@jbrowse/bandage-core 4.0.27 → 4.0.28

package/dist/chunks/{chunk-VNCGWA2N.js → chunk-G3HO75W7.js}

@@ -3153,7 +3153,7 @@ function nodeInk(graph, nodeById, contigThickness, nodeWidth2) {
 }
 
 // src/renderer/GeometryBuilder.ts
-import { packAbgr as packAbgr2 } from "@jbrowse/core/util/colorBits";
+import { abgrToCssRgba, packAbgr as packAbgr2 } from "@jbrowse/core/util/colorBits";
 
 // src/renderer/colorBits.ts
 import {
@@ -3227,6 +3227,9 @@ var EDGE_DELETION_COLOR = packAbgr2(24, 24, 28, 240);
 var DELETION_THICKNESS_FACTOR = 2.2;
 var LIFT_BACKDROP_COLOR = packAbgr2(160, 160, 160, 255);
 var FADED_ALPHA = 0.18;
+var LIFT_BACKDROP_CSS = abgrToCssRgba(
+  fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA)
+);
 var DELETION_DASH_PX = 11;
 var MIN_PATH_STRIPE_PX = 1.2;
 var MIN_WALK_LANE_PX = 4;
@@ -3880,7 +3883,7 @@ function buildGeometry(options) {
 
 // src/renderer/Canvas2DRenderer.ts
 import {
-  abgrToCssRgba,
+  abgrToCssRgba as abgrToCssRgba2,
   normalizedRgbToCssRgba
 } from "@jbrowse/core/util/colorBits";
 import { syncCanvasSize } from "@jbrowse/render-core/canvas2dUtils";
@@ -3949,7 +3952,7 @@ var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
       weight: e.thickness,
       last: inRun(hl, i)
     }))) {
-      ctx.strokeStyle = abgrToCssRgba(color);
+      ctx.strokeStyle = abgrToCssRgba2(color);
       ctx.lineWidth = items[0].thickness * 2 * t.dpr;
       ctx.beginPath();
       for (const e of items) {
@@ -3992,7 +3995,7 @@ var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
         last: factor !== void 0
       };
     })) {
-      ctx.strokeStyle = abgrToCssRgba(color);
+      ctx.strokeStyle = abgrToCssRgba2(color);
       ctx.lineWidth = items[0].thickness * 2 * t.dpr;
       ctx.beginPath();
       for (const s of items) {
@@ -4021,7 +4024,7 @@ var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
       weight: 0,
       last: inRun(hl, i)
     }))) {
-      ctx.fillStyle = abgrToCssRgba(color);
+      ctx.fillStyle = abgrToCssRgba2(color);
       ctx.beginPath();
       for (const a of items) {
         const [tip, left, notch, right] = arrowheadOutline(a, t);
@@ -4738,7 +4741,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.0.27";
+var version = "4.0.28";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -5406,15 +5409,57 @@ function nodeLimitError(error, limit, windowBp) {
     return new NodeLimitError(limit, windowBp, Math.max(fits, 1));
   }
 }
+var GBZ_CUT_DEFAULTS = {
+  context: 1e3,
+  snarls: "contained",
+  limit: 1e5
+};
+async function referencePieces(db, query, start, end) {
+  const inside = (await db.paths()).filter(
+    ({ isIndexed, name }) => isIndexed && name.sample === query.sample && name.haplotype === query.haplotype && name.contig === query.contig && name.fragment > start && name.fragment < end
+  ).map((path) => path.name.fragment);
+  const bounds = [start, ...[...new Set(inside)].sort((a, b) => a - b), end];
+  return bounds.slice(1).map((pieceEnd, i) => ({
+    start: bounds[i],
+    end: pieceEnd
+  }));
+}
+function joinCuts(gfas) {
+  const cuts = gfas.map((gfa) => gfa.split("\n").filter((line) => line !== ""));
+  const ofType = (cut, type) => cut.filter((line) => line.startsWith(type));
+  const lines = /* @__PURE__ */ new Set([
+    ...ofType(cuts[0] ?? [], "H"),
+    ...cuts.flatMap((cut) => ofType(cut, "S")),
+    ...cuts.flatMap((cut) => ofType(cut, "L")),
+    ...cuts.flatMap((cut) => ofType(cut, "W").slice(0, 1)),
+    ...cuts.flatMap((cut) => ofType(cut, "W").slice(1))
+  ]);
+  return lines.size === 0 ? "" : `${[...lines].join("\n")}
+`;
+}
 async function cutWindowGFA(db, query, start, end, { keep, ...opts }) {
-  const subgraph = query ? await db.getSubgraphForRange(query, start, end, {
-    ...opts,
-    haplotypes: "all",
-    ...keep === void 0 ? {} : { keep }
-  }).catch((error) => {
-    throw nodeLimitError(error, opts.limit, end - start) ?? error;
-  }) : void 0;
-  return subgraph ? subgraph.toGFA({ names: "resolved" }) : "";
+  if (!query) {
+    return "";
+  }
+  const pieces = await referencePieces(db, query, start, end);
+  const subgraphs = await Promise.all(
+    pieces.map(
+      (piece) => db.getSubgraphForRange(query, piece.start, piece.end, {
+        ...opts,
+        haplotypes: "all",
+        ...keep === void 0 ? {} : { keep }
+      }).catch((error) => {
+        throw nodeLimitError(error, opts.limit, end - start) ?? error;
+      })
+    )
+  );
+  return joinCuts(
+    await Promise.all(
+      subgraphs.flatMap(
+        (subgraph) => subgraph ? [subgraph.toGFA({ names: "resolved" })] : []
+      )
+    )
+  );
 }
 
 // src/gbzCut.ts
@@ -5427,7 +5472,6 @@ function haplotypeIndexBeside(db) {
   const GBZ_DB = /\.gbz\.db$/i;
   return GBZ_DB.test(db) ? db.replace(GBZ_DB, ".haplotype-index.db") : void 0;
 }
-var WALK_LIMIT = 1e5;
 function parseRegion(text) {
   const m = /^\s*([^:\s]+):([\d,]+)-([\d,]+)\s*$/.exec(text);
   if (!m) {
@@ -5466,9 +5510,9 @@ async function cutGbzRegion({ base, referenceSamples }, src, signal) {
   signal?.throwIfAborted();
   const wanted = src.haplotypes?.length ? src.haplotypes : void 0;
   const text = await cutWindowGFA(base, query, region.start, region.end, {
-    context: src.context ?? 1e3,
-    snarls: src.snarls ?? "contained",
-    limit: WALK_LIMIT,
+    context: src.context ?? GBZ_CUT_DEFAULTS.context,
+    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,
+    limit: GBZ_CUT_DEFAULTS.limit,
     signal,
     ...wanted ? { keep: (name) => haplotypeWanted(name, wanted) } : {}
   });
@@ -5528,10 +5572,8 @@ export {
   nodeWidthPx,
   maxNodeWidthPx,
   nodeInk,
-  fadeAbgr,
   baseEdgeCurves,
-  LIFT_BACKDROP_COLOR,
-  FADED_ALPHA,
+  LIFT_BACKDROP_CSS,
   REFERENCE_RAMP_MAX_HUE,
   computeReferenceRamp,
   computeColorSchemeRange,

package/dist/cli/figure.js

@@ -17,7 +17,7 @@ import {
   openGbz,
   parseRegion,
   refNameBinding
-} from "../chunks/chunk-VNCGWA2N.js";
+} from "../chunks/chunk-G3HO75W7.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";

package/dist/index.js

@@ -5,7 +5,6 @@ import {
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
-  FADED_ALPHA,
   FIT_PADDING,
   FORCE_LAYOUT_LABEL,
   HALO_FACTOR,
@@ -15,7 +14,7 @@ import {
   LABEL_PX,
   LAYOUT_MODES,
   LEGEND_INSET_PX,
-  LIFT_BACKDROP_COLOR,
+  LIFT_BACKDROP_CSS,
   NODE_WIDTHS,
   REFERENCE_RAMP_MAX_HUE,
   ROW_HEIGHT_PX,
@@ -43,7 +42,6 @@ import {
   facetCells,
   facetGrid,
   facetLifts,
-  fadeAbgr,
   featuresOnBackbone,
   figureSvg,
   fitTransform,
@@ -102,7 +100,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-VNCGWA2N.js";
+} from "./chunks/chunk-G3HO75W7.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -478,7 +476,6 @@ var REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8;
 var OVERHANG_PX = 8;
 var OVERHANG_CAP_PX = OVERHANG_PX + 3;
 var MIN_STAGGER_PX = 12;
-var PALE = abgrToCssRgba(fadeAbgr(LIFT_BACKDROP_COLOR, FADED_ALPHA));
 function referenceStripBlocks(graph, {
   colorScheme,
   referenceRamp,
@@ -490,14 +487,14 @@ function referenceStripBlocks(graph, {
     if (isBackbone(node)) {
       const colors = walks ? walks.map((w) => {
         const lane = w.colors.get(node.id);
-        return lane === void 0 ? PALE : abgrToCssRgba(lane);
+        return lane === void 0 ? LIFT_BACKDROP_CSS : abgrToCssRgba(lane);
       }) : [abgrToCssRgba(getNodeColor(node, index, colorScheme, range))];
       out.push({
         node: node.id,
         bp0: node.stable.start,
         bp1: node.stable.start + node.length,
         colors,
-        faded: colors.includes(PALE)
+        faded: colors.includes(LIFT_BACKDROP_CSS)
       });
     }
   });

package/dist/types/gbzWindow.d.ts

@@ -24,4 +24,13 @@ export interface GbzWindowOptions {
     keep?: (name: PathName) => boolean;
     signal?: AbortSignal;
 }
+export declare const GBZ_CUT_DEFAULTS: {
+    readonly context: 1000;
+    readonly snarls: "contained";
+    readonly limit: 100000;
+};
+export declare function referencePieces(db: GBZBase, query: PathQuery, start: number, end: number): Promise<{
+    start: number;
+    end: number;
+}[]>;
 export declare function cutWindowGFA(db: GBZBase, query: PathQuery | undefined, start: number, end: number, { keep, ...opts }: GbzWindowOptions): Promise<string>;

package/dist/types/renderer/GeometryBuilder.d.ts

@@ -6,6 +6,7 @@ import type { RenderBatch } from './types.js';
 import type { AxisScale, BezierCurve } from '../util/geometry.js';
 export declare const LIFT_BACKDROP_COLOR: number;
 export declare const FADED_ALPHA = 0.18;
+export declare const LIFT_BACKDROP_CSS: string;
 export interface BuildOptions {
     nodePositions: Record<string, NodeSegment[]>;
     graph: Graph;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.0.27";
+export declare const version = "4.0.28";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.27",
+  "version": "4.0.28",
   "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": {