taxonium-component/dist/SNPCoverageAdapter-B0LRA71f.js

React component for exploring large phylogenetic trees in the browser

import { B as E } from "./index-CpJXUZUB.js";
import { r as F } from "./rxjs-L4bS73F7.js";
import { S as k } from "./simpleFeature-DimH8SQV.js";
import { u as A, bs as O, O as $, bN as N, $ as P, a0 as R } from "./JBrowsePanel-BNE3gNW1.js";
import { g as T, a as B } from "./getMethBins-CvqMYb7k.js";
function I({ feature: s, bins: e, region: t }) {
  const o = s.get("start"), r = s.get("end"), n = s.get("strand"), d = t.end - t.start;
  for (let i = o; i < r + 1; i++) {
    const c = i - t.start;
    c >= 0 && c < d && (e[c] === void 0 && (e[c] = {
      depth: 0,
      readsCounted: 0,
      ref: {
        probabilities: [],
        entryDepth: 0,
        "-1": 0,
        0: 0,
        1: 0
      },
      snps: {},
      mods: {},
      nonmods: {},
      delskips: {},
      noncov: {}
    }), i !== r && (e[c].depth++, e[c].readsCounted++, e[c].ref.entryDepth++, e[c].ref[n]++));
  }
}
function L(s) {
  return q(s.type) ? 1 : s.length;
}
function q(s) {
  return s === "softclip" || s === "hardclip" || s === "insertion";
}
function x(s, e, t, o) {
  let r = s[t][o];
  r === void 0 && (r = s[t][o] = {
    entryDepth: 0,
    probabilities: [],
    "-1": 0,
    0: 0,
    1: 0
  }), r.entryDepth++, r[e]++;
}
function D(s, e, t, o, r) {
  let n = s[t][o];
  n === void 0 && (n = s[t][o] = {
    entryDepth: 0,
    probabilities: [],
    "-1": 0,
    0: 0,
    1: 0
  }), n.entryDepth++, n.probabilities.push(r), n[e]++;
}
function G({ feature: s, region: e, bins: t, skipmap: o }) {
  var r;
  const n = s.get("start"), d = s.get("strand"), i = (r = s.get("mismatches")) !== null && r !== void 0 ? r : [];
  for (const c of i) {
    const p = n + c.start, l = L(c), h = p + l;
    for (let a = p; a < p + l; a++) {
      const f = a - e.start;
      if (f >= 0 && f < t.length) {
        const b = t[f], { base: u, altbase: m, type: g } = c, S = q(g);
        g === "deletion" || g === "skip" ? (x(b, d, "delskips", g), b.depth--) : S ? x(b, d, "noncov", g) : (x(b, d, "snps", u), b.ref.entryDepth--, b.ref[d]--, b.refbase = m);
      }
    }
    if (c.type === "skip") {
      const a = s.get("tags"), f = (a == null ? void 0 : a.XS) || (a == null ? void 0 : a.TS), b = a == null ? void 0 : a.ts, u = f === "+" ? 1 : f === "-" ? -1 : (b === "+" ? 1 : f === "-" ? -1 : 0) * d, m = `${p}_${h}_${u}`;
      o[m] === void 0 && (o[m] = {
        feature: s,
        start: p,
        end: h,
        strand: d,
        effectiveStrand: u,
        score: 0
      }), o[m].score++;
    }
  }
}
function V({ feature: s, colorBy: e, region: t, bins: o, regionSequence: r }) {
  var n, d, i;
  const c = s.get("start"), p = s.get("strand"), l = s.get("end"), h = (n = e == null ? void 0 : e.modifications) === null || n === void 0 ? void 0 : n.twoColor, a = (d = e == null ? void 0 : e.modifications) === null || d === void 0 ? void 0 : d.isolatedModification;
  (i = T(s)) === null || i === void 0 || i.forEach(({ allProbs: f, prob: b, type: u }, m) => {
    if (a && u !== a)
      return;
    const g = m + c - t.start;
    if (g >= 0 && g < o.length && m + c < l) {
      o[g] === void 0 && (o[g] = {
        depth: 0,
        readsCounted: 0,
        snps: {},
        ref: {
          probabilities: [],
          entryDepth: 0,
          "-1": 0,
          0: 0,
          1: 0
        },
        mods: {},
        nonmods: {},
        delskips: {},
        noncov: {}
      });
      const S = 1 - A.sum(f), v = o[g];
      v.refbase = r[g], h && S > A.max(f) ? D(v, p, "nonmods", `nonmod_${u}`, S) : D(v, p, "mods", `mod_${u}`, b);
    }
    m++;
  });
}
function W({ feature: s, region: e, bins: t, regionSequence: o }) {
  var r;
  const n = s.get("start"), d = s.get("end"), i = s.get("strand"), c = s.get("seq"), p = (r = s.get("mismatches")) !== null && r !== void 0 ? r : [], l = o.toLowerCase();
  if (c) {
    const h = O(s.get("CIGAR")), { methBins: a, methProbs: f } = B(s, h), b = p.filter((u) => u.type === "deletion");
    for (let u = 0; u < d - n; u++) {
      const m = u + n, g = l[m - e.start + 1], S = l[m - e.start + 2];
      if (g === "c" && S === "g") {
        const v = t[m - e.start], y = t[m - e.start + 1], M = a[u], j = a[u + 1], C = f[u], _ = f[u + 1];
        M && (C === void 0 || C > 0.5) || j && (_ === void 0 || _ > 0.5) ? (v && (D(v, i, "mods", "cpg_meth", C || 0), v.ref.entryDepth--, v.ref[i]--), y && (D(y, i, "mods", "cpg_meth", _ || 0), y.ref.entryDepth--, y.ref[i]--)) : (v && (b.some((w) => A.doesIntersect2(m, m + 1, w.start + n, w.start + n + w.length)) || (D(v, i, "nonmods", "cpg_unmeth", 1 - (C || 0)), v.ref.entryDepth--, v.ref[i]--)), y && (b.some((w) => A.doesIntersect2(m + 1, m + 2, w.start + n, w.start + n + w.length)) || (D(y, i, "nonmods", "cpg_unmeth", 1 - (_ || 0)), y.ref.entryDepth--, y.ref[i]--)));
      }
    }
  }
}
async function X({ fetchSequence: s, features: e, region: t, opts: o }) {
  const { stopToken: r, colorBy: n } = o, d = {}, i = [], c = Math.max(0, t.start - 1), p = t.start - c;
  let l = performance.now();
  for (const h of e) {
    if (performance.now() - l > 400 && ($.checkStopToken(r), l = performance.now()), I({
      feature: h,
      bins: i,
      region: t
    }), (n == null ? void 0 : n.type) === "modifications") {
      const a = await s({
        ...t,
        start: c,
        end: t.end + 1
      }) || "";
      V({
        feature: h,
        colorBy: n,
        bins: i,
        region: t,
        regionSequence: a.slice(p)
      });
    } else if ((n == null ? void 0 : n.type) === "methylation") {
      const a = await s({
        ...t,
        start: c,
        end: t.end + 1
      }) || "";
      W({
        feature: h,
        bins: i,
        region: t,
        regionSequence: a
      });
    }
    G({ feature: h, skipmap: d, bins: i, region: t });
  }
  for (const h of i)
    h && (h.mods = Object.fromEntries(Object.entries(h.mods).map(([a, f]) => [
      a,
      {
        ...f,
        avgProbability: f.probabilities.length ? A.sum(f.probabilities) / f.probabilities.length : void 0
      }
    ])), h.nonmods = Object.fromEntries(Object.entries(h.nonmods).map(([a, f]) => [
      a,
      {
        ...f,
        avgProbability: f.probabilities.length ? A.sum(f.probabilities) / f.probabilities.length : void 0
      }
    ])));
  return {
    bins: i,
    skipmap: d
  };
}
class U extends E.BaseFeatureDataAdapter {
  async configure() {
    var e, t;
    const o = this.getConf("subadapter"), r = o.sequenceAdapter, n = await ((e = this.getSubAdapter) === null || e === void 0 ? void 0 : e.call(this, o)), d = r ? await ((t = this.getSubAdapter) === null || t === void 0 ? void 0 : t.call(this, r)) : void 0;
    if (!n)
      throw new Error("Failed to get subadapter");
    return {
      subadapter: n.dataAdapter,
      sequenceAdapter: d == null ? void 0 : d.dataAdapter
    };
  }
  async fetchSequence(e) {
    const { sequenceAdapter: t } = await this.configure();
    if (t)
      return N(e, t);
  }
  getFeatures(e, t = {}) {
    return F.ObservableCreate(async (o) => {
      const { subadapter: r } = await this.configure(), n = await P(r.getFeatures(e, t).pipe(R())), { bins: d, skipmap: i } = await X({
        features: n,
        region: e,
        opts: t,
        fetchSequence: (p) => this.fetchSequence(p)
      });
      let c = 0;
      for (const p of d) {
        if (p) {
          const l = e.start + c;
          o.next(new k({
            id: `${this.id}-${l}`,
            data: {
              score: p.depth,
              snpinfo: p,
              start: l,
              end: l + 1,
              refName: e.refName
            }
          }));
        }
        c++;
      }
      for (const [p, l] of Object.entries(i))
        o.next(new k({
          id: p,
          data: {
            type: "skip",
            start: l.start,
            end: l.end,
            strand: l.strand,
            score: l.score,
            effectiveStrand: l.effectiveStrand
          }
        }));
      o.complete();
    }, t.stopToken);
  }
  async getMultiRegionFeatureDensityStats(e, t) {
    const { subadapter: o } = await this.configure();
    return o.getMultiRegionFeatureDensityStats(e, t);
  }
  async getRefNames(e = {}) {
    const { subadapter: t } = await this.configure();
    return t.getRefNames(e);
  }
}
export {
  U as default
};
//# sourceMappingURL=SNPCoverageAdapter-B0LRA71f.js.map