taxonium-component/dist/AlignmentsFeatureDetail-C3anQ2Ub.js

React component for exploring large phylogenetic trees in the browser

import { jsxs as l, jsx as n, Fragment as d } from "react/jsx-runtime";
import { useState as c, lazy as m } from "react";
import { F as f } from "./FeatureDetails-8c1_Dsqv.js";
import { bQ as p, m as h, F as g, b0 as b, u as y, o as u, P as C } from "./JBrowsePanel-uJIA-L6s.js";
import { B as S } from "./BaseCard-CrWzwjYv.js";
import { g as v } from "./index-dFotuATn.js";
import { F as q } from "./FormControlLabel-CwjOxa71.js";
import { C as w } from "./Checkbox-BG4jcGUl.js";
import { L as F } from "./Link-CZ78-213.js";
var k = p();
const R = /* @__PURE__ */ v(k), P = h()({
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    paddingTop: 0,
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}), O = [
  "read paired",
  "read mapped in proper pair",
  "read unmapped",
  "mate unmapped",
  "read reverse strand",
  "mate reverse strand",
  "first in pair",
  "second in pair",
  "not primary alignment",
  "read fails platform/vendor quality checks",
  "read is PCR or optical duplicate",
  "supplementary alignment"
];
function T(t) {
  const { classes: a } = P(), { flags: e } = t;
  return l(S, { ...t, title: "Flags", children: [n(R, { name: "Flag", value: e }), n(g, { children: O.map((i, o) => {
    const r = e & 1 << o, s = `${i}_${r}`;
    return n(q, { control: n(w, { className: a.compact, checked: !!r, name: i, readOnly: !0 }), label: i }, s);
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}
function x({ value: t }) {
  const [a, e] = c(!1), [i, o] = c(!1), r = String(t);
  return r.length > 100 ? l(d, { children: [n("button", { type: "button", onClick: () => {
    b(r), o(!0), setTimeout(() => {
      o(!1);
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  }, children: i ? "Copied to clipboard" : "Copy" }), n("button", { type: "button", onClick: () => {
    e((s) => !s);
  }, children: a ? "Show less" : "Show more" }), n("div", { children: a ? r : `${r.slice(0, 100)}...` })] }) : n("div", { children: r });
}
function A(t, a) {
  var e;
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}
async function M(t, a) {
  const e = y.getSession(a), { view: i } = a;
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    console.error(o), e.notify(`${o}`);
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}
function Q({ locString: t, model: a }) {
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    e.preventDefault(), M(t, a);
  }, href: "#", children: t });
}
const B = {
  AM: "The smallest template-independent mapping quality in the template",
  AS: "Alignment score generated by aligner",
  BC: "Barcode sequence identifying the sample",
  BQ: "Offset to base alignment quality (BAQ)",
  BZ: "Phred quality of the unique molecular barcode bases in the {OX} tag",
  CB: "Cell identifier",
  CC: "Reference name of the next hit",
  CM: "Edit distance between the color sequence and the color reference (see also {NM})",
  CO: "Free-text comments",
  CP: "Leftmost coordinate of the next hit",
  CQ: "Color read base qualities",
  CR: "Cellular barcode sequence bases (uncorrected)",
  CS: "Color read sequence",
  CT: "Complete read annotation tag, used for consensus annotation dummy features",
  CY: "Phred quality of the cellular barcode sequence in the {CR} tag",
  E2: "The 2nd most likely base calls",
  FI: "The index of segment in the template",
  FS: "Segment suffix",
  FZ: "Flow stopToken intensities",
  GC: "Reserved for backwards compatibility reasons",
  GQ: "Reserved for backwards compatibility reasons",
  GS: "Reserved for backwards compatibility reasons",
  H0: "Number of perfect hits",
  H1: "Number of 1-difference hits (see also {NM})",
  H2: "Number of 2-difference hits",
  HI: "Query hit index",
  IH: "Query hit total count",
  LB: "Library",
  MC: "CIGAR string for mate/next segment",
  MD: "String encoding mismatched and deleted reference bases",
  MF: "Reserved for backwards compatibility reasons",
  MI: "Molecular identifier; a string that uniquely identifies the molecule from which the record was derived",
  ML: "Base modification probabilities",
  MM: "Base modifications / methylation ",
  MQ: "Mapping quality of the mate/next segment",
  NH: "Number of reported alignments that contain the query in the current record",
  NM: "Edit distance to the reference",
  OA: "Original alignment",
  OC: "Original CIGAR (deprecated; use {OA} instead)",
  OP: "Original mapping position (deprecated; use {OA} instead)",
  OQ: "Original base quality",
  OX: "Original unique molecular barcode bases",
  PG: "Program",
  PQ: "Phred likelihood of the template",
  PT: "Read annotations for parts of the padded read sequence",
  PU: "Platform unit",
  Q2: "Phred quality of the mate/next segment sequence in the {R2} tag",
  QT: "Phred quality of the sample barcode sequence in the {BC} tag",
  QX: "Quality score of the unique molecular identifier in the {RX} tag",
  R2: "Sequence of the mate/next segment in the template",
  RG: "Read group",
  RT: "Reserved for backwards compatibility reasons",
  RX: "Sequence bases of the (possibly corrected) unique molecular identifier",
  S2: "Reserved for backwards compatibility reasons",
  SA: "Other canonical alignments in a chimeric alignment",
  SM: "Template-independent mapping quality",
  SQ: "Reserved for backwards compatibility reasons",
  TC: "The number of segments in the template",
  TS: "Transcript strand",
  U2: "Phred probability of the 2nd call being wrong conditional on the best being wrong",
  UQ: "Phred likelihood of the segment, conditional on the mapping being correct"
}, N = m(() => import("./SupplementaryAlignments-BrM2eOAz.js")), L = m(() => import("./LinkedPairedAlignments-ndwsoOzz.js")), D = u(function(t) {
  const { model: a, feat: e } = t, i = e.flags, o = A("SA", e);
  return l(C, { "data-testid": "alignment-side-drawer", children: [n(f, { ...t, descriptions: { tags: B }, feature: e, formatter: (r, s) => s === "next_segment_position" ? n(Q, { model: a, locString: r }) : n(x, { value: r }) }), o !== void 0 ? n(N, { model: a, tag: o, feature: e }) : null, i != null ? l(d, { children: [i & 1 ? n(L, { model: a, feature: e }) : null, n(T, { flags: i, ...t })] }) : null] });
}), G = u(function(t) {
  const { model: a } = t, { featureData: e } = a, i = structuredClone(e);
  return i ? n(D, { feat: i, ...t }) : n("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" });
}), Z = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty({
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}, Symbol.toStringTag, { value: "Module" }));
export {
  Z as A,
  M as n
};
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