@sjcrh/proteinpaint-client 2.192.0 → 2.193.0

package/dist/chunk-QSEGY3U5.js

@@ -0,0 +1,129 @@
+import {
+  keyupEnter
+} from "./chunk-L7VDSIM7.js";
+
+// src/block.mds.svcnv.share.js
+function rnabamtk_initparam(c) {
+  if (!c.dna_mintotalreads) c.dna_mintotalreads = 8;
+  if (!c.rna_mintotalreads) c.rna_mintotalreads = 8;
+  if (!c.hetsnp_minbaf) c.hetsnp_minbaf = 0.3;
+  if (!c.hetsnp_maxbaf) c.hetsnp_maxbaf = 0.7;
+  if (c.rnapileup_q == void 0) c.rnapileup_q = 0;
+  if (!c.rnapileup_Q) c.rnapileup_Q = 13;
+  if (!c.binompvaluecutoff) c.binompvaluecutoff = 0.05;
+  if (!c.clientcolor_snpinuse) c.clientcolor_snpinuse = "blue";
+  if (!c.clientcolor_markernotinuse) c.clientcolor_markernotinuse = "#bbb";
+}
+function configPanel_rnabam(tk, block, loadTk) {
+  const c = tk.checkrnabam;
+  if (!c) return;
+  tk.tkconfigtip.d.append("hr");
+  const d = tk.tkconfigtip.d.append("div").style("margin", "15px 0px");
+  d.append("div").style("opacity", 0.5).style("font-size", ".9em").text("Finding heterozygous SNPs in DNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("DNA minimum total read count ");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.dna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.dna_mintotalreads == v) {
+        return;
+      }
+      c.dna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.");
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_minbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_minbaf == v) {
+        return;
+      }
+      c.hetsnp_minbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("span").style("opacity", ".5").style("font-size", ".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.hetsnp_maxbaf).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.hetsnp_maxbaf == v) {
+        return;
+      }
+      c.hetsnp_maxbaf = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.");
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Counting alleles in RNA-seq BAM file");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip alignments with mapQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v < 0) return;
+      if (c.rnapileup_q == v) {
+        return;
+      }
+      c.rnapileup_q = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rnapileup_Q).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rnapileup_Q == v) {
+        return;
+      }
+      c.rnapileup_Q = v;
+      loadTk(tk, block);
+    });
+  }
+  d.append("div").style("margin-top", "20px").style("opacity", 0.5).style("font-size", ".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("P-value cutoff&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.binompvaluecutoff).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseFloat(event.target.value);
+      if (!v || v <= 0 || v >= 1) return;
+      if (c.binompvaluecutoff == v) {
+        return;
+      }
+      c.binompvaluecutoff = v;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = d.append("div").style("margin-top", "5px");
+    row.append("span").html("RNA minimum total read count&nbsp;");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", c.rna_mintotalreads).on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      let v = Number.parseInt(event.target.value);
+      if (!v || v <= 0) return;
+      if (c.rna_mintotalreads == v) {
+        return;
+      }
+      c.rna_mintotalreads = v;
+      loadTk(tk, block);
+    });
+    row.append("div").style("opacity", ".5").style("font-size", ".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.");
+  }
+}
+
+export {
+  rnabamtk_initparam,
+  configPanel_rnabam
+};
+//# sourceMappingURL=chunk-QSEGY3U5.js.map