@jbrowse/bandage-core 9.9.2 → 10.0.0

package/dist/chunks/chunk-RAEABQNW.js

@@ -0,0 +1,227 @@
+// src/pathVisits.ts
+var PathVisits = class {
+  constructor(columns) {
+    this.segments = columns.segments;
+    this.offsets = columns.offsets;
+    this.path = columns.path;
+    this.start = columns.start;
+    this.reversed = columns.reversed;
+    this.paths = columns.paths;
+    this.samples = columns.samples;
+    this.slots = new Map(this.segments.map((s, i) => [s, i]));
+  }
+  static from(entries) {
+    const builder = new PathVisitsBuilder();
+    for (const [segment, visits] of entries) {
+      builder.declare(segment);
+      for (const v of visits) {
+        builder.add(segment, v.path, v.sample, v.start, v.strand === "-");
+      }
+    }
+    return builder.build();
+  }
+  get size() {
+    return this.segments.length;
+  }
+  // the segment's index into `segments` and `offsets`, -1 when unvisited
+  slot(segment) {
+    return this.slots.get(segment) ?? -1;
+  }
+  pathIndex(path) {
+    return this.paths.indexOf(path);
+  }
+  // the first of `slot`'s visits by path `p`, -1 for none
+  firstBy(slot, p) {
+    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {
+      if (this.path[i] === p) {
+        return i;
+      }
+    }
+    return -1;
+  }
+  // Paths' steps replayed in walk order against their visits: the k-th call
+  // for one path and segment answers that path's k-th visit there, -1 past
+  // its last. A walk in pieces lists its pieces in path order, so replaying
+  // the pieces in order reads each step's own visit.
+  replay() {
+    const cursor = /* @__PURE__ */ new Map();
+    return (slot, p) => {
+      if (slot < 0 || p < 0) {
+        return -1;
+      }
+      const key = slot * this.paths.length + p;
+      const end = this.offsets[slot + 1];
+      let at = cursor.get(key) ?? this.offsets[slot];
+      while (at < end && this.path[at] !== p) {
+        at++;
+      }
+      cursor.set(key, at + 1);
+      return at < end ? at : -1;
+    };
+  }
+  // the visits of paths `keepPath` accepts, at segments `keepSegment` does
+  filter(keepPath, keepSegment = () => true) {
+    const kept = this.paths.map(keepPath);
+    const builder = new PathVisitsBuilder();
+    this.segments.forEach((segment, s) => {
+      if (!keepSegment(segment)) {
+        return;
+      }
+      const slot = builder.declare(segment);
+      for (let i = this.offsets[s]; i < this.offsets[s + 1]; i++) {
+        const p = this.path[i];
+        if (kept[p]) {
+          builder.addAt(
+            slot,
+            builder.pathOf(this.paths[p], this.samples[p]),
+            this.start[i],
+            this.reversed[i] === 1
+          );
+        }
+      }
+    });
+    return builder.build();
+  }
+  strand(i) {
+    return this.reversed[i] ? "-" : "+";
+  }
+  visit(i) {
+    const p = this.path[i];
+    return {
+      path: this.paths[p],
+      sample: this.samples[p],
+      start: this.start[i],
+      strand: this.strand(i)
+    };
+  }
+  visitsAt(slot) {
+    const out = [];
+    for (let i = this.offsets[slot]; i < this.offsets[slot + 1]; i++) {
+      out.push(this.visit(i));
+    }
+    return out;
+  }
+  get(segment) {
+    const slot = this.slot(segment);
+    return slot < 0 ? void 0 : this.visitsAt(slot);
+  }
+  has(segment) {
+    return this.slots.has(segment);
+  }
+  keys() {
+    return this.segments[Symbol.iterator]();
+  }
+  *values() {
+    for (let s = 0; s < this.segments.length; s++) {
+      yield this.visitsAt(s);
+    }
+  }
+  *entries() {
+    for (let s = 0; s < this.segments.length; s++) {
+      yield [this.segments[s], this.visitsAt(s)];
+    }
+  }
+  [Symbol.iterator]() {
+    return this.entries();
+  }
+};
+var Column = class {
+  constructor(data) {
+    this.data = data;
+    this.length = 0;
+  }
+  push(value) {
+    if (this.length === this.data.length) {
+      const grown = new this.data.constructor(
+        this.data.length * 2
+      );
+      grown.set(this.data);
+      this.data = grown;
+    }
+    this.data[this.length++] = value;
+  }
+};
+var PathVisitsBuilder = class {
+  constructor() {
+    this.segments = [];
+    this.slots = /* @__PURE__ */ new Map();
+    this.paths = [];
+    this.samples = [];
+    this.pathIndex = /* @__PURE__ */ new Map();
+    this.slot = new Column(new Int32Array(1024));
+    this.path = new Column(new Int32Array(1024));
+    this.start = new Column(new Float64Array(1024));
+    this.reversed = new Column(new Uint8Array(1024));
+  }
+  // a segment's place in iteration order, though it has no visits yet
+  declare(segment) {
+    let s = this.slots.get(segment);
+    if (s === void 0) {
+      s = this.segments.length;
+      this.slots.set(segment, s);
+      this.segments.push(segment);
+    }
+    return s;
+  }
+  // a path's index, so a caller adding many of its visits names it once
+  pathOf(path, sample) {
+    let p = this.pathIndex.get(path);
+    if (p === void 0) {
+      p = this.paths.length;
+      this.pathIndex.set(path, p);
+      this.paths.push(path);
+      this.samples.push(sample);
+    }
+    return p;
+  }
+  add(segment, path, sample, start, reversed) {
+    this.addAt(
+      this.declare(segment),
+      this.pathOf(path, sample),
+      start,
+      reversed
+    );
+  }
+  addAt(slot, path, start, reversed) {
+    this.slot.push(slot);
+    this.path.push(path);
+    this.start.push(start);
+    this.reversed.push(reversed ? 1 : 0);
+  }
+  build() {
+    const n = this.slot.length;
+    const segments = this.segments.length;
+    const offsets = new Int32Array(segments + 1);
+    const slot = this.slot.data;
+    for (let i = 0; i < n; i++) {
+      offsets[slot[i] + 1]++;
+    }
+    for (let s = 0; s < segments; s++) {
+      offsets[s + 1] += offsets[s];
+    }
+    const fill = offsets.slice(0, segments);
+    const path = new Int32Array(n);
+    const start = new Float64Array(n);
+    const reversed = new Uint8Array(n);
+    for (let i = 0; i < n; i++) {
+      const at = fill[slot[i]]++;
+      path[at] = this.path.data[i];
+      start[at] = this.start.data[i];
+      reversed[at] = this.reversed.data[i];
+    }
+    return new PathVisits({
+      segments: this.segments,
+      offsets,
+      path,
+      start,
+      reversed,
+      paths: this.paths,
+      samples: this.samples
+    });
+  }
+};
+
+export {
+  PathVisits,
+  PathVisitsBuilder
+};

package/dist/chunks/{chunk-EDASNMLY.js → chunk-REE4GUDM.js}

@@ -1,12 +1,12 @@
-import {
-  groupDigits
-} from "./chunk-3ZZSX5HN.js";
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
 import {
   isGenericSample
 } from "./chunk-BPLIXMH7.js";
+import {
+  groupDigits
+} from "./chunk-3ZZSX5HN.js";
 
 // src/pathColors.ts
 function nameHue(name) {

package/dist/chunks/{chunk-IZ3W5IU2.js → chunk-RJXPPYA7.js}

@@ -5,36 +5,48 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-MECWJY2R.js";
-import {
-  Canvas2DRenderer
-} from "./chunk-WBCOREDZ.js";
-import {
-  layoutGeometryInputs
-} from "./chunk-LOCJN3BZ.js";
+} from "./chunk-WI7ZHJ27.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-P6O4RSOQ.js";
+} from "./chunk-VZNKA3K2.js";
 import {
-  genePins
-} from "./chunk-BUBZ32IC.js";
+  Canvas2DRenderer
+} from "./chunk-WBCOREDZ.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
 } from "./chunk-3S3YVOJ7.js";
+import {
+  genePins
+} from "./chunk-BUBZ32IC.js";
+import {
+  geneLabelCandidates
+} from "./chunk-DRG4236Y.js";
+import {
+  nodesUnderBox
+} from "./chunk-FP4H7SFT.js";
+import {
+  serializeEl
+} from "./chunk-NNODIW4U.js";
+import {
+  layoutGeometryInputs
+} from "./chunk-LOCJN3BZ.js";
+import {
+  version
+} from "./chunk-CDPYXHVR.js";
 import {
   axisScaleOf
-} from "./chunk-ZBLKAWSD.js";
+} from "./chunk-OOLNLCIO.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-EE37PVQY.js";
+} from "./chunk-QIVPRZ4H.js";
 import {
   encodingStops
-} from "./chunk-F5BYHLIN.js";
+} from "./chunk-VOWI544A.js";
 import {
   rangeText,
   walkKey
@@ -42,30 +54,26 @@ import {
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-F4BKWWLS.js";
-import {
-  version
-} from "./chunk-BQ33OOLC.js";
+} from "./chunk-NP356MC2.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-TOVOJNT7.js";
+} from "./chunk-3APK25GI.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-EDASNMLY.js";
+} from "./chunk-REE4GUDM.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";
+import {
+  FIT_PADDING,
+  drawingBounds,
+  fitTransform
+} from "./chunk-W4GZCVUK.js";
 import {
   referenceLabel
 } from "./chunk-RAKOB6IV.js";
-import {
-  geneLabelCandidates
-} from "./chunk-DRG4236Y.js";
-import {
-  nodesUnderBox
-} from "./chunk-FP4H7SFT.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -77,8 +85,9 @@ import {
   resolveColorScheme
 } from "./chunk-JKJWSY4V.js";
 import {
-  serializeEl
-} from "./chunk-NNODIW4U.js";
+  deletionDrawing,
+  deletionEdges
+} from "./chunk-N6FECAXP.js";
 import {
   FACET_GAP_PX,
   FACET_PAD_PX,
@@ -87,15 +96,6 @@ import {
   facetGrid,
   facetSettingOf
 } from "./chunk-XV4P5KEQ.js";
-import {
-  FIT_PADDING,
-  drawingBounds,
-  fitTransform
-} from "./chunk-FPTI3WAV.js";
-import {
-  deletionDrawing,
-  deletionEdges
-} from "./chunk-N6FECAXP.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';

package/dist/chunks/{chunk-F5BYHLIN.js → chunk-VOWI544A.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-F4BKWWLS.js";
+} from "./chunk-NP356MC2.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-P6O4RSOQ.js → chunk-VZNKA3K2.js}

@@ -3,16 +3,16 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-YS7VA5SI.js";
+} from "./chunk-DCJC32QW.js";
+import {
+  el
+} from "./chunk-NNODIW4U.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-F4BKWWLS.js";
+} from "./chunk-NP356MC2.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
-import {
-  el
-} from "./chunk-NNODIW4U.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-FPTI3WAV.js → chunk-W4GZCVUK.js}

@@ -1,18 +1,18 @@
-import {
-  orientToReference
-} from "./chunk-PUG7LXDF.js";
 import {
   seededNodes
 } from "./chunk-IGVV37VI.js";
 import {
-  convertGFAToGraph
-} from "./chunk-J7YKQ5YW.js";
+  smoothChain
+} from "./chunk-OPPVSPEF.js";
 import {
-  gfaTables
-} from "./chunk-G45YY72K.js";
+  orientToReference
+} from "./chunk-PUG7LXDF.js";
+import {
+  convertGFAToGraph
+} from "./chunk-QXAB2FLJ.js";
 import {
   graphFromTables
-} from "./chunk-OA7RIMZ2.js";
+} from "./chunk-PSMKPSO4.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
@@ -23,7 +23,10 @@ import {
 } from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
+import {
+  gfaTables
+} from "./chunk-G45YY72K.js";
 import {
   mergeRuns,
   splitRuns
@@ -148,11 +151,13 @@ async function forceLayout(graph, settings, engine) {
   const drawn = new Map(
     scaling.nodes.map((n) => [n.id, drawnNodeLength(scaling.opts, n.length)])
   );
-  const positions = splitRuns(
-    result.nodePositions,
-    merged.runs,
-    (id) => drawn.get(id) ?? 0
+  const smoothed = Object.fromEntries(
+    Object.entries(result.nodePositions).map(([id, line]) => [
+      id,
+      smoothChain(line)
+    ])
   );
+  const positions = splitRuns(smoothed, merged.runs, (id) => drawn.get(id) ?? 0);
   const { nodePositions, deletionRoutes } = takeRoutes(
     graph.nodes.some(isBackbone) ? orientToReference(graph, positions) : positions,
     routed.routes

package/dist/chunks/{chunk-MECWJY2R.js → chunk-WI7ZHJ27.js}

@@ -2,16 +2,16 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-P6O4RSOQ.js";
-import {
-  LABEL_CHAR_PX
-} from "./chunk-AB35TJST.js";
+} from "./chunk-VZNKA3K2.js";
 import {
   el
 } from "./chunk-NNODIW4U.js";
 import {
   pathOrigin
-} from "./chunk-IGJCTPFB.js";
+} from "./chunk-EMUUNWRU.js";
+import {
+  LABEL_CHAR_PX
+} from "./chunk-AB35TJST.js";
 
 // src/layout/walkStrip.ts
 function walkStripApplies(o) {

package/dist/cli/figure.js

@@ -4,6 +4,24 @@ import {
   genesFromGff3Lines,
   genesFromText
 } from "../chunks/chunk-BXEPA4KS.js";
+import {
+  figureSvg
+} from "../chunks/chunk-RJXPPYA7.js";
+import "../chunks/chunk-47DYCZOK.js";
+import "../chunks/chunk-WI7ZHJ27.js";
+import {
+  genesOnRow,
+  placeRowGenes
+} from "../chunks/chunk-VZNKA3K2.js";
+import "../chunks/chunk-WBCOREDZ.js";
+import "../chunks/chunk-4BYTEJGW.js";
+import "../chunks/chunk-3S3YVOJ7.js";
+import "../chunks/chunk-BUBZ32IC.js";
+import "../chunks/chunk-DCJC32QW.js";
+import "../chunks/chunk-DRG4236Y.js";
+import "../chunks/chunk-FP4H7SFT.js";
+import "../chunks/chunk-MLSWIMZO.js";
+import "../chunks/chunk-NNODIW4U.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
@@ -14,15 +32,15 @@ import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-IJRNMO4D.js";
-import "../chunks/chunk-LOEA5IHZ.js";
-import "../chunks/chunk-HOZI3FBG.js";
+} from "../chunks/chunk-ICXMWYOA.js";
+import "../chunks/chunk-IM4SJUPO.js";
 import "../chunks/chunk-CWFNEKST.js";
+import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-HNQPEMYE.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-RVS2QCOX.js";
-import "../chunks/chunk-HNQPEMYE.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   HPRC_GBZ,
@@ -30,75 +48,59 @@ import {
   haplotypeIndexBeside,
   openGbz,
   parseRegion
-} from "../chunks/chunk-73RSLGZT.js";
-import "../chunks/chunk-LTUWJKHD.js";
+} from "../chunks/chunk-FLFBYSJO.js";
+import "../chunks/chunk-Q7LYHGGQ.js";
 import "../chunks/chunk-WSIFAZU7.js";
-import {
-  figureSvg
-} from "../chunks/chunk-IZ3W5IU2.js";
-import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-MECWJY2R.js";
-import "../chunks/chunk-WBCOREDZ.js";
-import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import {
-  genesOnRow,
-  placeRowGenes
-} from "../chunks/chunk-P6O4RSOQ.js";
-import "../chunks/chunk-BUBZ32IC.js";
-import "../chunks/chunk-3S3YVOJ7.js";
-import "../chunks/chunk-ZBLKAWSD.js";
-import "../chunks/chunk-EE37PVQY.js";
-import "../chunks/chunk-F5BYHLIN.js";
+import "../chunks/chunk-CDPYXHVR.js";
+import "../chunks/chunk-OOLNLCIO.js";
+import "../chunks/chunk-QIVPRZ4H.js";
+import "../chunks/chunk-VOWI544A.js";
 import "../chunks/chunk-2LQ5BWT7.js";
-import "../chunks/chunk-YS7VA5SI.js";
-import "../chunks/chunk-F4BKWWLS.js";
+import "../chunks/chunk-NP356MC2.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-BQ33OOLC.js";
-import "../chunks/chunk-TOVOJNT7.js";
+import "../chunks/chunk-WFB5TXRA.js";
+import "../chunks/chunk-3APK25GI.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-6PYZYBBF.js";
-import "../chunks/chunk-EDASNMLY.js";
+} from "../chunks/chunk-KAN2WTG5.js";
+import "../chunks/chunk-REE4GUDM.js";
 import "../chunks/chunk-PBENCR5L.js";
-import {
-  featuresOnBackbone,
-  graphBackbone,
-  refNameBinding
-} from "../chunks/chunk-RAKOB6IV.js";
-import "../chunks/chunk-DRG4236Y.js";
-import "../chunks/chunk-FP4H7SFT.js";
-import "../chunks/chunk-MLSWIMZO.js";
-import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-JKJWSY4V.js";
-import "../chunks/chunk-NNODIW4U.js";
-import "../chunks/chunk-XV4P5KEQ.js";
 import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-FPTI3WAV.js";
-import "../chunks/chunk-PUG7LXDF.js";
+} from "../chunks/chunk-W4GZCVUK.js";
 import "../chunks/chunk-IGVV37VI.js";
-import "../chunks/chunk-J7YKQ5YW.js";
-import "../chunks/chunk-G45YY72K.js";
-import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-OPPVSPEF.js";
+import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-QXAB2FLJ.js";
 import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-PSMKPSO4.js";
 import "../chunks/chunk-CDLPYR5O.js";
 import "../chunks/chunk-JVLURPFW.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-IGJCTPFB.js";
+import {
+  featuresOnBackbone,
+  graphBackbone,
+  refNameBinding
+} from "../chunks/chunk-RAKOB6IV.js";
+import "../chunks/chunk-G45YY72K.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-UVBGRJQX.js";
 import "../chunks/chunk-6JEWNXCQ.js";
+import "../chunks/chunk-JKJWSY4V.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-XV4P5KEQ.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";

package/dist/cli/fold.js

@@ -7,17 +7,19 @@ import {
 } from "../chunks/chunk-B4645SM2.js";
 import {
   loadGraph
-} from "../chunks/chunk-FPTI3WAV.js";
-import "../chunks/chunk-PUG7LXDF.js";
+} from "../chunks/chunk-W4GZCVUK.js";
 import "../chunks/chunk-IGVV37VI.js";
-import "../chunks/chunk-J7YKQ5YW.js";
-import "../chunks/chunk-G45YY72K.js";
-import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-OPPVSPEF.js";
+import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-QXAB2FLJ.js";
 import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-PSMKPSO4.js";
 import "../chunks/chunk-CDLPYR5O.js";
 import "../chunks/chunk-JVLURPFW.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-G45YY72K.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-UVBGRJQX.js";