@jbrowse/bandage-core 9.0.0 → 9.2.0

package/dist/types/index.d.ts

@@ -31,7 +31,7 @@ export type { AxisScale } from './util/geometry.js';
 export { wheelZoomFactor } from './util/wheelZoom.js';
 export { REFERENCE_STRIP_ZONE_PX, drawReferenceStrip, referenceStripBlocks, stripBlockAt, } from './referenceStrip.js';
 export type { StripBlock } from './referenceStrip.js';
-export { drawTubeMap, tubeMapMismatchAt, tubeMapPicture, tubeMapTrackAt, } from './tubeMap/draw.js';
+export { drawTubeMap, drawTubeMapHighlight, tubeMapMismatchAt, tubeMapPicture, tubeMapTrackAt, } from './tubeMap/draw.js';
 export type { TubeMapFrame, TubeMapPicture } from './tubeMap/draw.js';
 export { tubeMapNodeColors } from './tubeMap/nodeColors.js';
 export { referenceKnots, warpX } from './tubeMap/warp.js';
@@ -41,7 +41,7 @@ export { drawTubeMapRuler, referenceBoxes, rulerBoxes, tubeX, } from './tubeMap/
 export type { Box as TubeMapBox, ReferenceBox, ReferenceBoxes, } from './tubeMap/axis.js';
 export { drawTubeMapGenes, tubeMapGenes } from './tubeMap/genes.js';
 export type { TubeMapGene } from './tubeMap/genes.js';
-export { connectorAt, drawTubeMapConnectors, tubeMapConnectors, } from './tubeMap/connectors.js';
+export { connectorAt, drawLitConnector, drawTubeMapConnectors, tubeMapConnectors, } from './tubeMap/connectors.js';
 export type { Connector } from './tubeMap/connectors.js';
 export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
 export { deletionDrawing, deletionEdges } from './deletionEdges.js';
@@ -62,6 +62,7 @@ export { WALK_FIELDS, WALK_SCHEMES, encodingStops, encodingSwatchCss, resolveEnc
 export type { WalkEncoding, WalkField, WalkLayer, WalkScheme, } from './walkEncoding.js';
 export { pathColorsLegible, pathLegend, walkLabelsOf } from './pathColors.js';
 export { bubblesFromGraph } from './bubbles/bubblesFromGraph.js';
+export { graphBubbles, superbubblesFromGraph } from './bubbles/superbubbles.js';
 export { bubbleHalos } from './bubbles/bubbleHalos.js';
 export type { BubbleHalo } from './bubbles/bubbleHalos.js';
 export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble, } from './bubbles/classifyBubble.js';

package/dist/types/layout/trimToWindow.d.ts

@@ -3,3 +3,7 @@ export declare function trimToWindow(graph: Graph, window: {
     start: number;
     end: number;
 }): Graph;
+export declare function clipToWindow(graph: Graph, window: {
+    start: number;
+    end: number;
+}, reachBp: number): Graph;

package/dist/types/renderer/Canvas2DRenderer.d.ts

@@ -16,9 +16,12 @@ export declare class Canvas2DRenderer implements Renderer {
     setEdgeHighlight(edgeIndex: number | null, factor: number): void;
     updateTransform(transform: TransformUniform): void;
     render(clearColor: [number, number, number, number]): void;
-    private renderEdges;
-    private renderNodes;
-    private renderArrows;
+    renderHighlights(): void;
+    private edgeRun;
+    private liftedStrokes;
+    private strokeCurves;
+    private strokeNodes;
+    private fillArrows;
     dispose(): void;
 }
 export declare function arrowheadOutline(a: Arrowhead, t: TransformUniform): readonly [{

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

@@ -12,3 +12,4 @@ export declare function drawTubeMapConnectors(ctx: CanvasRenderingContext2D, con
     highlightNode?: string | null;
     darkMode?: boolean;
 }): void;
+export declare function drawLitConnector(ctx: CanvasRenderingContext2D, connectors: readonly Connector[], bottom: number, node: string | null | undefined): void;

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

@@ -69,6 +69,7 @@ export interface TubeMapFrame extends TubeMapTransform {
     nodeColors?: ReadonlyMap<string, string>;
 }
 export declare function drawTubeMap(ctx: CanvasRenderingContext2D, picture: TubeMapPicture, frame: TubeMapFrame): void;
+export declare function drawTubeMapHighlight(ctx: CanvasRenderingContext2D, picture: TubeMapPicture, frame: TubeMapFrame): void;
 export declare function mismatchesLegible(yScale: number): boolean;
 export declare function mismatchOnScreen(m: TubeMapMismatch, { x, width }: Pick<TubeMapFrame, 'x' | 'width'>): boolean;
 export declare function tubeMapTrackAt(picture: TubeMapPicture, { x, y }: TubeMapTransform, sx: number, sy: number): number | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.0.0";
+export declare const version = "9.2.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-AMS3MAFP.js";
+} from "./chunks/chunk-FM6XRXPX.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,19 +5,19 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-TL4B342F.js";
-import "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-XKM5OHQQ.js";
+import "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/walkEncoding.js

@@ -9,11 +9,11 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-DPV2CUIE.js";
-import "./chunks/chunk-HBEKUQO4.js";
+} from "./chunks/chunk-XPT66H6H.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/dist/walkHighlight.js

@@ -2,12 +2,12 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-MBB7ATM6.js";
-import "./chunks/chunk-DPV2CUIE.js";
-import "./chunks/chunk-HBEKUQO4.js";
+} from "./chunks/chunk-LFKMASER.js";
+import "./chunks/chunk-XPT66H6H.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "9.0.0",
+  "version": "9.2.0",
   "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": {
@@ -28,7 +28,8 @@
     "access": "public"
   },
   "bin": {
-    "bandage-figure": "dist/cli/figure.js"
+    "bandage-figure": "dist/cli/figure.js",
+    "bandage-fold": "dist/cli/fold.js"
   },
   "files": [
     "dist"

package/dist/chunks/{chunk-HBEKUQO4.js → chunk-BR25DGIJ.js}

@@ -3,16 +3,16 @@ import {
   fadeAbgr,
   packAbgr
 } from "./chunk-G2FD7S3C.js";
-import {
-  meanDepth,
-  nodeWidthPx
-} from "./chunk-PBENCR5L.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
 } from "./chunk-7GBL7SJY.js";
+import {
+  meanDepth,
+  nodeWidthPx
+} from "./chunk-PBENCR5L.js";
 import {
   baseEdgeCurves
 } from "./chunk-WFB5TXRA.js";

package/dist/chunks/{chunk-WNUZP3WQ.js → chunk-M7SRZJ32.js}

@@ -1,12 +1,12 @@
+import {
+  sampleRowLayout
+} from "./chunk-LOEA5IHZ.js";
 import {
   hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
 } from "./chunk-INJ2UVOT.js";
-import {
-  sampleRowLayout
-} from "./chunk-LOEA5IHZ.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";

package/dist/chunks/{chunk-5OIVTEF7.js → chunk-ZGRYFUXE.js}

@@ -7,12 +7,17 @@ import {
 import {
   convertGFAToGraph
 } from "./chunk-OCMBULGN.js";
+import {
+  graphFromTables
+} from "./chunk-OA7RIMZ2.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
 import {
-  graphFromTables
-} from "./chunk-OA7RIMZ2.js";
+  routeNodes,
+  takeRoutes,
+  withDeletionRoutes
+} from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -20,11 +25,6 @@ import {
   mergeRuns,
   splitRuns
 } from "./chunk-TAMCZHLW.js";
-import {
-  routeNodes,
-  takeRoutes,
-  withDeletionRoutes
-} from "./chunk-JVLURPFW.js";
 import {
   spreadFor
 } from "./chunk-UVBGRJQX.js";