!alignment.isMapped()) return false
         if (this.vendorFailed && alignment.isFailsVendorQualityCheck()) return false
         if (this.duplicate && alignment.isDuplicate()) return false
         if (this.secondary && alignment.isSecondary()) return false
@@ -76476,7 +76674,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.7.1";
+const _version = "3.7.3";
 function version() {
     return _version
 }
@@ -76540,10 +76738,13 @@ class ChromosomeSelectWidget {
             genome.wgChromosomeNames.map(nm => genome.getChromosomeDisplayName(nm)) :
             [];
 
+        const alreadyAdded = genome.wgChromosomeNames ? new Set(genome.wgChromosomeNames) : new Set();
+
         if (this.showAllChromosomes && genome.chromosomeNames.length > 1) {
             const exclude = new Set(list);
-            let count = 0;
+            let count = alreadyAdded.size;
             for (let nm of genome.chromosomeNames) {
+                if(alreadyAdded.has(nm)) continue
                 if (++count === 1000) {
                     list.push(maximumSequenceCountExceeded);
                     break
@@ -79129,6 +79330,15 @@ class ChromAliasFile {
         }
     }
 
+    /**
+     * Search for chromosome alias record.  If found, cache results in the alias -> chr map
+     *
+     * An alias record is an object with keys corresponding to the chromosome name set (e.g. "ucsc", "refseq", etc) and
+     * value the corresponding chromosome alias for that name set.
+     *
+     * @param alias - the sequence name or alias
+     * @returns {Promise<any>} promise to resolve to the alias record.
+     */
     async search(alias) {
         if(this.aliasRecordCache.size === 0) {
             await this.loadAliases();
@@ -79476,7 +79686,7 @@ class Genome {
         this.ucscID = config.ucscID || ucsdIDMap.get(this.id) || this.id;
         this.blatDB = config.blatDB || this.ucscID;
         this.name = config.name;
-        this.nameSet = config.nameSet || 'ucsc';
+        this.nameSet = config.nameSet;
     }
 
 
@@ -80778,7 +80988,7 @@ class Browser {
             }
         }
 
-        const genomeOrReference = session.reference || session.genome;
+        const genomeOrReference = session.reference || session.genome || session.genarkAccession;
         if (!genomeOrReference) {
             console.warn("No genome or reference object specified");
             return
@@ -80995,6 +81205,15 @@ class Browser {
         return genome
     }
 
+    async expandGenarkAccession(genarkAccession) {
+
+        const url = convertToHubURL(genarkAccession);
+        const hub = await loadHub(url);
+        const genomeConfig = hub.getGenomeConfig();
+        genomeConfig.nameSet = "ucsc";
+        return genomeConfig
+    }
+
     /**
      * Load a genome, defined by a string ID or a json-like configuration object. This includes a fasta reference
      * as well as optional cytoband and annotation tracks.
@@ -81004,31 +81223,33 @@ class Browser {
      */
     async loadGenome(idOrConfig) {
 
-        if (idOrConfig.genarkAccession) {
-            idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
-        }
+        let genomeConfig;
 
-        // Translate the generic "url" field, used by clients such as igv-webapp
-        if (idOrConfig.url) {
-            if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
-                idOrConfig.hubURL = idOrConfig.url;
-                delete idOrConfig.url;
-            } else if ("gbk" === getFileExtension(idOrConfig.url)) {
-                idOrConfig.gbkURL = idOrConfig.url;
-                delete idOrConfig.url;
+        if (idOrConfig.genarkAccession) {
+            genomeConfig = await this.expandGenarkAccession(idOrConfig.genarkAccession);
+        } else {
+            // Translate the generic "url" field, used by clients such as igv-webapp
+            if (idOrConfig.url) {
+                if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
+                    idOrConfig.hubURL = idOrConfig.url;
+                    delete idOrConfig.url;
+                } else if ("gbk" === getFileExtension(idOrConfig.url)) {
+                    idOrConfig.gbkURL = idOrConfig.url;
+                    delete idOrConfig.url;
+                }
             }
-        }
 
-        let genomeConfig;
-        const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
-        if (isHubGenome) {
-            const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
-            genomeConfig = hub.getGenomeConfig();
-        } else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
-            // Either an ID, a json string, or an object missing required properties.
-            genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
-        } else {
-            genomeConfig = idOrConfig;
+
+            const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
+            if (isHubGenome) {
+                const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
+                genomeConfig = hub.getGenomeConfig();
+            } else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
+                // Either an ID, a json string, or an object missing required properties.
+                genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
+            } else {
+                genomeConfig = idOrConfig;
+            }
         }
 
         await this.loadReference(genomeConfig);