@sjcrh/proteinpaint-client 2.193.0 → 2.195.0

package/dist/chunk-OEOYTMMY.js

@@ -0,0 +1,203 @@
+import {
+  tkt
+} from "./chunk-LYULXXGR.js";
+import {
+  stratinput
+} from "./chunk-PF4DSFDR.js";
+import {
+  stratify_default
+} from "./chunk-VQZ2Z5YU.js";
+
+// src/vcf.tkconvert.js
+function vcf2dstk(arg) {
+  const ds = {
+    id2vcf: {},
+    label: arg.name || "Unnamed VCF file"
+  };
+  let vcfobj;
+  if (arg.file) {
+    const id = Math.random().toString();
+    vcfobj = {
+      file: arg.file,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else if (arg.url) {
+    const id = Math.random().toString();
+    vcfobj = {
+      url: arg.url,
+      indexURL: arg.indexURL,
+      vcfid: id
+    };
+    ds.id2vcf[id] = vcfobj;
+  } else {
+    return ["no .file or .url"];
+  }
+  vcfobj.headernotloaded = true;
+  if (arg.samplenamemap) {
+    vcfobj.samplenamemap = arg.samplenamemap;
+  }
+  if (arg.variant2img) {
+    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
+  }
+  const tk = {
+    type: tkt.ds,
+    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
+    isvcf: true,
+    name: ds.label,
+    ds,
+    populationfrequencyfilter: arg.populationfrequencyfilter,
+    vcfinfofilter: arg.vcfinfofilter,
+    itemlabelname: arg.itemlabelname,
+    viewrangeupperlimit: arg.viewrangeupperlimit,
+    variant2img: arg.variant2img,
+    axisheight: arg.axisheight
+  };
+  if (arg.url4variant) {
+    const err = check_url4variant(arg.url4variant);
+    if (err) return [".url4variant error: " + err];
+    tk.url4variant = arg.url4variant;
+  }
+  if (arg.button4variant) {
+    const err = check_button4variant(arg.button4variant);
+    if (err) return [".button4variant error: " + err];
+    tk.button4variant = arg.button4variant;
+  }
+  if (arg.sampleannotation) {
+    const sn = arg.sampleannotation;
+    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
+    if (sn.levels) {
+      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
+      const lst = [];
+      for (const sample in sn.annotation) {
+        const o = { sample_name: sample };
+        for (const k in sn.annotation[sample]) {
+          o[k] = sn.annotation[sample][k];
+        }
+        lst.push(o);
+      }
+      const nodes = stratinput(lst, sn.levels);
+      sn.root = stratify_default()(nodes);
+      sn.root.sum((i) => i.value);
+    }
+    if (sn.variantsunburst) {
+      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
+    }
+    tk.ds.cohort = sn;
+  }
+  if (arg.vcfcohorttrack) {
+    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
+    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
+  }
+  if (arg.germline2dvafplot) {
+    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
+    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
+    if (arg.germline2dvafplot.yrightsampletype) {
+      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
+        return [".yrightsampletype should not be same as yleftsampletype"];
+    }
+    tk.ds.germline2dvafplot = arg.germline2dvafplot;
+  }
+  if (arg.vaf2coverageplot) {
+    if (arg.vaf2coverageplot.categorykey) {
+      if (!arg.vaf2coverageplot.categories)
+        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
+    }
+    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
+  }
+  if (arg.genotype2boxplot) {
+    if (arg.genotype2boxplot.boxplotvaluekey) {
+    } else if (arg.genotype2boxplot.sampleannotationkey) {
+      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
+      if (!tk.ds.cohort.annotation)
+        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
+      let found = false;
+      for (const k in tk.ds.cohort.annotation) {
+        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
+          found = true;
+          break;
+        }
+      }
+      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
+    } else {
+      return ["incomplete instruction for genotype2boxplot"];
+    }
+    tk.ds.genotype2boxplot = arg.genotype2boxplot;
+  }
+  if (arg.discardsymbolicallele) {
+    tk.ds.discardsymbolicallele = true;
+  }
+  if (arg.samplebynumericvalue) {
+    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
+    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
+    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
+    let found = false;
+    for (const k in tk.ds.cohort.annotation) {
+      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
+        found = true;
+        break;
+      }
+    }
+    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
+    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
+  }
+  {
+    const g = arg.genotypebynumericvalue;
+    if (g) {
+      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
+      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
+      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
+      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
+      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
+      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
+      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
+        if (!g.refref.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
+        if (!g.refalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
+        if (!g.altalt.genotypeCountInfokey)
+          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
+      }
+      tk.ds.genotypebynumericvalue = g;
+    }
+  }
+  if (arg.pointdown) {
+    tk.aboveprotein = false;
+  }
+  if (arg.dstk_novcferror) {
+    tk.dstk_novcferror = true;
+  }
+  return [null, tk];
+}
+function check_url4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makeurl) {
+      return ".makeurl missing";
+    }
+    if (typeof item.makeurl != "function") {
+      return ".makeurl must be a function";
+    }
+  }
+  return false;
+}
+function check_button4variant(lst) {
+  if (!Array.isArray(lst)) return "value is not an array";
+  for (const item of lst) {
+    if (!item.makebutton) {
+      return ".makebutton missing";
+    }
+    if (typeof item.makebutton != "function") {
+      return ".makebutton must be a function";
+    }
+  }
+  return false;
+}
+
+export {
+  vcf2dstk
+};
+//# sourceMappingURL=chunk-OEOYTMMY.js.map