npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 8.7.2 → 8.8.1 - Mend

jbrowse-plugin-graphgenomeviewer 8.7.2 → 8.8.1

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package/dist/chunks/chunk-CEMQHMDO.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@12.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-34BOZKIE.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@12.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-HKYXWZQS.js", "../../node_modules/.pnpm/@jbrowse+graph-stress-layout@1.0.0/node_modules/@jbrowse/graph-stress-layout/esm/stressPlacement.js", "../../node_modules/.pnpm/@jbrowse+graph-stress-layout@1.0.0/node_modules/@jbrowse/graph-stress-layout/esm/stressEngine.js"],
+  "sourcesContent": ["// src/layout/drawnScale.ts\nvar MEAN_NODE_LENGTH = 40;\nvar MIN_TOTAL_GRAPH_LENGTH = 500;\nvar BANDAGE_MINIMUM_NODE_LENGTH = 5;\nfunction drawnNodeLength(opts, length) {\n  return Math.max(\n    opts.nodeLengthPerMegabase * length / 1e6,\n    opts.minimumNodeLength\n  );\n}\nfunction bandageAutoScale(graph, minNodeLength = BANDAGE_MINIMUM_NODE_LENGTH) {\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const megabases = totalLength / 1e6;\n  const target = Math.max(\n    graph.nodes.length * MEAN_NODE_LENGTH,\n    MIN_TOTAL_GRAPH_LENGTH\n  );\n  return {\n    nodeLengthPerMegabase: megabases > 0 ? target / megabases : 1e4,\n    minimumNodeLength: Math.max(BANDAGE_MINIMUM_NODE_LENGTH, minNodeLength),\n    edgeLength: 5,\n    nodeSegmentLength: 20\n  };\n}\nvar PROPORTIONAL_LENGTH = { power: 1, effect: 1 };\nfunction isProportional(law) {\n  return law.power === 1 && law.effect === 1;\n}\nfunction drawnLengthFor(graph, law) {\n  const count = graph.nodes.length;\n  const totalLength = graph.nodes.reduce((sum, n) => sum + n.length, 0);\n  const meanBp = count > 0 ? totalLength / count : 0;\n  const meanDrawn = count > 0 ? Math.max(count * MEAN_NODE_LENGTH, MIN_TOTAL_GRAPH_LENGTH) / count : MEAN_NODE_LENGTH;\n  return (bp) => {\n    if (meanBp <= 0) {\n      return meanDrawn;\n    }\n    const relative = (bp / meanBp) ** law.power;\n    return Math.max(\n      meanDrawn * ((relative - 1) * law.effect + 1),\n      BANDAGE_MINIMUM_NODE_LENGTH\n    );\n  };\n}\nvar LAYOUT_LENGTH_PRECISION = 1e3;\nvar PROPORTIONAL_SPREAD = {\n  law: PROPORTIONAL_LENGTH,\n  minNodeLength: 0\n};\nfunction layoutScaling(graph, spread = PROPORTIONAL_SPREAD) {\n  const { law, minNodeLength } = spread;\n  const opts = bandageAutoScale(graph, minNodeLength);\n  if (isProportional(law)) {\n    return { nodes: graph.nodes, opts };\n  }\n  const drawn = drawnLengthFor(graph, law);\n  return {\n    nodes: graph.nodes.map((node) => ({\n      ...node,\n      length: Math.round(drawn(node.length) * LAYOUT_LENGTH_PRECISION)\n    })),\n    opts: {\n      ...opts,\n      nodeLengthPerMegabase: 1e6 / LAYOUT_LENGTH_PRECISION,\n      // Bandage's own floor only. A law and a raised floor are alternatives\n      // rather than a stack: the law has already lifted the small end, and a\n      // floor on top of it would flatten exactly what it just spread.\n      minimumNodeLength: BANDAGE_MINIMUM_NODE_LENGTH\n    }\n  };\n}\nfunction drawnLengthOf(graph, spread = PROPORTIONAL_SPREAD) {\n  if (isProportional(spread.law)) {\n    const opts = bandageAutoScale(graph, spread.minNodeLength);\n    return (bp) => drawnNodeLength(opts, bp);\n  }\n  return drawnLengthFor(graph, spread.law);\n}\n\nexport {\n  MEAN_NODE_LENGTH,\n  drawnNodeLength,\n  bandageAutoScale,\n  PROPORTIONAL_LENGTH,\n  drawnLengthFor,\n  layoutScaling,\n  drawnLengthOf\n};\n", "import {\n  MEAN_NODE_LENGTH,\n  PROPORTIONAL_LENGTH\n} from \"./chunk-34BOZKIE.js\";\n\n// src/bubbleSpreads.ts\nvar BUBBLE_SPREADS = [\n  {\n    value: \"auto\",\n    label: \"Proportional\",\n    description: \"Bandage's own scale: a node draws proportional to its length, so a 1 bp allele is a speck.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 0\n  },\n  {\n    value: \"open\",\n    label: \"Open bubbles\",\n    description: \"Give every allele a drawn length, so a bubble reads as two arms rather than a knot.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 2.5\n  },\n  {\n    value: \"wide\",\n    label: \"Wide bubbles\",\n    description: \"As open, spread further. Best on a window of a dozen bubbles.\",\n    law: PROPORTIONAL_LENGTH,\n    minNodeFactor: 10\n  },\n  {\n    value: \"compress\",\n    label: \"Compress lengths\",\n    description: \"Pull the longest and shortest nodes towards the graph\\u2019s mean, so a cut spanning kb and bp fits one pane.\",\n    law: { power: 0.5, effect: 0.5 },\n    minNodeFactor: 0\n  }\n];\nvar BUBBLE_SPREAD_VALUES = BUBBLE_SPREADS.map((s) => s.value);\nfunction spreadFor(spread) {\n  const entry = BUBBLE_SPREADS.find((s) => s.value === spread);\n  return {\n    law: entry?.law ?? PROPORTIONAL_LENGTH,\n    minNodeLength: (entry?.minNodeFactor ?? 0) * MEAN_NODE_LENGTH\n  };\n}\n\nexport {\n  BUBBLE_SPREADS,\n  BUBBLE_SPREAD_VALUES,\n  spreadFor\n};\n", "// A node whose id starts with this is a deletion's route rather than sequence,\n// placed as an arch over the backbone.\nexport const ROUTE_ID = '\\u0000deletion:';\n// Where the stress engine starts an anchored graph. The backbone lies straight\n// along x at drawn length (its seeds). Every other node belongs to a piece: a\n// connected set of unplaced nodes, anchored where its links meet chains already\n// placed. A piece whose anchors sit on one placed curve is drawn in that\n// curve's frame (arc length along it, depth out of it): two anchors give a\n// spine along a circular arc of the piece's drawn length, a lens when it fits\n// its gap and a teardrop when longer, pushed out (legs, then a dropped chord,\n// then a tilt) until it clears what is drawn; a spine shorter than its gap is\n// a straight bar under it, hung deeper the wider the gap so its links leave\n// the lane; one anchor gives a straight tip. Anchors on\n// different curves use the chord between them. What a spine leaves unplaced\n// becomes pieces anchored on it, so nesting recurses. Deletion routes arch\n// above the backbone. Components with no backbone stay NaN for the engine's\n// random start.\nconst MIN_DEPTH = 12;\nconst LANE_GAP = 15;\nconst CLEAR = LANE_GAP * 0.7;\nconst TIP_ANGLE = (25 * Math.PI) / 180;\n// how deep a deletion arch rises, or a short bar hangs, per unit of its gap\nconst BOW = 0.25;\nconst BOW_CAP = 150;\n// a teardrop beside another leans away from it rather than dropping\nconst TEARDROP_TILTS = [0, -0.35, 0.35, -0.7, 0.7, -1.05, 1.05, -1.4, 1.4];\nconst SIDES = [0, 1];\nfunction other(side) {\n    return side ? 0 : 1;\n}\nfunction unit(a, b) {\n    const dx = b.x - a.x;\n    const dy = b.y - a.y;\n    const m = Math.hypot(dx, dy) || 1;\n    return { x: dx / m, y: dy / m };\n}\nfunction lerp(a, b, f) {\n    return { x: a.x + (b.x - a.x) * f, y: a.y + (b.y - a.y) * f };\n}\nfunction centroidOf(pts) {\n    let x = 0;\n    let y = 0;\n    for (const p of pts) {\n        x += p.x;\n        y += p.y;\n    }\n    return { x: x / pts.length, y: y / pts.length };\n}\nfunction arcLengths(pts) {\n    const arc = new Float64Array(pts.length);\n    for (let i = 1; i < pts.length; i++) {\n        arc[i] =\n            arc[i - 1] +\n                Math.hypot(pts[i].x - pts[i - 1].x, pts[i].y - pts[i - 1].y);\n    }\n    return arc;\n}\nfunction polylineLength(pts) {\n    var _a;\n    return (_a = arcLengths(pts)[pts.length - 1]) !== null && _a !== void 0 ? _a : 0;\n}\n// arc angle theta in (0, 2pi) with L/c = theta / (2 sin(theta/2)); a piece's\n// candidates ask for a handful of ratios hundreds of times\nconst arcAngles = new Map();\nfunction arcAngle(ratio) {\n    const known = arcAngles.get(ratio);\n    if (known !== undefined) {\n        return known;\n    }\n    const angle = solveArcAngle(ratio);\n    if (arcAngles.size > 10000) {\n        arcAngles.clear();\n    }\n    arcAngles.set(ratio, angle);\n    return angle;\n}\nfunction solveArcAngle(ratio) {\n    let lo = 1e-6;\n    let hi = 2 * Math.PI - 1e-6;\n    for (let i = 0; i < 60; i++) {\n        const mid = (lo + hi) / 2;\n        if (mid / (2 * Math.sin(mid / 2)) < ratio) {\n            lo = mid;\n        }\n        else {\n            hi = mid;\n        }\n    }\n    return (lo + hi) / 2;\n}\n// arc length of the circular arc with chord c and sagitta s\nfunction archLength(c, s) {\n    if (c < 1e-9) {\n        return Math.PI * s;\n    }\n    const R = ((c * c) / 4 + s * s) / (2 * s);\n    const theta = 2 * Math.asin(Math.min(1, c / (2 * R)));\n    return R * (s > R ? 2 * Math.PI - theta : theta);\n}\n// from (0, drop) to (c, drop) in `length`: legs of h along v joined by a\n// circular arc\nfunction arcFlat(c, length, h, drop) {\n    const arc = length - 2 * h;\n    const theta = c < 1e-9 ? 2 * Math.PI : arcAngle(arc / c);\n    const R = arc / theta;\n    const cos = Math.cos(theta / 2);\n    const cu = c / 2;\n    const cv = drop + h - R * cos;\n    return {\n        at: t => {\n            if (t <= h) {\n                return { u: 0, v: drop + t };\n            }\n            if (t >= length - h) {\n                return { u: c, v: drop + length - t };\n            }\n            const a = (t - h) / R - theta / 2;\n            return { u: cu + R * Math.sin(a), v: cv + R * Math.cos(a) };\n        },\n        apex: drop + h + R * (1 - cos),\n        length,\n    };\n}\n// The flat curve rotated about its chord's midpoint, which moves its feet\n// off the anchors by (c/2) sin(angle): one up, one down. A shear that kept\n// the feet swung a deep loop across its neighbours and raised link crossings\n// by half on the KIV-2 eight-haplotype cut.\nfunction tilted(flat, c, angle) {\n    if (!angle) {\n        return flat;\n    }\n    const cos = Math.cos(angle);\n    const sin = Math.sin(angle);\n    return {\n        ...flat,\n        at: t => {\n            const { u, v } = flat.at(t);\n            const du = u - c / 2;\n            return { u: c / 2 + du * cos - v * sin, v: du * sin + v * cos };\n        },\n    };\n}\n// whether any of the flat curve lies behind its frame: a loop's top poking\n// up through the reference line, which read as a glitch on every walk panel\nfunction behindFrame(flat) {\n    for (let i = 0; i <= 32; i++) {\n        if (flat.at((flat.length * i) / 32).v < -1e-6) {\n            return true;\n        }\n    }\n    return false;\n}\nfunction lineFlat(u0, v0, du, dv, length) {\n    return {\n        at: t => ({ u: u0 + du * t, v: v0 + dv * t }),\n        apex: v0 + Math.max(0, dv) * length,\n        length,\n    };\n}\n// A placed curve: dense samples with cumulative arc length and outward normals.\nclass Curve {\n    constructor(pts, normals, straight = false) {\n        var _a;\n        this.pts = pts;\n        this.normals = normals;\n        this.straight = straight;\n        this.arc = arcLengths(pts);\n        this.total = (_a = this.arc[pts.length - 1]) !== null && _a !== void 0 ? _a : 0;\n    }\n    segment(t) {\n        const { arc } = this;\n        let lo = 1;\n        let hi = arc.length - 1;\n        while (lo < hi) {\n            const mid = (lo + hi) >> 1;\n            if (arc[mid] < t) {\n                lo = mid + 1;\n            }\n            else {\n                hi = mid;\n            }\n        }\n        return lo;\n    }\n    fraction(i, t) {\n        const span = this.arc[i] - this.arc[i - 1];\n        return span > 0 ? (t - this.arc[i - 1]) / span : 0;\n    }\n    pointAt(t) {\n        const { pts } = this;\n        const last = pts.length - 1;\n        if (last === 0) {\n            return { ...pts[0] };\n        }\n        if (t <= 0) {\n            const d = unit(pts[0], pts[1]);\n            return { x: pts[0].x + d.x * t, y: pts[0].y + d.y * t };\n        }\n        if (t >= this.total) {\n            const d = unit(pts[last - 1], pts[last]);\n            const r = t - this.total;\n            return { x: pts[last].x + d.x * r, y: pts[last].y + d.y * r };\n        }\n        const i = this.segment(t);\n        return lerp(pts[i - 1], pts[i], this.fraction(i, t));\n    }\n    normalAt(t) {\n        const { normals } = this;\n        if (normals.length === 1 || t <= 0) {\n            return normals[0];\n        }\n        if (t >= this.total) {\n            return normals[normals.length - 1];\n        }\n        const i = this.segment(t);\n        const { x, y } = lerp(normals[i - 1], normals[i], this.fraction(i, t));\n        const m = Math.hypot(x, y) || 1;\n        return { x: x / m, y: y / m };\n    }\n}\n// A polyline's outward normals: the perpendicular pointing away from its\n// centroid where the shape is fat enough to say, else the frame's own outward.\nfunction outwardNormals(pts, outRef) {\n    const centroid = centroidOf(pts);\n    return pts.map((p, i) => {\n        const t = unit(pts[Math.max(0, i - 1)], pts[Math.min(pts.length - 1, i + 1)]);\n        const n = { x: -t.y, y: t.x };\n        const rx = p.x - centroid.x;\n        const ry = p.y - centroid.y;\n        const rm = Math.hypot(rx, ry);\n        const dot = n.x * rx + n.y * ry;\n        const ref = outRef[i];\n        const sign = rm > 1e-9 && Math.abs(dot) > 0.3 * rm\n            ? Math.sign(dot)\n            : Math.sign(n.x * ref.x + n.y * ref.y) || 1;\n        return { x: n.x * sign, y: n.y * sign };\n    });\n}\n// the flat curve carried into the frame from arc length tA, outward by sign,\n// sampled every `step` at most\nfunction mapFlat(frame, tA, sign, flat, step) {\n    const ds = Math.min(step, Math.max(flat.length / 24, 0.5));\n    const pts = [];\n    const refs = [];\n    for (let t = 0; t <= flat.length + 1e-9; t += ds) {\n        const { u, v } = flat.at(Math.min(t, flat.length));\n        const q = frame.pointAt(tA + u);\n        const nr = frame.normalAt(tA + u);\n        const ox = nr.x * sign;\n        const oy = nr.y * sign;\n        pts.push({ x: q.x + ox * v, y: q.y + oy * v });\n        refs.push({ x: ox, y: oy });\n    }\n    return { pts, refs };\n}\nconst FINE_STEP = 5;\nconst COARSE_STEP = CLEAR / 2;\n// the flat curve whose image in a curved frame has the asked length, within\n// a tenth of a percent or six tries\nfunction fitted(frame, tA, sign, make, length, step) {\n    let flatLength = length;\n    let mapped = mapFlat(frame, tA, sign, make(flatLength), step);\n    if (frame.straight) {\n        return mapped;\n    }\n    for (let i = 0; i < 6; i++) {\n        const got = polylineLength(mapped.pts);\n        if (!(got > 0) || Math.abs(got / length - 1) < 1e-3) {\n            break;\n        }\n        flatLength *= length / got;\n        mapped = mapFlat(frame, tA, sign, make(flatLength), step);\n    }\n    return mapped;\n}\nfunction depths(from, n) {\n    return Array.from({ length: n }, (_, i) => from + (i * LANE_GAP) / 2);\n}\nfunction spanOf(anchors) {\n    if (anchors.length === 0) {\n        return Infinity;\n    }\n    let lo = Infinity;\n    let hi = -Infinity;\n    for (const a of anchors) {\n        lo = Math.min(lo, a.point.x);\n        hi = Math.max(hi, a.point.x);\n    }\n    return hi - lo;\n}\nfunction cellKey(gx, gy) {\n    return (gx * 73856093) ^ (gy * 19349663);\n}\nclass Placer {\n    constructor(c) {\n        this.c = c;\n        this.grid = new Map();\n        const { ids, first, count, per, seedX, seedY, backbone } = c;\n        const N = ids.length;\n        this.points = Array.from({ length: N }, () => undefined);\n        this.params = Array.from({ length: N }, () => undefined);\n        this.curves = Array.from({ length: N }, () => undefined);\n        this.links = c.links.map((sides, k) => sides.map(out => out.filter(([v]) => v !== k)));\n        this.route = ids.map(id => id.startsWith(ROUTE_ID));\n        let min = Infinity;\n        let max = -Infinity;\n        for (let k = 0; k < N; k++) {\n            const start = first[k];\n            if (!backbone[start] || Number.isNaN(seedX[start])) {\n                continue;\n            }\n            min = Math.min(min, seedX[start]);\n            max = Math.max(max, seedX[start] + per[k] * (count[k] - 1));\n        }\n        this.backbone = new Curve([\n            { x: min, y: 0 },\n            { x: max, y: 0 },\n        ], [\n            { x: 0, y: 1 },\n            { x: 0, y: 1 },\n        ], true);\n        this.backboneCentroid = { x: (min + max) / 2, y: 0 };\n        for (let k = 0; k < N; k++) {\n            const start = first[k];\n            if (!backbone[start] || Number.isNaN(seedX[start])) {\n                continue;\n            }\n            const pts = [];\n            const ts = [];\n            for (let i = 0; i < count[k]; i++) {\n                const x = seedX[start] + i * per[k];\n                pts.push({ x, y: seedY[start] });\n                ts.push(x - min);\n            }\n            this.points[k] = pts;\n            this.params[k] = ts;\n            this.curves[k] = this.backbone;\n            this.occupy(pts, this.backbone);\n        }\n    }\n    static hasBackbone(c) {\n        for (let k = 0; k < c.ids.length; k++) {\n            const start = c.first[k];\n            if (c.backbone[start] && !Number.isNaN(c.seedX[start])) {\n                return true;\n            }\n        }\n        return false;\n    }\n    run() {\n        const free = [];\n        for (let k = 0; k < this.points.length; k++) {\n            if (!this.points[k]) {\n                free.push(k);\n            }\n        }\n        // Narrow pieces first, short before long, except that pieces on the same\n        // feet go longest first so an inner loop nests inside the outer one rather\n        // than crossing it. A wide loop whose foot lies inside a narrower loop's\n        // disc still drives its leg through it; making the narrow loop yield and\n        // re-place after the wide one freed it but re-placed it as a hairpin on\n        // long legs, 243/411/13 to 229/459/21 link-node/link-link/node-node\n        // crossings on the KIV-2 eight-haplotype cut at twice the time, and\n        // leaning the re-placed loop by shear at 0.1-0.4 rad gave 310/480/25.\n        const pieces = this.componentsOf(free)\n            .map(members => ({ members, anchors: this.anchorsOf(members) }))\n            .filter(p => p.anchors.length)\n            .map(p => ({\n            members: p.members,\n            span: spanOf(p.anchors),\n            drawn: p.members.reduce((s, k) => s + this.drawn(k), 0),\n            feet: p.anchors\n                .map(a => `${a.point.x},${a.point.y}`)\n                .sort()\n                .join(' '),\n        }))\n            .sort((a, b) => a.span - b.span ||\n            (a.feet === b.feet ? b.drawn - a.drawn : a.drawn - b.drawn));\n        for (const p of pieces) {\n            this.placePiece(p.members, this.backboneCentroid);\n        }\n    }\n    write(X, Y) {\n        const { first } = this.c;\n        this.points.forEach((pts, k) => {\n            pts === null || pts === void 0 ? void 0 : pts.forEach((p, i) => {\n                X[first[k] + i] = p.x;\n                Y[first[k] + i] = p.y;\n            });\n        });\n    }\n    drawn(k) {\n        return this.c.per[k] * (this.c.count[k] - 1);\n    }\n    endIndex(k, side) {\n        return side ? this.c.count[k] - 1 : 0;\n    }\n    occupy(pts, curve) {\n        for (const p of pts) {\n            const key = cellKey(Math.floor(p.x / CLEAR), Math.floor(p.y / CLEAR));\n            const list = this.grid.get(key);\n            const occupant = { x: p.x, y: p.y, curve };\n            if (list) {\n                list.push(occupant);\n            }\n            else {\n                this.grid.set(key, [occupant]);\n            }\n        }\n    }\n    // placed points within CLEAR of the candidate, off the exempt curve and\n    // beyond a lane of the anchors, up to `limit`. Exempting two lanes let\n    // teardrops off adjacent anchors cross at the neck: 3 node crossings on the\n    // HPRC KIV-2 cut against 1, and 2 on MHC class II against 0.\n    violations(pts, exempt, anchorPts, limit) {\n        var _a;\n        let n = 0;\n        for (const p of pts) {\n            if (anchorPts.some(a => Math.hypot(p.x - a.x, p.y - a.y) < LANE_GAP)) {\n                continue;\n            }\n            const cx = Math.floor(p.x / CLEAR);\n            const cy = Math.floor(p.y / CLEAR);\n            for (let gx = cx - 1; gx <= cx + 1; gx++) {\n                for (let gy = cy - 1; gy <= cy + 1; gy++) {\n                    for (const q of (_a = this.grid.get(cellKey(gx, gy))) !== null && _a !== void 0 ? _a : []) {\n                        if (q.curve !== exempt &&\n                            Math.hypot(p.x - q.x, p.y - q.y) < CLEAR) {\n                            n++;\n                            if (n >= limit) {\n                                return n;\n                            }\n                        }\n                    }\n                }\n            }\n        }\n        return n;\n    }\n    // The first candidate that clears what is drawn, else the least crowded.\n    // Exempting only the feet of pieces at the same anchor, or adding\n    // candidates with legs splayed a lane or more out from the anchors, moved\n    // no count that mattered on the HPRC cuts.\n    choose(candidates, exempt, anchorPts) {\n        let best;\n        let bestV = Infinity;\n        for (const candidate of candidates) {\n            const v = this.violations(candidate(COARSE_STEP).pts, exempt, anchorPts, bestV);\n            if (v === 0) {\n                return candidate(FINE_STEP);\n            }\n            if (v < bestV) {\n                bestV = v;\n                best = candidate;\n            }\n        }\n        return best(FINE_STEP);\n    }\n    anchorsOf(members) {\n        const set = new Set(members);\n        const out = [];\n        for (const u of members) {\n            for (const uSide of SIDES) {\n                for (const [v, vSide] of this.links[u][uSide]) {\n                    const pts = this.points[v];\n                    if (set.has(v) || !pts) {\n                        continue;\n                    }\n                    const i = this.endIndex(v, vSide);\n                    out.push({\n                        u,\n                        uSide,\n                        v,\n                        vSide,\n                        point: pts[i],\n                        curve: this.curves[v],\n                        t: this.params[v][i],\n                    });\n                }\n            }\n        }\n        return out;\n    }\n    componentsOf(members) {\n        const set = new Set(members);\n        const seen = new Set();\n        const comps = [];\n        for (const s of members) {\n            if (seen.has(s)) {\n                continue;\n            }\n            const queue = [s];\n            seen.add(s);\n            for (const u of queue) {\n                for (const side of SIDES) {\n                    for (const [v] of this.links[u][side]) {\n                        if (set.has(v) && !seen.has(v)) {\n                            seen.add(v);\n                            queue.push(v);\n                        }\n                    }\n                }\n            }\n            comps.push(queue);\n        }\n        return comps;\n    }\n    // side-consistent BFS over (node, entered side) within the piece; without a\n    // target, the path to the farthest state\n    spinePath(members, from, fromSide, to, toExitSide) {\n        const set = new Set(members);\n        const key = (k, s) => k * 2 + s;\n        const reached = (k, s) => k === to && other(s) === toExitSide;\n        const prev = new Map([[key(from, fromSide), -1]]);\n        const queue = [[from, fromSide]];\n        let far = [from, fromSide];\n        for (const [k, s] of queue) {\n            far = [k, s];\n            if (to !== undefined && reached(k, s)) {\n                break;\n            }\n            for (const [v, t] of this.links[k][other(s)]) {\n                if (!set.has(v) || prev.has(key(v, t))) {\n                    continue;\n                }\n                prev.set(key(v, t), key(k, s));\n                queue.push([v, t]);\n            }\n        }\n        if (to !== undefined && !reached(far[0], far[1])) {\n            return undefined;\n        }\n        const path = [];\n        for (let cur = key(far[0], far[1]); cur !== -1; cur = prev.get(cur)) {\n            path.push({ k: cur >> 1, enter: (cur & 1) });\n        }\n        return path.reverse();\n    }\n    loosePath(members, from, to) {\n        const set = new Set(members);\n        const prev = new Map([[from, -1]]);\n        const side = new Map([[from, 0]]);\n        const queue = [from];\n        for (const k of queue) {\n            if (k === to) {\n                break;\n            }\n            for (const s of SIDES) {\n                for (const [v, t] of this.links[k][s]) {\n                    if (!set.has(v) || prev.has(v)) {\n                        continue;\n                    }\n                    prev.set(v, k);\n                    side.set(v, t);\n                    queue.push(v);\n                }\n            }\n        }\n        const path = [];\n        for (let cur = to; cur !== -1; cur = prev.get(cur)) {\n            path.push({ k: cur, enter: side.get(cur) });\n        }\n        return path.reverse();\n    }\n    spineLength(spine) {\n        const { link } = this.c;\n        return spine.reduce((s, { k }) => s + this.drawn(k) + link, link);\n    }\n    // the spine's chains along the curve from arc length t0, at their own\n    // spacing unless one is given\n    layAlong(spine, curve, t0, spacing) {\n        const { count, per, link } = this.c;\n        let t = t0;\n        const all = [];\n        for (const { k, enter } of spine) {\n            const step = spacing !== null && spacing !== void 0 ? spacing : per[k];\n            const pts = [];\n            const ts = [];\n            for (let i = 0; i < count[k]; i++) {\n                pts.push(curve.pointAt(t + i * step));\n                ts.push(t + i * step);\n            }\n            if (enter === 1) {\n                pts.reverse();\n                ts.reverse();\n            }\n            this.points[k] = pts;\n            this.params[k] = ts;\n            this.curves[k] = curve;\n            all.push(...pts);\n            t += step * (count[k] - 1) + link;\n        }\n        return all;\n    }\n    arcCandidates(frame, tA, sign, c, L) {\n        const hMax = (L - c) / 2 - 1e-6;\n        const tilts = L > 2 * c ? TEARDROP_TILTS : [0];\n        const candidates = [];\n        for (const drop of depths(0, 8)) {\n            for (const tilt of tilts) {\n                for (let i = 0; i <= 16; i++) {\n                    const h = (hMax * i) / 16;\n                    const flat = tilted(arcFlat(c, L, h, drop), c, tilt);\n                    if ((i < 16 && flat.apex < MIN_DEPTH) || behindFrame(flat)) {\n                        continue;\n                    }\n                    candidates.push(step => fitted(frame, tA, sign, length => tilted(arcFlat(c, length, Math.min(h, (length - c) / 2 - 1e-6), drop), c, tilt), L, step));\n                }\n            }\n        }\n        return candidates;\n    }\n    placePiece(members, parent) {\n        var _a;\n        const { count, link } = this.c;\n        const anchors = this.anchorsOf(members);\n        if (anchors.length === 0) {\n            return;\n        }\n        const route = members.every(k => this.route[k]);\n        const shared = anchors.every(a => a.curve === anchors[0].curve)\n            ? anchors[0].curve\n            : undefined;\n        let frame;\n        let tA;\n        let tB;\n        let sign;\n        if (shared) {\n            anchors.sort((a, b) => a.t - b.t);\n            frame = shared;\n            tA = anchors[0].t;\n            tB = anchors[anchors.length - 1].t;\n            sign = frame === this.backbone && route ? -1 : 1;\n        }\n        else {\n            // A piece between curves hangs on the chord, and its links stay long.\n            // Relaxing just these pieces over their links with the rest held\n            // stretched the junction nodes across the gap instead: on the KIV-2\n            // eight-haplotype cut, chain length error 0.3% to 57% and node\n            // crossings 22 to 48. Hanging the piece on the curve with most anchors\n            // more than doubled that cut's link crossings.\n            anchors.sort((a, b) => a.point.x - b.point.x || a.point.y - b.point.y);\n            const a = anchors[0].point;\n            const b = anchors[anchors.length - 1].point;\n            const chord = Math.hypot(b.x - a.x, b.y - a.y);\n            const u = chord > 1e-9 ? unit(a, b) : { x: 1, y: 0 };\n            const n = { x: -u.y, y: u.x };\n            const mid = lerp(a, b, 0.5);\n            sign = anchors.some(x => x.curve === this.backbone)\n                ? (route ? -1 : 1) * (Math.sign(n.y) || 1)\n                : (mid.x - parent.x) * n.x + (mid.y - parent.y) * n.y >= 0\n                    ? 1\n                    : -1;\n            frame = new Curve([a, b], [n, n], true);\n            tA = 0;\n            tB = chord;\n        }\n        const A = anchors[0];\n        const B = anchors[anchors.length - 1];\n        const c = tB - tA;\n        const single = anchors.length === 1 || (A.u === B.u && A.uSide === B.uSide && c < 1e-9);\n        const anchorPts = [A.point, B.point];\n        const pick = (candidates) => this.choose(candidates, shared, anchorPts);\n        let spine;\n        let mapped;\n        let start = link;\n        let spacing;\n        if (single) {\n            spine = this.spinePath(members, A.u, A.uSide);\n            const L = this.spineLength(spine);\n            const next = A.vSide\n                ? Math.max(0, count[A.v] - 2)\n                : Math.min(1, count[A.v] - 1);\n            const dirU = A.t >= this.params[A.v][next] ? 1 : -1;\n            const du = dirU * Math.cos(TIP_ANGLE);\n            const dv = Math.sin(TIP_ANGLE);\n            mapped = pick(depths(0, 12).map(drop => (step) => fitted(frame, tA, sign, length => lineFlat(0, drop, du, dv, length), L, step)));\n        }\n        else {\n            spine =\n                (_a = this.spinePath(members, A.u, A.uSide, B.u, B.uSide)) !== null && _a !== void 0 ? _a : this.loosePath(members, A.u, B.u);\n            const L = this.spineLength(spine);\n            if (route) {\n                const d0 = Math.max(MIN_DEPTH, Math.min(BOW * c, BOW_CAP));\n                mapped = pick(depths(d0, 12).map(d => (step) => mapFlat(frame, tA, sign, arcFlat(c, archLength(c, d), 0, 0), step)));\n                const total = polylineLength(mapped.pts);\n                spacing = Math.max(1e-3, (total - 2 * link) / (count[spine[0].k] - 1));\n            }\n            else if (L > c + 1e-6) {\n                mapped = pick(this.arcCandidates(frame, tA, sign, c, L));\n            }\n            else {\n                const bar = L - 2 * link;\n                const d0 = Math.max(MIN_DEPTH, Math.min(BOW * (c - bar), BOW_CAP));\n                mapped = pick(depths(d0, 12).map(d => (step) => fitted(frame, tA, sign, length => lineFlat(c / 2 - length / 2, d, 1, 0, length), bar, step)));\n                start = 0;\n            }\n        }\n        const curve = new Curve(mapped.pts, outwardNormals(mapped.pts, mapped.refs));\n        const placed = this.layAlong(spine, curve, start, spacing);\n        this.occupy(placed, curve);\n        const centroid = centroidOf(placed);\n        const rest = members.filter(k => !this.points[k]);\n        const subs = this.componentsOf(rest)\n            .map(m => ({ members: m, span: spanOf(this.anchorsOf(m)) }))\n            .sort((a, b) => a.span - b.span);\n        for (const sub of subs) {\n            this.placePiece(sub.members, centroid);\n        }\n    }\n}\n// Initial positions per point, NaN where the placement reached nothing.\nexport function stressPlacement(c) {\n    const X = new Float64Array(c.n).fill(NaN);\n    const Y = new Float64Array(c.n).fill(NaN);\n    if (Placer.hasBackbone(c)) {\n        const placer = new Placer(c);\n        placer.run();\n        placer.write(X, Y);\n    }\n    return { X, Y };\n}\n", "import { stressPlacement } from \"./stressPlacement.js\";\n// A layout taking the Bandage engine's request: each node is the chain of\n// points FMMM would build, and the result is a polyline per node.\n//\n// A component with a seeded backbone is drawn by stressPlacement: the\n// backbone straight along x, every other node hung off it. The rest is a\n// stress layout by stochastic gradient descent (Zheng, Pawar & Goodman 2019)\n// with target distances from random walks, after odgi's path-guided SGD:\n// every point starts a few walks of log-uniform length each iteration, and\n// how far a walk got is how far apart its ends should sit, so a repeat's loop\n// draws as a ring of its own circumference. Stress has no repulsion, so a\n// final pass pushes apart points that are close but not joined.\n//\n// Running the schedule on a placed component twists its loops, since a walk\n// from a loop's leg runs on along the backbone and pulls the leg to lie along\n// it: 32 node crossings on HPRC MHC class II against the placement's 4.\n// walks per point and iterations by the quality the request names\nconst QUALITY = [\n    { walks: 2, iterations: 15 },\n    { walks: 4, iterations: 30 },\n    { walks: 8, iterations: 60 },\n    { walks: 12, iterations: 90 },\n    { walks: 16, iterations: 120 },\n];\nconst UNTANGLE_PASSES = 20;\n// the untangle radius, in link lengths\nconst UNTANGLE_LINKS = 3;\nconst UNTANGLE_PUSH = 0.3;\nconst SMOOTH_PASSES = 2;\n// a 20-link cap balls a 3k-node graph up\nconst MAX_HOPS = 200;\n// the step size the schedule ends on, as a share of the smallest pair's\nconst EPS = 0.1;\n// the share of the schedule a seeded component skips\nconst WARM = 0.5;\nconst isBackbone = (node) => { var _a; return ((_a = node.stable) === null || _a === void 0 ? void 0 : _a.rank) === 0; };\nfunction flipped(strand, name) {\n    const own = name.at(-1);\n    return ((strand === '+' || strand === '-') &&\n        (own === '+' || own === '-') &&\n        strand !== own);\n}\nfunction xorshift(seed) {\n    let s = Math.imul(seed, 2654435761) >>> 0 || 1;\n    return () => {\n        s ^= s << 13;\n        s >>>= 0;\n        s ^= s >>> 17;\n        s ^= s << 5;\n        s >>>= 0;\n        return s / 4294967296;\n    };\n}\nexport function num(value, fallback) {\n    return typeof value === 'number' && Number.isFinite(value) ? value : fallback;\n}\n// A node's drawn length, in layout units, from its bp\nexport function drawnLength(options, bp) {\n    return Math.max((num(options.nodeLengthPerMegabase, 1000) * bp) / 1000000, num(options.minimumNodeLength, 1));\n}\nexport function chains(request) {\n    const { nodes, edges } = request.graph;\n    const o = request.options;\n    const segment = num(o.nodeSegmentLength, 1);\n    const link = num(o.edgeLength, 1);\n    const ids = nodes.map(n => n.id);\n    const first = new Int32Array(nodes.length);\n    const count = new Int32Array(nodes.length);\n    const per = new Float64Array(nodes.length);\n    let n = 0;\n    nodes.forEach((node, k) => {\n        const drawn = drawnLength(o, node.length);\n        const steps = Math.max(1, Math.ceil(drawn / segment));\n        first[k] = n;\n        count[k] = steps + 1;\n        per[k] = drawn / steps;\n        n += steps + 1;\n    });\n    const chainOf = new Int32Array(n);\n    const indexOf = new Int32Array(n);\n    const seedX = new Float64Array(n).fill(NaN);\n    const seedY = new Float64Array(n).fill(NaN);\n    const backbone = new Uint8Array(n);\n    const adjacent = Array.from({ length: n }, () => []);\n    nodes.forEach((node, k) => {\n        const seeded = typeof node.x === 'number' && typeof node.y === 'number';\n        const reference = isBackbone(node) ? 1 : 0;\n        for (let i = 0; i < count[k]; i++) {\n            const v = first[k] + i;\n            chainOf[v] = k;\n            indexOf[v] = i;\n            backbone[v] = reference;\n            if (seeded) {\n                seedX[v] = node.x + i * per[k];\n                seedY[v] = node.y;\n            }\n            if (i > 0) {\n                adjacent[v - 1].push([v, per[k]]);\n                adjacent[v].push([v - 1, per[k]]);\n            }\n        }\n    });\n    const index = new Map(ids.map((id, k) => [id, k]));\n    const links = nodes.map(() => [[], []]);\n    for (const edge of edges) {\n        const a = index.get(edge.from);\n        const b = index.get(edge.to);\n        if (a === undefined || b === undefined) {\n            continue;\n        }\n        // a self link on a chain of one step has nowhere to go, as in FMMM\n        if (a === b && count[a] <= 2) {\n            continue;\n        }\n        const fromSide = flipped(edge.fromStrand, edge.from) ? 0 : 1;\n        const toSide = flipped(edge.toStrand, edge.to) ? 1 : 0;\n        const u = first[a] + (fromSide ? count[a] - 1 : 0);\n        const v = first[b] + (toSide ? count[b] - 1 : 0);\n        adjacent[u].push([v, link]);\n        adjacent[v].push([u, link]);\n        links[a][fromSide].push([b, toSide]);\n        links[b][toSide].push([a, fromSide]);\n    }\n    const off = new Int32Array(n + 1);\n    for (let i = 0; i < n; i++) {\n        off[i + 1] = off[i] + adjacent[i].length;\n    }\n    const nb = new Int32Array(off[n]);\n    const wt = new Float64Array(off[n]);\n    for (let i = 0; i < n; i++) {\n        adjacent[i].forEach(([v, w], k) => {\n            nb[off[i] + k] = v;\n            wt[off[i] + k] = w;\n        });\n    }\n    return {\n        ids,\n        first,\n        count,\n        per,\n        links,\n        chainOf,\n        indexOf,\n        seedX,\n        seedY,\n        backbone,\n        off,\n        nb,\n        wt,\n        n,\n        link,\n    };\n}\n// each point's connected component, and the points of each component\nfunction components(c) {\n    const { n, off, nb } = c;\n    const comp = new Int32Array(n).fill(-1);\n    const members = [];\n    for (let s = 0; s < n; s++) {\n        if (comp[s] >= 0) {\n            continue;\n        }\n        const queue = [s];\n        comp[s] = members.length;\n        for (const u of queue) {\n            for (let e = off[u]; e < off[u + 1]; e++) {\n                const v = nb[e];\n                if (comp[v] < 0) {\n                    comp[v] = members.length;\n                    queue.push(v);\n                }\n            }\n        }\n        members.push(queue);\n    }\n    return { comp, members };\n}\nexport function stressLayout(request, opts = {}) {\n    var _a, _b, _c;\n    const c = chains(request);\n    const { n, off, nb, wt, seedX, seedY, first, count, per, link } = c;\n    const o = request.options;\n    const quality = QUALITY[Math.max(0, Math.min(4, num((_a = opts.quality) !== null && _a !== void 0 ? _a : o.quality, 2)))];\n    const gap = num((_b = opts.componentSeparation) !== null && _b !== void 0 ? _b : o.componentSeparation, 15);\n    const rand = xorshift(num((_c = opts.seed) !== null && _c !== void 0 ? _c : o.seed, 1));\n    const X = new Float64Array(n);\n    const Y = new Float64Array(n);\n    const nodePositions = {};\n    if (n === 0) {\n        return { nodePositions };\n    }\n    const { comp, members } = components(c);\n    let dmin = Infinity;\n    let total = 0;\n    for (let e = 0; e < nb.length; e++) {\n        dmin = Math.min(dmin, wt[e]);\n        total += wt[e];\n    }\n    total /= 2;\n    let anySeed = false;\n    for (let i = 0; i < n; i++) {\n        if (!Number.isNaN(seedX[i])) {\n            anySeed = true;\n            break;\n        }\n    }\n    const placed = anySeed ? stressPlacement(c) : undefined;\n    const side = Math.sqrt(n) * 20;\n    for (let i = 0; i < n; i++) {\n        if (placed && !Number.isNaN(placed.X[i])) {\n            X[i] = placed.X[i];\n            Y[i] = placed.Y[i];\n        }\n        else if (anySeed && !Number.isNaN(seedX[i])) {\n            X[i] = seedX[i] + rand() - 0.5;\n            Y[i] = seedY[i] + rand() - 0.5;\n        }\n        else {\n            X[i] = rand() * side;\n            Y[i] = rand() * side;\n        }\n    }\n    // the points the schedule moves: those of components the placement did not\n    // draw whole, in index order so the schedule runs as it would alone\n    const drawn = members.map(points => placed !== undefined && points.every(i => !Number.isNaN(placed.X[i])));\n    const loose = [];\n    let looseSeeded = true;\n    for (let i = 0; i < n; i++) {\n        if (!drawn[comp[i]]) {\n            loose.push(i);\n            looseSeeded && (looseSeeded = !Number.isNaN(seedX[i]));\n        }\n    }\n    const dmax = Math.max(total / 4, dmin * 10);\n    const etaMax = dmax * dmax;\n    const etaMin = EPS * dmin * dmin;\n    const { walks, iterations } = quality;\n    const lambda = Math.log(etaMax / etaMin) / Math.max(1, iterations - 1);\n    const logMin = Math.log(dmin);\n    const logMax = Math.log(dmax);\n    const move = (i, j, d, eta) => {\n        let mu = eta / (d * d);\n        if (mu > 1) {\n            mu = 1;\n        }\n        const dx = X[i] - X[j];\n        const dy = Y[i] - Y[j];\n        const mag = Math.sqrt(dx * dx + dy * dy) || 1e-9;\n        const r = (mu * (mag - d)) / (2 * mag);\n        const rx = r * dx;\n        const ry = r * dy;\n        X[i] = X[i] - rx;\n        Y[i] = Y[i] - ry;\n        X[j] = X[j] + rx;\n        Y[j] = Y[j] + ry;\n    };\n    // The end of a walk of up to `length` from point i, with how far it got in\n    // `walked`: a walk stops short at a free chain end.\n    let walked = 0;\n    const walk = (i, length) => {\n        let chain = c.chainOf[i];\n        let idx = c.indexOf[i];\n        let dir = rand() < 0.5 ? -1 : 1;\n        let remaining = length;\n        for (let hops = 0; hops < MAX_HOPS; hops++) {\n            const points = count[chain];\n            const step = per[chain];\n            const toEnd = (dir > 0 ? points - 1 - idx : idx) * step;\n            if (remaining <= toEnd) {\n                const steps = Math.round(remaining / step);\n                walked = length - remaining + steps * step;\n                return first[chain] + idx + dir * steps;\n            }\n            remaining -= toEnd;\n            const out = c.links[chain][dir > 0 ? 1 : 0];\n            if (out.length === 0) {\n                walked = length - remaining;\n                return first[chain] + (dir > 0 ? points - 1 : 0);\n            }\n            const [next, enterSide] = out[Math.floor(rand() * out.length)];\n            remaining -= link;\n            chain = next;\n            dir = enterSide === 0 ? 1 : -1;\n            idx = enterSide === 0 ? 0 : count[next] - 1;\n            if (remaining <= 0) {\n                walked = length - remaining;\n                return first[chain] + idx;\n            }\n        }\n        return -1;\n    };\n    const adjacentTerms = (i, eta) => {\n        for (let e = off[i]; e < off[i + 1]; e++) {\n            const j = nb[e];\n            if (j > i) {\n                move(i, j, wt[e], eta);\n            }\n        }\n    };\n    const order = Int32Array.from(loose);\n    const warm = looseSeeded ? Math.floor(WARM * iterations) : 0;\n    for (let t = loose.length ? warm : iterations; t < iterations; t++) {\n        const eta = etaMax * Math.exp(-lambda * t);\n        for (let k = order.length - 1; k > 0; k--) {\n            const r = Math.floor(rand() * (k + 1));\n            const tmp = order[k];\n            order[k] = order[r];\n            order[r] = tmp;\n        }\n        for (const i of order) {\n            adjacentTerms(i, eta);\n            for (let w = 0; w < walks; w++) {\n                const length = Math.exp(logMin + rand() * (logMax - logMin));\n                const j = walk(i, length);\n                if (j >= 0 && j !== i && walked > 0) {\n                    move(i, j, walked, eta);\n                }\n            }\n        }\n    }\n    // untangle: points closer than the radius and not joined push apart, then\n    // a sweep over the links pulls each back towards its length\n    const radius = UNTANGLE_LINKS * link;\n    const key = (x, y) => (Math.floor(x / radius) * 73856093) ^ (Math.floor(y / radius) * 19349663);\n    for (let u = 0; u < (loose.length ? 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Smoothing\n// shortens a curve, so the interior first bulges out from the chord between\n// the ends until the length is back, and the points then take their full\n// spacing. 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+//# sourceMappingURL=chunk-CLO4ZOOD.js.map

package/dist/chunks/{chunk-VPZZ6XMM.js.map → chunk-CLO4ZOOD.js.map} RENAMED Viewed

@@ -1,6 +1,6 @@
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[\"M\", \"MT\"] : [bare];\n  return [.../* @__PURE__ */ new Set([contig, ...forms.flatMap((f) => [f, `chr${f}`])])];\n}\nfunction refNameBinding(refNames, aliases = {}) {\n  const exact = new Set(refNames);\n  const byName = /* @__PURE__ */ new Map();\n  for (const refName of exact) {\n    const contig = panSNContig(refName);\n    const alias = aliases[contig];\n    for (const name of /* @__PURE__ */ new Set([\n      ...contigNames(contig),\n      ...alias ? [alias] : []\n    ])) {\n      byName.set(name, byName.has(name) ? void 0 : refName);\n    }\n  }\n  return (name) => exact.has(name) ? name : byName.get(name);\n}\nfunction featuresOnBackbone(features, backbone, aliases) {\n  const bind = refNameBinding(\n    backbone.contigs.map((c) => c.refName),\n    aliases\n  );\n  return features.flatMap((f) => {\n    const refName = bind(f.refName);\n    return refName === void 0 ? [] : [refName === f.refName ? f : { ...f, refName }];\n  });\n}\n\nexport {\n  WELL_KNOWN_SAMPLES,\n  wellKnownSample,\n  graphBackbone,\n  referenceLabel,\n  backboneAssembly,\n  assemblyWalk,\n  contigNames,\n  refNameBinding,\n  featuresOnBackbone\n};\n", "import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-D7ZTAGDM.js\";\nimport {\n  Column\n} from \"./chunk-BEUTROKU.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? 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{ sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(text) {\n  const line = text.trimEnd();\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line);\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
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