@jbrowse/bandage-core 4.6.0 → 4.7.0

package/dist/chunks/{chunk-XANWHEE7.js → chunk-NUCLM4VR.js}

@@ -5058,6 +5058,12 @@ function alongRow(axis, start, end) {
 function rowSpan(axis, bp) {
   return axis.reversed ? { start: axis.start - bp, end: axis.start } : { start: axis.start, end: axis.start + bp };
 }
+function genesOnRow(row, genes) {
+  const contig = row.axis?.contig;
+  return genes.filter(
+    (g) => g.refName === contig || g.refName.endsWith(`#${contig}`)
+  );
+}
 function placeRowGenes(rows, byRow) {
   const placed = /* @__PURE__ */ new Map();
   for (const row of rows) {
@@ -5716,7 +5722,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.6.0";
+var version = "4.7.0";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -6773,6 +6779,7 @@ export {
   runPaint,
   alongRow,
   rowSpan,
+  genesOnRow,
   placeRowGenes,
   rowGeneBoxes,
   walkRowsKey,

package/dist/cli/figure.js

@@ -10,6 +10,7 @@ import {
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   graphBackbone,
   haplotypeIndexBeside,
   layoutModeByValue,
@@ -17,9 +18,10 @@ import {
   loadGraph,
   openGbz,
   parseRegion,
+  placeRowGenes,
   refNameBinding,
   walkRows
-} from "../chunks/chunk-XANWHEE7.js";
+} from "../chunks/chunk-NUCLM4VR.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -178,12 +180,25 @@ async function renderSpec(spec, base) {
     ...bars,
     rows: filterSamples(bars.rows, spec.walkRowSamples)
   };
+  const genes = spec.genes ? await readGenes(spec.genes, graph, resolve) : void 0;
+  const reference = stripRows?.reference;
+  const rowGenes = reference && genes?.length ? placeRowGenes(
+    [reference],
+    /* @__PURE__ */ new Map([[reference.name, genesOnRow(reference, genes)]])
+  ) : void 0;
   return figureSvg(graph, layout, {
     ...spec,
-    walkStrip: stripRows && { rows: stripRows },
+    walkStrip: stripRows && {
+      rows: stripRows,
+      rowGenes,
+      rowGeneGaps: rowGenes && {
+        untracked: stripRows.rows.length,
+        unread: 0
+      }
+    },
     walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w),
     region: source.region,
-    genes: spec.genes ? await readGenes(spec.genes, graph, resolve) : void 0,
+    genes,
     spec
   });
 }

package/dist/index.js

@@ -67,6 +67,7 @@ import {
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   getNodeColor,
   graphBackbone,
   haplotypeWanted,
@@ -137,7 +138,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-XANWHEE7.js";
+} from "./chunks/chunk-NUCLM4VR.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -1866,6 +1867,7 @@ export {
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   getDpr,
   graphBackbone,
   haplotypeWanted,

package/dist/types/index.d.ts

@@ -56,7 +56,7 @@ 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 } 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, coalesceRuns, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.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, coalesceRuns, genesOnRow, 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 { 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';

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

@@ -49,6 +49,7 @@ export interface RowGene {
         end: number;
     }[];
 }
+export declare function genesOnRow(row: WalkRow, genes: GeneModel[]): GeneModel[];
 export declare function placeRowGenes(rows: WalkRow[], byRow: Map<string, GeneModel[]>): Map<string, RowGene[]>;
 export declare function boxesGenes(rowPx: number, barPx: number): boolean;
 export interface GeneBox {

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.6.0";
+export declare const version = "4.7.0";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.6.0",
+  "version": "4.7.0",
   "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": {