@jbrowse/bandage-core 4.0.24 → 4.0.26

package/dist/types/gbzCut.d.ts

@@ -0,0 +1,33 @@
+import { GBZBase } from '@gmod/gbz-base';
+import type { ByteSource, RangeOptions } from '@gmod/gbz-base';
+export interface GbzSource {
+    db: string;
+    index?: string;
+    region: string;
+    haplotypes?: string[];
+    referenceSample?: string;
+    context?: number;
+    snarls?: RangeOptions['snarls'];
+}
+export declare const HPRC_GBZ: {
+    db: string;
+    index: string;
+};
+export declare function parseRegion(text: string): {
+    refName: string;
+    start: number;
+    end: number;
+};
+export declare function openGbz(db: ByteSource, index?: ByteSource): Promise<{
+    base: GBZBase;
+    referenceSamples: string[];
+}>;
+export declare function cutGbzRegion({ base, referenceSamples }: Awaited<ReturnType<typeof openGbz>>, src: Omit<GbzSource, 'db' | 'index'>, signal?: AbortSignal): Promise<{
+    text: string;
+    region: {
+        refName: string;
+        start: number;
+        end: number;
+    };
+    sample: string;
+}>;

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

@@ -0,0 +1,10 @@
+import type { GeneModel } from './genePins.js';
+type Interval = GeneModel['exons'][number];
+export declare function mergedIntervals(intervals: Interval[]): {
+    start: number;
+    end: number;
+}[];
+export declare function genesFromGff3Lines(lines: Iterable<string>): GeneModel[];
+export declare function genesFromBed(text: string): GeneModel[];
+export declare function genesFromText(text: string): GeneModel[];
+export {};

package/dist/types/index.d.ts

@@ -19,7 +19,8 @@ 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, tubeMapPicture } from './tubeMap/draw.js';
-export type { TubeMapFrame, TubeMapPicture } from './tubeMap/draw.js';
+export type { TubeMapColors, TubeMapFrame, TubeMapPicture, } from './tubeMap/draw.js';
+export { tubeMapNodeColors } from './tubeMap/nodeColors.js';
 export { referenceKnots, warpX } from './tubeMap/warp.js';
 export { tubeMapFrame, tubeMapNodeAt } from './tubeMap/frame.js';
 export type { TubeMapTransform, TubeMapView } from './tubeMap/frame.js';
@@ -33,8 +34,12 @@ export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
 export { deletionEdges } from './deletionEdges.js';
 export type { DeletionEdge } from './deletionEdges.js';
 export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
-export { rangeText, walkKey } from './walkKey.js';
+export { rangeText, walkKey, walkPosition } from './walkKey.js';
 export { figureSvg } from './figure.js';
+export { genesFromBed, genesFromGff3Lines, genesFromText, } from './genes/geneFiles.js';
+export { HPRC_GBZ, cutGbzRegion, openGbz, parseRegion } from './gbzCut.js';
+export type { GbzSource } from './gbzCut.js';
+export { version } from './version.js';
 export type { FigureOptions } from './figure.js';
 export { svgCanvas } from './renderer/svgCanvas.js';
 export { FACET_GAP_PX, FACET_PAD_PX, FACET_TITLE_PX, facetCells, facetGrid, } from './facetGrid.js';

package/dist/types/labelLayout.d.ts

@@ -46,4 +46,18 @@ export interface LabelLayout {
     sizes: GraphLabel[];
 }
 export declare function geneCoverageNote(pin: GenePin): string | undefined;
+export declare function geneLabelCandidates(pins: GenePin[], screen: (p: {
+    x: number;
+    y: number;
+}) => {
+    x: number;
+    y: number;
+}, contigThickness: number): {
+    item: GenePin;
+    x: number;
+    y: number;
+    text: string;
+    fallback: string | undefined;
+    stack: number;
+}[];
 export declare function layoutLabels(m: LabelLayoutSource): LabelLayout;

package/dist/types/pathAnchoring.d.ts

@@ -1,4 +1,4 @@
-import type { Graph, PathOrigin, PathVisit } from './types.js';
+import type { Graph, GraphPath, PathOrigin, PathVisit } from './types.js';
 export declare function pathOrigin(pathName: string): {
     name: string;
     start: number;
@@ -18,3 +18,7 @@ export declare function surveyPaths(paths: PathSteps[], lengthOf: (segmentId: st
 export declare function chooseReferencePath(anchorPaths: PathOrigin[], preferred: string | undefined): PathOrigin | undefined;
 export declare function anchorFromPaths(graph: Graph, preferred: string | undefined): Graph;
 export declare function anchorGraph(graph: Graph, preferred: string | undefined): Graph;
+export declare function trimOrigins(origins: PathOrigin[], paths: GraphPath[], stretches: Map<string, {
+    dropped: number;
+    bp: number;
+}>): PathOrigin[];

package/dist/types/referenceStrip.d.ts

@@ -41,12 +41,13 @@ export interface StripLit {
         y: number;
     };
 }
-export declare function stripPixels(blocks: readonly StripBlock[], frame: BpFrame, width: number, dpr: number): {
+export interface StripPixel {
     colors: string[];
     x0: number;
     x1: number;
-    tier: number;
-}[];
+    tier?: number;
+}
+export declare function stripPixels(blocks: readonly StripBlock[], frame: BpFrame, width: number, dpr: number): StripPixel[];
 export declare function drawReferenceStrip(ctx: CanvasRenderingContext2D, blocks: readonly StripBlock[], frame: BpFrame, { width, lit, darkMode, dpr, }: {
     width: number;
     lit?: StripLit;

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

@@ -54,10 +54,15 @@ export interface TubeMapPicture {
         commands: Command[];
         x0: number;
         x1: number;
+        color?: string;
     }[];
     mismatches: TubeMapMismatch[];
 }
-export declare function tubeMapPicture(layout: TubeMapLayout): TubeMapPicture;
+export interface TubeMapColors {
+    tubes?: readonly string[];
+    nodes?: ReadonlyMap<string, string>;
+}
+export declare function tubeMapPicture(layout: TubeMapLayout, colors?: TubeMapColors): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

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

@@ -0,0 +1,4 @@
+import type { ResolvedColorScheme } from '../colorSchemes.js';
+import type { ReferenceRamp } from '../renderer/GeometryBuilder.js';
+import type { Graph } from '../types.js';
+export declare function tubeMapNodeColors(graph: Graph, colorScheme: ResolvedColorScheme, referenceRamp?: ReferenceRamp): Map<string, string> | undefined;

package/dist/types/version.d.ts

@@ -0,0 +1 @@
+export declare const version = "4.0.26";

package/dist/types/walkKey.d.ts

@@ -11,3 +11,4 @@ export declare function walkKey(walk: LiftedWalk, reference?: {
     scale: string | undefined;
     hover: string | undefined;
 };
+export declare function walkPosition(walk: LiftedWalk, nodeId: string, length: number): string | undefined;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.24",
+  "version": "4.0.26",
   "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": {
@@ -31,7 +31,8 @@
     "dist"
   ],
   "dependencies": {
-    "@gmod/gbz-base": "^4.0.0",
+    "@gmod/gbz-base": "^4.1.0",
+    "@gmod/tabix": "^3.9.0",
     "@gmod/tubemap-core": "^0.1.0",
     "@jbrowse/core": "5.0.0-beta.9",
     "@jbrowse/render-core": "5.0.0-beta.9"