@jbrowse/bandage-core 9.8.0 → 9.8.1

package/dist/chunks/{chunk-75HR3756.js → chunk-G3SZWUPA.js}

@@ -4,6 +4,9 @@ import {
 import {
   readColor
 } from "./chunk-CWFNEKST.js";
+import {
+  pathOrigin
+} from "./chunk-ST2IBUAN.js";
 
 // src/tubeMap/draw.ts
 import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";
@@ -53,9 +56,9 @@ function extentOf(commands) {
   }
   return { x0, x1 };
 }
-function shapeOf(d, color, id, haplotype) {
+function shapeOf(d, color, id, haplotype, reference) {
   const commands = parsePath(d);
-  return { commands, color, id, haplotype, ...extentOf(commands) };
+  return { commands, color, id, haplotype, reference, ...extentOf(commands) };
 }
 function trackColors(layout, pathColors) {
   return new Map(
@@ -65,30 +68,43 @@ function trackColors(layout, pathColors) {
     ])
   );
 }
-function layerOf(layout, type, colors) {
+function layerOf(layout, type, colors, referenceIds) {
   const { shapes } = layout;
   const haplotype = type === "haplotype";
   const colorOf = (s) => colors.get(s.id);
+  const isReference = (s) => haplotype && referenceIds.has(s.id);
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
     color: colorOf(r),
     id: r.id,
     haplotype,
+    reference: isReference(r),
     x0: r.xStart,
     x1: r.xEnd + 1,
     y0: r.yStart,
     y1: r.yEnd + 1
   }));
   const curves = curvePaths(shapes.curves, type).map(
-    (c) => shapeOf(c.path, colorOf(c), c.id, haplotype)
+    (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));
+  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c)));
   return { rects, shapes: [...curves, ...corners] };
 }
+function referenceTrackIds(graph) {
+  const ids = /* @__PURE__ */ new Set();
+  graph?.paths?.forEach((path, i) => {
+    if (pathOrigin(path.name).name === graph.referencePath) {
+      ids.add(i);
+    }
+  });
+  return ids;
+}
 function tubeMapPicture({
   layout,
-  pathColors
+  pathColors,
+  graph
 }) {
   const colors = trackColors(layout, pathColors);
+  const referenceIds = referenceTrackIds(graph);
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
@@ -99,8 +115,8 @@ function tubeMapPicture({
   return {
     bounds: layout.bounds,
     layers: [
-      layerOf(layout, "haplotype", colors),
-      layerOf(layout, "read", colors)
+      layerOf(layout, "haplotype", colors, referenceIds),
+      layerOf(layout, "read", colors, referenceIds)
     ],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
@@ -181,14 +197,29 @@ function drawTubeMap(ctx, picture, frame) {
   const colorOf = (item) => item.haplotype && frame.tubeColors?.[item.id] || item.color;
   ctx.globalAlpha = 1;
   for (const layer of picture.layers) {
-    fillByColor(ctx, layer.rects, visible, colorOf, (r) => {
-      const left = x(r.x0);
-      const top = y(r.y0);
-      ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);
-    });
-    fillByColor(ctx, layer.shapes, visible, colorOf, (s) => {
-      trace(ctx, s.commands, x, y);
-    });
+    for (const reference of [false, true]) {
+      const inPass = (item) => item.reference === reference;
+      fillByColor(
+        ctx,
+        layer.rects,
+        (r) => inPass(r) && visible(r),
+        colorOf,
+        (r) => {
+          const left = x(r.x0);
+          const top = y(r.y0);
+          ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);
+        }
+      );
+      fillByColor(
+        ctx,
+        layer.shapes,
+        (s) => inPass(s) && visible(s),
+        colorOf,
+        (s) => {
+          trace(ctx, s.commands, x, y);
+        }
+      );
+    }
   }
   const stroke = frame.darkMode ? "#d0d0d0" : "#000000";
   const fill = frame.darkMode ? "rgba(40,40,40,0.4)" : "rgba(255,255,255,0.4)";

package/dist/chunks/chunk-IJYFJVIT.js

@@ -0,0 +1,77 @@
+// src/tubeMap/warp.ts
+var MAX_GAP_PX = 24;
+var MAX_GAP_SHARE = 0.5;
+var isReal = (c) => c.bp1 > c.bp0;
+function referenceKnots(columns, bpToScreen) {
+  const real = columns.filter(isReal);
+  if (real.length === 0) {
+    const first = columns[0];
+    return first ? [{ tx: first.x0, sx: bpToScreen(first.bp0) }] : [];
+  }
+  const tx = [];
+  const target = [];
+  const gap = [];
+  real.forEach((c, i) => {
+    tx.push(c.x0, c.x1);
+    target.push(bpToScreen(c.bp0), bpToScreen(c.bp1));
+    gap.push(i === 0 ? 0 : Math.min(c.x0 - real[i - 1].x1, MAX_GAP_PX), 0);
+  });
+  const span = target.at(-1) - target[0];
+  const demand = gap.reduce((a, b) => a + b, 0);
+  const scale = demand > 0 ? Math.min(1, MAX_GAP_SHARE * span / demand) : 1;
+  return spread(target, gap, scale).map((sx, k) => ({ tx: tx[k], sx }));
+}
+function spread(target, gap, scale) {
+  const offset = [];
+  let sum = 0;
+  for (const g of gap) {
+    sum += g * scale;
+    offset.push(sum);
+  }
+  const blocks = [];
+  target.forEach((t, k) => {
+    let block = { mean: t - offset[k], n: 1 };
+    let last = blocks.at(-1);
+    while (last && last.mean >= block.mean) {
+      blocks.pop();
+      const n = last.n + block.n;
+      block = { mean: (last.mean * last.n + block.mean * block.n) / n, n };
+      last = blocks.at(-1);
+    }
+    blocks.push(block);
+  });
+  return blocks.flatMap((b) => Array(b.n).fill(b.mean)).map((q, k) => q + offset[k]);
+}
+function warpX(knots, tx) {
+  const n = knots.length;
+  if (n === 0) {
+    return tx;
+  }
+  const first = knots[0];
+  const last = knots[n - 1];
+  if (tx <= first.tx) {
+    return first.sx + (tx - first.tx);
+  }
+  if (tx >= last.tx) {
+    return last.sx + (tx - last.tx);
+  }
+  let lo = 0;
+  let hi = n - 1;
+  while (hi - lo > 1) {
+    const mid = lo + hi >> 1;
+    if (knots[mid].tx <= tx) {
+      lo = mid;
+    } else {
+      hi = mid;
+    }
+  }
+  const a = knots[lo];
+  const b = knots[hi];
+  const span = b.tx - a.tx;
+  return span > 0 ? a.sx + (tx - a.tx) / span * (b.sx - a.sx) : a.sx;
+}
+
+export {
+  referenceKnots,
+  warpX
+};

package/dist/chunks/{chunk-VZQ4FKLR.js → chunk-JABM3MUS.js}

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

package/dist/chunks/{chunk-CG77WIFD.js → chunk-JRADQSGK.js}

@@ -45,7 +45,7 @@ import {
 } from "./chunk-BOHK5BD3.js";
 import {
   version
-} from "./chunk-JEF73V3A.js";
+} from "./chunk-YMMZUMYE.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/chunks/{chunk-JEF73V3A.js → chunk-YMMZUMYE.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "9.8.0";
+var version = "9.8.1";
 
 export {
   version

package/dist/cli/figure.js

@@ -35,7 +35,7 @@ import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import {
   figureSvg
-} from "../chunks/chunk-CG77WIFD.js";
+} from "../chunks/chunk-JRADQSGK.js";
 import "../chunks/chunk-QMJXHYVQ.js";
 import "../chunks/chunk-WBCOREDZ.js";
 import "../chunks/chunk-4BYTEJGW.js";
@@ -54,7 +54,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-QG5IVMRS.js";
 import "../chunks/chunk-BOHK5BD3.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-JEF73V3A.js";
+import "../chunks/chunk-YMMZUMYE.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-CG77WIFD.js";
+} from "./chunks/chunk-JRADQSGK.js";
 import "./chunks/chunk-QMJXHYVQ.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
@@ -16,7 +16,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-QG5IVMRS.js";
 import "./chunks/chunk-BOHK5BD3.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-JEF73V3A.js";
+import "./chunks/chunk-YMMZUMYE.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";

package/dist/index.js

@@ -29,16 +29,16 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "./chunks/chunk-75HR3756.js";
+} from "./chunks/chunk-G3SZWUPA.js";
 import "./chunks/chunk-XXT2JCAC.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "./chunks/chunk-VZQ4FKLR.js";
+} from "./chunks/chunk-JABM3MUS.js";
 import {
   referenceKnots,
   warpX
-} from "./chunks/chunk-KQFOCDFY.js";
+} from "./chunks/chunk-IJYFJVIT.js";
 import {
   createForceLayoutCache
 } from "./chunks/chunk-BV64PQ2C.js";
@@ -122,7 +122,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-CG77WIFD.js";
+} from "./chunks/chunk-JRADQSGK.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -222,7 +222,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-JEF73V3A.js";
+} from "./chunks/chunk-YMMZUMYE.js";
 import {
   walkRowLabels,
   walkRowsExtent

package/dist/tubeMap/draw.js

@@ -8,10 +8,13 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-75HR3756.js";
+} from "../chunks/chunk-G3SZWUPA.js";
 import "../chunks/chunk-XXT2JCAC.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
 export {
   drawTubeMap,
   drawTubeMapHighlight,

package/dist/tubeMap/frame.js

@@ -1,8 +1,8 @@
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "../chunks/chunk-VZQ4FKLR.js";
-import "../chunks/chunk-KQFOCDFY.js";
+} from "../chunks/chunk-JABM3MUS.js";
+import "../chunks/chunk-IJYFJVIT.js";
 export {
   tubeMapFrame,
   tubeMapNodeAt

package/dist/tubeMap/warp.js

@@ -1,7 +1,7 @@
 import {
   referenceKnots,
   warpX
-} from "../chunks/chunk-KQFOCDFY.js";
+} from "../chunks/chunk-IJYFJVIT.js";
 export {
   referenceKnots,
   warpX

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

@@ -34,6 +34,7 @@ interface Filled {
     color: string;
     id: number;
     haplotype: boolean;
+    reference: boolean;
     x0: number;
     x1: number;
 }
@@ -60,7 +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, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'>): TubeMapPicture;
+export declare function tubeMapPicture({ layout, pathColors, graph, }: Pick<TubeMapDrawing, 'layout' | 'pathColors'> & Partial<Pick<TubeMapDrawing, 'graph'>>): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.8.0";
+export declare const version = "9.8.1";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-JEF73V3A.js";
+} from "./chunks/chunk-YMMZUMYE.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.8.0",
+  "version": "9.8.1",
   "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": {

package/dist/chunks/chunk-KQFOCDFY.js

@@ -1,73 +0,0 @@
-// src/tubeMap/warp.ts
-var MAX_GAP_PX = 24;
-var isReal = (c) => c.bp1 > c.bp0;
-function referenceKnots(columns, bpToScreen) {
-  const real = columns.filter(isReal);
-  if (real.length === 0) {
-    const first = columns[0];
-    return first ? [{ tx: first.x0, sx: bpToScreen(first.bp0) }] : [];
-  }
-  const screen = real.map((c) => ({
-    c,
-    s0: bpToScreen(c.bp0),
-    s1: bpToScreen(c.bp1),
-    trimLeft: 0,
-    trimRight: 0
-  }));
-  for (let i = 0; i + 1 < screen.length; i++) {
-    const left = screen[i];
-    const right = screen[i + 1];
-    const demand = Math.min(right.c.x0 - left.c.x1, MAX_GAP_PX);
-    const short = demand - (right.s0 - left.s1);
-    if (short > 0) {
-      const capLeft = (left.s1 - left.s0) / 2;
-      const capRight = (right.s1 - right.s0) / 2;
-      let fromLeft = Math.min(short / 2, capLeft);
-      const fromRight = Math.min(short - fromLeft, capRight);
-      fromLeft = Math.min(short - fromRight, capLeft);
-      left.trimRight = fromLeft;
-      right.trimLeft = fromRight;
-    }
-  }
-  const knots = [];
-  for (const { c, s0, s1, trimLeft, trimRight } of screen) {
-    knots.push(
-      { tx: c.x0, sx: s0 + trimLeft },
-      { tx: c.x1, sx: s1 - trimRight }
-    );
-  }
-  return knots;
-}
-function warpX(knots, tx) {
-  const n = knots.length;
-  if (n === 0) {
-    return tx;
-  }
-  const first = knots[0];
-  const last = knots[n - 1];
-  if (tx <= first.tx) {
-    return first.sx + (tx - first.tx);
-  }
-  if (tx >= last.tx) {
-    return last.sx + (tx - last.tx);
-  }
-  let lo = 0;
-  let hi = n - 1;
-  while (hi - lo > 1) {
-    const mid = lo + hi >> 1;
-    if (knots[mid].tx <= tx) {
-      lo = mid;
-    } else {
-      hi = mid;
-    }
-  }
-  const a = knots[lo];
-  const b = knots[hi];
-  const span = b.tx - a.tx;
-  return span > 0 ? a.sx + (tx - a.tx) / span * (b.sx - a.sx) : a.sx;
-}
-
-export {
-  referenceKnots,
-  warpX
-};