@sjcrh/proteinpaint-client 2.224.2 → 2.226.0

package/dist/Disco.UI-UDUXNCZX.js

@@ -0,0 +1,239 @@
+import {
+  launch
+} from "./chunk-EARMOT6Q.js";
+import {
+  makeBtn,
+  makeFileUpload,
+  makeGenomeDropDown,
+  makePrompt,
+  makeResetBtn,
+  makeTextAreaInput
+} from "./chunk-5EBRF6Z7.js";
+import "./chunk-4WFXCUT4.js";
+import "./chunk-W2SBSEKT.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-LMONIWPI.js";
+import {
+  Tabs,
+  appear,
+  sayerror
+} from "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/disco/Disco.UI.ts
+function init_discoplotUI(holder, genomes, debugmode) {
+  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
+    "font-family",
+    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
+  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true).classed("sjpp-disco-ui", true);
+  const obj = {
+    data: []
+  };
+  makePrompt(wrapper, "Select Genome").style("font-size", "1.15em").style("padding", "10px 0px").style("color", "#003366");
+  genomeSelection(wrapper, genomes, obj);
+  makePrompt(wrapper, "Provide Data").style("font-size", "1.15em").style("padding", "10px 0px 5px 0px").style("color", "#003366");
+  wrapper.append("div").style("opacity", 0.75).style("padding", "10px 10px 15px 20px").style("width", "65vw").style("line-height", "1.5em").html(
+    '<p>The plot accepts multiple data types. Input fields for each data type are available in the tabs below. Upload a file or paste data in at least one data type tab and click "Create Disco Plot". <a href="https://proteinpaint.stjude.org/ppdemo/hg38/disco/discoDemoData.tar.gz" target="Demo data">Download example files</a></p>'
+  );
+  const dataTypeTabs_div = wrapper.append("div").style("margin-left", "2vw");
+  makeDataTypeTabs(dataTypeTabs_div, obj);
+  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("padding", "15px 0px");
+  submitButton(controlBtns_div, obj, genomes, wrapper, holder);
+  makeResetBtn(controlBtns_div, obj, ".disco_input");
+  if (debugmode) window["doms"] = obj;
+  return obj;
+}
+function genomeSelection(div, genomes, obj) {
+  const genome_div = div.append("div").style("margin-left", "40px");
+  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
+  obj.genome = g.node();
+}
+function makeDataTypeTabs(dataTypeTabs_div, obj) {
+  const tabs = [
+    {
+      label: "SNV Indel",
+      active: true,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "snv";
+        const listHTML = `<ol>
+					<li>chr</li>
+					<li>position</li>
+					<li>gene</li>
+					<li>aachange</li>
+					<li>class</li>
+					<li>DNA total reads (optional)</li>
+					<li>DNA alt reads (optional)</li>
+					<li>RNA total reads (optional)</li>
+					<li>RNA alt reads (optional)</li></ol>
+					<p>Example:</p>
+<pre style="margin-left: 10px;">
+chr1	226252135	H3F3A	K28M	M	100	25	80	16
+chr2	98765432	TestGene	TestMutation	F
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    },
+    {
+      label: "SV",
+      active: false,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "sv";
+        const listHTML = `<ol>
+					<li>chrA</li>
+					<li>posA</li>
+					<li>geneA (optional)</li>
+					<li>chrB</li>
+					<li>posB</li>
+					<li>geneB (optional)</li>
+				</ol>
+				<p>Example (with genes):</p>
+<pre style="margin-left: 10px;">
+chr6	3067605	MDC1	chr12	61521661	KMT2D
+</pre>
+				<p>Example (without genes):</p>
+<pre style="margin-left: 10px;">
+chr6	3067605	chr12	61521661
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    },
+    {
+      label: "CNV",
+      active: false,
+      callback: async (event, dataTypeTab) => {
+        dataTypeTab.key = "cnv";
+        const listHTML = `<ol>
+				<li>chr</li>
+				<li>start</li>
+				<li>stop</li>
+				<li>value</li>
+				</ol>
+				<p>Example:</p>
+<pre style="margin-left: 10px;">
+chr1	1	100000000	0.5
+chr1	100000000	200000000	-0.5
+</pre>`;
+        mainTabCallback(dataTypeTab, obj, listHTML);
+      }
+    }
+  ];
+  new Tabs({ holder: dataTypeTabs_div, tabs, tabsPosition: "vertical", linePosition: "right" }).main();
+}
+function mainTabCallback(dataTypeTab, obj, listHTML) {
+  dataTypeTab.contentHolder.style("border", "none").style("display", "block").style("padding-left", "30px");
+  makeDataInputTabs(dataTypeTab, obj);
+  dataTypeTab.contentHolder.append("div").style("padding", "15px 0px 0px 10px").style("opacity", 0.75).text(`Provide ${dataTypeTab.label} data in tab delimited format with the following columns:`).append("span").html(listHTML);
+  delete dataTypeTab.callback;
+}
+function makeDataInputTabs(dataTypeTab, obj) {
+  const width = 95;
+  const tabs = [
+    // //TODO: implement file upload and file path input once launch.adhoc is ready
+    {
+      label: "Select File",
+      active: true,
+      width,
+      callback: async (event, tab) => {
+        const key = dataTypeTab.key;
+        tab.contentHolder.style("border", "none").style("display", "block");
+        appear(tab.contentHolder);
+        tab.contentHolder.append("div").style("padding", "0px 0px 5px 15px").style("opacity", 0.65).text(`Select a local file`);
+        makeFileUpload2(tab, obj, key);
+        delete tab.callback;
+      }
+    },
+    // {
+    // 	label: 'File Path',
+    // 	active: false,
+    // 	width,
+    // 	callback: async (tab: Tab) => {
+    // 		const key = dataTypeTab.key
+    // 		tab.contentHolder.style('border', 'none').style('display', 'block')
+    // 		appear(tab.contentHolder)
+    // 		tab.contentHolder
+    // 			.append('div')
+    // 			.html(`<p style="margin-left: 10px; opacity: 0.65;">Provide a URL file path.</p>`)
+    // 		uiutils.makePrompt(tab.contentHolder, 'URL')
+    // 		makeTextEntryFilePathInput(tab.contentHolder, obj, key)
+    // 		delete tab.callback
+    // 	}
+    // },
+    {
+      label: "Paste Data",
+      active: false,
+      width,
+      callback: async (event, tab) => {
+        const key = dataTypeTab.key;
+        tab.contentHolder.style("border", "none").style("display", "block");
+        appear(tab.contentHolder);
+        makeCopyPasteInput(tab, obj, key);
+        delete tab.callback;
+      }
+    }
+  ];
+  new Tabs({ holder: dataTypeTab.contentHolder, tabs }).main();
+}
+function makeFileUpload2(tab, obj, key) {
+  const upload_div = tab.contentHolder.append("div").style("display", "inline-block");
+  const upload = makeFileUpload(upload_div).classed("disco_input", true);
+  upload.on("change", (event) => {
+    const file = event.target.files[0];
+    const reader = new FileReader();
+    reader.onload = (event2) => {
+      obj.data[key + "Text"] = event2.target.result;
+    };
+    reader.readAsText(file, "utf8");
+  });
+}
+function makeCopyPasteInput(tab, obj, key) {
+  const paste_div = tab.contentHolder.append("div").style("display", "block");
+  const paste = makeTextAreaInput({ div: paste_div, cols: 50 }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("disco_input", true).on("keyup", async () => {
+    obj.data[key + "Text"] = paste.property("value").trim();
+  });
+}
+function submitButton(div, obj, genomes, wrapper, holder) {
+  const submit = makeBtn({ div, text: "Create Disco Plot" });
+  const errorMessage_div = div.append("div");
+  submit.style("margin-right", "10px").style("font-size", "16px").classed("sjpp-ui-submitBtn", true).attr("type", "submit").on("click", () => {
+    if (!obj.data || obj.data == void 0) {
+      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
+      sayerror(sayerrorDiv, "Please provide data");
+      setTimeout(() => sayerrorDiv.remove(), 2e3);
+    } else {
+      const genomeObj = genomes[obj.genome.options[obj.genome.selectedIndex].text];
+      wrapper.remove();
+      launch(obj.data, genomeObj, holder);
+      backButton(holder, genomes);
+    }
+  });
+}
+function backButton(holder, genomes) {
+  holder.append("button").html("&#171; Back").on("click", () => {
+    holder.selectAll("*").remove();
+    init_discoplotUI(holder, genomes, false);
+  });
+}
+export {
+  init_discoplotUI
+};
+//# sourceMappingURL=Disco.UI-UDUXNCZX.js.map

package/dist/DmrPlot-FZCD6FTX.js

@@ -0,0 +1,366 @@
+import {
+  DmrViewModel,
+  getDefaultDMRSettings
+} from "./chunk-XKWLP433.js";
+import {
+  PlotBase,
+  startElapsedTimer,
+  table2col
+} from "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import {
+  dofetch3,
+  formatElapsedTime
+} from "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/dmr/model/DmrModel.ts
+var DmrModel = class {
+  constructor(config, vocab) {
+    this.config = config;
+    this.vocab = vocab;
+  }
+  async fetchDmr(chr, start, stop, signal) {
+    const { group1, group2, settings } = this.config;
+    const { genome, dslabel } = this.vocab;
+    return dofetch3("termdb/dmr", {
+      signal,
+      body: {
+        genome,
+        dslabel,
+        chr,
+        start,
+        stop,
+        group1,
+        group2,
+        lambda: settings.dmr.lambda,
+        C: settings.dmr.C,
+        fdr_cutoff: settings.dmr.fdr_cutoff,
+        group1Name: this.config.group1Name,
+        group2Name: this.config.group2Name,
+        blockWidth: settings.dmr.blockWidth,
+        devicePixelRatio: typeof window !== "undefined" ? window.devicePixelRatio : 1,
+        maxLoessRegion: settings.dmr.maxLoessRegion,
+        colors: settings.dmr.colors,
+        scanChromosomes: this.config.scanChromosomes,
+        backgroundCorrection: this.config.backgroundCorrection,
+        minCpgs: this.config.minCpgs,
+        yAxis: this.config.yAxis,
+        filter0: this.config.filter0
+      }
+    });
+  }
+};
+
+// plots/dmr/view/DmrView.ts
+var DmrView = class {
+  constructor(dom) {
+    this.dom = dom;
+  }
+  async renderBlock(viewData, genomeObj, settings, chr, start, stop, onCoordinateChange) {
+    const { Block } = await import("./block-YGQFUK5L.js");
+    return new Block({
+      holder: this.dom.holder,
+      genome: genomeObj,
+      chr,
+      start,
+      stop,
+      tklst: viewData.tklst,
+      nobox: true,
+      width: settings.blockWidth,
+      onCoordinateChange
+    });
+  }
+  updateTracks(viewData, blockInstance) {
+    for (const tk of blockInstance.tklst) {
+      const updated = viewData.tklst.find((t) => t.name === tk.name);
+      if (!updated) continue;
+      if (tk.type === "bedj" && updated.bedItems) {
+        tk.bedItems = updated.bedItems;
+        blockInstance.tk_load(tk);
+      } else if (tk.type === "bigwig" && updated.imgData) {
+        tk.imgData = updated.imgData;
+        blockInstance.tk_load(tk);
+      }
+    }
+  }
+  updateLegend(blockInstance, legendRows) {
+    if (!blockInstance?.legend?.holder) return;
+    const labels = ["Per-CpG Means", "DMR", "Sig. CpGs"];
+    blockInstance.legend.holder.selectAll("tr").filter((_d, i, nodes) => {
+      const td = nodes[i].querySelector("td");
+      return td && labels.includes(td.textContent);
+    }).remove();
+    this.renderLegend(blockInstance, legendRows);
+  }
+  renderLegend(blockInstance, legendRows) {
+    if (!blockInstance?.legend?.holder) return;
+    const { legendcolor, vpad } = blockInstance.legend;
+    for (const row of legendRows) {
+      const tr = blockInstance.legend.holder.append("tr");
+      tr.append("td").text(row.label).attr("style", `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`);
+      const td = tr.append("td");
+      for (const entry of row.items) {
+        const item = td.append("div").attr("style", `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`);
+        if (entry.style === "shaded") {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`
+          );
+        } else if (entry.style === "dashed") {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`
+          );
+        } else {
+          item.append("div").attr(
+            "style",
+            `display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`
+          );
+        }
+        item.append("div").attr("style", "display:inline-block;color:#555;font-size:.8em").text(entry.text);
+      }
+    }
+  }
+  renderDiagnostics(diagnostic, dmrs, fdr_cutoff) {
+    const panel = this.dom.diagnosticPanel;
+    panel.selectAll("*").remove();
+    panel.style("display", "block");
+    const { probes } = diagnostic;
+    const toggle = panel.append("div").attr("style", "cursor:default;font-size:12px;color:#888;padding:2px 0");
+    const statsContent = panel.append("div").style("display", "none");
+    let expanded = false;
+    toggle.text("+ Diagnostic details").on("click", () => {
+      expanded = !expanded;
+      toggle.text((expanded ? "\u2212 " : "+ ") + "Diagnostic details");
+      statsContent.style("display", expanded ? "block" : "none");
+    });
+    const spacings = diagnostic.probe_spacings;
+    const medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0;
+    const maxGap = spacings.length ? Math.max(...spacings) : 0;
+    const gapsOver1kb = spacings.filter((s) => s > 1e3).length;
+    const density = probes.positions.length > 1 ? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1e3) : 0;
+    const sigFdrCount = probes.sig.filter(Boolean).length;
+    const minDeltaBeta = 0.05;
+    const sigDualCount = probes.sig.filter((s, i) => {
+      if (!s) return false;
+      const m1 = probes.mean_group1[i];
+      const m2 = probes.mean_group2[i];
+      if (m1 == null || m2 == null) return false;
+      return Math.abs(m2 - m1) >= minDeltaBeta;
+    }).length;
+    const t = table2col({ holder: statsContent, disableScroll: true });
+    for (const [k, v] of [
+      ["Probes in region", String(probes.positions.length)],
+      ["FDR significant", `${sigFdrCount} (FDR < ${fdr_cutoff})`],
+      ["FDR + effect size", `${sigDualCount} (FDR < ${fdr_cutoff} & |\u0394\u03B2| \u2265 ${minDeltaBeta})`],
+      ["Probe density", `${density.toFixed(1)} probes/kb`],
+      ["Median spacing", `${medianSpacing.toFixed(0)} bp`],
+      ["Max gap", `${maxGap.toFixed(0)} bp`],
+      ["Gaps > 1kb", String(gapsOver1kb)],
+      ["DMRs called", String(dmrs.length)],
+      ...diagnostic.total_probes_analyzed ? [["Probes analyzed (genome-wide)", diagnostic.total_probes_analyzed.toLocaleString()]] : [],
+      ...diagnostic.elapsed_ms != null ? [["Analysis time", formatElapsedTime(diagnostic.elapsed_ms)]] : [],
+      ...diagnostic.peak_memory_mb != null ? [["Peak memory", `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : []
+    ]) {
+      t.addRow(k, v);
+    }
+  }
+  showOverlay() {
+    this.dom.loadingOverlay.style("display", "");
+  }
+  hideOverlay() {
+    this.dom.loadingOverlay.style("display", "none");
+  }
+  clearDiagnostics() {
+    this.dom.diagnosticPanel.selectAll("*").remove();
+    this.dom.diagnosticPanel.style("display", "none");
+  }
+  /** The view model's notes, one line each, under the plot */
+  showNotes(notes) {
+    this.dom.note.selectAll("*").remove();
+    for (const text of notes)
+      this.dom.note.append("div").attr("class", "sjpp-dmr-note").style("color", "#666").style("font-size", ".85em").style("padding", "4px 0").style("max-width", "900px").text(text);
+  }
+};
+
+// plots/dmr/DmrPlot.ts
+var LOADING_TEXT = "Running DMR analysis\u2026 A comparison not yet cached first runs DMRcate over the whole genome, which can take minutes.";
+var DmrPlot = class _DmrPlot extends PlotBase {
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _DmrPlot.type;
+    this.blockInstance = null;
+    this.analyzedRegion = null;
+    /** counts the requests that showed the loading text; see showLoading() */
+    this.loadingRequest = 0;
+    const wrapper = opts.holder.append("div").style("position", "relative");
+    const loadingOverlay = wrapper.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("z-index", "10").style("background-color", "rgba(255,255,255,0.65)");
+    this.dom = {
+      header: opts?.header,
+      holder: wrapper.append("div"),
+      loadingOverlay,
+      error: opts.holder.append("div"),
+      note: opts.holder.append("div"),
+      loading: opts.holder.append("div").style("display", "none"),
+      diagnosticPanel: opts.holder.append("div").style("display", "none")
+    };
+    this.view = new DmrView(this.dom);
+  }
+  static {
+    this.type = "dmr";
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    if (!config) throw new Error(`No plot with id='${this.id}' found`);
+    return { config };
+  }
+  async init(appState) {
+    const { config } = this.getState(appState);
+    validateConfig(config);
+    if (this.dom.header) this.dom.header.text(config.headerText || "DMR Analysis");
+    this.genomeObj = this.app.opts.genome;
+    this.model = new DmrModel(config, this.app.vocabApi.vocab);
+  }
+  async main() {
+    const config = this.state.config;
+    this.model = new DmrModel(config, this.app.vocabApi.vocab);
+    const c = config.coordinateOverride;
+    if (!c) return;
+    const pad = config.settings.dmr.pad;
+    const chr = c.chr;
+    const start = Math.max(0, Number(c.start) - pad);
+    const stop = Number(c.stop) + pad;
+    const a = this.analyzedRegion;
+    const coordsChanged = a && (chr !== a.chr || start !== a.start || stop !== a.stop);
+    if (a && coordsChanged) {
+      this.view.showOverlay();
+      const hideLoading = this.showLoading();
+      try {
+        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
+        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
+        if ("error" in dmrResult) throw new Error(dmrResult.error);
+        this.analyzedRegion = { chr, start, stop };
+        const blkRegion = this.blockInstance?.rglst?.[0];
+        const viewStart = blkRegion?.start ?? start;
+        const viewStop = blkRegion?.stop ?? stop;
+        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop);
+        this.view.updateTracks(vm.viewData, this.blockInstance);
+        this.view.updateLegend(this.blockInstance, vm.viewData.legendRows);
+        this.view.showNotes(vm.viewData.notes);
+        this.view.clearDiagnostics();
+        if (vm.viewData.diagnostic)
+          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
+      } catch (e) {
+        if (this.app.isAbortError(e)) return;
+        this.view.hideOverlay();
+        throw e;
+      } finally {
+        hideLoading();
+      }
+      this.view.hideOverlay();
+    } else {
+      this.dom.holder.selectAll("*").remove();
+      const hideLoading = this.showLoading();
+      this.blockInstance = null;
+      try {
+        checkRegionSize(stop - start, config.settings.dmr.maxRegionSize);
+        const dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal());
+        if ("error" in dmrResult) throw new Error(dmrResult.error);
+        this.analyzedRegion = { chr, start, stop };
+        const vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop);
+        this.blockInstance = await this.view.renderBlock(
+          vm.viewData,
+          this.genomeObj,
+          config.settings.dmr,
+          chr,
+          start,
+          stop,
+          (rglst) => this.onBlockCoordinateChange(rglst)
+        );
+        this.view.renderLegend(this.blockInstance, vm.viewData.legendRows);
+        this.view.showNotes(vm.viewData.notes);
+        if (vm.viewData.diagnostic)
+          this.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs, config.settings.dmr.fdr_cutoff);
+      } catch (e) {
+        if (this.app.isAbortError(e)) return;
+        throw e;
+      } finally {
+        hideLoading();
+      }
+    }
+  }
+  /** Shows the loading text with its elapsed timer. The returned cleanup stops this request's timer and hides the text
+   * only when no newer request has shown it since: an aborted request ending late must not hide a newer one's. */
+  showLoading() {
+    const request = ++this.loadingRequest;
+    this.dom.loading.style("display", "block");
+    const stopTimer = startElapsedTimer(this.dom.loading, LOADING_TEXT);
+    return () => {
+      stopTimer();
+      if (request == this.loadingRequest) this.dom.loading.style("display", "none");
+    };
+  }
+  onBlockCoordinateChange(rglst) {
+    if (!this.analyzedRegion || !rglst.length) return;
+    const r = rglst[0];
+    if (r.start >= r.stop || r.start < 0) return;
+    const a = this.analyzedRegion;
+    if (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return;
+    this.app.dispatch({
+      type: "plot_edit",
+      id: this.id,
+      config: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }
+    });
+  }
+};
+var componentInit = getCompInit(DmrPlot);
+function getPlotConfig(opts, app) {
+  validateConfig(opts);
+  const config = {
+    settings: {
+      // app is passed through so the defaults can tell a CpG-level dataset from an
+      // element-level one; opts alone does not carry termdbConfig
+      dmr: getDefaultDMRSettings({ ...opts, app })
+    }
+  };
+  return copyMerge(config, opts);
+}
+function validateConfig(opts) {
+  if (!opts.coordinateOverride) throw new Error("coordinateOverride (chr/start/stop) is required for DMR plot");
+  if (!opts.group1) throw new Error("group1 is required for DMR plot");
+  if (!opts.group2) throw new Error("group2 is required for DMR plot");
+}
+function checkRegionSize(span, maxRegionSize) {
+  if (span > maxRegionSize) {
+    const mbLimit = (maxRegionSize / 1e6).toFixed(0);
+    const mbSpan = (span / 1e6).toFixed(1);
+    throw new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`);
+  }
+}
+export {
+  componentInit,
+  getPlotConfig
+};
+//# sourceMappingURL=DmrPlot-FZCD6FTX.js.map

package/dist/DmrPlot-FZCD6FTX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/dmr/model/DmrModel.ts", "../plots/dmr/view/DmrView.ts", "../plots/dmr/DmrPlot.ts"],
+  "sourcesContent": ["import { dofetch3 } from '#common/dofetch'\nimport type { TermdbDmrResponse } from '#types'\nimport type { DmrConfig } from '../DmrTypes.ts'\n\nexport class DmrModel {\n\tprivate config: DmrConfig\n\tprivate vocab: { genome: string; dslabel: string }\n\n\tconstructor(config: DmrConfig, vocab: { genome: string; dslabel: string }) {\n\t\tthis.config = config\n\t\tthis.vocab = vocab\n\t}\n\n\tasync fetchDmr(chr: string, start: number, stop: number, signal?: AbortSignal): Promise<TermdbDmrResponse> {\n\t\tconst { group1, group2, settings } = this.config\n\t\tconst { genome, dslabel } = this.vocab\n\t\treturn dofetch3('termdb/dmr', {\n\t\t\tsignal,\n\t\t\tbody: {\n\t\t\t\tgenome,\n\t\t\t\tdslabel,\n\t\t\t\tchr,\n\t\t\t\tstart,\n\t\t\t\tstop,\n\t\t\t\tgroup1,\n\t\t\t\tgroup2,\n\t\t\t\tlambda: settings.dmr.lambda,\n\t\t\t\tC: settings.dmr.C,\n\t\t\t\tfdr_cutoff: settings.dmr.fdr_cutoff,\n\t\t\t\tgroup1Name: this.config.group1Name,\n\t\t\t\tgroup2Name: this.config.group2Name,\n\t\t\t\tblockWidth: settings.dmr.blockWidth,\n\t\t\t\tdevicePixelRatio: typeof window !== 'undefined' ? window.devicePixelRatio : 1,\n\t\t\t\tmaxLoessRegion: settings.dmr.maxLoessRegion,\n\t\t\t\tcolors: settings.dmr.colors,\n\t\t\t\tscanChromosomes: this.config.scanChromosomes,\n\t\t\t\tbackgroundCorrection: this.config.backgroundCorrection,\n\t\t\t\tminCpgs: this.config.minCpgs,\n\t\t\t\tyAxis: this.config.yAxis,\n\t\t\t\tfilter0: this.config.filter0\n\t\t\t}\n\t\t}) as Promise<TermdbDmrResponse>\n\t}\n}\n", "import { table2col } from '#dom'\nimport { formatElapsedTime } from '#shared'\nimport type { DmrDiagnostic } from '#types'\nimport type { DmrDom, LegendRow, DmrViewData } from '../DmrTypes.ts'\n\nexport class DmrView {\n\tprivate dom: DmrDom\n\n\tconstructor(dom: DmrDom) {\n\t\tthis.dom = dom\n\t}\n\n\tasync renderBlock(\n\t\tviewData: DmrViewData,\n\t\tgenomeObj: any,\n\t\tsettings: { blockWidth: number },\n\t\tchr: string,\n\t\tstart: number,\n\t\tstop: number,\n\t\tonCoordinateChange: (rglst: { chr: string; start: number; stop: number }[]) => void\n\t) {\n\t\tconst { Block } = await import('#src/block')\n\t\treturn new Block({\n\t\t\tholder: this.dom.holder,\n\t\t\tgenome: genomeObj,\n\t\t\tchr,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\ttklst: viewData.tklst,\n\t\t\tnobox: true,\n\t\t\twidth: settings.blockWidth,\n\t\t\tonCoordinateChange\n\t\t})\n\t}\n\n\tupdateTracks(viewData: DmrViewData, blockInstance: any) {\n\t\tfor (const tk of blockInstance.tklst) {\n\t\t\tconst updated = viewData.tklst.find((t: any) => t.name === tk.name)\n\t\t\tif (!updated) continue\n\t\t\tif (tk.type === 'bedj' && updated.bedItems) {\n\t\t\t\ttk.bedItems = updated.bedItems\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t} else if (tk.type === 'bigwig' && updated.imgData) {\n\t\t\t\ttk.imgData = updated.imgData\n\t\t\t\tblockInstance.tk_load(tk)\n\t\t\t}\n\t\t}\n\t}\n\n\tupdateLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst labels = ['Per-CpG Means', 'DMR', 'Sig. CpGs']\n\t\tblockInstance.legend.holder\n\t\t\t.selectAll('tr')\n\t\t\t.filter((_d: any, i: number, nodes: any) => {\n\t\t\t\tconst td = nodes[i].querySelector('td')\n\t\t\t\treturn td && labels.includes(td.textContent)\n\t\t\t})\n\t\t\t.remove()\n\t\tthis.renderLegend(blockInstance, legendRows)\n\t}\n\n\trenderLegend(blockInstance: any, legendRows: LegendRow[]) {\n\t\tif (!blockInstance?.legend?.holder) return\n\t\tconst { legendcolor, vpad } = blockInstance.legend\n\n\t\tfor (const row of legendRows) {\n\t\t\tconst tr = blockInstance.legend.holder.append('tr')\n\t\t\ttr.append('td')\n\t\t\t\t.text(row.label)\n\t\t\t\t.attr('style', `padding-right:10px;text-align:right;color:#555;border-right:solid 1px ${legendcolor}`)\n\t\t\tconst td = tr.append('td')\n\t\t\tfor (const entry of row.items) {\n\t\t\t\tconst item = td\n\t\t\t\t\t.append('div')\n\t\t\t\t\t.attr('style', `display:inline-block;white-space:nowrap;padding:${vpad} 20px ${vpad} 0`)\n\t\t\t\tif (entry.style === 'shaded') {\n\t\t\t\t\t// Shaded region with line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:10px;background:${entry.color}20;border-top:2px solid ${entry.color};margin-right:5px;vertical-align:middle;border-radius:1px`\n\t\t\t\t\t\t)\n\t\t\t\t} else if (entry.style === 'dashed') {\n\t\t\t\t\t// Dashed line marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:18px;height:0;border-top:2px dashed ${entry.color};margin-right:5px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t} else {\n\t\t\t\t\t// Default square marker\n\t\t\t\t\titem\n\t\t\t\t\t\t.append('div')\n\t\t\t\t\t\t.attr(\n\t\t\t\t\t\t\t'style',\n\t\t\t\t\t\t\t`display:inline-block;width:12px;height:12px;background:${entry.color};margin-right:5px;border-radius:2px;vertical-align:middle`\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t\titem.append('div').attr('style', 'display:inline-block;color:#555;font-size:.8em').text(entry.text)\n\t\t\t}\n\t\t}\n\t}\n\n\trenderDiagnostics(\n\t\tdiagnostic: DmrDiagnostic,\n\t\tdmrs: { start: number; stop: number; direction: string }[],\n\t\tfdr_cutoff: number\n\t) {\n\t\tconst panel = this.dom.diagnosticPanel\n\t\tpanel.selectAll('*').remove()\n\t\tpanel.style('display', 'block')\n\n\t\tconst { probes } = diagnostic\n\n\t\tconst toggle = panel.append('div').attr('style', 'cursor:default;font-size:12px;color:#888;padding:2px 0')\n\t\tconst statsContent = panel.append('div').style('display', 'none')\n\t\tlet expanded = false\n\t\ttoggle.text('+ Diagnostic details').on('click', () => {\n\t\t\texpanded = !expanded\n\t\t\ttoggle.text((expanded ? '\\u2212 ' : '+ ') + 'Diagnostic details')\n\t\t\tstatsContent.style('display', expanded ? 'block' : 'none')\n\t\t})\n\n\t\tconst spacings = diagnostic.probe_spacings\n\t\tconst medianSpacing = spacings.length ? spacings.slice().sort((a, b) => a - b)[Math.floor(spacings.length / 2)] : 0\n\t\tconst maxGap = spacings.length ? Math.max(...spacings) : 0\n\t\tconst gapsOver1kb = spacings.filter(s => s > 1000).length\n\t\tconst density =\n\t\t\tprobes.positions.length > 1\n\t\t\t\t? probes.positions.length / ((probes.positions[probes.positions.length - 1] - probes.positions[0]) / 1000)\n\t\t\t\t: 0\n\t\tconst sigFdrCount = probes.sig.filter(Boolean).length\n\t\tconst minDeltaBeta = 0.05\n\t\tconst sigDualCount = probes.sig.filter((s, i) => {\n\t\t\tif (!s) return false\n\t\t\tconst m1 = probes.mean_group1[i]\n\t\t\tconst m2 = probes.mean_group2[i]\n\t\t\tif (m1 == null || m2 == null) return false\n\t\t\treturn Math.abs(m2 - m1) >= minDeltaBeta\n\t\t}).length\n\n\t\tconst t = table2col({ holder: statsContent, disableScroll: true })\n\t\tfor (const [k, v] of [\n\t\t\t['Probes in region', String(probes.positions.length)],\n\t\t\t['FDR significant', `${sigFdrCount} (FDR < ${fdr_cutoff})`],\n\t\t\t['FDR + effect size', `${sigDualCount} (FDR < ${fdr_cutoff} & |\\u0394\\u03B2| \\u2265 ${minDeltaBeta})`],\n\t\t\t['Probe density', `${density.toFixed(1)} probes/kb`],\n\t\t\t['Median spacing', `${medianSpacing.toFixed(0)} bp`],\n\t\t\t['Max gap', `${maxGap.toFixed(0)} bp`],\n\t\t\t['Gaps > 1kb', String(gapsOver1kb)],\n\t\t\t['DMRs called', String(dmrs.length)],\n\t\t\t...(diagnostic.total_probes_analyzed\n\t\t\t\t? [['Probes analyzed (genome-wide)', diagnostic.total_probes_analyzed.toLocaleString()]]\n\t\t\t\t: []),\n\t\t\t...(diagnostic.elapsed_ms != null ? [['Analysis time', formatElapsedTime(diagnostic.elapsed_ms)]] : []),\n\t\t\t...(diagnostic.peak_memory_mb != null ? [['Peak memory', `${diagnostic.peak_memory_mb.toFixed(1)} MB`]] : [])\n\t\t] as [string, string][]) {\n\t\t\tt.addRow(k, v)\n\t\t}\n\t}\n\n\tshowOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', '')\n\t}\n\n\thideOverlay() {\n\t\tthis.dom.loadingOverlay.style('display', 'none')\n\t}\n\n\tclearDiagnostics() {\n\t\tthis.dom.diagnosticPanel.selectAll('*').remove()\n\t\tthis.dom.diagnosticPanel.style('display', 'none')\n\t}\n\n\t/** The view model's notes, one line each, under the plot */\n\tshowNotes(notes: string[]) {\n\t\tthis.dom.note.selectAll('*').remove()\n\t\tfor (const text of notes)\n\t\t\tthis.dom.note\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-dmr-note')\n\t\t\t\t.style('color', '#666')\n\t\t\t\t.style('font-size', '.85em')\n\t\t\t\t.style('padding', '4px 0')\n\t\t\t\t.style('max-width', '900px')\n\t\t\t\t.text(text)\n\t}\n}\n", "import { PlotBase } from '../PlotBase.ts'\nimport { getCompInit, copyMerge, type RxComponent, type ComponentApi } from '#rx'\nimport type { DmrConfig, DmrDom } from './DmrTypes.ts'\nimport { getDefaultDMRSettings } from './settings/defaults.ts'\nimport { DmrModel } from './model/DmrModel.ts'\nimport { DmrViewModel } from './viewModel/DmrViewModel.ts'\nimport { DmrView } from './view/DmrView.ts'\nimport { startElapsedTimer } from '#dom'\n\n/* Says why a wait can be long: a view on a comparison whose genome-wide run is not cached, such as a saved\nsession's, runs it first */\nconst LOADING_TEXT =\n\t'Running DMR analysis\\u2026 A comparison not yet cached first runs DMRcate over the whole genome, which can take minutes.'\n\nclass DmrPlot extends PlotBase implements RxComponent {\n\tstatic type = 'dmr'\n\n\ttype = DmrPlot.type\n\tdeclare dom: DmrDom\n\tblockInstance: InstanceType<any> | null = null\n\tanalyzedRegion: { chr: string; start: number; stop: number } | null = null\n\t/** counts the requests that showed the loading text; see showLoading() */\n\tprivate loadingRequest = 0\n\tview!: DmrView\n\tprivate model!: DmrModel\n\tprivate genomeObj: any\n\n\tconstructor(opts: any, api: ComponentApi) {\n\t\tsuper(opts, api)\n\t\tconst wrapper = opts.holder.append('div').style('position', 'relative')\n\t\tconst loadingOverlay = wrapper\n\t\t\t.append('div')\n\t\t\t.attr('class', 'sjpp-spinner')\n\t\t\t.style('display', 'none')\n\t\t\t.style('position', 'absolute')\n\t\t\t.style('z-index', '10')\n\t\t\t.style('background-color', 'rgba(255,255,255,0.65)')\n\t\tthis.dom = {\n\t\t\theader: opts?.header,\n\t\t\tholder: wrapper.append('div'),\n\t\t\tloadingOverlay,\n\t\t\terror: opts.holder.append('div'),\n\t\t\tnote: opts.holder.append('div'),\n\t\t\tloading: opts.holder.append('div').style('display', 'none'),\n\t\t\tdiagnosticPanel: opts.holder.append('div').style('display', 'none')\n\t\t}\n\t\tthis.view = new DmrView(this.dom)\n\t}\n\n\tgetState(appState: { plots: DmrConfig[] }): { config: DmrConfig } {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\tif (!config) throw new Error(`No plot with id='${this.id}' found`)\n\t\treturn { config }\n\t}\n\n\tasync init(appState: any) {\n\t\tconst { config } = this.getState(appState)\n\t\tvalidateConfig(config)\n\t\tif (this.dom.header) this.dom.header.text(config.headerText || 'DMR Analysis')\n\t\tthis.genomeObj = this.app.opts.genome\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\t/* No fetch here. main() runs right after init and its full-rebuild branch does the first\n\t\trender, so there is one code path for rendering and, more to the point, one for failing:\n\t\tan error thrown from main() is shown by the framework (PlotBase.printError) and re-shown on\n\t\tevery update until it is resolved, where an error caught inside init and written into\n\t\tdom.error was wiped by the very next update() before anyone saw it. */\n\t}\n\n\tasync main() {\n\t\tconst config = this.state.config as DmrConfig\n\t\tthis.model = new DmrModel(config, this.app.vocabApi.vocab)\n\n\t\tconst c = config.coordinateOverride\n\t\tif (!c) return\n\t\tconst pad = config.settings.dmr.pad\n\t\tconst chr = c.chr\n\t\tconst start = Math.max(0, Number(c.start) - pad)\n\t\tconst stop = Number(c.stop) + pad\n\n\t\tconst a = this.analyzedRegion\n\t\tconst coordsChanged = a && (chr !== a.chr || start !== a.start || stop !== a.stop)\n\n\t\tif (a && coordsChanged) {\n\t\t\t// New coordinates \u2014 re-fetch and update tracks in place\n\t\t\tthis.view.showOverlay()\n\t\t\t// a pan onto another chromosome can wait on a fresh DMRcate run, so it gets the timer too\n\t\t\tconst hideLoading = this.showLoading()\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) throw new Error(dmrResult.error)\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst blkRegion = this.blockInstance?.rglst?.[0]\n\t\t\t\tconst viewStart = blkRegion?.start ?? start\n\t\t\t\tconst viewStop = blkRegion?.stop ?? stop\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, viewStart, viewStop)\n\n\t\t\t\tthis.view.updateTracks(vm.viewData, this.blockInstance)\n\t\t\t\tthis.view.updateLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showNotes(vm.viewData.notes)\n\t\t\t\tthis.view.clearDiagnostics()\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tthis.view.hideOverlay()\n\t\t\t\tthrow e\n\t\t\t} finally {\n\t\t\t\thideLoading()\n\t\t\t}\n\t\t\tthis.view.hideOverlay()\n\t\t} else {\n\t\t\t// First render, or same coordinates with changed settings (e.g. a settings change) \u2014 full build\n\t\t\tthis.dom.holder.selectAll('*').remove()\n\t\t\tconst hideLoading = this.showLoading()\n\t\t\tthis.blockInstance = null\n\n\t\t\ttry {\n\t\t\t\tcheckRegionSize(stop - start, config.settings.dmr.maxRegionSize)\n\t\t\t\tconst dmrResult = await this.model.fetchDmr(chr, start, stop, this.api?.getAbortSignal())\n\t\t\t\tif ('error' in dmrResult) throw new Error(dmrResult.error)\n\n\t\t\t\tthis.analyzedRegion = { chr, start, stop }\n\t\t\t\tconst vm = new DmrViewModel(dmrResult, config, this.genomeObj, chr, start, stop)\n\n\t\t\t\tthis.blockInstance = await this.view.renderBlock(\n\t\t\t\t\tvm.viewData,\n\t\t\t\t\tthis.genomeObj,\n\t\t\t\t\tconfig.settings.dmr,\n\t\t\t\t\tchr,\n\t\t\t\t\tstart,\n\t\t\t\t\tstop,\n\t\t\t\t\trglst => this.onBlockCoordinateChange(rglst)\n\t\t\t\t)\n\t\t\t\tthis.view.renderLegend(this.blockInstance, vm.viewData.legendRows)\n\t\t\t\tthis.view.showNotes(vm.viewData.notes)\n\t\t\t\tif (vm.viewData.diagnostic)\n\t\t\t\t\tthis.view.renderDiagnostics(vm.viewData.diagnostic, vm.viewData.dmrs!, config.settings.dmr.fdr_cutoff)\n\t\t\t} catch (e: unknown) {\n\t\t\t\tif (this.app.isAbortError(e)) return\n\t\t\t\tthrow e\n\t\t\t} finally {\n\t\t\t\thideLoading()\n\t\t\t}\n\t\t}\n\t}\n\n\t/** Shows the loading text with its elapsed timer. The returned cleanup stops this request's timer and hides the text\n\t * only when no newer request has shown it since: an aborted request ending late must not hide a newer one's. */\n\tprivate showLoading(): () => void {\n\t\tconst request = ++this.loadingRequest\n\t\tthis.dom.loading.style('display', 'block')\n\t\tconst stopTimer = startElapsedTimer(this.dom.loading, LOADING_TEXT)\n\t\treturn () => {\n\t\t\tstopTimer()\n\t\t\tif (request == this.loadingRequest) this.dom.loading.style('display', 'none')\n\t\t}\n\t}\n\n\tonBlockCoordinateChange(rglst: { chr: string; start: number; stop: number }[]) {\n\t\tif (!this.analyzedRegion || !rglst.length) return\n\t\tconst r = rglst[0]\n\t\tif (r.start >= r.stop || r.start < 0) return\n\t\tconst a = this.analyzedRegion\n\t\tif (r.chr === a.chr && r.start === a.start && r.stop === a.stop) return\n\t\tthis.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: this.id,\n\t\t\tconfig: { coordinateOverride: { chr: r.chr, start: r.start, stop: r.stop } }\n\t\t})\n\t}\n}\n\nexport const componentInit = getCompInit(DmrPlot)\n\nexport function getPlotConfig(opts: Partial<DmrConfig>, app?: any): DmrConfig {\n\tvalidateConfig(opts)\n\n\tconst config = {\n\t\tsettings: {\n\t\t\t// app is passed through so the defaults can tell a CpG-level dataset from an\n\t\t\t// element-level one; opts alone does not carry termdbConfig\n\t\t\tdmr: getDefaultDMRSettings({ ...opts, app })\n\t\t}\n\t}\n\treturn copyMerge(config, opts)\n}\n\n/** Runs in both getPlotConfig and main() because will only run in main()\n * when plot is loaded from a saved state (e.g. mass session file).*/\nfunction validateConfig(opts) {\n\tif (!opts.coordinateOverride) throw new Error('coordinateOverride (chr/start/stop) is required for DMR plot')\n\tif (!opts.group1) throw new Error('group1 is required for DMR plot')\n\tif (!opts.group2) throw new Error('group2 is required for DMR plot')\n}\n\n/** Client-side region size guard (configurable via settings.dmr.maxRegionSize, default 5 Mb).\n *  The server also enforces a hard safety cap (10 Mb) to catch direct API calls or buggy clients. */\nfunction checkRegionSize(span: number, maxRegionSize: number) {\n\tif (span > maxRegionSize) {\n\t\tconst mbLimit = (maxRegionSize / 1_000_000).toFixed(0)\n\t\tconst mbSpan = (span / 1_000_000).toFixed(1)\n\t\tthrow new Error(`Region too large for DMR analysis (${mbSpan} Mb). Maximum is ${mbLimit} Mb.`)\n\t}\n}\n"],
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