@jbrowse/bandage-core 4.0.30 → 4.1.1

package/dist/cli/figure.js

@@ -17,7 +17,7 @@ import {
   openGbz,
   parseRegion,
   refNameBinding
-} from "../chunks/chunk-P7UDDVHK.js";
+} from "../chunks/chunk-QWZLIWOJ.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -34,10 +34,6 @@ function byteSource(location) {
           headers: { range: `bytes=${position}-${position + length - 1}` }
         });
         return new Uint8Array(await res.arrayBuffer());
-      },
-      async stat() {
-        const res = await fetchOk(location, { method: "HEAD" });
-        return { size: Number(res.headers.get("content-length")) };
       }
     };
   }
@@ -47,9 +43,6 @@ function byteSource(location) {
       const buffer = new Uint8Array(length);
       const { bytesRead } = await (await handle).read(buffer, 0, length, position);
       return buffer.subarray(0, bytesRead);
-    },
-    async stat() {
-      return { size: (await (await handle).stat()).size };
     }
   };
 }

package/dist/index.js

@@ -1,12 +1,16 @@
 import {
+  BAR_PX,
   BUBBLE_SPREADS,
   COLOR_SCHEMES,
   Canvas2DRenderer,
+  DISAGREES,
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
   FIT_PADDING,
   FORCE_LAYOUT_LABEL,
+  GAP_PX,
+  GENE_INK,
   HALO_FACTOR,
   HPRC_GBZ,
   LABEL_CHAR_PX,
@@ -16,11 +20,16 @@ import {
   LEGEND_INSET_PX,
   LIFT_BACKDROP_CSS,
   NODE_WIDTHS,
+  OFF_REFERENCE,
+  ON_REFERENCE,
+  OUTSIDE_CUT,
+  RAMP_GRADIENT_CSS,
   REFERENCE_RAMP_MAX_HUE,
   ROW_HEIGHT_PX,
   WALK_FIELDS,
   WALK_SCHEMES,
   WELL_KNOWN_SAMPLES,
+  alongRow,
   assemblyWalk,
   axisScaleOf,
   backboneAssembly,
@@ -35,6 +44,7 @@ import {
   cutWindowGFA,
   deletionEdges,
   drawingBounds,
+  el,
   encodingStops,
   encodingSwatchCss,
   engineKey,
@@ -64,6 +74,7 @@ import {
   loadGraph,
   maxNodeWidthPx,
   meanDepth,
+  mergeOverlappingByName,
   modeUsesLayoutEngine,
   nodeInk,
   nodeWidthPx,
@@ -76,7 +87,12 @@ import {
   pathColorsLegible,
   pathLegend,
   pathRibbonOffsets,
+  placeRowGenes,
+  rampHue,
+  rampHueCss,
+  rampStops,
   rangeText,
+  readoutPlacement,
   refNameBinding,
   referenceOrder,
   referencePathQuery,
@@ -84,24 +100,33 @@ import {
   resolveColorScheme,
   resolveEncoding,
   resolveReferenceSample,
+  rowGeneBoxes,
+  rowSpan,
+  runPaint,
   schemeCss,
   screenToLayout,
+  serializeEl,
   svgCanvas,
   svgPath,
   translateCurves,
   trimOrigins,
+  unitTicks,
   version,
   viewportOf,
   walkHighlight,
   walkKey,
   walkLift,
   walkPosition,
+  walkRowReadout,
   walkRows,
   walkRowsExtent,
+  walkRowsKey,
+  walkRowsKeyTree,
+  walkRowsTree,
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-P7UDDVHK.js";
+} from "./chunks/chunk-QWZLIWOJ.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -1764,12 +1789,21 @@ export {
   LAYOUT_MODES,
   LEGEND_INSET_PX,
   NODE_WIDTHS,
+  RAMP_GRADIENT_CSS,
   REFERENCE_RAMP_MAX_HUE,
   REFERENCE_STRIP_ZONE_PX,
   ROW_HEIGHT_PX,
+  BAR_PX as WALK_BAR_PX,
+  DISAGREES as WALK_DISAGREES,
   WALK_FIELDS,
+  GAP_PX as WALK_GAP_PX,
+  GENE_INK as WALK_GENE_INK,
+  OFF_REFERENCE as WALK_OFF_REFERENCE,
+  ON_REFERENCE as WALK_ON_REFERENCE,
+  OUTSIDE_CUT as WALK_OUTSIDE_CUT,
   WALK_SCHEMES,
   WELL_KNOWN_SAMPLES,
+  alongRow,
   assemblyWalk,
   axisScaleOf,
   backboneAssembly,
@@ -1792,6 +1826,7 @@ export {
   drawTubeMapGenes,
   drawTubeMapRuler,
   drawingBounds,
+  el,
   encodingStops,
   encodingSwatchCss,
   engineKey,
@@ -1822,6 +1857,7 @@ export {
   loadGraph,
   maxNodeWidthPx,
   meanDepth,
+  mergeOverlappingByName,
   modeUsesLayoutEngine,
   nodeInk,
   nodeWidthPx,
@@ -1833,7 +1869,12 @@ export {
   parseRegion,
   pathColorsLegible,
   pathLegend,
+  placeRowGenes,
+  rampHue,
+  rampHueCss,
+  rampStops,
   rangeText,
+  readoutPlacement,
   refNameBinding,
   referenceBoxes,
   referenceKnots,
@@ -1844,9 +1885,13 @@ export {
   resolveColorScheme,
   resolveEncoding,
   resolveReferenceSample,
+  rowGeneBoxes,
+  rowSpan,
   rulerBoxes,
+  runPaint,
   schemeCss,
   screenToLayout,
+  serializeEl,
   stripBlockAt,
   svgCanvas,
   tubeMapConnectors,
@@ -1856,14 +1901,19 @@ export {
   tubeMapNodeColors,
   tubeMapPicture,
   tubeX,
+  unitTicks,
   version,
   viewportOf,
   walkHighlight,
   walkKey,
   walkLift,
   walkPosition,
+  walkRowReadout,
   walkRows,
   walkRowsExtent,
+  walkRowsKey,
+  walkRowsKeyTree,
+  walkRowsTree,
   warpX,
   wellKnownSample,
   wheelZoomFactor,

package/dist/types/el.d.ts

@@ -0,0 +1,8 @@
+export type ElAttrs = Record<string, string | number | undefined>;
+export interface El {
+    tag: string;
+    attrs: ElAttrs;
+    children: (El | string)[];
+}
+export declare function el(tag: string, attrs?: ElAttrs, ...children: (El | string | undefined | false)[]): El;
+export declare function serializeEl(node: El | string): string;

package/dist/types/figure.d.ts

@@ -1,6 +1,7 @@
 import type { ColorScheme } from './colorSchemes.js';
 import type { FacetInput } from './facetGrid.js';
 import type { GeneModel } from './genes/genePins.js';
+import type { GeneGaps, RowGene, WalkRowsWithCalls } from './layout/walkRowDraw.js';
 import type { NodeWidth } from './nodeWidths.js';
 import type { Graph, LayoutResult } from './types.js';
 import type { WalkLayer } from './walkEncoding.js';
@@ -26,5 +27,8 @@ export interface FigureOptions {
     fitToDrawing?: boolean;
     genes?: GeneModel[];
     spec?: unknown;
+    walkRows?: WalkRowsWithCalls;
+    rowGenes?: Map<string, RowGene[]>;
+    rowGeneGaps?: GeneGaps;
 }
 export declare function figureSvg(graph: Graph, layout: LayoutResult, o?: FigureOptions): string;

package/dist/types/gbzCut.d.ts

@@ -1,5 +1,5 @@
 import { GBZBase } from '@gmod/gbz-base';
-import type { ByteSource, RangeOptions } from '@gmod/gbz-base';
+import type { ByteSource, SnarlOutput } from '@gmod/gbz-base';
 export interface GbzSource {
     db: string;
     index?: string;
@@ -7,7 +7,7 @@ export interface GbzSource {
     haplotypes?: string[];
     referenceSample?: string;
     context?: number;
-    snarls?: RangeOptions['snarls'];
+    snarls?: SnarlOutput;
 }
 export declare const HPRC_GBZ: {
     db: string;

package/dist/types/gbzWindow.d.ts

@@ -1,4 +1,4 @@
-import type { GBZBase, PathName, PathQuery, RangeOptions } from '@gmod/gbz-base';
+import type { GBZBase, PathName, PathQuery, SnarlOutput } from '@gmod/gbz-base';
 export declare class NoReferenceSampleError extends Error {
     name: string;
     constructor(anchor: string, referenceSamples: string[]);
@@ -16,21 +16,17 @@ export declare function resolveReferenceSample({ configured, anchorPrefix, refer
     referenceSamples: string[];
 }): string;
 export declare function referencePathQuery(db: GBZBase, referenceSample: string, refName: string): Promise<PathQuery | undefined>;
-export declare function nodeLimitError(error: unknown, limit: number, windowBp: number, walkedFrom?: number): NodeLimitError | undefined;
+export declare function nodeLimitError(error: unknown, limit: number, windowBp: number): NodeLimitError | undefined;
 export interface GbzWindowOptions {
     context: number;
-    snarls: RangeOptions['snarls'];
+    snarls: SnarlOutput;
     limit: number;
-    keep?: (name: PathName) => boolean;
-    signal?: AbortSignal;
+    keep?: ((name: PathName) => boolean) | undefined;
+    signal?: AbortSignal | undefined;
 }
 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>;
+export declare function cutWindowGFA(db: GBZBase, query: PathQuery | undefined, start: number, end: number, opts: GbzWindowOptions): Promise<string>;

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

@@ -5,6 +5,7 @@ export declare function mergedIntervals(intervals: Interval[]): {
     end: number;
 }[];
 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 {};

package/dist/types/index.d.ts

@@ -36,7 +36,7 @@ export type { DeletionEdge } from './deletionEdges.js';
 export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
 export { rangeText, walkKey, walkPosition } from './walkKey.js';
 export { figureSvg } from './figure.js';
-export { genesFromBed, genesFromGff3Lines, genesFromText, } from './genes/geneFiles.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';
 export { version } from './version.js';
@@ -55,7 +55,12 @@ export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble
 export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
 export { walkRows } from './layout/walkRows.js';
-export type { WalkRows } from './layout/walkRows.js';
+export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
+export { BAR_PX as WALK_BAR_PX, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, alongRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
+export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
+export { el, serializeEl } from './el.js';
+export type { El, ElAttrs } from './el.js';
+export { RAMP_GRADIENT_CSS, rampHue, rampHueCss, rampStops, } from './referenceRampCss.js';
 export { walkRowsExtent } from './layout/walkRowLayout.js';
 export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, geneCoverageNote, layoutLabels, } from './labelLayout.js';

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

@@ -0,0 +1,125 @@
+import type { WalkAxis, WalkRow, WalkRows, WalkRun } from './walkRows.js';
+import type { El } from '../el.js';
+import type { GeneModel } from '../genes/genePins.js';
+export declare const ON_REFERENCE = "#2f8fd6";
+export declare const OFF_REFERENCE = "#8e3fbf";
+export declare const OUTSIDE_CUT = "#bdbdbd";
+export declare const GENE_INK = "#1c1c22";
+export declare const BAR_PX = 12;
+export declare const GAP_PX = 4;
+export declare function kb(bp: number): string;
+export interface ReadoutCall {
+    bp: number;
+    spanningReads?: number;
+    agrees?: boolean;
+}
+export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
+export declare function readoutPlacement(text: string, endX: number, width: number): {
+    x: number;
+    anchor: "start";
+    halo: boolean;
+} | {
+    x: number;
+    anchor: "end";
+    halo: boolean;
+};
+export declare function unitTicks(bp: number, unit: number, pxPerBp: number): number[];
+export declare function runPaint(run: WalkRun, ramp: {
+    start: number;
+    end: number;
+} | undefined): {
+    fill: string;
+} | {
+    stops: string[];
+};
+export declare function alongRow(axis: WalkAxis, start: number, end: number): {
+    start: number;
+    end: number;
+};
+export declare function rowSpan(axis: WalkAxis, bp: number): {
+    start: number;
+    end: number;
+};
+export interface RowGene {
+    name: string;
+    start: number;
+    end: number;
+    exons: {
+        start: number;
+        end: number;
+    }[];
+}
+export declare function placeRowGenes(rows: WalkRow[], byRow: Map<string, GeneModel[]>): Map<string, RowGene[]>;
+export interface GeneBox {
+    name: string;
+    x: number;
+    y: number;
+    w: number;
+    h: number;
+    exons: {
+        x: number;
+        w: number;
+    }[];
+    label?: {
+        x: number;
+        y: number;
+        size: number;
+    };
+}
+export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => number, y: number): GeneBox[];
+export type KeySwatch = {
+    kind: 'bar';
+    fill: string;
+} | {
+    kind: 'gap';
+    fill: string;
+} | {
+    kind: 'gene';
+};
+export interface KeyEntry {
+    swatch: KeySwatch;
+    label: string;
+    note?: true;
+}
+export interface GeneGaps {
+    untracked: number;
+    unplaced?: number;
+    unread: number;
+}
+export declare function walkRowsKey(bars: WalkRows, o?: {
+    ramp?: {
+        start: number;
+        end: number;
+    };
+    rampCss?: string;
+    genes?: GeneGaps;
+}): KeyEntry[];
+export type WalkRowsWithCalls = Omit<WalkRows, 'reference' | 'rows'> & {
+    reference: WalkRow & {
+        call?: ReadoutCall;
+    };
+    rows: (WalkRow & {
+        call?: ReadoutCall;
+    })[];
+};
+export declare const DISAGREES = "#c62828";
+export declare function walkRowsKeyTree(entries: KeyEntry[], x: number, y: number): {
+    width: number;
+    tree: El;
+};
+export interface WalkRowsFrame {
+    scaleX: number;
+    scaleY: number;
+    translateX: number;
+    translateY: number;
+    width: number;
+    height: number;
+}
+export declare function walkRowsTree(bars: WalkRowsWithCalls, frame: WalkRowsFrame, o?: {
+    ramp?: {
+        start: number;
+        end: number;
+    };
+    rowGenes?: Map<string, RowGene[]>;
+    idPrefix?: string;
+}): El;

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

@@ -7,6 +7,11 @@ export interface WalkRun {
     reversed?: true;
     gap?: true;
 }
+export interface WalkAxis {
+    contig: string;
+    start: number;
+    reversed: boolean;
+}
 export interface WalkRow {
     name: string;
     label: string;
@@ -17,6 +22,7 @@ export interface WalkRow {
     gapBp: number;
     complete: boolean;
     runs: WalkRun[];
+    axis?: WalkAxis;
 }
 export interface WalkRows {
     origin: number;

package/dist/types/layoutModes.d.ts

@@ -42,7 +42,7 @@ export declare const LAYOUT_MODES: readonly [{
 }, {
     readonly value: "walkrows";
     readonly label: "Walk rows";
-    readonly description: "x is each walk's own bp: one bar per haplotype, sequence the reference also carries in blue and sequence it does not in purple, so a repeat expansion reads as bar length. Needs W or P lines.";
+    readonly description: "x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs W or P lines.";
     readonly run: typeof walkRowLayout;
     readonly cutMargins: false;
     readonly wholeWalks: true;
@@ -116,7 +116,7 @@ export declare function layoutModeByValue(value: string): {
 } | {
     readonly value: "walkrows";
     readonly label: "Walk rows";
-    readonly description: "x is each walk's own bp: one bar per haplotype, sequence the reference also carries in blue and sequence it does not in purple, so a repeat expansion reads as bar length. Needs W or P lines.";
+    readonly description: "x is each walk's own bp: one bar per haplotype, blue on the reference's path and purple off it, so a repeat expansion reads as bar length, and each bar boxes its haplotype's own genes where the session has them. Needs W or P lines.";
     readonly run: typeof walkRowLayout;
     readonly cutMargins: false;
     readonly wholeWalks: true;

package/dist/types/referenceRampCss.d.ts

@@ -0,0 +1,14 @@
+export declare function rampHueCss(hue: number): string;
+export declare function rampHue(bp: number, domain: {
+    start: number;
+    end: number;
+}): number;
+export declare function rampStops({ start, bp, reversed }: {
+    start: number;
+    bp: number;
+    reversed?: boolean;
+}, domain: {
+    start: number;
+    end: number;
+}): number[];
+export declare const RAMP_GRADIENT_CSS: string;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.0.30";
+export declare const version = "4.1.1";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.30",
+  "version": "4.1.1",
   "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 +31,7 @@
     "dist"
   ],
   "dependencies": {
-    "@gmod/gbz-base": "^5.0.0",
+    "@gmod/gbz-base": "^6.0.1",
     "@gmod/tabix": "^3.9.0",
     "@gmod/tubemap-core": "^0.1.0",
     "@jbrowse/core": "5.0.0-beta.9",