igv 2.15.1 → 2.15.3

package/dist/igv.esm.js

@@ -18360,7 +18360,7 @@ async function getAccessToken(scope) {
 
 function getScopeForURL(url) {
     if (isGoogleDriveURL(url)) {
-        return "https://www.googleapis.com/auth/drive.file"
+        return "https://www.googleapis.com/auth/drive.readonly"
     } else if (isGoogleStorageURL(url)) {
         return "https://www.googleapis.com/auth/devstorage.read_only"
     } else {
@@ -18389,7 +18389,8 @@ async function getDriveFileInfo(googleDriveURL) {
     const response = await fetch(endPoint);
     let json = await response.json();
     if (json.error && json.error.code === 404) {
-        const access_token = await getAccessToken("https://www.googleapis.com/auth/drive.readonly");
+        let scope = "https://www.googleapis.com/auth/drive.readonly";
+        const access_token = await getAccessToken(scope);
         if (access_token) {
             const response = await fetch(endPoint, {
                 headers: {
@@ -18656,6 +18657,8 @@ class IGVXhr {
 
     async _loadURL(url, options) {
 
+        const self = this;
+
         //console.log(`${Date.now()}   ${url}`)
         url = mapUrl$1(url);
 
@@ -18745,7 +18748,7 @@ class IGVXhr {
                         // 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 && !this.RANGE_WARNING_GIVEN) {
+                        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));
@@ -18774,8 +18777,9 @@ class IGVXhr {
             xhr.onerror = function (event) {
                 if (isGoogleURL(url) && !options.retries) {
                     tryGoogleAuth();
+                } else {
+                    handleError("Error accessing resource: " + url + " Status: " + xhr.status);
                 }
-                handleError("Error accessing resource: " + url + " Status: " + xhr.status);
             };
 
             xhr.ontimeout = function (event) {
@@ -18790,7 +18794,11 @@ class IGVXhr {
             try {
                 xhr.send(sendData);
             } catch (e) {
-                reject(e);
+                if (isGoogleURL(url) && !options.retries) {
+                    tryGoogleAuth();
+                } else {
+                    handleError(e);
+                }
             }
 
 
@@ -18807,7 +18815,7 @@ class IGVXhr {
                     const accessToken = await fetchGoogleAccessToken(url);
                     options.retries = 1;
                     options.oauthToken = accessToken;
-                    const response = await this._load(url, options);
+                    const response = await self.load(url, options);
                     resolve(response);
                 } catch (e) {
                     if (e.error) {
@@ -18863,29 +18871,41 @@ class IGVXhr {
         this.oauth.setToken(token, host);
     }
 
+    /**
+     * Return an oauth token for the URL if we have one.  This method does not force sign-in, and the token may
+     * or may not be valid.  Sign-in is triggered on request failure.
+     * *
+     * @param url
+     * @returns {*}
+     */
     getOauthToken(url) {
 
         // Google is the default provider, don't try to parse host for google URLs
         const host = isGoogleURL(url) ?
             undefined :
             parseUri(url).host;
+
+        // First check the explicit settings (i.e. token set through the API)
         let token = this.oauth.getToken(host);
         if (token) {
             return token
         } else if (host === undefined) {
+            // Now try Google oauth tokens previously obtained.  This will return undefined if google oauth is not
+            // configured.
             const googleToken = getCurrentGoogleAccessToken();
             if (googleToken && googleToken.expires_at > Date.now()) {
                 return googleToken.access_token
             }
         }
     }
-
 }
 
 function isGoogleStorageSigned(url) {
     return url.indexOf("X-Goog-Signature") > -1
 }
 
+
+
 /**
  * Return a Google oAuth token, triggering a sign in if required.   This method should not be called until we know
  * a token is required, that is until we've tried the url and received a 401, 403, or 404.
@@ -18953,14 +18973,16 @@ function addTeamDrive(url) {
  */
 function mapUrl$1(url) {
 
-    if (url.includes("//www.dropbox.com")) {
+    if (url.startsWith("https://www.dropbox.com")) {
         return url.replace("//www.dropbox.com", "//dl.dropboxusercontent.com")
-    } else if (url.includes("//drive.google.com")) {
+    } else if (url.startsWith("https://drive.google.com")) {
         return getDriveDownloadURL(url)
     } else if (url.includes("//www.broadinstitute.org/igvdata")) {
         return url.replace("//www.broadinstitute.org/igvdata", "//data.broadinstitute.org/igvdata")
     } else if (url.includes("//igvdata.broadinstitute.org")) {
-        return url.replace("//igvdata.broadinstitute.org", "https://dn7ywbm9isq8j.cloudfront.net")
+        return url.replace("//igvdata.broadinstitute.org", "//s3.amazonaws.com/igv.broadinstitute.org")
+    } else if (url.includes("//igv.genepattern.org")) {
+        return url.replace("//igv.genepattern.org", "//igv-genepattern-org.s3.amazonaws.com")
     } else if (url.startsWith("ftp://ftp.ncbi.nlm.nih.gov/geo")) {
         return url.replace("ftp://", "https://")
     } else {
@@ -23922,7 +23944,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.15.1";
+const _version = "2.15.3";
 function version() {
     return _version
 }
@@ -25759,15 +25781,15 @@ function decodeGTF(tokens, header) {
  * @param keyValueDelim
  * @returns {[]}
  */
-function parseAttributeString(attributeString, keyValueDelim) {
+function parseAttributeString(attributeString, keyValueDelim, relaxed = false) {
     // parse 'attributes' string (see column 9 docs in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
     var attributes = [];
     for (let kv of attributeString.split(';')) {
         kv = kv.trim();
         const idx = kv.indexOf(keyValueDelim);
         if (idx > 0 && idx < kv.length - 1) {
-            const key = kv.substring(0, idx);
-            let value = stripQuotes(decodeGFFAttribute(kv.substring(idx + 1).trim()));
+            const key = stripQuotes(decodeGFFAttribute(kv.substring(0, idx).trim(), relaxed));
+            let value = stripQuotes(decodeGFFAttribute(kv.substring(idx + 1).trim(), relaxed));
             attributes.push([key, value]);
         }
     }
@@ -25806,11 +25828,14 @@ const encodings = new Map([
     ["%2C", ","]
 ]);
 
-function decodeGFFAttribute(str) {
+function decodeGFFAttribute(str, relaxed = false) {
 
     if (!str.includes("%")) {
         return str
     }
+    if (relaxed) {
+        return decodeURIComponent(str);
+    }
     let decoded = "";
     for (let i = 0; i < str.length; i++) {
 
@@ -25868,7 +25893,7 @@ function decodeBed(tokens, header) {
 
             // Potentially parse name field as GFF column 9 style streng.
             if (tokens[3].indexOf(';') > 0 && tokens[3].indexOf('=') > 0) {
-                const attributeKVs = parseAttributeString(tokens[3], '=');
+                const attributeKVs = parseAttributeString(tokens[3], '=', true);
                 feature.attributes = {};
                 for (let kv of attributeKVs) {
                     feature.attributes[kv[0]] = kv[1];
@@ -27269,6 +27294,8 @@ class TrackBase {
                         }
                         tracklineConfg.autoscale = false;
                         tracklineConfg.dataRange = {min, max};
+                        this.viewLimitMin = min;
+                        this.viewLimitMax = max;
                     }
                 case "name":
                     tracklineConfg[key] = properties[key];
@@ -29167,9 +29194,9 @@ function optimizeChunks(chunks, lowest) {
  * @returns {boolean|boolean}
  */
 function canMerge(chunk1, chunk2) {
-    const gap = chunk2.minv.block - chunk1.maxv.block;
+    chunk2.minv.block - chunk1.maxv.block;
     const sizeEstimate = chunk1.maxv.block - chunk1.minv.block;
-    return gap < 65000 && sizeEstimate < 5000000
+    return sizeEstimate < 5000000
 }
 
 // Represents a CSI Bam or Tabix index
@@ -40792,8 +40819,8 @@ class FeatureTrack extends TrackBase {
             color = IGVColor.addAlpha(color, feature.alpha);
         } else if (this.useScore && feature.score && !Number.isNaN(feature.score)) {
             // UCSC useScore option, for scores between 0-1000.  See https://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK
-            const min = this.config.min ? this.config.min : 0; //getViewLimitMin(track);
-            const max = this.config.max ? this.config.max : 1000; //getViewLimitMax(track);
+            const min = this.config.min ? this.config.min : this.viewLimitMin ? this.viewLimitMin : 0;
+            const max = this.config.max ? this.config.max : this.viewLimitMax ? this.viewLimitMax : 1000;
             const alpha = getAlpha(min, max, feature.score);
             feature.alpha = alpha;    // Avoid computing again
             color = IGVColor.addAlpha(color, alpha);
@@ -40852,6 +40879,10 @@ class RegionTableBase {
         this.browser = config.browser;
 
         this.container = domUtils.div({ class: 'igv-roi-table' });
+        if(config.width) {
+            this.container.style.width = config.width;
+
+        }
 
         config.parent.appendChild(this.container);
 
@@ -41033,6 +41064,7 @@ class BlatTable extends RegionTableBase {
     set columnTitleDOM(columnFormat) {
 
         const dom = domUtils.div({ class: 'igv-roi-table-column-titles' });
+        this.columnTitlesDiv = dom;
         this.container.appendChild(dom);
 
         for (const format of columnFormat) {
@@ -41050,13 +41082,16 @@ class BlatTable extends RegionTableBase {
 
             let dom;
 
-            const found = this.container.querySelector('.igv-roi-table-column-titles');
             dom = domUtils.div({ class: 'igv-roi-table-description' });
-            this.container.insertBefore(dom, found);
+            this.container.insertBefore(dom, this.columnTitlesDiv);
+            dom.innerHTML = `BLAT result for query sequence:`;
+
+            dom = domUtils.div({ class: 'igv-roi-table-description' });
+            this.container.insertBefore(dom, this.columnTitlesDiv);
             dom.innerHTML = config.description;
 
             dom = domUtils.div({ class: 'igv-roi-table-goto-explainer' });
-            this.container.insertBefore(dom, found);
+            this.container.insertBefore(dom, this.columnTitlesDiv);
             dom.innerHTML = `Select one or more rows and click Go To to view the regions`;
 
         }
@@ -41174,16 +41209,16 @@ http://genome.ucsc.edu/cgi-bin/hgBlat
 &output=json
  */
 
-
 //const blatServer = "https://genome.ucsc.edu/cgi-bin/hgBlat"
-const blatServer = "https://igv.org/services/blat.php";
+const defaultBlatServer = "https://igv.org/services/blatUCSC.php";
+//const blatServer = "http://localhost:8000/blatUCSC.php"
 
 
-async function blat(userSeq, db) {
+async function blat({url, userSeq, db}) {
 
-    const url = `${blatServer}?userSeq=${userSeq}&type=DNA&db=${db}&output=json`;
+    url = url || defaultBlatServer;
 
-    const results = await igvxhr.loadJson(url, {});
+    const results = await postData(url, userSeq, db);
 
     results.fields;
 
@@ -41192,8 +41227,19 @@ async function blat(userSeq, db) {
     return features
 }
 
-class BlatTrack extends FeatureTrack {
+async function postData(url = "", userSeq, db) {
+
+    const data = new URLSearchParams();
+    data.append("userSeq", userSeq);
+    data.append("db", db);
 
+    const response = await fetch(url, { method: "post", body: data });
+    return response.json(); // parses JSON response into native JavaScript objects
+}
+
+const maxSequenceSize = 25000;
+
+class BlatTrack extends FeatureTrack {
 
     constructor(config, browser) {
         super(config, browser);
@@ -41229,7 +41275,7 @@ class BlatTrack extends FeatureTrack {
                     browser: this.browser,
                     parent: this.browser.parent,
                     headerTitle: this.config.title,
-                    description: `BLAT result for query sequence:<br>${ this.sequence }`,
+                    description: this.sequence,
                     dismissHandler: () => {
                         this.table.dismiss();
                         this.table.dispose();
@@ -41278,21 +41324,34 @@ class BlatTrack extends FeatureTrack {
 
 async function createBlatTrack({sequence, browser, name, title}) {
 
+    if (sequence.length > maxSequenceSize) {
+        browser.alert.present(`Sequence size exceeds maximum allowed length (${sequence.length} > ${maxSequenceSize})`);
+        return
+    }
+
     const db = browser.genome.id;   // TODO -- blat specific property
 
-    const features = await blat(sequence, db);
+    const url = browser.config["blatServerURL"];
 
-    const trackConfig = {
-        type: 'blat',
-        name: name || 'blat results',
-        title: title || 'blat results',
-        sequence: sequence,
-        features: features
-    };
+    try {
+
+        const features = await blat({url, userSeq: sequence, db});
+        const trackConfig = {
+            type: 'blat',
+            name: name || 'blat results',
+            title: title || 'blat results',
+            sequence: sequence,
+            altColor: 'rgb(176, 176, 236)',
+            color: 'rgb(236, 176, 176)',
+            features: features
+        };
 
-    const track = await browser.loadTrack(trackConfig);
+        const track = await browser.loadTrack(trackConfig);
+        track.openTableView();
 
-    track.openTableView();
+    } catch (e) {
+        browser.alert.present(`Error performing blat search:  ${e}`);
+    }
 
 }
 
@@ -42645,18 +42704,21 @@ class AlignmentTrack {
                 // TODO if genome supports blat
                 const seqstring = clickedAlignment.seq;
                 if (seqstring && "*" != seqstring) {
-                    list.push({
-                        label: 'BLAT read sequence',
-                        click: () => {
-                            const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(seqstring) : seqstring;
-                            const name = `${clickedAlignment.readName} - blat`;
-                            const title = `${this.parent.name} - ${name}`;
-                            createBlatTrack({sequence, browser: this.browser, name, title});
-                        }
-                    });
+
+                    if(seqstring.length < maxSequenceSize) {
+                        list.push({
+                            label: 'BLAT read sequence',
+                            click: () => {
+                                const sequence = clickedAlignment.isNegativeStrand() ? reverseComplementSequence(seqstring) : seqstring;
+                                const name = `${clickedAlignment.readName} - blat`;
+                                const title = `${this.parent.name} - ${name}`;
+                                createBlatTrack({sequence, browser: this.browser, name, title});
+                            }
+                        });
+                    }
 
                     const softClips = clickedAlignment.softClippedBlocks();
-                    if (softClips.left && softClips.left.len > MINIMUM_BLAT_LENGTH) {
+                    if (softClips.left && softClips.left.len > MINIMUM_BLAT_LENGTH && softClips.left.len < maxSequenceSize) {
                         list.push({
                             label: 'BLAT left soft-clipped sequence',
                             click: () => {
@@ -42668,7 +42730,7 @@ class AlignmentTrack {
                             }
                         });
                     }
-                    if (softClips.right && softClips.right.length > MINIMUM_BLAT_LENGTH) {
+                    if (softClips.right && softClips.right.len > MINIMUM_BLAT_LENGTH && softClips.right.len < maxSequenceSize) {
                         list.push({
                             label: 'BLAT right soft-clipped sequence',
                             click: () => {
@@ -54162,11 +54224,13 @@ class HDF5Reader {
 
         // console.log(h5_obj_keys)
         let signal_bin = new ParseSignals(h5_obj_keys);
-        this.rd_bins = signal_bin.get_rd_bins();
+        let rd_bins = signal_bin.get_rd_bins();
+        let snp_bins = signal_bin.get_snp_bins();
+        this.available_bins = [...new Set(rd_bins, snp_bins)];
 
         // let bin_size = this.bin_size
-        if(! this.rd_bins.includes(bin_size)){
-            bin_size = this.rd_bins[rd_bins.length-1];    
+        if(! this.available_bins.includes(bin_size)){
+            bin_size = this.available_bins.at(-1);    
         }
 
         const chr_ds = await h5_obj.get("rd_chromosomes");
@@ -54210,6 +54274,9 @@ class HDF5Reader {
             let signal_baf_1 = `snp_likelihood_${chrom}_${bin_size}_mask`;
             let chr_wig_bafs = await this.get_baf_signals(h5_obj, h5_obj_keys, chrom, bin_size, signal_baf_1);
 
+            // let signal_baf_1 = `snp_i1_${chrom}_${bin_size}_mask`
+            // let chr_wig_bafs = await this.get_baf_signals_v2(h5_obj, h5_obj_keys, chrom, bin_size, signal_baf_1)
+
             wigFeatures_baf1 = wigFeatures_baf1.concat(chr_wig_bafs[0]);
             wigFeatures_baf2 = wigFeatures_baf2.concat(chr_wig_bafs[1]);
             // this.rd_call_combined(h5_obj, h5_obj_keys, chrom, bin_size, rd_stat)
@@ -54334,6 +54401,28 @@ class HDF5Reader {
         }
         return [chr_wig_1, chr_wig_2]
     }
+
+    async get_baf_signals_v2(h5_obj, h5_obj_keys, chrom, bin_size, signal_name){
+        
+        /* return two list of dictionary*/
+        let chr_wig_1 = [];
+        let chr_wig_2 = [];
+        if (h5_obj_keys.includes(signal_name)){
+            let chrom_dataset = await h5_obj.get(signal_name);
+            let chrom_data = await chrom_dataset.to_array(); //create_nested_array(value, shape)
+            chrom_data.forEach((lh, bin_idx) => {
+                if (!isNaN(lh)){
+                    chr_wig_1.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 * ( 0.5 - lh )});
+                    if(lh != 0.5){
+                        chr_wig_2.push({chr:chrom, start: bin_idx*bin_size, end: (bin_idx+1) * bin_size, value: -2 * ( 0.5 + lh )});
+                    }
+                }
+            });
+        }
+        console.log(chrom, chr_wig_1, chr_wig_2);
+        return [chr_wig_1, chr_wig_2]
+
+    }
 }
 
 class ParseSignals{
@@ -54374,6 +54463,53 @@ class ParseSignals{
     }
 }
 
+class GetFit {
+  constructor(allBins) {
+      this.allBins = allBins;
+  }
+  getValues() {
+      const bins = Object.values(this.allBins).reduce(
+          (binResult, bin) => { return binResult.concat(bin.filter(a => a.binScore > 0).map(a => a.binScore)) }, []);
+      return bins
+  }
+  getMean(data) {
+      return (data.reduce(function (a, b) { return a + b; }) / data.length);
+  }
+  fit_data() {
+      let rd_list = this.getValues();
+      let distParmas = getDistParams(rd_list);
+      return distParmas
+  }
+
+  histogram(data, bins) {
+      const step = bins[1] - bins[0];
+      const hist_bins = [];
+
+      data.forEach((value, index) => {
+          bins.forEach((bin_value, bin_index) => {
+              if (!hist_bins[bin_value]) {
+                  hist_bins[bin_value] = { count: 0 };
+              }
+              if (bin_value <= value && value < bin_value + step) {
+                  hist_bins[bin_value].count++;
+                  return false;
+              }
+          });
+      });
+      const dist_p = [];
+      hist_bins.forEach((bin, index) => { dist_p.push(bin.count); });
+      return dist_p
+  }
+
+}
+
+function range_function(start, stop, step) {
+  const data_array = Array(Math.ceil((stop - start) / step))
+    .fill(start)
+    .map((x, y) => x + y * step);
+  return data_array;
+}
+
 function filterOutliers(someArray) {
 
   if (someArray.length < 4)
@@ -54406,6 +54542,21 @@ function getDistParams(bins) {
   return [mean, std]
 }
 
+function linspace(a, b, n) {
+  if (typeof n === "undefined") n = Math.max(Math.round(b - a) + 1, 1);
+  if (n < 2) {
+      return n === 1 ? [a] : [];
+  }
+  var ret = Array(n);
+  n--;
+  for (let i = n; i >= 0; i--) {
+      ret[i] = (i * b + (n - i) * a) / n;
+  }
+  return ret;
+}
+
+var g_utils = { range_function, getDistParams, linspace, GetFit};
+
 /** 
 * Evaluates the cumulative distribution function (CDF) for a Student's t distribution with degrees of freedom `v` at a value `t`.
 *
@@ -54550,48 +54701,507 @@ function lgamma(xg){
     return Math.log(gamma(xg))
 }
 
-var t_dist = {TdistributionCDF, gamma};
+function t_test_1_sample$1(mean, m, s, n) {
+    if (s == 0) s = 1;
+    var t = ((mean - m) / s) * Math.sqrt(n);
+    var p = 1.0 - TdistributionCDF(Math.abs(t), (n - 1));
+    return p
+}
 
-class GetFit {
-    constructor(allBins) {
-        this.allBins = allBins;
-    }
-    getValues() {
-        const bins = Object.values(this.allBins).reduce(
-            (binResult, bin) => { return binResult.concat(bin.filter(a => a.binScore > 0).map(a => a.binScore)) }, []);
-        return bins
+function t_test_2_samples$1(m1, s1, n1, m2, s2, n2) {
+    if (s1 == 0) s1 = 1;
+    if (s2 == 0) s2 = 1;
+    var t = (m1 - m2) / Math.sqrt(s1 ** 2 / n1 + s2 ** 2 / n2);
+    var df = ((s1 ** 2 / n1 + s2 ** 2 / n2) ** 2 * (n1 - 1) * (n2 - 1)) /
+        ((s1 ** 4 * (n2 - 1)) / n1 ** 2 + (s2 ** 4 * (n1 - 1)) / n2 ** 2);
+
+    var p = 1.0 - TdistributionCDF(Math.abs(t), parseInt(df + 0.5));
+
+    return p
+}
+
+var t_dist = {TdistributionCDF, gamma, t_test_1_sample: t_test_1_sample$1, t_test_2_samples: t_test_2_samples$1};
+
+class CombinedCaller{
+    constructor(wigFeatures, binSize) {
+        this.wigFeatures = wigFeatures;
+        this.binSize = binSize;
+        // let fit_obj = this.get_fit()
+        // this.globalMean = fit_obj.globalMean
+        // this.globalStd = fit_obj.globalStd
     }
-    getMean(data) {
-        return (data.reduce(function (a, b) { return a + b; }) / data.length);
+    get_fit(){
+        var fit_info = new g_utils.GetFit(this.wigFeatures);
+        var [globalMean, globalStd] = fit_info.fit_data();
+
+        return {globalMean:globalMean, globalStd:globalStd}
+       
     }
-    fit_data() {
-        let rd_list = this.getValues();
-        let distParmas = getDistParams(rd_list);
-        return distParmas
+    async call_2d(omin=null, mcount=null, event_type="both", max_distance=0.1, baf_threshold=0, max_copy_number=10, min_cell_fraction=0.0){
+        
+        let fit_obj = this.get_fit();
+        this.globalMean = fit_obj.globalMean;
+        this.globalStd = fit_obj.globalStd;
+        
+        let overlap_min = omin==null ?  0.05 * this.binSize / 3e9: omin ;
+        let min_count = mcount == null ? parseInt(this.binSize / 10000) : mcount ;
+
+        let gstat_rd0 = [];
+        let gstat_rd_all = [];
+        let gstat_rd = [];
+        let gstat_error = [];
+        let gstat_lh = [];
+        let gstat_n = [];
+        
+        for (const [chr, wig] of Object.entries(this.wigFeatures)) {
+            let segments = [];
+            let levels = [];
+            let likelihoods = [];
+            
+            wig.forEach((bin, bin_idx) => {
+                if (bin.hets_count > 4 ){
+                    
+                    if( bin.dp_count > min_count ){
+                        segments.push([bin_idx]);
+                        levels.push(bin.binScore);
+                        likelihoods.push(bin.likelihood_score);
+                        delete bin.likelihood_score;
+                        
+                    }
+                }
+            });
+
+            let diff_level = [];
+            for(let i=1; i<levels.length; i++){
+                diff_level.push(Math.abs(levels[i] - levels[i-1]));
+            }
+            let min_flank = [0];
+            for(let i=1; i<diff_level.length; i++){
+                min_flank.push(Math.min(diff_level[i-1], diff_level[i]));    
+            }
+            min_flank.push(0);
+
+            let error  = levels.map((x, x_idx) => {return Math.sqrt(Math.sqrt(x) ** 2 + this.globalStd ** 2 + Math.pow(min_flank[x_idx]/2, 2));});
+            
+            let overlaps = [];
+            
+            for(let i=0; i< segments.length-1; i++){
+                
+                let lh_overlap = 0;
+                try{
+                    lh_overlap = likelihood_overlap(likelihoods[i], likelihoods[i+1]);
+                }catch{
+                    console.log("Overlap failed: ", i, likelihoods[i], segments[i+1], likelihoods[i+1]);
+                }
+                
+                let rd_overlap = normal_overlap_approx(levels[i], error[i], levels[i+1], error[i+1]);
+                overlaps.push(rd_overlap * lh_overlap);
+                
+            }
+            
+            while(overlaps.length >0) {
+                overlaps = overlaps.filter(num => typeof num === "number");
+                
+                let max_overlap = arrayMax(overlaps);
+                if(isNaN(max_overlap)){
+                    console.log('NaN value', overlaps);
+                }
+                if(max_overlap < overlap_min){
+                    // console.log("maxoverlap ",max_overlap,  "is smaller than overlap min")
+                    break
+                }
+                let i = overlaps.indexOf(max_overlap);
+                
+                let merge_level = normal_merge(levels[i], error[i], levels[i + 1], error[i + 1]);
+                
+                let nlh;
+                let nlh_sum;
+                try{
+                    nlh = likelihoods[i].map((l_value, l_idx) => { return l_value * likelihoods[i+1][l_idx]});
+                
+                    nlh_sum = nlh.reduce((a, c_value) => {return a + c_value});
+                    
+                }catch{
+                    console.log(likelihoods);
+                    console.log('max_overlap:', max_overlap, i, overlaps.length);
+                    console.log('likelihood: ', i ,likelihoods[i], likelihoods[i+1]);
+                    console.log('nlh: ', nlh_sum);
+                }
+                // nlh_sum = nlh.reduce((a, c_value) => {return a + c_value});
+
+                levels[i] = merge_level.nl;
+                error[i] = merge_level.ne;
+                
+                likelihoods[i] = nlh.map(function(item) { return item/nlh_sum } );
+                
+                segments[i].push(...segments[i+1]);
+
+                levels.splice(i + 1, 1);
+                error.splice(i + 1, 1);
+                segments.splice(i + 1, 1);
+                likelihoods.splice(i + 1, 1);
+                overlaps.splice(i, 1);
+                
+                if(i < overlaps.length){
+                    
+                    let rd_overlap = normal_overlap_approx(levels[i], error[i], levels[i+1], error[i+1]);
+                    let new_overlap = rd_overlap * likelihood_overlap(likelihoods[i], likelihoods[i + 1]);
+                    
+                    overlaps[i] = new_overlap;
+                }
+                if(i > 0){
+                    let new_overlap = normal_overlap_approx(levels[i - 1], error[i - 1], levels[i], error[i]) 
+                    * likelihood_overlap(likelihoods[i - 1], likelihoods[i]);
+                    overlaps[i - 1] = new_overlap;
+                }
+
+            }
+            let ons = -1;
+            while(true){
+                overlaps = [];
+                for(let i=0; i< levels.length; i++){
+                    for(let j=i; j<levels.length; j++){
+                        if(segments[j][0] - segments[i].at(-1) < max_distance * (segments[i].length + segments[j].length)){
+                            overlaps.push(normal_overlap_approx(levels[i], error[i], levels[j], error[j]) * likelihood_overlap(likelihoods[i], likelihoods[j]));
+                        }
+                    }
+                }
+                
+                if(overlaps.length == 0){
+                    break
+                }
+                let max_overlap = arrayMax(overlaps);
+                if(max_overlap < overlap_min){
+                    break
+                }
+                let i = 0; 
+                let j = 1;
+                while (i < segments.length - 1){
+                    let overlap_value = normal_overlap_approx(levels[i], error[i], levels[j], error[j]) * likelihood_overlap(likelihoods[i], likelihoods[j]);
+
+                    if((segments[j][0] - segments[i].at(-1)) < max_distance * (segments[i].length + segments[j].length) && overlap_value == max_overlap){
+                        let merge_level = normal_merge(levels[i], error[i], levels[i + 1], error[i + 1]);
+
+                        levels[i] = merge_level.nl;
+                        error[i] = merge_level.ne;
+                        let nlh = likelihoods[i].map((l_value, l_idx) => { return l_value * likelihoods[i+1][l_idx]});
+                        let nlh_sum = nlh.reduce((a, c_value) => {return a + c_value});
+                        likelihoods[i] = nlh.map(function(item) { return item/nlh_sum } );
+
+                        
+                        segments[i].push(...segments[i+1]);
+                        segments[i] = segments[i].sort((a,b) => a-b);
+
+                        levels.splice(j, 1);
+                        error.splice(j, 1);
+                        segments.splice(j, 1);
+                        likelihoods.splice(j, 1);
+                        
+                        if(j >= segments.length){
+                            i += 1;
+                            j = i + 1;
+                        }
+
+                    }else {
+                        j += 1;
+                        if(j >= segments.length){
+                            i += 1;
+                            j = i + 1;
+                        }
+                    }
+                }
+                if(ons == segments.length){
+                    break
+                }
+                ons = segments.length;
+            }
+            // console.log('final segments', segments)
+            
+            segments.forEach((seg_value, seg_idx) => {
+                let baf_info = likelihood_baf_pval(likelihoods[seg_idx]);
+                if(seg_value.length > 1){
+
+                    seg_value.forEach((bin, bin_idx) =>{
+                        gstat_rd_all.push(wig[bin]);
+                        if(baf_info.mean <= baf_threshold){
+                            gstat_rd0.push(wig[bin]);
+                        }
+                        wig[bin].segment_score = levels[seg_idx];
+                    });
+                    gstat_rd.push(levels[seg_idx]);
+                    gstat_error.push(error[seg_idx]);
+                    gstat_lh.push(likelihoods[seg_idx]);
+
+                }
+
+            });
+
+            continue
+        }
+        
+        // Third stage for call
+        
+        // let data = gstat_rd0.lengthn == 0 ?  gstat_rd_all: gstat_rd0 ;
+        
+        let points = parseInt(1000 * (1 - min_cell_fraction));
+        if(points == 0){
+            points = 1;
+        }
+        let x = g_utils.linspace(min_cell_fraction, 1, points);
+        let master_lh = {};
+        let germline_lh = {};
+        for(let cn=10; cn > -1; cn--){
+            for(let h1=0; h1 < (cn/2+1); h1++){
+                let h2 = cn - h1;
+                let mrd = x.map((v, idx) => {return 1-v +v*cn/2});
+                let g_mrd = cn / 2;
+                let g_mbaf;
+                let mbaf;
+                if(cn > 0){
+                    g_mbaf = 0.5 - (h1 / (h1 + h2));
+                    mbaf = x.map((v, idx) => {return 0.5 - (1 - v + v * h1) / (2 - 2 * v + (h1 + h2) * v)});
+                   
+                }else {
+                    g_mbaf = 0;
+                    mbaf =  x.map((v, idx) => {return 0*v});
+                }
+                
+                for( let ei=0; ei < gstat_rd.length; ei++){
+                        
+                    let g_lh = normal(g_mrd * this.globalMean, 1, gstat_rd[ei], gstat_error[ei]) * likelihood_of_baf(gstat_lh[ei], 0.5 + g_mbaf);
+                    if(ei in germline_lh){
+                        germline_lh[ei].push([cn, h1, h2, g_lh, 1.0]);
+                    }else {
+                        germline_lh[ei] = [cn, h1, h2, g_lh, 1.0];
+                    }
+                    let slh = 0;
+                    let max_lh = 0;
+                    let max_x = 0;
+                    mrd.forEach((mi, idx) => {
+                        if(!isNaN(mbaf[idx])){
+                            let tmpl = normal(mi * this.globalMean, 1, gstat_rd[ei], gstat_error[ei]) * likelihood_of_baf(gstat_lh[ei], 0.5 + mbaf[idx]);
+                            slh += tmpl;
+                            if(tmpl > max_lh){
+                                max_lh = tmpl;
+                                max_x = x[idx];
+                            }
+                        }
+                    });
+                    if(ei in master_lh){
+                        master_lh[ei].push([cn, h1, h2, slh / x.length, max_x]);
+                    }else {
+                        master_lh[ei] = [cn, h1, h2, slh / x.length, max_x];
+                    }
+                }
+                
+                for( let ei=0; ei < gstat_rd.length; ei++){
+                    if(event_type == "germline"){
+                        master_lh[ei].sort((a, b) => a[3] - b[3]);
+                    }
+                    else {
+                        master_lh[ei].sort((a, b) => a[3] - b[3]);
+                        if(event_type == "both"){
+                            
+                            germline_lh[ei].sort((a, b) => a[3] - b[3]);
+                            if(germline_lh[ei][0][3] > master_lh[ei][0][3]){
+                                //let tmp_list = list(filter( lambda x: x[0] != germline_lh[ei][0][0] and x[1] != germline_lh[ei][0][1], master_lh[ei]))
+                                let tmp_list = master_lh[ei].filter((x) => (x[0] != germline_lh[ei][0][0]) && (x[1] <= germline_lh[ei][0][1]));
+                                // console.log('tmp_list', tmp_list)
+                                // master_lh[ei] = [germline_lh[ei][0]] + tmp_list
+                                master_lh[ei] = [germline_lh[ei][0]].push(...tmp_list);
+                            }
+                        }
+                    }
+                }
+                for( let ei=0; ei < gstat_rd.length; ei++){
+                    if(master_lh[ei][0][0] > 2);
+                    if(master_lh[ei][0][0] < 2);
+                    gstat_rd[ei] / this.globalMean;
+                    t_dist.t_test_1_sample(this.globalMean, gstat_rd[ei], gstat_error[ei], gstat_n[ei]);
+                    // console.log(etype)
+
+                }
+                
+
+                // break
+            }
+            
+        }
+        
+        var rawbinScore = this.formatDataStructure(this.wigFeatures, 'binScore', this.globalMean);
+        var callScore = this.formatDataStructure(this.wigFeatures, 'segment_score', this.globalMean);
+        
+        return {binScore: rawbinScore, segment_score: callScore}
+        
     }
 
-    histogram(data, bins) {
-        const step = bins[1] - bins[0];
-        const hist_bins = [];
+    formatDataStructure(wigFeatures, feature_column, scaling_factor = 1) {
+        const results = [];
+        for (const [chr, wig] of Object.entries(wigFeatures)) {
 
-        data.forEach((value, index) => {
-            bins.forEach((bin_value, bin_index) => {
-                if (!hist_bins[bin_value]) {
-                    hist_bins[bin_value] = { count: 0 };
+            wig.forEach(sample => {
+                var new_sample = { ...sample };
+                if (scaling_factor != 1) {
+                    new_sample.value = sample[feature_column] / scaling_factor * 2;
                 }
-                if (bin_value <= value && value < bin_value + step) {
-                    hist_bins[bin_value].count++;
-                    return false;
+                results.push(new_sample);
+            });
+        }
+
+        return results
+    }
+
+    formatDataStructure_BAF(feature_column, scaling_factor = 2) {
+        const baf1 = [];
+        const baf2 = [];
+        for (const [chr, wig] of Object.entries(this.wigFeatures)) {
+
+            wig.forEach(sample => {
+                
+                var baf1_value = { ...sample };
+                var baf2_value = { ...sample };
+                
+                let value = sample[feature_column];
+                if (value != 0.5){
+                    baf2_value.value = -2 * (1 - value);
+                    baf2.push(baf2_value);
                 }
+                baf1_value.value = -2 * value;
+                baf1.push(baf1_value);
+                    
             });
-        });
-        const dist_p = [];
-        hist_bins.forEach((bin, index) => { dist_p.push(bin.count); });
-        return dist_p
+        }
+        
+
+        return [baf1, baf2]
+    }
+}
+
+function arrayMax(arr) {
+    return arr.reduce(function (p, v) {
+      return ( p > v ? p : v );
+    });
+  }
+
+/**
+ * Normal distribution.
+ * 
+ * @param {float} x - Variable.
+ * @param {float} a - area
+ * @param {float} x0 -  Mean value
+ * @param {float} sigma - Sigma
+ * @returns {float} - Value of distribution in x.
+ */
+function normal(x, a, x0, sigma){
+  
+  return a * Math.exp(-1* (x - x0) ** 2 / (2 * sigma ** 2)) / Math.sqrt(2 * Math.PI) / sigma
+
+}
+
+/**
+ *  Calculates two normal distributions overlap area.
+ * 
+ * @param {float} m1 - Mean value of the first distribution
+ * @param {float} s1 - Sigma of the first distribution
+ * @param {float} m2 - Mean value for second distribution
+ * @param {float} s2 - Sigma of the second distribution
+ * 
+ * @returns {float} area - Area of overlap
+ */
+function normal_overlap_approx(m1, s1, m2, s2){
+   
+    return Math.exp(-1* (m1-m2)**2/ (s1**2+s2**2))
+}
+
+
+/**
+ * Returns overlap area of two likelihood functions.
+ * 
+ * @param {*} lk1 - First likelihood function.
+ * @param {*} lk2 - Second likelihood function.
+ * 
+ * @returns {float}  - Overlap area.
+ */
+function likelihood_overlap(likelihood_1, likelihood_2){
+    let sum;
+    try{
+        sum = likelihood_1.reduce((accumulator, currentValue, currentIndex) => {return accumulator + Math.min(currentValue, likelihood_2[currentIndex])});
+    }catch{
+        console.log("Failed to find likelihood overlap: ", likelihood_1, likelihood_2);
+        return 0
+    }
+
+    return sum
+}
+
+/**
+ * Calculates normal distribution that is product of two given normal distributions.
+ * 
+ * @param {float} m1 - Mean value of the first distribution
+ * @param {float} s1 - Sigma of the first distribution
+ * @param {float} m2 - Mean value for second distribution
+ * @param {float} s2 - Sigma of the second distribution
+ * @returns {Object} An object representing the first distribution
+ * @property {float} nl - Mean value of the first distribution
+ * @property {float} ne - Sigma of the first distribution
+ */
+function normal_merge(m1, s1, m2, s2){
+   
+    if((s1 == 0) && (s2 == 0)){
+        return {nl: 0.5 * (m1 + m2), ne: 0}
     }
+    else {
+        return {nl: (m1 * s2 * s2 + m2 * s1 * s1) / (s1 * s1 + s2 * s2), ne: Math.sqrt(s1 * s1 * s2 * s2 / (s1 * s1 + s2 * s2))}
+    }
+}
 
+/**
+ * Calculates likelihood for given baf
+ * @param {*} likelihood 
+ * @param {*} baf 
+ * @returns {float}  likelihood value
+ */
+function likelihood_of_baf(likelihood, baf){
+   
+    let bin = parseInt(baf * (likelihood.length - 1));
+    let fr = baf * (likelihood.length - 1) - bin;
+    if(bin < likelihood.length - 1){
+        return likelihood[bin] * (1 - fr) + likelihood[bin + 1] * fr
+    }
+    else {
+        return likelihood[bin]
+    }
 }
 
+/**
+ * 
+ * Calculates baf level and p-value for given likelihood function.
+ * 
+ * @param {*} likelihood 
+ * @returns {Object} An object representing BAF
+ * @property {float} mean  BAF level (difference from 1/2)
+ * @property {float} p  p-value for event different than 1/2
+ */
+function likelihood_baf_pval(likelihood) {
+    const res = likelihood.length;
+    const max_lh = Math.max(...likelihood);
+    let ix = likelihood.indexOf(max_lh);
+    if (ix > Math.floor(res / 2)) {
+      ix = res - 1 - ix;
+    }
+    const b = (res / 2 - ix) / (res + 1);
+  
+    const ix1 = Math.floor((res / 2 + ix) / 2);
+    const ix2 = res - 1 - ix1;
+    let p = likelihood.slice(ix1, ix2 + 1).reduce((acc, val) => acc + val, 0) / likelihood.reduce((acc, val) => acc + val, 0);
+    if (ix === Math.floor(res / 2)) {
+      p = 1.0;
+    }
+    return {mean:b, p:p};
+  }
+
+  var combined_caller = {CombinedCaller};
+
 function erf(x) {
     var m = 1.0, s = 1.0, sum = x * 1.0;
     for (var i = 1; i < 50; i++) {
@@ -55239,6 +55849,10 @@ class Partition {
     }
 }
 
+
+
+var read_depth_caller = { Partition };
+
 class CNVpytorVCF {
     constructor(allVariants, binSize) {
         this.allVariants = allVariants;
@@ -55366,13 +55980,11 @@ class CNVpytorVCF {
     readDepthMeanshift(wigFeatures) {
 
         // Get global mean and standrad deviation
-        var fit_info = new GetFit(wigFeatures);
+        var fit_info = new g_utils.GetFit(wigFeatures);
         var [globamMean, globalStd] = fit_info.fit_data();
-        // console.log('Fitter', globamMean, globalStd)
-
 
         // Apply partition method
-        var partition = new Partition(wigFeatures, globamMean, globalStd);
+        var partition = new read_depth_caller.Partition(wigFeatures, globamMean, globalStd);
         var partition_array = partition.meanShiftCaller();
         var caller_array = partition.cnv_calling();
 
@@ -55403,86 +56015,10 @@ class CNVpytorVCF {
                 results.push(new_sample);
             });
         }
-        // console.log(feature_column, results)
 
         return results
     }
 
-    // function for baf likelihood calculations
-    async computeBAF() {
-        const chromosomes = Object.keys(this.allVariants);
-        const wigFeatures = {};
-        const results = [];
-
-        for (let chr of chromosomes) {
-            const variants = this.allVariants[chr];
-            if (variants.length === 0) continue
-            var featureBin;
-            for (let snp of variants) {
-                featureBin = Math.max(Math.floor(snp.start / this.binSize), 0);
-
-                if (!wigFeatures[chr]) {
-                    wigFeatures[chr] = [];
-                }
-                if (!wigFeatures[chr][featureBin]) {
-                    if (featureBin > 0) {
-                        // calculating the BAF likelihood for previous bin
-                        let previous_featureBin = featureBin - 1;
-                        if (wigFeatures[chr][previous_featureBin]) {
-
-                            const updated_bin = this.get_max_min_score(wigFeatures[chr][previous_featureBin]);
-                            wigFeatures[chr][previous_featureBin] = updated_bin;
-                            results.push(wigFeatures[chr][previous_featureBin]);
-                        }
-                    }
-                    wigFeatures[chr][featureBin] = {
-                        chr,
-                        start: featureBin * this.binSize,
-                        end: (featureBin + 1) * this.binSize,
-                        value: 0,
-                        count: 0,
-                        likelihood_score: [],
-                        min_score: 0,
-                    };
-                }
-                const calls = snp.calls[9];
-                let genotype = calls.genotype;
-                let ad_score = calls.info["AD"].split(',');
-                let ad_a = ad_score[0], ad_b = ad_score[1];
-
-                if ((genotype[0] == 0 && genotype[1] == 1) || (genotype[0] == 1 && genotype[1] == 0)) {
-                    //apply the beta function
-                    if (wigFeatures[chr][featureBin].likelihood_score.length == 0) {
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 200).map((value, index) => {
-                            return beta(ad_a, ad_b, value);
-                        });
-                    } else {
-                        var sum = 0;
-
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 200).map((value, index) => {
-                            var likelihood_value = wigFeatures[chr][featureBin].likelihood_score[index] * beta(ad_a, ad_b, value);
-                            sum = sum + likelihood_value;
-                            return likelihood_value;
-                        });
-
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 200).map((value, index) => {
-                            return wigFeatures[chr][featureBin].likelihood_score[index] / sum;
-                        });
-                    }
-                    wigFeatures[chr][featureBin].count++;
-                }
-            }
-
-            // last feature bin
-            const updated_bin = this.get_max_min_score(wigFeatures[chr][featureBin]);
-            wigFeatures[chr][featureBin] = updated_bin;
-            results.push(wigFeatures[chr][featureBin]);
-        }
-
-        const baf2_result = this.format_BAF_likelihood(wigFeatures);
-        return [results, baf2_result]
-
-    }
     async computeBAF_v2() {
 
         const chromosomes = Object.keys(this.allVariants);
@@ -55537,19 +56073,19 @@ class CNVpytorVCF {
                 if ((genotype[0] == 0 && genotype[1] == 1) || (genotype[0] == 1 && genotype[1] == 0)) {
                     //apply the beta function
                     if (wigFeatures[chr][featureBin].likelihood_score.length == 0) {
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                        wigFeatures[chr][featureBin].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                             return beta(ad_a, ad_b, value);
                         });
                     } else {
                         var sum = 0;
 
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                        wigFeatures[chr][featureBin].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                             var likelihood_value = wigFeatures[chr][featureBin].likelihood_score[index] * beta(ad_a, ad_b, value);
                             sum = sum + likelihood_value;
                             return likelihood_value;
                         });
 
-                        wigFeatures[chr][featureBin].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                        wigFeatures[chr][featureBin].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                             return wigFeatures[chr][featureBin].likelihood_score[index] / sum;
                         });
                     }
@@ -55595,7 +56131,6 @@ class CNVpytorVCF {
         if (sample.likelihood_score.length > 0) {
             const max = Math.max(...sample.likelihood_score);
             const res = sample.likelihood_score.indexOf(max);
-            sample.likelihood_score = [];
             sample.value = Math.max(res / 100, 1 - res / 100);
             sample.min_score = Math.min(res / 100, 1 - res / 100);
 
@@ -55611,7 +56146,7 @@ class CNVpytorVCF {
 
         //console.log('getAllbins', bins["value"])
 
-        const fitter = new GetFit(bins);
+        const fitter = new g_utils.GetFit(bins);
 
         fitter.fit_data();
         //  dconsole.log('rd list', distParams)
@@ -55619,7 +56154,7 @@ class CNVpytorVCF {
         return bins
     }
 
-    async read_rd_baf(){
+    async read_rd_baf(caller='ReadDepth'){
         
         const chromosomes = Object.keys(this.allVariants);
         var wigFeatures = {};
@@ -55665,13 +56200,22 @@ class CNVpytorVCF {
             }
         
         }
-        
+    
         var avgbin = this.adjust_bin_size(wigFeatures);
+        var finalFeatureSet;
+        if(caller == 'ReadDepth'){
+            finalFeatureSet = this.readDepthMeanshift(avgbin);
+            var baf = this.formatDataStructure_BAF(avgbin, 'max_likelihood');
+        }else if(caller=='2D'){
+            
+            let caller_obj = new combined_caller.CombinedCaller(avgbin,  this.binSize);        
+            let processed_bins = await caller_obj.call_2d();
+            
+            finalFeatureSet = [processed_bins.binScore, [], processed_bins.segment_score];
+    
+            var baf = caller_obj.formatDataStructure_BAF('max_likelihood');
+        }
         
-        let finalFeatureSet = this.readDepthMeanshift(avgbin);
-        
-        //var rawbinScore = this.formatDataStructure(avgbin, 'binScore', globamMean)
-        var baf = this.formatDataStructure_BAF(avgbin, 'max_likelihood');
 
         return [finalFeatureSet, baf]
     }
@@ -55734,19 +56278,19 @@ class CNVpytorVCF {
                             
                             wigFeatures[chr][j].hets.forEach((hets, hets_idx) => {
                                 if(avgbin[chr][k].likelihood_score.length == 0){
-                                    avgbin[chr][k].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                                    avgbin[chr][k].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                                         return beta(hets.ref, hets.alt, value);
                                     });
                                 }
                                 else {
                                     var likelihood_sum = 0;
-                                    avgbin[chr][k].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                                    avgbin[chr][k].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                                         var likelihood_value = avgbin[chr][k].likelihood_score[index] * beta(hets.ref, hets.alt, value);
                                         likelihood_sum += likelihood_value;
                                         return likelihood_value;
                                     });
 
-                                    avgbin[chr][k].likelihood_score = linspace(0, 1, 100).map((value, index) => {
+                                    avgbin[chr][k].likelihood_score = g_utils.linspace(0, 1, 100).map((value, index) => {
                                         return avgbin[chr][k].likelihood_score[index] / likelihood_sum;
                                     });
                        
@@ -55771,19 +56315,6 @@ function beta(a, b, p, phased = true) {
     return p ** a * (1 - p) ** b + p ** b * (1 - p) ** a;
 }
 
-function linspace(a, b, n) {
-    if (typeof n === "undefined") n = Math.max(Math.round(b - a) + 1, 1);
-    if (n < 2) {
-        return n === 1 ? [a] : [];
-    }
-    var ret = Array(n);
-    n--;
-    for (let i = n; i >= 0; i--) {
-        ret[i] = (i * b + (n - i) * a) / n;
-    }
-    return ret;
-}
-
 /*
 * The MIT License (MIT)
 *
@@ -55894,29 +56425,43 @@ class CNVPytorTrack extends TrackBase {
             }, Object.create(null));
 
             const cnvpytor_obj = new CNVpytorVCF(allVariants, this.bin_size);
-            //const wigFeatures = await cnvpytor_obj.computeReadDepth()
-            //const bafFeatures = await cnvpytor_obj.computeBAF_v2()
-            const dataWigs = await cnvpytor_obj.read_rd_baf();
-            const wigFeatures = dataWigs[0];
-            const bafFeatures = dataWigs[1];
             
+            let wigFeatures;
+            let bafFeatures;
             this.wigFeatures_obj = {};
-            this.wigFeatures_obj[this.bin_size] = {
-                "RD_Raw": wigFeatures[0],
-                "RD_Raw_gc_coor": wigFeatures[1],
-                "ReadDepth": wigFeatures[2],
-                "2D": [],
-                "BAF1": bafFeatures[0],
-                "BAF2": bafFeatures[1]
-            };
-            this.rd_bins = [this.bin_size];
-            this.available_callers = ["ReadDepth"];
+            this.wigFeatures_obj[this.bin_size] = {};
+
+            let dataWigs;
+            if(this.config.cnv_caller == '2D'){
+                
+                dataWigs = await cnvpytor_obj.read_rd_baf('2D');
+
+                wigFeatures = dataWigs[0];
+                bafFeatures = dataWigs[1];
+                this.wigFeatures_obj[this.bin_size]['2D'] = wigFeatures[2];
+
+                this.available_callers = ['2D'];
+            }else {
+                dataWigs = await cnvpytor_obj.read_rd_baf();
+                wigFeatures = dataWigs[0];
+                bafFeatures = dataWigs[1];
+                this.wigFeatures_obj[this.bin_size]['ReadDepth'] = wigFeatures[2];
+                this.available_callers = ['ReadDepth'];
+            }
+            
+            this.wigFeatures_obj[this.bin_size]['RD_Raw'] = wigFeatures[0];
+            this.wigFeatures_obj[this.bin_size]['RD_Raw_gc_coor'] = wigFeatures[1];
+            this.wigFeatures_obj[this.bin_size]['BAF1'] = bafFeatures[0];
+            this.wigFeatures_obj[this.bin_size]['BAF2'] = bafFeatures[1];
+            
+            this.available_bins = [this.bin_size];
+            
             this.set_available_callers();
 
         } else {
             this.cnvpytor_obj =   new HDF5Reader(this.config.url, this.bin_size);
             this.wigFeatures_obj = await this.cnvpytor_obj.get_rd_signal(this.bin_size);
-            this.rd_bins = this.cnvpytor_obj.rd_bins;
+            this.available_bins = this.cnvpytor_obj.available_bins;
             this.available_callers = this.cnvpytor_obj.callers;
             this.set_available_callers();
         }
@@ -56029,7 +56574,7 @@ class CNVPytorTrack extends TrackBase {
 
         items.push('<hr/>');
         items.push("Bin Sizes");
-        for (let rd_bin of this.rd_bins) {
+        for (let rd_bin of this.available_bins) {
             const checkBox = createCheckbox(rd_bin, rd_bin === this.bin_size);
             items.push({
                 object: $$1(checkBox),
@@ -60426,6 +60971,7 @@ class Browser {
 
     updateLocusSearchWidget() {
 
+        if(!this.referenceFrameList) return
         const referenceFrameList = this.referenceFrameList;
 
         // Update end position of reference frames based on pixel widths.  This is hacky, but its been done here
@@ -60479,6 +61025,8 @@ class Browser {
 
     async zoomWithScaleFactor(scaleFactor, centerBPOrUndefined, referenceFrameOrUndefined) {
 
+        if(!this.referenceFrameList) return
+
         const viewportWidth = this.calculateViewportWidth(this.referenceFrameList.length);
 
         let referenceFrames = referenceFrameOrUndefined ? [referenceFrameOrUndefined] : this.referenceFrameList;
@@ -60497,6 +61045,8 @@ class Browser {
      */
     async addMultiLocusPanel(chr, start, end, referenceFrameLeft) {
 
+        if(!this.referenceFrameList) return
+
         // account for reduced viewport width as a result of adding right mate pair panel
         const viewportWidth = this.calculateViewportWidth(1 + this.referenceFrameList.length);
         const scaleFactor = this.calculateViewportWidth(this.referenceFrameList.length) / this.calculateViewportWidth(1 + this.referenceFrameList.length);
@@ -61110,6 +61660,8 @@ class Browser {
  */
 async function resize() {
 
+    if(!this.referenceFrameList) return
+
     const viewportWidth = this.calculateViewportWidth(this.referenceFrameList.length);
 
     for (let referenceFrame of this.referenceFrameList) {
@@ -61514,7 +62066,7 @@ async function createTrack(config, browser) {
 
 function embedCSS() {
 
-    var css = '.igv-navbar {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  box-sizing: border-box;\n  width: 100%;\n  color: #444;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  line-height: 32px;\n  padding-left: 8px;\n  padding-right: 8px;\n  margin-top: 2px;\n  margin-bottom: 6px;\n  height: 32px;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n  width: 34px;\n  height: 32px;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n  height: 32px;\n  margin-left: 4px;\n  margin-right: 4px;\n  user-select: none;\n  line-height: 32px;\n  vertical-align: middle;\n  text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n  height: 100%;\n  width: 125px;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n  display: block;\n  cursor: pointer;\n  width: 100px;\n  height: 75%;\n  outline: none;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  margin-left: 8px;\n  height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 210px;\n  height: 22px;\n  line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n  cursor: text;\n  width: 85%;\n  height: 22px;\n  line-height: 22px;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  text-align: left;\n  padding-left: 8px;\n  margin-right: 8px;\n  outline: none;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n  cursor: pointer;\n  height: 16px;\n  width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n  margin-left: 4px;\n  user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n  margin-left: 0;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n  margin-left: 0;\n  margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n  display: block;\n  height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n  display: block;\n  width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n  display: none;\n}\n\n.igv-navbar-button {\n  display: block;\n  box-sizing: unset;\n  padding-left: 6px;\n  padding-right: 6px;\n  height: 18px;\n  text-transform: capitalize;\n  user-select: none;\n  line-height: 18px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 11px;\n  font-weight: 200;\n  color: #737373;\n  background-color: #f3f3f3;\n  border-color: #737373;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n  color: white;\n  background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n  cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n  z-index: 1024;\n  position: absolute;\n  top: 8px;\n  left: 50%;\n  transform: translate(-50%, 0%);\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n  background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-top: 2px;\n  padding-bottom: 2px;\n  width: 100%;\n  height: 100%;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n  position: absolute;\n  top: 10px;\n  left: 50%;\n}\n.igv-zoom-in-notice div {\n  position: relative;\n  left: -50%;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #3f3f3f;\n  background-color: rgba(255, 255, 255, 0.51);\n  z-index: 64;\n}\n\n.igv-container-spinner {\n  position: absolute;\n  top: 90%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  z-index: 1024;\n  width: 24px;\n  height: 24px;\n  pointer-events: none;\n  color: #737373;\n}\n\n.igv-multi-locus-close-button {\n  position: absolute;\n  top: 2px;\n  right: 0;\n  padding-left: 2px;\n  padding-right: 2px;\n  width: 12px;\n  height: 12px;\n  color: #666666;\n  background-color: white;\n  z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n  vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n  cursor: pointer;\n  color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n  z-index: 64;\n  position: absolute;\n  top: 2px;\n  left: 0;\n  width: 100%;\n  height: 12px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label > div {\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 12px;\n  color: rgb(16, 16, 16);\n  background-color: white;\n}\n.igv-multi-locus-ruler-label > div {\n  cursor: pointer;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n  z-index: 64;\n  position: absolute;\n  left: 50%;\n  top: 5%;\n  transform: translate(-50%, 0%);\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n  width: 14px;\n  height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n  margin-left: 16px;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n}\n\n.igv-ruler-sweeper {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 26px;\n  bottom: 0;\n  left: 0;\n  width: 0;\n  z-index: 99999;\n  background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n  pointer-events: none;\n  z-index: 128;\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 1px;\n  height: 32px;\n  background-color: transparent;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-ruler-tooltip > div {\n  pointer-events: none;\n  width: 128px;\n  height: auto;\n  padding: 1px;\n  color: #373737;\n  font-size: 10px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  background-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-color: #373737;\n}\n\n.igv-track-label {\n  position: absolute;\n  left: 8px;\n  top: 8px;\n  width: auto;\n  height: auto;\n  max-width: 50%;\n  padding-left: 4px;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  text-align: center;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-color: #444;\n  border-radius: 2px;\n  border-style: solid;\n  border-width: thin;\n  background-color: white;\n  z-index: 128;\n  cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n  background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-top: 4px;\n}\n\n.igv-center-line {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  transform: translateX(-50%);\n  z-index: 8;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-left-style: dashed;\n  border-left-width: thin;\n  border-right-style: dashed;\n  border-right-width: thin;\n}\n\n.igv-center-line-wide {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n  display: none;\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  left: 0;\n  right: 0;\n  top: 50%;\n  height: 1px;\n  z-index: 1;\n  margin-left: 50px;\n  margin-right: 54px;\n  border-top-style: dotted;\n  border-top-width: thin;\n  border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  width: 1px;\n  z-index: 1;\n  border-left-style: dotted;\n  border-left-width: thin;\n  border-left-color: rgba(127, 127, 127, 0.76);\n  display: none;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-generic-dialog-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 300px;\n  height: 200px;\n  border-color: #7F7F7F;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  z-index: 2048;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n  color: #373737;\n  width: 95%;\n  height: 24px;\n  line-height: 24px;\n  text-align: left;\n  margin-top: 8px;\n  padding-left: 8px;\n  overflow-wrap: break-word;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n  margin-top: 8px;\n  width: 95%;\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  padding-left: 8px;\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n  width: 30%;\n  height: 100%;\n  font-size: 16px;\n  text-align: right;\n  padding-right: 8px;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  width: 50%;\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n  margin-top: 8px;\n  width: calc(100% - 16px);\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n  width: 100%;\n  height: 28px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n  margin-top: 32px;\n  color: white;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  width: 75px;\n  height: 28px;\n  line-height: 28px;\n  text-align: center;\n  border-color: transparent;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n  margin-left: 32px;\n  margin-right: 0;\n  background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n  margin-left: 0;\n  margin-right: 32px;\n  background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n  cursor: pointer;\n  background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n  cursor: pointer;\n  background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n  width: 100%;\n  height: 36px;\n  margin-top: 32px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n  width: 98px;\n  height: 36px;\n  line-height: 36px;\n  text-align: center;\n  color: white;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  border-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 4px;\n  background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n  cursor: pointer;\n  background-color: #25597f;\n}\n\n.igv-generic-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  z-index: 2048;\n  background-color: white;\n  cursor: pointer;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: wrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-container div:first-child {\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  height: 24px;\n  width: 100%;\n  background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n  display: block;\n  color: #5f5f5f;\n  cursor: pointer;\n  width: 14px;\n  height: 14px;\n  margin-right: 8px;\n  margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: max-content;\n  z-index: 4096;\n  cursor: pointer;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background: white;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-end;\n  text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n  width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n  background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n  padding-left: 4px;\n  padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n  background: #efefef;\n}\n\n.igv-menu-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-bottom: 1px;\n  padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n  position: relative;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-menu-popup-header div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n.igv-menu-popup-check-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 100%;\n  height: 20px;\n  margin-right: 4px;\n  background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n  padding-top: 2px;\n  padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n  position: relative;\n  width: 12px;\n  height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n  position: absolute;\n  width: 12px;\n  height: 12px;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-loading-spinner-container {\n  z-index: 1024;\n  position: absolute;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 32px;\n  height: 32px;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-loading-spinner-container > div {\n  box-sizing: border-box;\n  width: 100%;\n  height: 100%;\n  border-radius: 50%;\n  border: 4px solid rgba(128, 128, 128, 0.5);\n  border-top-color: rgb(255, 255, 255);\n  animation: spin 1s ease-in-out infinite;\n  -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n@-webkit-keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n.igv-roi-menu-next-gen {\n  position: absolute;\n  z-index: 512;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background-color: white;\n  width: 192px;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu-next-gen > div:first-child {\n  height: 24px;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-roi-menu-next-gen > div:first-child > div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-roi-menu-next-gen > div:first-child > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-menu-next-gen > div:last-child {\n  background-color: white;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  text-align: start;\n  vertical-align: middle;\n}\n.igv-roi-menu-next-gen > div:last-child > div {\n  height: 24px;\n  padding-left: 4px;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  border-bottom-color: #7f7f7f;\n}\n.igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n  background-color: rgba(127, 127, 127, 0.1);\n}\n.igv-roi-menu-next-gen > div:last-child div:first-child {\n  font-style: italic;\n  text-align: center;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-menu-next-gen > div:last-child > div:last-child {\n  border-bottom-width: 0;\n  border-bottom-color: transparent;\n}\n\n.igv-roi-placeholder {\n  font-style: normal;\n  color: rgba(75, 75, 75, 0.6);\n}\n\n.igv-roi-table {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  cursor: default;\n}\n.igv-roi-table > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table > .igv-roi-table-description {\n  height: fit-content;\n  padding: 4px;\n  margin-left: 4px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-roi-table > .igv-roi-table-goto-explainer {\n  margin-left: 4px;\n  color: #7F7F7F;\n  font-style: italic;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: left;\n  margin-left: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  border-right-color: #7f7f7f;\n  border-right-style: solid;\n  border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\n  border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n  resize: both;\n  overflow: scroll;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: left;\n  margin-left: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  border-right-color: transparent;\n  border-right-style: solid;\n  border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\n  border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-row-selected {\n  background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n  cursor: pointer;\n  height: 20px;\n  user-select: none;\n  line-height: 20px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 13px;\n  font-weight: 400;\n  color: black;\n  padding-left: 6px;\n  padding-right: 6px;\n  background-color: rgb(239, 239, 239);\n  border-color: black;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n  font-weight: 400;\n  background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n  z-index: 64;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  pointer-events: none;\n  overflow: visible;\n  margin-top: 44px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-region > div {\n  position: relative;\n  width: 100%;\n  height: 8px;\n  pointer-events: auto;\n}\n\n.igv-roi-menu {\n  position: absolute;\n  z-index: 1024;\n  width: 144px;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n  border-bottom-color: rgba(128, 128, 128, 0.5);\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-menu > div:first-child {\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-color: transparent;\n  border-top-style: solid;\n  border-top-width: 0;\n}\n.igv-roi-menu > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n}\n\n.igv-roi-menu-row {\n  height: 24px;\n  padding-left: 8px;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n  background-color: white;\n}\n\n.igv-roi-menu-row-edit-description {\n  width: -webkit-fill-available;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  background-color: white;\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-bottom: 4px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-menu-row-edit-description > label {\n  margin-left: 2px;\n  margin-bottom: 0;\n  display: block;\n  width: -webkit-fill-available;\n}\n.igv-roi-menu-row-edit-description > input {\n  display: block;\n  margin-left: 2px;\n  margin-right: 2px;\n  margin-bottom: 1px;\n  width: -webkit-fill-available;\n}\n\n.igv-container {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  padding-top: 4px;\n  user-select: none;\n  -webkit-user-select: none;\n  -ms-user-select: none;\n}\n\n.igv-viewport {\n  position: relative;\n  margin-top: 5px;\n  line-height: 1;\n  overflow-x: hidden;\n  overflow-y: hidden;\n}\n\n.igv-viewport-content {\n  position: relative;\n  width: 100%;\n}\n.igv-viewport-content > canvas {\n  position: relative;\n  display: block;\n}\n\n.igv-column-container {\n  position: relative;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  width: 100%;\n}\n\n.igv-column-shim {\n  width: 1px;\n  margin-left: 2px;\n  margin-right: 2px;\n  background-color: #545453;\n}\n\n.igv-column {\n  position: relative;\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-axis-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 50px;\n}\n.igv-axis-column > div {\n  margin-top: 5px;\n  width: 100%;\n}\n\n.igv-sample-name-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-scrollbar-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 14px;\n}\n.igv-scrollbar-column > div {\n  position: relative;\n  margin-top: 5px;\n  width: 14px;\n}\n.igv-scrollbar-column > div > div {\n  cursor: pointer;\n  position: absolute;\n  top: 0;\n  left: 2px;\n  width: 8px;\n  border-width: 1px;\n  border-style: solid;\n  border-color: #c4c4c4;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n  background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 12px;\n  background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n  z-index: 512;\n  position: relative;\n  cursor: pointer;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n  border-top-right-radius: 6px;\n  border-bottom-right-radius: 6px;\n  background-color: #c4c4c4;\n}\n.igv-track-drag-column .igv-track-drag-handle-hover {\n  background-color: #787878;\n}\n.igv-track-drag-column > .igv-track-drag-shim {\n  position: relative;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n}\n\n.igv-gear-menu-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 28px;\n}\n.igv-gear-menu-column > div {\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  margin-top: 5px;\n  width: 100%;\n  background: white;\n}\n.igv-gear-menu-column > div > div {\n  position: relative;\n  margin-top: 4px;\n  width: 16px;\n  height: 16px;\n  color: #7F7F7F;\n}\n.igv-gear-menu-column > div > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n/*# sourceMappingURL=dom.css.map */\n';
+    var css = '.igv-navbar {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  box-sizing: border-box;\n  width: 100%;\n  color: #444;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  line-height: 32px;\n  padding-left: 8px;\n  padding-right: 8px;\n  margin-top: 2px;\n  margin-bottom: 6px;\n  height: 32px;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: #f3f3f3;\n}\n.igv-navbar .igv-navbar-left-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-left-container .igv-logo {\n  width: 34px;\n  height: 32px;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-left-container .igv-current-genome {\n  height: 32px;\n  margin-left: 4px;\n  margin-right: 4px;\n  user-select: none;\n  line-height: 32px;\n  vertical-align: middle;\n  text-align: center;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container {\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n  height: 100%;\n  width: 125px;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-chromosome-select-widget-container select {\n  display: block;\n  cursor: pointer;\n  width: 100px;\n  height: 75%;\n  outline: none;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  margin-left: 8px;\n  height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 210px;\n  height: 22px;\n  line-height: 22px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container input.igv-search-input {\n  cursor: text;\n  width: 85%;\n  height: 22px;\n  line-height: 22px;\n  font-size: 12px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  text-align: left;\n  padding-left: 8px;\n  margin-right: 8px;\n  outline: none;\n  border-style: solid;\n  border-radius: 3px;\n  border-width: thin;\n  border-color: #bfbfbf;\n  background-color: white;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-search-container .igv-search-icon-container {\n  cursor: pointer;\n  height: 16px;\n  width: 16px;\n}\n.igv-navbar .igv-navbar-left-container .igv-navbar-genomic-location .igv-locus-size-group .igv-windowsize-panel-container {\n  margin-left: 4px;\n  user-select: none;\n}\n.igv-navbar .igv-navbar-right-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 32px;\n  line-height: 32px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n  height: 100%;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div {\n  margin-left: 0;\n  margin-right: 4px;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container div:last-child {\n  margin-left: 0;\n  margin-right: 0;\n}\n.igv-navbar .igv-navbar-right-container .igv-navbar-toggle-button-container-750 {\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget div:nth-child(even) {\n  display: block;\n  height: fit-content;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget input {\n  display: block;\n  width: 125px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 {\n  color: #737373;\n  font-size: 18px;\n  height: 32px;\n  line-height: 32px;\n  margin-left: 8px;\n  user-select: none;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div {\n  cursor: pointer;\n  margin-left: unset;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:first-child {\n  height: 24px;\n  width: 24px;\n  margin-left: unset;\n  margin-right: 8px;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:last-child {\n  height: 24px;\n  width: 24px;\n  margin-left: 8px;\n  margin-right: unset;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 div:nth-child(even) {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 input {\n  width: 0;\n  height: 0;\n  display: none;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-900 svg {\n  display: block;\n}\n.igv-navbar .igv-navbar-right-container .igv-zoom-widget-hidden {\n  display: none;\n}\n\n.igv-navbar-button {\n  display: block;\n  box-sizing: unset;\n  padding-left: 6px;\n  padding-right: 6px;\n  height: 18px;\n  text-transform: capitalize;\n  user-select: none;\n  line-height: 18px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 11px;\n  font-weight: 200;\n  color: #737373;\n  background-color: #f3f3f3;\n  border-color: #737373;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 6px;\n}\n\n.igv-navbar-button-clicked {\n  color: white;\n  background-color: #737373;\n}\n\n.igv-navbar-button:hover {\n  cursor: pointer;\n}\n\n.igv-zoom-in-notice-container {\n  z-index: 1024;\n  position: absolute;\n  top: 8px;\n  left: 50%;\n  transform: translate(-50%, 0%);\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n  background-color: white;\n}\n.igv-zoom-in-notice-container > div {\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-top: 2px;\n  padding-bottom: 2px;\n  width: 100%;\n  height: 100%;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: #3f3f3f;\n}\n\n.igv-zoom-in-notice {\n  position: absolute;\n  top: 10px;\n  left: 50%;\n}\n.igv-zoom-in-notice div {\n  position: relative;\n  left: -50%;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #3f3f3f;\n  background-color: rgba(255, 255, 255, 0.51);\n  z-index: 64;\n}\n\n.igv-container-spinner {\n  position: absolute;\n  top: 90%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  z-index: 1024;\n  width: 24px;\n  height: 24px;\n  pointer-events: none;\n  color: #737373;\n}\n\n.igv-multi-locus-close-button {\n  position: absolute;\n  top: 2px;\n  right: 0;\n  padding-left: 2px;\n  padding-right: 2px;\n  width: 12px;\n  height: 12px;\n  color: #666666;\n  background-color: white;\n  z-index: 1000;\n}\n.igv-multi-locus-close-button > svg {\n  vertical-align: top;\n}\n\n.igv-multi-locus-close-button:hover {\n  cursor: pointer;\n  color: #434343;\n}\n\n.igv-multi-locus-ruler-label {\n  z-index: 64;\n  position: absolute;\n  top: 2px;\n  left: 0;\n  width: 100%;\n  height: 12px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label > div {\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 12px;\n  color: rgb(16, 16, 16);\n  background-color: white;\n}\n.igv-multi-locus-ruler-label > div {\n  cursor: pointer;\n}\n\n.igv-multi-locus-ruler-label-square-dot {\n  z-index: 64;\n  position: absolute;\n  left: 50%;\n  top: 5%;\n  transform: translate(-50%, 0%);\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-multi-locus-ruler-label-square-dot > div:first-child {\n  width: 14px;\n  height: 14px;\n}\n.igv-multi-locus-ruler-label-square-dot > div:last-child {\n  margin-left: 16px;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  color: rgb(16, 16, 16);\n}\n\n.igv-ruler-sweeper {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 26px;\n  bottom: 0;\n  left: 0;\n  width: 0;\n  z-index: 99999;\n  background-color: rgba(68, 134, 247, 0.25);\n}\n\n.igv-ruler-tooltip {\n  pointer-events: none;\n  z-index: 128;\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 1px;\n  height: 32px;\n  background-color: transparent;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-ruler-tooltip > div {\n  pointer-events: none;\n  width: 128px;\n  height: auto;\n  padding: 1px;\n  color: #373737;\n  font-size: 10px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  background-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-color: #373737;\n}\n\n.igv-track-label {\n  position: absolute;\n  left: 8px;\n  top: 8px;\n  width: auto;\n  height: auto;\n  max-width: 50%;\n  padding-left: 4px;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  text-align: center;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-color: #444;\n  border-radius: 2px;\n  border-style: solid;\n  border-width: thin;\n  background-color: white;\n  z-index: 128;\n  cursor: pointer;\n}\n\n.igv-track-label:hover,\n.igv-track-label:focus,\n.igv-track-label:active {\n  background-color: #e8e8e8;\n}\n\n.igv-track-label-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-top: 4px;\n}\n\n.igv-center-line {\n  display: none;\n  pointer-events: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  transform: translateX(-50%);\n  z-index: 8;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  border-left-style: dashed;\n  border-left-width: thin;\n  border-right-style: dashed;\n  border-right-width: thin;\n}\n\n.igv-center-line-wide {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(127, 127, 127, 0.51);\n}\n\n.igv-center-line-thin {\n  background-color: rgba(0, 0, 0, 0);\n  border-left-color: rgba(127, 127, 127, 0.51);\n  border-right-color: rgba(0, 0, 0, 0);\n}\n\n.igv-cursor-guide-horizontal {\n  display: none;\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  left: 0;\n  right: 0;\n  top: 50%;\n  height: 1px;\n  z-index: 1;\n  margin-left: 50px;\n  margin-right: 54px;\n  border-top-style: dotted;\n  border-top-width: thin;\n  border-top-color: rgba(127, 127, 127, 0.76);\n}\n\n.igv-cursor-guide-vertical {\n  pointer-events: none;\n  user-select: none;\n  -moz-user-select: none;\n  -webkit-user-select: none;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  left: 50%;\n  width: 1px;\n  z-index: 1;\n  border-left-style: dotted;\n  border-left-width: thin;\n  border-left-color: rgba(127, 127, 127, 0.76);\n  display: none;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-generic-dialog-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: 300px;\n  height: 200px;\n  border-color: #7F7F7F;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  z-index: 2048;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-generic-dialog-container .igv-generic-dialog-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-generic-dialog-container .igv-generic-dialog-one-liner {\n  color: #373737;\n  width: 95%;\n  height: 24px;\n  line-height: 24px;\n  text-align: left;\n  margin-top: 8px;\n  padding-left: 8px;\n  overflow-wrap: break-word;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input {\n  margin-top: 8px;\n  width: 95%;\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  padding-left: 8px;\n  background-color: white;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input div {\n  width: 30%;\n  height: 100%;\n  font-size: 16px;\n  text-align: right;\n  padding-right: 8px;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-label-input input {\n  width: 50%;\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input {\n  margin-top: 8px;\n  width: calc(100% - 16px);\n  height: 24px;\n  color: #373737;\n  line-height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  display: block;\n  height: 100%;\n  width: 100%;\n  padding-left: 4px;\n  font-family: \"Open Sans\", sans-serif;\n  font-weight: 400;\n  color: #373737;\n  text-align: left;\n  outline: none;\n  border-style: solid;\n  border-width: thin;\n  border-color: #7F7F7F;\n  background-color: white;\n}\n.igv-generic-dialog-container .igv-generic-dialog-input input {\n  font-size: 16px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel {\n  width: 100%;\n  height: 28px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div {\n  margin-top: 32px;\n  color: white;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 14px;\n  font-weight: 400;\n  width: 75px;\n  height: 28px;\n  line-height: 28px;\n  text-align: center;\n  border-color: transparent;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 2px;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child {\n  margin-left: 32px;\n  margin-right: 0;\n  background-color: #5ea4e0;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child {\n  margin-left: 0;\n  margin-right: 32px;\n  background-color: #c4c4c4;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:first-child:hover {\n  cursor: pointer;\n  background-color: #3b5c7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok-cancel div:last-child:hover {\n  cursor: pointer;\n  background-color: #7f7f7f;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok {\n  width: 100%;\n  height: 36px;\n  margin-top: 32px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div {\n  width: 98px;\n  height: 36px;\n  line-height: 36px;\n  text-align: center;\n  color: white;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  border-color: white;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 4px;\n  background-color: #2B81AF;\n}\n.igv-generic-dialog-container .igv-generic-dialog-ok div:hover {\n  cursor: pointer;\n  background-color: #25597f;\n}\n\n.igv-generic-container {\n  position: absolute;\n  top: 0;\n  left: 0;\n  z-index: 2048;\n  background-color: white;\n  cursor: pointer;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: wrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-generic-container div:first-child {\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n  height: 24px;\n  width: 100%;\n  background-color: #dddddd;\n}\n.igv-generic-container div:first-child i {\n  display: block;\n  color: #5f5f5f;\n  cursor: pointer;\n  width: 14px;\n  height: 14px;\n  margin-right: 8px;\n  margin-bottom: 4px;\n}\n\n.igv-menu-popup {\n  position: absolute;\n  top: 0;\n  left: 0;\n  width: max-content;\n  z-index: 4096;\n  cursor: pointer;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background: white;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-end;\n  text-align: left;\n}\n.igv-menu-popup > div:not(:first-child) {\n  width: 100%;\n}\n.igv-menu-popup > div:not(:first-child) > div {\n  background: white;\n}\n.igv-menu-popup > div:not(:first-child) > div.context-menu {\n  padding-left: 4px;\n  padding-right: 4px;\n}\n.igv-menu-popup > div:not(:first-child) > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-menu-popup > div:not(:first-child) > div:hover {\n  background: #efefef;\n}\n\n.igv-menu-popup-shim {\n  padding-left: 8px;\n  padding-right: 8px;\n  padding-bottom: 1px;\n  padding-top: 1px;\n}\n\n.igv-menu-popup-header {\n  position: relative;\n  width: 100%;\n  height: 24px;\n  cursor: move;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-menu-popup-header div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-menu-popup-header div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n.igv-menu-popup-check-container {\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  width: 100%;\n  height: 20px;\n  margin-right: 4px;\n  background-color: transparent;\n}\n.igv-menu-popup-check-container div {\n  padding-top: 2px;\n  padding-left: 8px;\n}\n.igv-menu-popup-check-container div:first-child {\n  position: relative;\n  width: 12px;\n  height: 12px;\n}\n.igv-menu-popup-check-container div:first-child svg {\n  position: absolute;\n  width: 12px;\n  height: 12px;\n}\n\n.igv-user-feedback {\n  position: fixed;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 512px;\n  height: 360px;\n  z-index: 2048;\n  background-color: white;\n  border-color: #a2a2a2;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: medium;\n  font-weight: 400;\n  color: #444;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n}\n.igv-user-feedback div:first-child {\n  position: relative;\n  height: 24px;\n  width: 100%;\n  background-color: white;\n  border-bottom-color: #a2a2a2;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-user-feedback div:first-child div {\n  position: absolute;\n  top: 2px;\n  width: 16px;\n  height: 16px;\n  background-color: transparent;\n}\n.igv-user-feedback div:first-child div:first-child {\n  left: 8px;\n}\n.igv-user-feedback div:first-child div:last-child {\n  cursor: pointer;\n  right: 8px;\n}\n.igv-user-feedback div:last-child {\n  width: 100%;\n  height: calc(100% - 24px);\n  border-width: 0;\n}\n.igv-user-feedback div:last-child div {\n  width: auto;\n  height: auto;\n  margin: 8px;\n}\n\n.igv-loading-spinner-container {\n  z-index: 1024;\n  position: absolute;\n  top: 50%;\n  left: 50%;\n  transform: translate(-50%, -50%);\n  width: 32px;\n  height: 32px;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: center;\n  align-items: center;\n}\n.igv-loading-spinner-container > div {\n  box-sizing: border-box;\n  width: 100%;\n  height: 100%;\n  border-radius: 50%;\n  border: 4px solid rgba(128, 128, 128, 0.5);\n  border-top-color: rgb(255, 255, 255);\n  animation: spin 1s ease-in-out infinite;\n  -webkit-animation: spin 1s ease-in-out infinite;\n}\n\n@keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n@-webkit-keyframes spin {\n  to {\n    -webkit-transform: rotate(360deg);\n    transform: rotate(360deg);\n  }\n}\n.igv-roi-menu-next-gen {\n  position: absolute;\n  z-index: 512;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: small;\n  font-weight: 400;\n  color: #4b4b4b;\n  background-color: white;\n  width: 192px;\n  border-radius: 4px;\n  border-color: #7F7F7F;\n  border-style: solid;\n  border-width: thin;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu-next-gen > div:first-child {\n  height: 24px;\n  border-top-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-color: #7F7F7F;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: flex-end;\n  align-items: center;\n}\n.igv-roi-menu-next-gen > div:first-child > div {\n  margin-right: 4px;\n  height: 12px;\n  width: 12px;\n  color: #7F7F7F;\n}\n.igv-roi-menu-next-gen > div:first-child > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-menu-next-gen > div:last-child {\n  background-color: white;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  text-align: start;\n  vertical-align: middle;\n}\n.igv-roi-menu-next-gen > div:last-child > div {\n  height: 24px;\n  padding-left: 4px;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  border-bottom-color: #7f7f7f;\n}\n.igv-roi-menu-next-gen > div:last-child > div:not(:first-child):hover {\n  background-color: rgba(127, 127, 127, 0.1);\n}\n.igv-roi-menu-next-gen > div:last-child div:first-child {\n  font-style: italic;\n  text-align: center;\n  padding-right: 4px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n}\n.igv-roi-menu-next-gen > div:last-child > div:last-child {\n  border-bottom-width: 0;\n  border-bottom-color: transparent;\n}\n\n.igv-roi-placeholder {\n  font-style: normal;\n  color: rgba(75, 75, 75, 0.6);\n}\n\n.igv-roi-table {\n  position: absolute;\n  z-index: 1024;\n  width: fit-content;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 12px;\n  font-weight: 400;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  cursor: default;\n}\n.igv-roi-table > div {\n  height: 24px;\n  font-size: 14px;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n}\n.igv-roi-table > div:first-child {\n  border-color: transparent;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-width: 0;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n  background-color: #eee;\n  cursor: move;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-between;\n  align-items: center;\n}\n.igv-roi-table > div:first-child > div:first-child {\n  text-align: center;\n  width: calc(100% - 4px - 12px);\n}\n.igv-roi-table > div:first-child > div:last-child {\n  margin-right: 4px;\n  margin-bottom: 2px;\n  height: 12px;\n  width: 12px;\n  color: #7f7f7f;\n}\n.igv-roi-table > div:first-child > div:last-child > svg {\n  display: block;\n}\n.igv-roi-table > div:first-child > div:last-child:hover {\n  cursor: pointer;\n  color: #444;\n}\n.igv-roi-table > .igv-roi-table-description {\n  height: fit-content;\n  padding: 4px;\n  margin-left: 4px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  word-break: break-all;\n  max-height: 300px;\n  overflow-y: auto;\n}\n.igv-roi-table > .igv-roi-table-goto-explainer {\n  margin-left: 4px;\n  color: #7F7F7F;\n  font-style: italic;\n  border-top: solid lightgray;\n  margin-top: 5px;\n}\n.igv-roi-table > .igv-roi-table-column-titles {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n  padding-right: 16px;\n  background-color: white;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: #7f7f7f;\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: left;\n  margin-left: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  border-right-color: #7f7f7f;\n  border-right-style: solid;\n  border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-column-titles > div:last-child {\n  border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container {\n  overflow: scroll;\n  min-height: 72px;\n  height: 144px;\n  max-height: 480px;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row {\n  height: 24px;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div {\n  font-size: 14px;\n  vertical-align: middle;\n  line-height: 24px;\n  text-align: left;\n  margin-left: 4px;\n  height: 24px;\n  white-space: nowrap;\n  overflow: hidden;\n  text-overflow: ellipsis;\n  border-right-color: transparent;\n  border-right-style: solid;\n  border-right-width: thin;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row > div:last-child {\n  border-right: unset;\n}\n.igv-roi-table > .igv-roi-table-row-container > .igv-roi-table-row-hover {\n  background-color: rgba(0, 0, 0, 0.04);\n}\n.igv-roi-table > div:last-child {\n  height: 32px;\n  line-height: 32px;\n  border-top-color: #7f7f7f;\n  border-top-style: solid;\n  border-top-width: thin;\n  border-bottom-color: transparent;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-width: 0;\n  background-color: #eee;\n  display: flex;\n  flex-flow: row;\n  flex-wrap: nowrap;\n  justify-content: space-around;\n  align-items: center;\n}\n\n.igv-roi-table-row-selected {\n  background-color: rgba(0, 0, 0, 0.125);\n}\n\n.igv-roi-table-button {\n  cursor: pointer;\n  height: 20px;\n  user-select: none;\n  line-height: 20px;\n  text-align: center;\n  vertical-align: middle;\n  font-family: \"Open Sans\", sans-serif;\n  font-size: 13px;\n  font-weight: 400;\n  color: black;\n  padding-left: 6px;\n  padding-right: 6px;\n  background-color: rgb(239, 239, 239);\n  border-color: black;\n  border-style: solid;\n  border-width: thin;\n  border-radius: 3px;\n}\n\n.igv-roi-table-button:hover {\n  font-weight: 400;\n  background-color: rgba(0, 0, 0, 0.13);\n}\n\n.igv-roi-region {\n  z-index: 64;\n  position: absolute;\n  top: 0;\n  bottom: 0;\n  pointer-events: none;\n  overflow: visible;\n  margin-top: 44px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-region > div {\n  position: relative;\n  width: 100%;\n  height: 8px;\n  pointer-events: auto;\n}\n\n.igv-roi-menu {\n  position: absolute;\n  z-index: 1024;\n  width: 144px;\n  border-color: #7f7f7f;\n  border-radius: 4px;\n  border-style: solid;\n  border-width: thin;\n  font-family: \"Open Sans\", sans-serif;\n  background-color: white;\n  display: flex;\n  flex-flow: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n}\n.igv-roi-menu > div:not(:last-child) {\n  border-bottom-color: rgba(128, 128, 128, 0.5);\n  border-bottom-style: solid;\n  border-bottom-width: thin;\n}\n.igv-roi-menu > div:first-child {\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-top-color: transparent;\n  border-top-style: solid;\n  border-top-width: 0;\n}\n.igv-roi-menu > div:last-child {\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n  border-bottom-color: transparent;\n  border-bottom-style: solid;\n  border-bottom-width: 0;\n}\n\n.igv-roi-menu-row {\n  height: 24px;\n  padding-left: 8px;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  line-height: 24px;\n  background-color: white;\n}\n\n.igv-roi-menu-row-edit-description {\n  width: -webkit-fill-available;\n  font-size: small;\n  text-align: start;\n  vertical-align: middle;\n  background-color: white;\n  padding-left: 4px;\n  padding-right: 4px;\n  padding-bottom: 4px;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: stretch;\n  align-items: stretch;\n}\n.igv-roi-menu-row-edit-description > label {\n  margin-left: 2px;\n  margin-bottom: 0;\n  display: block;\n  width: -webkit-fill-available;\n}\n.igv-roi-menu-row-edit-description > input {\n  display: block;\n  margin-left: 2px;\n  margin-right: 2px;\n  margin-bottom: 1px;\n  width: -webkit-fill-available;\n}\n\n.igv-container {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  padding-top: 4px;\n  user-select: none;\n  -webkit-user-select: none;\n  -ms-user-select: none;\n}\n\n.igv-viewport {\n  position: relative;\n  margin-top: 5px;\n  line-height: 1;\n  overflow-x: hidden;\n  overflow-y: hidden;\n}\n\n.igv-viewport-content {\n  position: relative;\n  width: 100%;\n}\n.igv-viewport-content > canvas {\n  position: relative;\n  display: block;\n}\n\n.igv-column-container {\n  position: relative;\n  display: flex;\n  flex-direction: row;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: stretch;\n  width: 100%;\n}\n\n.igv-column-shim {\n  width: 1px;\n  margin-left: 2px;\n  margin-right: 2px;\n  background-color: #545453;\n}\n\n.igv-column {\n  position: relative;\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-axis-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 50px;\n}\n.igv-axis-column > div {\n  margin-top: 5px;\n  width: 100%;\n}\n\n.igv-sample-name-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n}\n\n.igv-scrollbar-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 14px;\n}\n.igv-scrollbar-column > div {\n  position: relative;\n  margin-top: 5px;\n  width: 14px;\n}\n.igv-scrollbar-column > div > div {\n  cursor: pointer;\n  position: absolute;\n  top: 0;\n  left: 2px;\n  width: 8px;\n  border-width: 1px;\n  border-style: solid;\n  border-color: #c4c4c4;\n  border-top-left-radius: 4px;\n  border-top-right-radius: 4px;\n  border-bottom-left-radius: 4px;\n  border-bottom-right-radius: 4px;\n}\n.igv-scrollbar-column > div > div:hover {\n  background-color: #c4c4c4;\n}\n\n.igv-track-drag-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 12px;\n  background-color: white;\n}\n.igv-track-drag-column > .igv-track-drag-handle {\n  z-index: 512;\n  position: relative;\n  cursor: pointer;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n  border-top-right-radius: 6px;\n  border-bottom-right-radius: 6px;\n  background-color: #c4c4c4;\n}\n.igv-track-drag-column .igv-track-drag-handle-hover {\n  background-color: #787878;\n}\n.igv-track-drag-column > .igv-track-drag-shim {\n  position: relative;\n  margin-top: 5px;\n  width: 100%;\n  border-style: solid;\n  border-width: 0;\n}\n\n.igv-gear-menu-column {\n  position: relative;\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: flex-start;\n  box-sizing: border-box;\n  height: 100%;\n  width: 28px;\n}\n.igv-gear-menu-column > div {\n  display: flex;\n  flex-direction: column;\n  flex-wrap: nowrap;\n  justify-content: flex-start;\n  align-items: center;\n  margin-top: 5px;\n  width: 100%;\n  background: white;\n}\n.igv-gear-menu-column > div > div {\n  position: relative;\n  margin-top: 4px;\n  width: 16px;\n  height: 16px;\n  color: #7F7F7F;\n}\n.igv-gear-menu-column > div > div:hover {\n  cursor: pointer;\n  color: #444;\n}\n\n/*# sourceMappingURL=dom.css.map */\n';
 
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