@jbrowse/bandage-core 10.3.1 → 11.0.0

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

@@ -0,0 +1,59 @@
+import type { PathStop, StopChunk } from '../types.js';
+export declare const START_STOP_TAG = "ws";
+export declare const END_STOP_TAG = "we";
+export type GapCause = 'missing' | 'elsewhere' | 'unknown';
+export declare const GAP_CAUSE_TEXT: Record<GapCause, string>;
+export declare const OUTSIDE_TEXT = "outside the extracted subgraph";
+export interface GapPart {
+    bp: number;
+    cause?: GapCause;
+    chunk?: StopChunk;
+}
+/**
+ * A gap of `bp` in contig order, split by the stops either side: the bp each
+ * side's cut trimmed, outside the extracted subgraph, then the bp a record
+ * break beside either side says the graph lacks, and the rest between, on
+ * nodes filed elsewhere when either side goes on in a chunk the cut did not
+ * read. A gap neither side states a stop for stays whole, with no cause.
+ */
+export declare function gapParts(bp: number, after: PathStop | undefined, before: PathStop | undefined): GapPart[];
+export interface WalkStopTable {
+    kinds: Uint8Array;
+    kindNames: string[];
+    bp: Float64Array;
+    trimmed: Float64Array;
+    chunkRefs: Int32Array;
+    chunkStarts: Float64Array;
+    chunkRefNames: string[];
+}
+export declare function stopAt(table: WalkStopTable, i: number): PathStop | undefined;
+/**
+ * A stop as a Z tag's value: its kind, then `bp=`, `trimmed=` and
+ * `chunk=refName:start` where it states them, comma-joined:
+ * `break,bp=19021`, `elsewhere,bp=34110,chunk=GRCh38#0#chr22:20316160`
+ */
+export declare function stopTag(stop: PathStop): string;
+export declare function parseStopTag(value: string): PathStop | undefined;
+export declare function stopFields(before: PathStop | undefined, after: PathStop | undefined): {
+    after?: PathStop | undefined;
+    before?: PathStop | undefined;
+};
+export declare function walkStopFields(tags: Record<string, string | number>): {
+    after?: PathStop | undefined;
+    before?: PathStop | undefined;
+};
+export declare function walkStopTags(walks: {
+    before?: WalkStopTable;
+    after?: WalkStopTable;
+}, p: number): string;
+export declare class StopColumns {
+    kinds: number[];
+    bp: number[];
+    trimmed: number[];
+    chunkRefs: number[];
+    chunkStarts: number[];
+    chunkRefNames: string[];
+    private refIndex;
+    push(stop: PathStop): void;
+    table(): WalkStopTable;
+}

package/dist/types/index.d.ts

@@ -73,7 +73,7 @@ export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
 export { filterSamples, walkRows } from './layout/walkRows.js';
 export type { WalkAxis, WalkRow, WalkRows, WalkRun, WalkStop, } from './layout/walkRows.js';
-export { BAR_PX as WALK_BAR_PX, CALL_TICK as WALK_CALL_TICK, 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, UNBACKED_TICK as WALK_UNBACKED_TICK, alongRow, callTickInk, coalesceRuns, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowPitch, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
+export { BAR_PX as WALK_BAR_PX, CALL_TICK as WALK_CALL_TICK, 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, UNBACKED_TICK as WALK_UNBACKED_TICK, alongRow, callTickInk, coalesceRuns, gapStyle, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowPitch, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
 export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, RowPitch, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
 export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';
 export type { StripFrame, StripMark } from './layout/walkStrip.js';
@@ -92,12 +92,14 @@ export type { GeneModel, GenePin } from './genes/genePins.js';
 export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone, graphBackbone, refNameBinding, referenceLabel, wellKnownSample, } from './reference.js';
 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 type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, PathStop, StopChunk, } from './types.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 { END_STOP_TAG, GAP_CAUSE_TEXT, OUTSIDE_TEXT, START_STOP_TAG, gapParts, parseStopTag, stopTag, } from './gfa/walkStops.js';
+export type { GapCause, GapPart, WalkStopTable } from './gfa/walkStops.js';
 export { PathVisits, PathVisitsBuilder } from './pathVisits.js';
 export { engineKey } from './pipeline.js';
 export { axisScaleOf, contains, padded, screenToLayout, viewportOf, zoomAbout, } from './viewport.js';

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

@@ -1,19 +1,25 @@
 import type { WalkAxis, WalkRow, WalkRows, WalkRun } from './walkRows.js';
 import type { El } from '../el.js';
 import type { GeneModel } from '../genes/genePins.js';
+import type { GapCause } from '../gfa/walkStops.js';
 export declare const ON_REFERENCE = "#2f8fd6";
 export declare const OFF_REFERENCE = "#8e3fbf";
 export declare const OUTSIDE_CUT = "#bdbdbd";
+export declare const MISSING_INK = "#8a8a8a";
+export declare const UNKNOWN_GAP = "#e2e2e2";
 export declare const GENE_INK = "#1c1c22";
 export declare const BAR_PX = 12;
 export declare const GAP_PX = 4;
+export declare const MISSING_PX = 1;
 export declare const LABELLED_ROW_PX = 12;
 export interface ReadoutCall {
     bp: number;
     spanningReads?: number;
     agrees?: boolean;
 }
-export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
+export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'> & {
+    runs?: WalkRun[];
+}, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
 export declare function readoutPlacement(text: string, endX: number, width: number): {
     x: number;
     anchor: "start";
@@ -24,6 +30,11 @@ export declare function readoutPlacement(text: string, endX: number, width: numb
     halo: boolean;
 };
 export declare function unitTicks(bp: number, unit: number, pxPerBp: number): number[];
+export declare function gapStyle(cause: GapCause | undefined): {
+    fill: string;
+    px: number;
+    label: string;
+};
 export declare function runPaint(run: WalkRun, ramp: {
     start: number;
     end: number;
@@ -79,6 +90,7 @@ export type KeySwatch = {
 } | {
     kind: 'gap';
     fill: string;
+    px: number;
 } | {
     kind: 'gene';
 };
@@ -134,6 +146,7 @@ export interface WalkRowsFrame {
     rowPx?: number;
     barPx?: number;
     readouts?: boolean;
+    bars?: boolean;
 }
 export declare function coalesceRuns(runs: WalkRun[], pxPerBp: number): WalkRun[];
 export declare function walkRowsTree(bars: WalkRowsWithCalls, frame: WalkRowsFrame, o?: {

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

@@ -1,4 +1,5 @@
-import type { Graph } from '../types.js';
+import type { GapCause } from '../gfa/walkStops.js';
+import type { Graph, StopChunk } from '../types.js';
 export interface WalkRun {
     start: number;
     bp: number;
@@ -6,6 +7,8 @@ export interface WalkRun {
     referenceStart?: number;
     reversed?: true;
     gap?: true;
+    cause?: GapCause;
+    chunk?: StopChunk;
 }
 export interface WalkAxis {
     contig: string;

package/dist/types/types.d.ts

@@ -25,6 +25,25 @@ export interface GraphPath {
     haplotype?: number;
     contig?: string;
     members?: string[];
+    before?: PathStop;
+    after?: PathStop;
+}
+export type PathStop = ({
+    kind: 'elsewhere';
+    chunk: StopChunk;
+    bp?: number;
+} | {
+    kind: 'break';
+    bp: number;
+    chunk?: StopChunk;
+} | {
+    kind: 'end';
+}) & {
+    trimmed?: number;
+};
+export interface StopChunk {
+    refName: string;
+    start: number;
 }
 export interface PathOrigin {
     name: string;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "10.3.1";
+export declare const version = "11.0.0";

package/dist/types/walkHighlight.d.ts

@@ -15,6 +15,8 @@ export interface WalkHighlight {
         start: number;
         end: number;
     };
+    missingBp: number;
+    unknownBp: number;
 }
 export interface LiftedWalk extends WalkHighlight {
     encoding: WalkEncoding;

package/dist/types/walkKey.d.ts

@@ -6,7 +6,7 @@ export declare function walkKey(walk: LiftedWalk, reference?: {
     end: number;
 }): {
     delta: string;
-    outside: string;
+    gaps: string;
     reversed: string;
     shades: boolean;
     scale: string | undefined;

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-AQCOIE5R.js";
+} from "./chunks/chunk-6OP4HPXG.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,19 +5,20 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-BKEZLETL.js";
-import "./chunks/chunk-KMBE2Q42.js";
+} from "./chunks/chunk-AI5PTOSV.js";
+import "./chunks/chunk-KDU4EF66.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-VPE4AYP7.js";
-import "./chunks/chunk-NZTYV3JL.js";
+import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-DBLV7PGG.js";
+import "./chunks/chunk-3XSRT7RQ.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
-import "./chunks/chunk-Z6XZWPXK.js";
+import "./chunks/chunk-DZR37KXT.js";
+import "./chunks/chunk-EIY2SKD3.js";
 import "./chunks/chunk-ZPZ7GNBT.js";
 import "./chunks/chunk-BZFOFC4D.js";
 import "./chunks/chunk-HKYXWZQS.js";

package/dist/walkHighlight.js

@@ -2,7 +2,7 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-YZQI35UJ.js";
+} from "./chunks/chunk-C3NT37C3.js";
 import "./chunks/chunk-DO62DG26.js";
 import "./chunks/chunk-SWCULW6S.js";
 import "./chunks/chunk-G2FD7S3C.js";
@@ -12,6 +12,7 @@ import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
+import "./chunks/chunk-EIY2SKD3.js";
 import "./chunks/chunk-ZPZ7GNBT.js";
 import "./chunks/chunk-PFRQBCGC.js";
 import "./chunks/chunk-HMXCN6PG.js";

package/dist/walkKey.js

@@ -2,7 +2,8 @@ import {
   rangeText,
   walkKey,
   walkPosition
-} from "./chunks/chunk-CGFPFBT2.js";
+} from "./chunks/chunk-D4ZFRBB4.js";
+import "./chunks/chunk-EIY2SKD3.js";
 import "./chunks/chunk-PFRQBCGC.js";
 import "./chunks/chunk-HMXCN6PG.js";
 import "./chunks/chunk-AB35TJST.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.3.1",
+  "version": "11.0.0",
   "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": {