@jbrowse/bandage-core 10.2.2 → 10.2.3

package/dist/layoutModes.js

@@ -4,27 +4,27 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-4R6QNG23.js";
+} from "./chunks/chunk-WL6ZKUVC.js";
 import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-DK5P2YOL.js";
+import "./chunks/chunk-XI3ZUTWF.js";
 import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
-import "./chunks/chunk-HNQPEMYE.js";
 import "./chunks/chunk-C44YRP5F.js";
+import "./chunks/chunk-CM6LO6OC.js";
 import "./chunks/chunk-RVS2QCOX.js";
-import "./chunks/chunk-C7MZJSPT.js";
+import "./chunks/chunk-54POIBVC.js";
 import "./chunks/chunk-RIPAA7OK.js";
-import "./chunks/chunk-TWRLC3KK.js";
+import "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/nodeWidths.js

@@ -1,15 +1,13 @@
 import {
   NODE_WIDTHS,
-  NODE_WIDTH_VALUES,
   depthWidthFactor,
   maxNodeWidthPx,
   meanDepth,
   nodeInk,
   nodeWidthPx
-} from "./chunks/chunk-PBENCR5L.js";
+} from "./chunks/chunk-JBCZIBFC.js";
 export {
   NODE_WIDTHS,
-  NODE_WIDTH_VALUES,
   depthWidthFactor,
   maxNodeWidthPx,
   meanDepth,

package/dist/pathColors.js

@@ -9,15 +9,15 @@ import {
   pathHueAt,
   pathLegend,
   walkLabelsOf
-} from "./chunks/chunk-TWRLC3KK.js";
+} from "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/pipeline.js

@@ -11,25 +11,25 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-XTCNEKO5.js";
+} from "./chunks/chunk-2QLLQJ72.js";
+import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-VPE4AYP7.js";
-import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-IW6CYVX2.js";
+import "./chunks/chunk-AR4BUBMU.js";
 import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-5I3K4R2G.js";
 import "./chunks/chunk-PSMKPSO4.js";
-import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-G45YY72K.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-TAMCZHLW.js";
+import "./chunks/chunk-N73TI3VG.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/referenceRampCss.js

@@ -4,21 +4,21 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-ZIUKZUPJ.js";
-import "./chunks/chunk-SBMJNRTV.js";
+} from "./chunks/chunk-XL472HHD.js";
+import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-TWRLC3KK.js";
-import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-ZY2AFL4Y.js";
+import "./chunks/chunk-3XSM4OZU.js";
+import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/referenceStrip.js

@@ -7,21 +7,21 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-5BGP5Z64.js";
-import "./chunks/chunk-SBMJNRTV.js";
+} from "./chunks/chunk-JLSJMCDJ.js";
+import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-TWRLC3KK.js";
-import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-ZY2AFL4Y.js";
+import "./chunks/chunk-3XSM4OZU.js";
+import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-BPLIXMH7.js";
-import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-PTABFYQ7.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-N6FECAXP.js";
-import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-N73TI3VG.js";
+import "./chunks/chunk-24WITXQY.js";
+import "./chunks/chunk-7SRWJLSC.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/renderer/Canvas2DRenderer.js

@@ -1,8 +1,8 @@
 import {
   Canvas2DRenderer,
   arrowheadOutline
-} from "../chunks/chunk-WBCOREDZ.js";
-import "../chunks/chunk-4BYTEJGW.js";
+} from "../chunks/chunk-QLWI2PZ3.js";
+import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-G2FD7S3C.js";
 export {
   Canvas2DRenderer,

package/dist/renderer/GeometryBuilder.js

@@ -11,20 +11,20 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-SBMJNRTV.js";
+} from "../chunks/chunk-A4PFFC4Q.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-TWRLC3KK.js";
-import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-ZY2AFL4Y.js";
+import "../chunks/chunk-3XSM4OZU.js";
+import "../chunks/chunk-JBCZIBFC.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/renderer/canvas.js

@@ -3,7 +3,7 @@ import {
   MAX_DPR,
   getDpr,
   syncCanvasSize
-} from "../chunks/chunk-4BYTEJGW.js";
+} from "../chunks/chunk-RBCE2OQH.js";
 export {
   MAX_CANVAS_DIM_PX,
   MAX_DPR,

package/dist/renderer/svgCanvas.js

@@ -1,6 +1,6 @@
 import {
   svgCanvas
-} from "../chunks/chunk-47DYCZOK.js";
+} from "../chunks/chunk-RUCH6ZFL.js";
 export {
   svgCanvas
 };

package/dist/tubeMap/axis.js

@@ -6,12 +6,12 @@ import {
   rulerMarks,
   tubeSpan,
   tubeX
-} from "../chunks/chunk-BPRXQ2SS.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+} from "../chunks/chunk-XMW266WS.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/tubeMap/bundle.js

@@ -1,18 +1,18 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-PKFMP65V.js";
-import "../chunks/chunk-DK5P2YOL.js";
+} from "../chunks/chunk-5GMFEPWR.js";
+import "../chunks/chunk-XI3ZUTWF.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-TWRLC3KK.js";
+import "../chunks/chunk-3XSM4OZU.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/tubeMap/coarsen.js

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "../chunks/chunk-DK5P2YOL.js";
+} from "../chunks/chunk-XI3ZUTWF.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-TWRLC3KK.js";
+import "../chunks/chunk-3XSM4OZU.js";
 import {
   pathOrigin
 } from "../chunks/chunk-M6LK4GII.js";
@@ -11,11 +11,11 @@ import {
   PathVisitsBuilder
 } from "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import {
   isBackbone

package/dist/tubeMap/deviations.js

@@ -1,11 +1,11 @@
 import {
   referenceBoxes
-} from "../chunks/chunk-BPRXQ2SS.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+} from "../chunks/chunk-XMW266WS.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 

package/dist/tubeMap/draw.js

@@ -8,7 +8,7 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-IUDJKOLB.js";
+} from "../chunks/chunk-B6IW3IRE.js";
 import "../chunks/chunk-XXT2JCAC.js";
 import "../chunks/chunk-HK5Y2YWV.js";
 import "../chunks/chunk-CWFNEKST.js";

package/dist/tubeMap/genes.js

@@ -3,13 +3,13 @@ import {
   drawTubeMapGenes,
   tubeMapGeneRows,
   tubeMapGenes
-} from "../chunks/chunk-WEDZ76AK.js";
-import "../chunks/chunk-BPRXQ2SS.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+} from "../chunks/chunk-4DRQTBBE.js";
+import "../chunks/chunk-XMW266WS.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/tubeMap/nodeColors.js

@@ -1,20 +1,20 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-GNTTI6LA.js";
-import "../chunks/chunk-SBMJNRTV.js";
+} from "../chunks/chunk-T2PCSAFY.js";
+import "../chunks/chunk-A4PFFC4Q.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-TWRLC3KK.js";
-import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-ZY2AFL4Y.js";
+import "../chunks/chunk-3XSM4OZU.js";
+import "../chunks/chunk-JBCZIBFC.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-PTABFYQ7.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-N6FECAXP.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/types/bubbles/bubblesFromGraph.d.ts

@@ -5,6 +5,7 @@ export interface Routes {
     max: number;
     n: number;
 }
+export declare function relax<K>(best: Map<K, Routes>, to: K, cur: Routes, add: number): void;
 export declare function bubblesFromGraph(graph: Graph): MinigraphBubble[];
 export type WalkIndex = Map<string, Int32Array>;
 export declare function walkIndexOf(graph: Graph, ids: Iterable<string>): WalkIndex | undefined;

package/dist/types/bubbles/classifyBubble.d.ts

@@ -9,7 +9,6 @@ export interface RepeatSpan {
     end: number;
     name?: string;
 }
-export declare function formatBp(bp: number): string;
 export declare function classifyBubble(b: MinigraphBubble, repeats?: readonly RepeatSpan[]): BubbleClass;
 export declare const BUBBLE_KIND_COLORS: Record<BubbleKind, string>;
 export declare const BUBBLE_KIND_NAMES: Record<BubbleKind, string>;

package/dist/types/cli/decodeText.d.ts

@@ -0,0 +1 @@
+export declare function decodeText(bytes: Uint8Array): string;

package/dist/types/cli/figure.d.ts

@@ -1,27 +1,16 @@
-import type { BubbleSpread } from '../bubbleSpreads.js';
 import type { FigureOptions } from '../figure.js';
+import type { GfaFigureSpec } from '../figureData.js';
 import type { GbzSource } from '../gbzCut.js';
-import type { LayoutEngineKind } from '../layoutEngines.js';
-import type { LayoutModeValue } from '../layoutModes.js';
-import type { WalkLayer } from '../walkEncoding.js';
-export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {
+import type { GeneFormat } from '../genes/geneFiles.js';
+export interface FigureSpec extends GfaFigureSpec, Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {
     gfa?: string;
     gbz?: GbzSource;
-    region?: string;
-    referencePath?: string;
-    layout?: LayoutModeValue;
-    quality?: number;
-    bubbleSpread?: BubbleSpread;
-    engine?: LayoutEngineKind;
-    spacing?: number;
-    componentSeparation?: number;
-    walks?: (string | WalkLayer)[];
     walkStrip?: boolean;
     walkRowSamples?: string[];
     genes?: {
         file: string;
         index?: string;
-        format?: 'gff3' | 'bed';
+        format?: GeneFormat;
         refNames?: Record<string, string>;
     };
 }

package/dist/types/deletionEdges.d.ts

@@ -1,4 +1,4 @@
-import type { Graph, NodeSegment } from './types.js';
+import type { Graph, GraphEdge, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
 export interface DeletionEdge {
     edgeIndex: number;
@@ -19,10 +19,8 @@ export declare function bypassedPoints(nodePositions: Record<string, {
     x: number;
     y: number;
 }[];
-export declare function deletionArcCurves(nodePositions: Record<string, {
-    x: number;
-    y: number;
-}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[], stranded?: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
+export declare function deletionArcCurves(nodePositions: Record<string, NodeSegment[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[], stranded?: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
+export declare function edgeCurvesOf(nodePositions: Record<string, NodeSegment[]>, edge: GraphEdge, axis: AxisScale, bypassed: string[] | undefined, route: NodeSegment[] | undefined, stranded: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
 export declare function deletionEdges(graph: Graph): DeletionEdge[];
 export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
 export interface DeletionDrawing {

package/dist/types/el.d.ts

@@ -5,4 +5,5 @@ export interface El {
     children: (El | string)[];
 }
 export declare function el(tag: string, attrs?: ElAttrs, ...children: (El | string | undefined | false)[]): El;
+export declare function escapeAttr(s: string): string;
 export declare function serializeEl(node: El | string): string;

package/dist/types/figureData.d.ts

@@ -1,34 +1,10 @@
 import type { BubbleSpread } from './bubbleSpreads.js';
-import type { ColorScheme } from './colorSchemes.js';
-import type { FacetInput } from './facetGrid.js';
+import type { FigureOptions } from './figure.js';
 import type { LayoutEngineKind } from './layoutEngines.js';
 import type { LayoutModeValue } from './layoutModes.js';
-import type { NodeWidth } from './nodeWidths.js';
 import type { Graph, LayoutResult } from './types.js';
 import type { WalkLayer } from './walkEncoding.js';
-export interface FigureDataOptions {
-    width?: number;
-    height?: number;
-    walks?: WalkLayer[];
-    facet?: FacetInput;
-    colorScheme?: ColorScheme;
-    nodeWidth?: NodeWidth;
-    showDeletionEdges?: boolean;
-    linearLayout?: boolean;
-    contigThickness?: number;
-    connectorThickness?: number;
-    region?: {
-        refName: string;
-        start: number;
-        end: number;
-    };
-    referenceName?: string;
-    colorDomain?: {
-        start: number;
-        end: number;
-    };
-    fitToDrawing?: boolean;
-}
+export type FigureDataOptions = Pick<FigureOptions, 'width' | 'height' | 'walks' | 'facet' | 'colorScheme' | 'nodeWidth' | 'showDeletionEdges' | 'linearLayout' | 'contigThickness' | 'connectorThickness' | 'region' | 'referenceName' | 'colorDomain' | 'fitToDrawing'>;
 type Columns<T> = {
     [K in keyof T]: T[K][];
 };
@@ -112,6 +88,11 @@ export interface GfaFigureSpec extends Omit<FigureDataOptions, 'region' | 'walks
     spacing?: number;
     componentSeparation?: number;
 }
+export declare function laidOutGraph(text: string, name: string, region: FigureOptions['region'], spec: GfaFigureSpec): Promise<{
+    graph: Graph;
+    layout: LayoutResult;
+}>;
+export declare function walkLayers(walks: GfaFigureSpec['walks']): WalkLayer[] | undefined;
 export declare function gfaFigureData(text: string, name: string, spec?: GfaFigureSpec): Promise<{
     meta: {
         generator: string;

package/dist/types/figureScene.d.ts

@@ -0,0 +1,31 @@
+import type { FigureOptions } from './figure.js';
+import type { Graph, LayoutResult } from './types.js';
+import type { AxisScale } from './util/geometry.js';
+import type { WalkLift } from './walkHighlight.js';
+export type FigureSceneOptions = Pick<FigureOptions, 'walks' | 'facet' | 'colorScheme' | 'nodeWidth' | 'showDeletionEdges' | 'linearLayout' | 'contigThickness' | 'connectorThickness' | 'region' | 'referenceName' | 'colorDomain' | 'fitToDrawing' | 'walkRows' | 'walkRowPitch'>;
+export declare function figureScene(graph: Graph, layout: LayoutResult, o: FigureSceneOptions): {
+    bounds: {
+        minX: number;
+        minY: number;
+        w: number;
+        h: number;
+    };
+    nodeById: Map<string, import("./types.js").GraphNode>;
+    colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
+    referenceRamp: import("./renderer/GeometryBuilder.js").ReferenceRamp | undefined;
+    drawnDeletions: import("./deletionEdges.js").DeletionDrawing;
+    layers: import("./walkEncoding.js").WalkLayer[];
+    lift: WalkLift | undefined;
+    facet: import("./facetGrid.js").FacetSetting;
+    panels: WalkLift[] | undefined;
+    labelOf: (name: string) => string;
+    referenceName: string | undefined;
+    reference: {
+        name: string | undefined;
+        start: number;
+        end: number;
+    } | undefined;
+    contigThickness: number;
+    nodeWidth: "depth" | "uniform";
+    geometry: (highlight: WalkLift | undefined, axis: AxisScale) => import("./renderer/types.js").RenderBatch;
+};

package/dist/types/genes/geneFiles.d.ts

@@ -7,5 +7,6 @@ export declare function mergedIntervals(intervals: Interval[]): {
 export declare function genesFromGff3Lines(lines: Iterable<string>): GeneModel[];
 export declare function mergeOverlappingByName(genes: GeneModel[]): GeneModel[];
 export declare function genesFromBed(text: string): GeneModel[];
-export declare function genesFromText(text: string): GeneModel[];
+export type GeneFormat = 'gff3' | 'bed';
+export declare function genesFromText(text: string, format?: GeneFormat): GeneModel[];
 export {};

package/dist/types/index.d.ts

@@ -102,5 +102,5 @@ export { PathVisits, PathVisitsBuilder } from './pathVisits.js';
 export { engineKey } from './pipeline.js';
 export { axisScaleOf, contains, padded, screenToLayout, viewportOf, zoomAbout, } from './viewport.js';
 export type { PaneTransform } from './viewport.js';
-export { default as loadBandage } from './loadBandage.js';
+export { loadFmmm as loadBandage } from '@jbrowse/graph-fmmm-layout';
 export { panSNContig, panSNHaplotype, panSNSample } from './pansn.js';

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

@@ -2,7 +2,7 @@ import type { BandageScaleOpts } from './drawnScale.js';
 import type { DeletionEdge } from '../deletionEdges.js';
 import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
 export type DeletionRoutes = Record<number, NodeSegment[]>;
-export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: Set<number>): {
+export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: ReadonlySet<number>): {
     graph: {
         nodes: {
             id: string;

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

@@ -1,9 +1,3 @@
 import type { Graph, LayoutResult } from '../types.js';
 export declare function referenceOrder(graph: Graph): string[];
-export interface LayeredGraph {
-    layers: string[][];
-    layerOf: Map<string, number>;
-    preds: Map<string, string[]>;
-}
-export declare function layerGraph(graph: Graph): LayeredGraph;
 export declare function orderedLayout(graph: Graph): LayoutResult | undefined;

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

@@ -1,6 +1,7 @@
 import type { RowPitch } from './walkRowDraw.js';
 import type { WalkRows } from './walkRows.js';
 import type { Graph, LayoutResult, RowLabel } from '../types.js';
+export declare const READOUT_ROOM = 1.3;
 export declare function walkRowsExtent(walks: WalkRows, pitch?: Pick<RowPitch, 'rowPx' | 'readouts'>): {
     maxX: number;
     maxY: number;

package/dist/types/nodeWidths.d.ts

@@ -10,7 +10,6 @@ export declare const NODE_WIDTHS: readonly [{
     readonly description: "Every node the same thickness.";
 }];
 export type NodeWidth = (typeof NODE_WIDTHS)[number]['value'];
-export declare const NODE_WIDTH_VALUES: ("depth" | "uniform")[];
 export declare function meanDepth(graph: Graph): number;
 export declare function depthWidthFactor(node: GraphNode, mean: number): number;
 export declare function nodeWidthPx(node: GraphNode, contigThickness: number, nodeWidth: NodeWidth, mean: number): number;

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

@@ -7,6 +7,7 @@ export declare class Canvas2DRenderer implements Renderer {
     private nodeHighlights;
     private highlightedEdge;
     private highlightFactor;
+    private fit;
     constructor(canvas: HTMLCanvasElement);
     setErrorHandler(_handler: (error: Error) => void): void;
     releaseOffscreenTargets(): void;

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

@@ -1,4 +1,4 @@
 export declare const MAX_DPR = 2;
 export declare const MAX_CANVAS_DIM_PX = 8192;
-export declare function getDpr(): number;
-export declare function syncCanvasSize(canvas: HTMLCanvasElement, width: number, height: number): void;
+export declare function getDpr(width?: number, height?: number): number;
+export declare function syncCanvasSize(canvas: HTMLCanvasElement, width: number, height: number): number;