taxonium-component/dist/getMethBins-CvqMYb7k.js

React component for exploring large phylogenetic trees in the browser

import { u as A, bq as I, br as x, bs as B } from "./JBrowsePanel-BNE3gNW1.js";
function q(s, e) {
  let n = 0, o = 0, t = 0;
  const c = [];
  for (let f = 0; f < s.length && t < e.length; f += 2) {
    const r = +s[f], i = s[f + 1];
    if (i === "S" || i === "I") {
      for (let l = 0; l < r && t < e.length; l++)
        e[t] === n + l && t++;
      n += r;
    } else if (i === "D" || i === "N")
      o += r;
    else if (i === "M" || i === "X" || i === "=") {
      for (let l = 0; l < r && t < e.length; l++)
        e[t] === n + l && (c.push({
          ref: o + l,
          idx: t
        }), t++);
      n += r, o += r;
    }
  }
  return c;
}
function R(s, e, n) {
  const o = n === -1 ? A.revcom(e) : e, t = s.split(";"), c = [];
  for (const f of t) {
    if (f === "")
      continue;
    const r = f.split(","), i = r[0], l = I.exec(i);
    if (!l)
      throw new Error(`bad format for MM tag: "${f}"`);
    const [, a, h, g] = l, m = g.split(/(\d+|.)/);
    h === "-" && (console.warn("unsupported negative strand modifications"), c.push({
      type: "unsupported",
      positions: [],
      base: a,
      strand: h
    }));
    for (const p of m) {
      if (p === "")
        continue;
      let d = 0;
      const b = [];
      for (let u = 1, M = r.length; u < M; u++) {
        let y = +r[u];
        do
          (a === "N" || a === o[d]) && y--, d++;
        while (y >= 0 && d < o.length);
        if (n === -1) {
          const P = o.length - d;
          P >= 0 && b.unshift(P);
        } else
          b.push(d - 1);
      }
      c.push({
        type: p,
        base: a,
        strand: h,
        positions: b
      });
    }
  }
  return c;
}
function w(s) {
  const e = x(s, "ML", "Ml") || [];
  if (e) {
    const n = [];
    if (typeof e == "string") {
      const o = e.split(",");
      for (let t = 0, c = o.length; t < c; t++)
        n.push(+o[t] / 255);
    } else
      for (let o = 0, t = e.length; o < t; o++)
        n.push(e[o] / 255);
    return n;
  } else {
    const n = x(s, "MP", "Mp");
    if (n) {
      const o = [];
      for (let t = 0, c = n.length; t < c; t++) {
        const f = n.charCodeAt(t) - 33;
        o.push(Math.min(1, f / 50));
      }
      return o;
    }
    return;
  }
}
function E(s, e) {
  const n = s.get("strand"), o = s.get("seq"), t = x(s, "MM", "Mm") || "", c = e || B(s.get("CIGAR"));
  if (o) {
    const f = R(t, o, n), r = w(s), i = [];
    let l = 0;
    for (const { type: a, positions: h } of f) {
      for (const { ref: g, idx: m } of q(c, h)) {
        const p = (r == null ? void 0 : r[l + (n === -1 ? h.length - 1 - m : m)]) || 0;
        if (!i[g])
          i[g] = {
            type: a,
            prob: p,
            allProbs: [p]
          };
        else {
          const d = i[g];
          i[g] = {
            allProbs: [...d.allProbs, p],
            prob: Math.max(d.prob, p),
            type: d.prob > p ? d.type : a
          };
        }
      }
      l += h.length;
    }
    return i;
  }
}
function N(s, e) {
  const n = s.get("start"), o = s.get("end"), t = s.get("strand"), c = o - n, f = x(s, "MM", "Mm") || "", r = [], i = [], l = [], a = [], h = s.get("seq");
  if (h) {
    const g = w(s), m = R(f, h, t);
    let p = 0;
    for (const { type: d, positions: b } of m) {
      for (const { ref: u, idx: M } of q(e, b)) {
        if (u < 0 || u >= c)
          continue;
        const P = p + (t === -1 ? b.length - 1 - M : M), v = (g == null ? void 0 : g[P]) || 0;
        d === "m" ? (r[u] = 1, l[u] = v) : d === "h" && (i[u] = 1, a[u] = v);
      }
      p += b.length;
    }
  }
  return {
    methBins: r,
    hydroxyMethBins: i,
    methProbs: l,
    hydroxyMethProbs: a
  };
}
export {
  N as a,
  E as g
};
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