@jbrowse/bandage-core 9.9.2 → 10.0.0

package/dist/layout/walkStrip.js

@@ -9,22 +9,23 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-MECWJY2R.js";
+} from "../chunks/chunk-WI7ZHJ27.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-P6O4RSOQ.js";
-import "../chunks/chunk-YS7VA5SI.js";
-import "../chunks/chunk-F4BKWWLS.js";
+} from "../chunks/chunk-VZNKA3K2.js";
+import "../chunks/chunk-DCJC32QW.js";
+import "../chunks/chunk-NNODIW4U.js";
+import "../chunks/chunk-NP356MC2.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-NNODIW4U.js";
+import "../chunks/chunk-REE4GUDM.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/layoutModes.js

@@ -4,23 +4,24 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-IJRNMO4D.js";
-import "./chunks/chunk-LOEA5IHZ.js";
-import "./chunks/chunk-HOZI3FBG.js";
+} from "./chunks/chunk-ICXMWYOA.js";
+import "./chunks/chunk-IM4SJUPO.js";
 import "./chunks/chunk-CWFNEKST.js";
+import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
+import "./chunks/chunk-HNQPEMYE.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-RVS2QCOX.js";
-import "./chunks/chunk-HNQPEMYE.js";
-import "./chunks/chunk-TOVOJNT7.js";
-import "./chunks/chunk-6PYZYBBF.js";
-import "./chunks/chunk-EDASNMLY.js";
-import "./chunks/chunk-3ZZSX5HN.js";
-import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-3APK25GI.js";
+import "./chunks/chunk-KAN2WTG5.js";
+import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-IGJCTPFB.js";
 import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/dist/pathAnchoring.js

@@ -5,7 +5,8 @@ import {
   pathOrigin,
   surveyPaths,
   trimOrigins
-} from "./chunks/chunk-IGJCTPFB.js";
+} from "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
 export {

package/dist/pathColors.js

@@ -9,11 +9,12 @@ import {
   pathHueAt,
   pathLegend,
   walkLabelsOf
-} from "./chunks/chunk-EDASNMLY.js";
+} from "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
+import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";
-import "./chunks/chunk-IGJCTPFB.js";
-import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/dist/pathVisits.js

@@ -0,0 +1,8 @@
+import {
+  PathVisits,
+  PathVisitsBuilder
+} from "./chunks/chunk-RAEABQNW.js";
+export {
+  PathVisits,
+  PathVisitsBuilder
+};

package/dist/pipeline.js

@@ -11,17 +11,19 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-FPTI3WAV.js";
-import "./chunks/chunk-PUG7LXDF.js";
+} from "./chunks/chunk-W4GZCVUK.js";
 import "./chunks/chunk-IGVV37VI.js";
-import "./chunks/chunk-J7YKQ5YW.js";
-import "./chunks/chunk-G45YY72K.js";
-import "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-OPPVSPEF.js";
+import "./chunks/chunk-PUG7LXDF.js";
+import "./chunks/chunk-QXAB2FLJ.js";
 import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-PSMKPSO4.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-JVLURPFW.js";
+import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-IGJCTPFB.js";
+import "./chunks/chunk-G45YY72K.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-UVBGRJQX.js";

package/dist/referenceRampCss.js

@@ -4,17 +4,18 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-YS7VA5SI.js";
-import "./chunks/chunk-F4BKWWLS.js";
+} from "./chunks/chunk-DCJC32QW.js";
+import "./chunks/chunk-NP356MC2.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-EDASNMLY.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3ZZSX5HN.js";
-import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-IGJCTPFB.js";
 import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/dist/referenceStrip.js

@@ -7,17 +7,18 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-RK3MF4FD.js";
-import "./chunks/chunk-F4BKWWLS.js";
+} from "./chunks/chunk-KJYSOHVN.js";
+import "./chunks/chunk-NP356MC2.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-EDASNMLY.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
-import "./chunks/chunk-3ZZSX5HN.js";
-import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-REE4GUDM.js";
+import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-EMUUNWRU.js";
+import "./chunks/chunk-RAEABQNW.js";
 import "./chunks/chunk-ES2N6V56.js";
-import "./chunks/chunk-IGJCTPFB.js";
 import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-3ZZSX5HN.js";
+import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-TAMCZHLW.js";
 import "./chunks/chunk-N6FECAXP.js";
 import "./chunks/chunk-2CVHXFK7.js";

package/dist/renderer/GeometryBuilder.js

@@ -11,16 +11,17 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-F4BKWWLS.js";
+} from "../chunks/chunk-NP356MC2.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-REE4GUDM.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/bundle.js

@@ -1,14 +1,15 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-WVBYR6Y7.js";
-import "../chunks/chunk-HOZI3FBG.js";
+} from "../chunks/chunk-FG762CCP.js";
+import "../chunks/chunk-IM4SJUPO.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-EDASNMLY.js";
+import "../chunks/chunk-REE4GUDM.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
+import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-IGJCTPFB.js";
-import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/tubeMap/coarsen.js

@@ -1,15 +1,18 @@
 import {
   pathSteps
-} from "../chunks/chunk-HOZI3FBG.js";
+} from "../chunks/chunk-IM4SJUPO.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-REE4GUDM.js";
 import {
   pathOrigin
-} from "../chunks/chunk-IGJCTPFB.js";
+} from "../chunks/chunk-EMUUNWRU.js";
+import {
+  PathVisitsBuilder
+} from "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";
@@ -231,7 +234,7 @@ function coarsenTubeMap(graph, sigma) {
   };
   const deviations = /* @__PURE__ */ new Map();
   const coarsePaths = [];
-  const pathVisits = /* @__PURE__ */ new Map();
+  const pathVisits = new PathVisitsBuilder();
   const edges = /* @__PURE__ */ new Map();
   const depth = /* @__PURE__ */ new Map();
   for (const { path, runs, gaps } of walks) {
@@ -299,14 +302,13 @@ function coarsenTubeMap(graph, sigma) {
     let pos = 0;
     steps.forEach(({ node, strand }, i) => {
       depth.set(node.id, (depth.get(node.id) ?? 0) + 1);
-      const visits = pathVisits.get(node.name) ?? [];
-      visits.push({
-        path: visitName,
-        sample: path.sample ?? visitName,
-        start: pos,
-        strand
-      });
-      pathVisits.set(node.name, visits);
+      pathVisits.add(
+        node.name,
+        visitName,
+        path.sample ?? visitName,
+        pos,
+        strand === "-"
+      );
       pos += node.length;
       const next = steps[i + 1];
       if (next) {
@@ -335,7 +337,7 @@ function coarsenTubeMap(graph, sigma) {
       nodes,
       edges: [...edges.values()],
       paths: coarsePaths,
-      pathVisits,
+      pathVisits: pathVisits.build(),
       reads: void 0
     },
     members,

package/dist/tubeMap/draw.js

@@ -8,12 +8,13 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-PIN7ZMTZ.js";
-import "../chunks/chunk-XXT2JCAC.js";
+} from "../chunks/chunk-EU6FBTQF.js";
 import "../chunks/chunk-HK5Y2YWV.js";
+import "../chunks/chunk-XXT2JCAC.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-IGJCTPFB.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/tubeMap/nodeColors.js

@@ -1,16 +1,17 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-KJEMKHVB.js";
-import "../chunks/chunk-F4BKWWLS.js";
+} from "../chunks/chunk-OEPCRURR.js";
+import "../chunks/chunk-NP356MC2.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-EDASNMLY.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
-import "../chunks/chunk-3ZZSX5HN.js";
-import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-REE4GUDM.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-EMUUNWRU.js";
+import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";
 import "../chunks/chunk-N6FECAXP.js";
 import "../chunks/chunk-2CVHXFK7.js";

package/dist/types/figureData.d.ts

@@ -0,0 +1,146 @@
+import type { BubbleSpread } from './bubbleSpreads.js';
+import type { ColorScheme } from './colorSchemes.js';
+import type { FacetInput } from './facetGrid.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;
+}
+type Columns<T> = {
+    [K in keyof T]: T[K][];
+};
+interface NodeRow {
+    panel: string;
+    node: string;
+    stroke: number;
+    x: number;
+    y: number;
+    color: string;
+    alpha: number;
+    width: number;
+}
+interface EdgeRow {
+    panel: string;
+    edge: number;
+    curve: number;
+    x0: number;
+    y0: number;
+    cx0: number;
+    cy0: number;
+    cx1: number;
+    cy1: number;
+    x1: number;
+    y1: number;
+    color: string;
+    alpha: number;
+    width: number;
+    deletion: boolean;
+}
+interface ArrowRow {
+    panel: string;
+    edge: number;
+    x: number;
+    y: number;
+    angle: number;
+    length: number;
+    halfWidth: number;
+    color: string;
+    alpha: number;
+}
+export declare function figureData(graph: Graph, layout: LayoutResult, o?: FigureDataOptions): {
+    meta: {
+        generator: string;
+        width: number;
+        scaleX: number;
+        scaleY: number;
+        pixelRows: boolean;
+        referenceAxis: boolean;
+        colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
+        referenceName: string | null;
+    };
+    panels: {
+        panel: string[];
+        key: string[];
+        range: string[];
+    };
+    nodes: Columns<NodeRow>;
+    edges: Columns<EdgeRow>;
+    arrows: Columns<ArrowRow>;
+    nodeInfo: {
+        node: string[];
+        name: string[];
+        length: number[];
+        depth: number[];
+        backbone: boolean[];
+    };
+    rowLabels: {
+        label: string[];
+        y: number[];
+    };
+};
+export interface GfaFigureSpec extends Omit<FigureDataOptions, 'region' | 'walks'> {
+    region?: string;
+    walks?: (string | WalkLayer)[];
+    layout?: LayoutModeValue;
+    referencePath?: string;
+    quality?: number;
+    bubbleSpread?: BubbleSpread;
+    engine?: LayoutEngineKind;
+    spacing?: number;
+    componentSeparation?: number;
+}
+export declare function gfaFigureData(text: string, name: string, spec?: GfaFigureSpec): Promise<{
+    meta: {
+        generator: string;
+        width: number;
+        scaleX: number;
+        scaleY: number;
+        pixelRows: boolean;
+        referenceAxis: boolean;
+        colorScheme: import("./colorSchemes.js").ResolvedColorScheme;
+        referenceName: string | null;
+    };
+    panels: {
+        panel: string[];
+        key: string[];
+        range: string[];
+    };
+    nodes: Columns<NodeRow>;
+    edges: Columns<EdgeRow>;
+    arrows: Columns<ArrowRow>;
+    nodeInfo: {
+        node: string[];
+        name: string[];
+        length: number[];
+        depth: number[];
+        backbone: boolean[];
+    };
+    rowLabels: {
+        label: string[];
+        y: number[];
+    };
+}>;
+export {};

package/dist/types/gbzWindow.d.ts

@@ -1,4 +1,5 @@
-import type { GBZBase, PathName, PathQuery, SnarlOutput } from '@gmod/gbz-base';
+import type { GraphTables } from './gfa/graphTables.js';
+import type { CompactSubgraph, GBZBase, PathName, PathQuery, SnarlOutput } from '@gmod/gbz-base';
 export declare class NoReferenceSampleError extends Error {
     name: string;
     constructor(anchor: string, referenceSamples: string[]);
@@ -32,3 +33,16 @@ export declare const GBZ_CUT_DEFAULTS: {
     readonly limit: 100000;
 };
 export declare function cutWindowGFA(db: GBZBase, query: PathQuery | undefined, start: number, end: number, opts: GbzWindowOptions): Promise<string>;
+/**
+ * The cut `cutWindowGFA` writes, as the tables `gfaTables` would read from
+ * it. A window on one reference fragment is one cut, whose typed arrays
+ * become the tables with no GFA written or read: writing an every-haplotype
+ * KIV-2 cut out and parsing it back was 2 s. A window over several
+ * fragments joins their GFA as text. Empty text for no indexed path.
+ */
+export declare function cutWindowTables(db: GBZBase, query: PathQuery | undefined, start: number, end: number, opts: GbzWindowOptions): Promise<GraphTables | string>;
+/**
+ * A gbz-base cut's typed arrays as the tables of the GFA `toGFA` writes for
+ * it: its segments, its links, and its walks in order, steps by GBWT handle
+ */
+export declare function compactTables(cut: CompactSubgraph): GraphTables;

package/dist/types/gfa/gfaConverter.d.ts

@@ -6,6 +6,6 @@ export declare function convertGFAToGraph(gfaGraph: GFAGraph, name?: string): {
     edges: GraphEdge[];
     paths: GraphPath[] | undefined;
     anchorPaths: import("../types.js").PathOrigin[] | undefined;
-    pathVisits: Map<string, import("../types.js").PathVisit[]> | undefined;
+    pathVisits: import("../index.js").PathVisits | undefined;
     anchoredBy: "tags" | undefined;
 };

package/dist/types/index.d.ts

@@ -50,6 +50,8 @@ export type { DeletionDrawing, DeletionEdge } from './deletionEdges.js';
 export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
 export { rangeText, walkKey, walkPosition } from './walkKey.js';
 export { figureSvg } from './figure.js';
+export { figureData, gfaFigureData } from './figureData.js';
+export type { FigureDataOptions, GfaFigureSpec } from './figureData.js';
 export { genesFromBed, genesFromGff3Lines, genesFromText, mergeOverlappingByName, } from './genes/geneFiles.js';
 export { HPRC_GBZ, cutGbzRegion, openGbz, parseRegion } from './gbzCut.js';
 export type { GbzSource } from './gbzCut.js';
@@ -91,11 +93,12 @@ export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone,
 export type { AssemblyNames, Backbone, BackboneContig } from './reference.js';
 export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
 export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';
-export { cutWindowGFA, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';
+export { compactTables, cutWindowGFA, cutWindowTables, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';
 export type { GbzWindowOptions } from './gbzWindow.js';
 export { gfaTables } from './gfa/gfaTables.js';
 export { graphFromTables, graphTablesGFA } from './gfa/graphTables.js';
 export type { GraphTables } from './gfa/graphTables.js';
+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';

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

@@ -15,7 +15,7 @@ export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge
         name: string;
         paths?: import("../types.js").GraphPath[];
         anchorPaths?: import("../types.js").PathOrigin[];
-        pathVisits?: Map<string, import("../types.js").PathVisit[]>;
+        pathVisits?: import("../index.js").PathVisits;
         anchoredBy?: "tags" | "paths";
         referencePath?: string;
         reads?: import("../gaf/parseGaf.js").GafRecord[];

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

@@ -0,0 +1,2 @@
+import type { NodeSegment } from '../types.js';
+export declare function smoothChain(line: NodeSegment[]): NodeSegment[];

package/dist/types/pathAnchoring.d.ts

@@ -1,4 +1,5 @@
-import type { Graph, PathOrigin, PathVisit } from './types.js';
+import type { PathVisits } from './pathVisits.js';
+import type { Graph, PathOrigin } from './types.js';
 export declare function pathOrigin(pathName: string): {
     name: string;
     start: number;
@@ -13,7 +14,7 @@ export interface PathSteps {
 }
 export declare function surveyPaths(paths: PathSteps[], lengthOf: (segmentId: string) => number): {
     anchorPaths: PathOrigin[];
-    pathVisits: Map<string, PathVisit[]>;
+    pathVisits: PathVisits;
 };
 export declare function chooseReferencePath(anchorPaths: PathOrigin[], preferred: string | undefined): PathOrigin | undefined;
 export declare function anchorFromPaths(graph: Graph, preferred: string | undefined): Graph;

package/dist/types/pathVisits.d.ts

@@ -0,0 +1,64 @@
+import type { PathVisit } from './types.js';
+/**
+ * Every visit each path makes to each segment, as columns rather than an
+ * object per visit: a gbz-base cut of every haplotype is millions of them.
+ * A segment's visits are contiguous and in walk order, and segments iterate in
+ * the order they were first visited. Reads as a map from segment name to its
+ * visits, each built when asked for; a pass over every segment reads the
+ * columns instead.
+ */
+export declare class PathVisits {
+    readonly segments: string[];
+    readonly offsets: Int32Array;
+    readonly path: Int32Array;
+    readonly start: Float64Array;
+    readonly reversed: Uint8Array;
+    readonly paths: string[];
+    readonly samples: string[];
+    private readonly slots;
+    constructor(columns: {
+        segments: string[];
+        offsets: Int32Array;
+        path: Int32Array;
+        start: Float64Array;
+        reversed: Uint8Array;
+        paths: string[];
+        samples: string[];
+    });
+    static from(entries: Iterable<readonly [string, readonly PathVisit[]]>): PathVisits;
+    get size(): number;
+    slot(segment: string): number;
+    pathIndex(path: string): number;
+    firstBy(slot: number, p: number): number;
+    replay(): (slot: number, p: number) => number;
+    filter(keepPath: (path: string) => boolean, keepSegment?: (segment: string) => boolean): PathVisits;
+    strand(i: number): '+' | '-';
+    visit(i: number): PathVisit;
+    private visitsAt;
+    get(segment: string): PathVisit[] | undefined;
+    has(segment: string): boolean;
+    keys(): ArrayIterator<string>;
+    values(): Generator<PathVisit[], void, unknown>;
+    entries(): Generator<[string, PathVisit[]]>;
+    [Symbol.iterator](): Generator<[string, PathVisit[]], any, any>;
+}
+/**
+ * Visits added in any order, grouped by segment on `build`, each segment's
+ * keeping the order they were added in
+ */
+export declare class PathVisitsBuilder {
+    private segments;
+    private slots;
+    private paths;
+    private samples;
+    private pathIndex;
+    private slot;
+    private path;
+    private start;
+    private reversed;
+    declare(segment: string): number;
+    pathOf(path: string, sample: string): number;
+    add(segment: string, path: string, sample: string, start: number, reversed: boolean): void;
+    addAt(slot: number, path: number, start: number, reversed: boolean): void;
+    build(): PathVisits;
+}

package/dist/types/types.d.ts

@@ -1,6 +1,7 @@
 import type { GafRecord } from './gaf/parseGaf.js';
 import type { StableCoordinate } from './gfa-core/index.js';
 import type { TubeMapDrawing } from './layout/tubeMapLayout.js';
+import type { PathVisits } from './pathVisits.js';
 export interface GraphNode {
     id: string;
     name: string;
@@ -43,7 +44,7 @@ export interface Graph {
     edges: GraphEdge[];
     paths?: GraphPath[];
     anchorPaths?: PathOrigin[];
-    pathVisits?: Map<string, PathVisit[]>;
+    pathVisits?: PathVisits;
     anchoredBy?: 'tags' | 'paths';
     referencePath?: string;
     reads?: GafRecord[];