loaderParagraph = { 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 title = params.get("title") || "COG-UK"; let loader = html`

Loading variant data...

`; loader.value = null; yield loader; let rd = await obtainSourceData( null, variant_url || "https://data.hyphy.org/web/SARS-CoV-2/variants.json.gz", 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 || "https://data.hyphy.org/web/SARS-CoV-2/meta.tsv.gz", true ); 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]] >= 0.1 && rd.keys[afc][rd.values[i + afc]] <= 0.25 ) { 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; let singlePoission = _.find( _.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]; } ), (d) => d[1] < -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]; yield retValue; }