@jbrowse/bandage-core 9.9.1 → 9.9.2

package/dist/chunks/{chunk-JABM3MUS.js → chunk-2CMYNW3E.js}

@@ -1,7 +1,7 @@
 import {
   referenceKnots,
   warpX
-} from "./chunk-IJYFJVIT.js";
+} from "./chunk-HK5Y2YWV.js";
 
 // src/tubeMap/frame.ts
 var MIN_TUBE_Y_SCALE = 0.05;

package/dist/chunks/{chunk-EC4UZHWQ.js → chunk-BQ33OOLC.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.9.1";
+var version = "9.9.2";
 
 export {
   version

package/dist/chunks/{chunk-IJYFJVIT.js → chunk-HK5Y2YWV.js}

@@ -72,6 +72,7 @@ function warpX(knots, tx) {
 }
 
 export {
+  MAX_GAP_PX,
   referenceKnots,
   warpX
 };

package/dist/chunks/{chunk-D4I6GGFX.js → chunk-IZ3W5IU2.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-F4BKWWLS.js";
 import {
   version
-} from "./chunk-EC4UZHWQ.js";
+} from "./chunk-BQ33OOLC.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/chunks/{chunk-2NROXCK3.js → chunk-PIN7ZMTZ.js}

@@ -1,6 +1,9 @@
 import {
   tubeMapMismatches
 } from "./chunk-XXT2JCAC.js";
+import {
+  MAX_GAP_PX
+} from "./chunk-HK5Y2YWV.js";
 import {
   readColor
 } from "./chunk-CWFNEKST.js";
@@ -68,7 +71,7 @@ function trackColors(layout, pathColors) {
     ])
   );
 }
-function layerOf(layout, type, colors, referenceIds) {
+function layerOf(layout, type, colors, referenceIds, gapWidth) {
   const { shapes } = layout;
   const haplotype = type === "haplotype";
   const colorOf = (s) => colors.get(s.id);
@@ -83,7 +86,7 @@ function layerOf(layout, type, colors, referenceIds) {
     y0: r.yStart,
     y1: r.yEnd + 1
   }));
-  const curves = curvePaths(shapes.curves, type).map(
+  const curves = curvePaths(shapes.curves, type, { gapWidth }).map(
     (c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c))
   );
   const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c)));
@@ -101,10 +104,12 @@ function referenceTrackIds(graph) {
 function tubeMapPicture({
   layout,
   pathColors,
-  graph
+  graph,
+  columns
 }) {
   const colors = trackColors(layout, pathColors);
   const referenceIds = referenceTrackIds(graph);
+  const gapWidth = columns ? MAX_GAP_PX : void 0;
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
@@ -115,8 +120,8 @@ function tubeMapPicture({
   return {
     bounds: layout.bounds,
     layers: [
-      layerOf(layout, "haplotype", colors, referenceIds),
-      layerOf(layout, "read", colors, referenceIds)
+      layerOf(layout, "haplotype", colors, referenceIds, gapWidth),
+      layerOf(layout, "read", colors, referenceIds, gapWidth)
     ],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
@@ -297,11 +302,60 @@ function drawMismatches(ctx, marks, frame) {
     }
   }
 }
+function outline(commands, x, y) {
+  const points = [];
+  let cx = 0;
+  let cy = 0;
+  const STEPS = 12;
+  for (const c of commands) {
+    if (c.op === "C" || c.op === "Q") {
+      for (let i = 1; i <= STEPS; i++) {
+        const t = i / STEPS;
+        const u = 1 - t;
+        const [px, py] = c.op === "C" ? [
+          u * u * u * cx + 3 * u * u * t * c.x1 + 3 * u * t * t * c.x2 + t * t * t * c.x,
+          u * u * u * cy + 3 * u * u * t * c.y1 + 3 * u * t * t * c.y2 + t * t * t * c.y
+        ] : [
+          u * u * cx + 2 * u * t * c.x1 + t * t * c.x,
+          u * u * cy + 2 * u * t * c.y1 + t * t * c.y
+        ];
+        points.push([x(px), y(py)]);
+      }
+    }
+    if (c.op !== "Z") {
+      cx = "x" in c ? c.x : cx;
+      cy = "y" in c ? c.y : cy;
+      if (c.op !== "C" && c.op !== "Q") {
+        points.push([x(cx), y(cy)]);
+      }
+    }
+  }
+  return points;
+}
+function inside(points, sx, sy) {
+  let hit = false;
+  for (let i = 0, j = points.length - 1; i < points.length; j = i++) {
+    const [xi, yi] = points[i];
+    const [xj, yj] = points[j];
+    if (yi > sy !== yj > sy && sx < (xj - xi) * (sy - yi) / (yj - yi) + xi) {
+      hit = !hit;
+    }
+  }
+  return hit;
+}
 function tubeMapTrackAt(picture, { x, y }, sx, sy) {
   for (let l = picture.layers.length - 1; l >= 0; l--) {
-    for (const r of picture.layers[l].rects) {
-      if (x(r.x0) <= sx && sx <= x(r.x1) && y(r.y0) <= sy && sy <= y(r.y1)) {
-        return r.id;
+    const { rects, shapes } = picture.layers[l];
+    for (const reference of [true, false]) {
+      for (const r of rects) {
+        if (r.reference === reference && x(r.x0) <= sx && sx <= x(r.x1) && y(r.y0) <= sy && sy <= y(r.y1)) {
+          return r.id;
+        }
+      }
+      for (const s of shapes) {
+        if (s.reference === reference && x(s.x0) <= sx && sx <= x(s.x1) && inside(outline(s.commands, x, y), sx, sy)) {
+          return s.id;
+        }
       }
     }
   }

package/dist/cli/figure.js

@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-D4I6GGFX.js";
+} from "../chunks/chunk-IZ3W5IU2.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-MECWJY2R.js";
 import "../chunks/chunk-WBCOREDZ.js";
@@ -54,7 +54,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-YS7VA5SI.js";
 import "../chunks/chunk-F4BKWWLS.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EC4UZHWQ.js";
+import "../chunks/chunk-BQ33OOLC.js";
 import "../chunks/chunk-TOVOJNT7.js";
 import {
   filterSamples,

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-D4I6GGFX.js";
+} from "./chunks/chunk-IZ3W5IU2.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-MECWJY2R.js";
 import "./chunks/chunk-WBCOREDZ.js";
@@ -16,7 +16,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-YS7VA5SI.js";
 import "./chunks/chunk-F4BKWWLS.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-EC4UZHWQ.js";
+import "./chunks/chunk-BQ33OOLC.js";
 import "./chunks/chunk-TOVOJNT7.js";
 import "./chunks/chunk-6PYZYBBF.js";
 import "./chunks/chunk-EDASNMLY.js";

package/dist/index.js

@@ -4,7 +4,7 @@ import {
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "./chunks/chunk-JABM3MUS.js";
+} from "./chunks/chunk-2CMYNW3E.js";
 import {
   drawTubeMapGenes,
   tubeMapGenes
@@ -12,10 +12,6 @@ import {
 import {
   tubeMapNodeColors
 } from "./chunks/chunk-KJEMKHVB.js";
-import {
-  referenceKnots,
-  warpX
-} from "./chunks/chunk-IJYFJVIT.js";
 import {
   bundleRoutes
 } from "./chunks/chunk-WVBYR6Y7.js";
@@ -37,8 +33,12 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "./chunks/chunk-2NROXCK3.js";
+} from "./chunks/chunk-PIN7ZMTZ.js";
 import "./chunks/chunk-XXT2JCAC.js";
+import {
+  referenceKnots,
+  warpX
+} from "./chunks/chunk-HK5Y2YWV.js";
 import {
   createForceLayoutCache
 } from "./chunks/chunk-YAN2ZPNV.js";
@@ -122,7 +122,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-D4I6GGFX.js";
+} from "./chunks/chunk-IZ3W5IU2.js";
 import {
   svgCanvas
 } from "./chunks/chunk-47DYCZOK.js";
@@ -222,7 +222,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-EC4UZHWQ.js";
+} from "./chunks/chunk-BQ33OOLC.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/tubeMap/draw.js

@@ -8,8 +8,9 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-2NROXCK3.js";
+} from "../chunks/chunk-PIN7ZMTZ.js";
 import "../chunks/chunk-XXT2JCAC.js";
+import "../chunks/chunk-HK5Y2YWV.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-IGJCTPFB.js";

package/dist/tubeMap/frame.js

@@ -1,8 +1,8 @@
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "../chunks/chunk-JABM3MUS.js";
-import "../chunks/chunk-IJYFJVIT.js";
+} from "../chunks/chunk-2CMYNW3E.js";
+import "../chunks/chunk-HK5Y2YWV.js";
 export {
   tubeMapFrame,
   tubeMapNodeAt

package/dist/tubeMap/warp.js

@@ -1,8 +1,10 @@
 import {
+  MAX_GAP_PX,
   referenceKnots,
   warpX
-} from "../chunks/chunk-IJYFJVIT.js";
+} from "../chunks/chunk-HK5Y2YWV.js";
 export {
+  MAX_GAP_PX,
   referenceKnots,
   warpX
 };

package/dist/types/tubeMap/draw.d.ts

@@ -61,7 +61,7 @@ export interface TubeMapPicture {
     mismatches: TubeMapMismatch[];
 }
 export declare function trackColors(layout: TubeMapLayout, pathColors: readonly string[]): ReadonlyMap<number, string>;
-export declare function tubeMapPicture({ layout, pathColors, graph, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph'>>): TubeMapPicture;
+export declare function tubeMapPicture({ layout, pathColors, graph, columns, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph' | 'columns'>>): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

package/dist/types/tubeMap/warp.d.ts

@@ -3,5 +3,6 @@ export interface Knot {
     tx: number;
     sx: number;
 }
+export declare const MAX_GAP_PX = 24;
 export declare function referenceKnots(columns: readonly TubeMapColumn[], bpToScreen: (bp: number) => number): Knot[];
 export declare function warpX(knots: readonly Knot[], tx: number): number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.9.1";
+export declare const version = "9.9.2";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-EC4UZHWQ.js";
+} from "./chunks/chunk-BQ33OOLC.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.9.1",
+  "version": "9.9.2",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -37,7 +37,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
-    "@jbrowse/tubemap-core": "^0.2.3"
+    "@jbrowse/tubemap-core": "^0.2.4"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",