loaderParagraph = { let predefURLs = _.fromPairs (_.map (manifest, (d)=>[d.label, d])); const baseURL = "https://raw.githubusercontent.com/veg/SARS-CoV-2/compact/intrahost/data/"; let params = new URLSearchParams(location.search); let variant_url = params.get ("variants"); let meta_url = params.get ("meta"); let attr_url = params.get ("attribution"); let pangolin_url = params.get ("pangolin"); let title = params.get ("title") || setToView; let loader = html`

Loading variant data...

`; loader.value = null; yield loader; let rd = await obtainSourceData (null, variant_url || baseURL + predefURLs[setToView].variants, false, true); let column_map = { "Sample" : 0, "AF" : 1, "variant_keys" : 2 }; let variant_key = { "POS" : 0, "REF": 1, "ALT" : 2, "EFFECT" : 3, "CODON" : 4, "TRID" : 5, "AA": 6 }; rd.top_cols = _.size (column_map); rd.inner_cols = _.size (variant_key); loader = html`

Loading metadata...

`; loader.value = null; yield loader; let an = await obtainSourceData (null, meta_url || baseURL + predefURLs[setToView].meta, true); loader = html`

Loading PANGOLIN annotation

`; yield loader; let pangolin = await obtainSourceData (null, pangolin_url || baseURL + predefURLs[setToView].pangolin, true); pangolin = _.chain (pangolin).map ((d)=>[d.taxon,d.lineage]).fromPairs().value(); loader = html`

Performing variant error filtering

`; yield loader; let cbp = _.map (_.range (29903), (d)=>0); let afc = column_map["AF"]; let var_key = column_map ["variant_keys"]; let posc = variant_key ["POS"]; for (let i = 0; i < rd.values.length; i += rd.top_cols) { if (rd.keys[afc][rd.values[i+afc]] >= 0.05 && rd.keys[afc][rd.values[i+afc]] <= 0.15) { const var_position = rd.variant_keys[posc][rd.keys[var_key][rd.values[i+var_key] * rd.inner_cols + posc]]; cbp [var_position] += 1; //pos.push (var_position); } } let bySiteCount = _.chain (cbp).countBy().toPairs().map ((d)=>{return {'samples' : +d[0], 'count' : d[1]}}).value(); let singleLambda = d3.sum (cbp) / cbp.length; let error_rate = singleLambda/29903; const poissonUndercount = _.map (_.filter (poissonSupport (singleLambda, _.map (bySiteCount, (d)=>d.samples), cbp.length), (d)=>d.count > 0.1), (d,i)=> {return [i,(d.count - bySiteCount[i].count)/d.count]}); let singlePoission = _.find (poissonUndercount, (d)=>d[1] < -1); if (!singlePoission)singlePoission = poissonUndercount[poissonUndercount.length-1]; let keep_in = {}; for (let i = 0; i < rd.values.length; i += rd.top_cols) { let vk = make_variant_key_long_encoded (rd.keys[var_key] , rd.values[i+var_key] * rd.inner_cols, variant_key); if (vk in keep_in) { keep_in[vk] += 1; } else { keep_in[vk] = 1; } } let before = rd.rows; //singlePoission[0] = 2; if (singlePoission[0] > 1) { let filtered_array = []; for (let i = 0; i < rd.values.length; i += rd.top_cols) { let vk = make_variant_key_long_encoded (rd.keys[var_key] , rd.values[i+var_key] * rd.inner_cols, variant_key); if (keep_in[vk] >= singlePoission[0]) { for (let j = 0; j < rd.top_cols; j+=1) { filtered_array.push (rd.values[i+j]); } } } rd.values = filtered_array; rd.rows = rd.values.length / rd.top_cols; } loader = html`

Rendering the dashboard

`; yield loader; let attributions = await d3.tsv (attr_url || "https://raw.githubusercontent.com/usegalaxy-eu/sars-cov-2-processing-requests/main/CONTRIBUTORS.tsv") let retValue = md`### Results computed using the [global platform for SARS-CoV-2 analysis](https://covid19.galaxyproject.org/genomics/global_platform/) Poisson modeling estimated the global error rate of ${floatFmt(error_rate)}/base; ${before-rd.rows} allelic variants (AV) occurring in fewer than ${singlePoission[0]} samples are deemed to be unreliable and have been removed. `; retValue.value = [rd,an, title, attributions, column_map, variant_key, pangolin]; yield retValue; }