igv 3.7.1 → 3.7.3

package/dist/igv.js

@@ -10638,7 +10638,7 @@
        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,
@@ -10945,7 +10945,7 @@
    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
@@ -11291,6 +11291,12 @@
          }
          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;
@@ -14765,13 +14771,12 @@
 
    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);
        }
@@ -14786,7 +14791,7 @@
    }
 
    function isCoding(type) {
-       return cdsTypes.has(type) || codonTypes.has(type)
+       return cdsTypes.has(type)
    }
 
    function isUTR(type) {
@@ -14966,12 +14971,17 @@
            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);
            }
 
@@ -14983,6 +14993,11 @@
            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;
@@ -15003,7 +15018,10 @@
                    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;
                    }
                }
@@ -31918,7 +31936,7 @@
            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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+       "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F378a1641-5894-475e-8614-bd016e8529d5%2F4DNFIMBPX8Q1.hic": "17880333903,22663"
    };
 
    const isNode = typeof process !== 'undefined' && process.versions != null && process.versions.node != null;
@@ -34010,6 +34187,8 @@
            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) {
@@ -34029,9 +34208,9 @@
                }
            } 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");
            }
        }
 
@@ -34056,15 +34235,15 @@
                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() {
@@ -34072,13 +34251,13 @@
            // 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();
 
@@ -34087,7 +34266,7 @@
            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;
@@ -34172,7 +34351,7 @@
                "version": this.version,
                "genome": this.genomeId,
                "chromosomes": this.chromosomes,
-               "resolutions": this.bpResolutions,
+               "resolutions": this.bpResolutions
            };
 
 
@@ -34280,14 +34459,14 @@
                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);
@@ -34310,7 +34489,7 @@
 
            const blocks = await this.getBlocks(region1, region2, units, binsize);
            if (!blocks || blocks.length === 0) {
-               return []
+               return [];
            }
 
            const contactRecords = [];
@@ -34376,23 +34555,23 @@
 
            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);
@@ -34423,7 +34602,7 @@
            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) {
@@ -34536,7 +34715,7 @@
 
            const index = normVectorIndex[key];
 
-           return undefined !== index
+           return undefined !== index;
 
        }
 
@@ -34562,20 +34741,20 @@
 
            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];
@@ -34602,37 +34781,44 @@
                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() {
@@ -34822,9 +35008,9 @@
 
        getFileChrName(chrAlias) {
            if (this.chrAliasTable.hasOwnProperty(chrAlias)) {
-               return this.chrAliasTable[chrAlias]
+               return this.chrAliasTable[chrAlias];
            } else {
-               return chrAlias
+               return chrAlias;
            }
        }
 
@@ -34853,7 +35039,7 @@
    }
 
    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 {
@@ -35592,6 +35778,11 @@
            }
 
            if (remainder) {
+
+               if (!riteExon) {
+                   return undefined
+               }
+
                stringA = sequenceInterval.getSequence(remainder.start, remainder.end);
 
                if (!stringA) {
@@ -50365,19 +50556,26 @@
 
    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
@@ -76482,7 +76680,7 @@ ${indent}columns: ${matrix.columns}
        })
    }
 
-   const _version = "3.7.1";
+   const _version = "3.7.3";
    function version() {
        return _version
    }
@@ -76546,10 +76744,13 @@ ${indent}columns: ${matrix.columns}
                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
@@ -79135,6 +79336,15 @@ ${indent}columns: ${matrix.columns}
            }
        }
 
+       /**
+        * 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();
@@ -79482,7 +79692,7 @@ ${indent}columns: ${matrix.columns}
            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;
        }
 
 
@@ -80784,7 +80994,7 @@ ${indent}columns: ${matrix.columns}
                }
            }
 
-           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
@@ -81001,6 +81211,15 @@ ${indent}columns: ${matrix.columns}
            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.
@@ -81010,31 +81229,33 @@ ${indent}columns: ${matrix.columns}
         */
        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);