@jbrowse/bandage-core 4.5.0 → 4.7.0

package/dist/chunks/{chunk-7KQ2IWLP.js → chunk-NUCLM4VR.js}

@@ -2212,6 +2212,11 @@ function sliceBetween(steps, span, region, flanked = true) {
     to: i1
   };
 }
+function filterSamples(rows, samples) {
+  return samples ? rows.filter((r) => samples.includes(r.sample)).sort(
+    (a, b) => samples.indexOf(a.sample) - samples.indexOf(b.sample) || a.label.localeCompare(b.label)
+  ) : rows;
+}
 function walkRows(graph, region, unit) {
   const paths = graph.paths ?? [];
   const isReference2 = (p) => pathOrigin(p.name).name === graph.referencePath;
@@ -4986,9 +4991,12 @@ function rampStops({ start, bp, reversed }, domain) {
     (_, i) => rampHue(start + bp * (reversed ? n2 - i : i) / n2, domain)
   );
 }
-var RAMP_GRADIENT_CSS = `linear-gradient(to right, ${Array.from(
-  { length: 7 },
-  (_, i) => `${rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)} ${i / 6 * 100}%`
+var RAMP_GRADIENT_STOPS = Array.from({ length: 7 }, (_, i) => ({
+  offset: i / 6,
+  color: rampHueCss(i / 6 * REFERENCE_RAMP_MAX_HUE)
+}));
+var RAMP_GRADIENT_CSS = `linear-gradient(to right, ${RAMP_GRADIENT_STOPS.map(
+  (s) => `${s.color} ${s.offset * 100}%`
 ).join(", ")})`;
 
 // src/layout/walkRowDraw.ts
@@ -5050,6 +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(`#${contig}`)
+  );
+}
 function placeRowGenes(rows, byRow) {
   const placed = /* @__PURE__ */ new Map();
   for (const row of rows) {
@@ -5122,10 +5136,7 @@ var rowsText = (n2) => `${n2} row${n2 === 1 ? "" : "s"}`;
 function walkRowsKey(bars, o = {}) {
   const entries = [
     {
-      swatch: {
-        kind: "bar",
-        fill: o.ramp ? o.rampCss ?? ON_REFERENCE : ON_REFERENCE
-      },
+      swatch: o.ramp ? { kind: "bar", fill: o.rampCss ?? RAMP_GRADIENT_CSS, ramp: true } : { kind: "bar", fill: ON_REFERENCE },
       label: `on ${bars.reference.label}'s path`
     },
     {
@@ -5180,9 +5191,17 @@ function walkRowsKey(bars, o = {}) {
 var CALL_TICK = "#111";
 var UNBACKED_TICK = "#9e9e9e";
 var DISAGREES = "#c62828";
-function walkRowsKeyTree(entries, x, y) {
+function walkRowsKeyTree(entries, x, y, idPrefix = "walk-key") {
   let at = 0;
-  const parts = entries.flatMap((e) => {
+  const parts = entries.flatMap((e, i) => {
+    const rampId = `${idPrefix}-ramp-${i}`;
+    const ramp = !e.note && e.swatch.kind === "bar" && e.swatch.ramp ? el(
+      "linearGradient",
+      { id: rampId },
+      ...RAMP_GRADIENT_STOPS.map(
+        (s) => el("stop", { offset: s.offset, "stop-color": s.color })
+      )
+    ) : void 0;
     const swatch = e.note ? void 0 : e.swatch.kind === "gene" ? el("rect", {
       x: at,
       y: 5,
@@ -5197,7 +5216,7 @@ function walkRowsKeyTree(entries, x, y) {
       width: 18,
       height: e.swatch.kind === "gap" ? GAP_PX : 8,
       rx: 2,
-      fill: e.swatch.fill
+      fill: ramp ? `url(#${rampId})` : e.swatch.fill
     });
     const text = el(
       "text",
@@ -5210,7 +5229,7 @@ function walkRowsKeyTree(entries, x, y) {
       e.label
     );
     at += (e.note ? 0 : 23) + e.label.length * LABEL_CHAR_PX + 16;
-    return swatch ? [swatch, text] : [text];
+    return [ramp, swatch, text].filter((p) => p !== void 0);
   });
   return {
     width: at,
@@ -5703,7 +5722,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.5.0";
+var version = "4.7.0";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -6006,7 +6025,8 @@ function figureSvg(graph, layout, o = {}) {
           genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
         }),
         x,
-        2
+        2,
+        "rows-key"
       );
       push({ width: key.width, markup: serializeEl(key.tree) });
     } else if (!lift && referenceRamp) {
@@ -6047,7 +6067,8 @@ function figureSvg(graph, layout, o = {}) {
         genes: stripGeneGaps(frame, strip.rowGenes, strip.rowGeneGaps)
       }),
       6,
-      height + frame.height
+      height + frame.height,
+      "strip-key"
     );
     parts.push(
       `<line x1="0" x2="${width}" y1="${height + 0.5}" y2="${height + 0.5}" stroke="#ddd"/>`,
@@ -6695,6 +6716,7 @@ export {
   formatBp,
   pathColorsLegible,
   pathLegend,
+  filterSamples,
   walkRows,
   walkRowsExtent,
   FORCE_LAYOUT_LABEL,
@@ -6757,6 +6779,7 @@ export {
   runPaint,
   alongRow,
   rowSpan,
+  genesOnRow,
   placeRowGenes,
   rowGeneBoxes,
   walkRowsKey,

package/dist/cli/figure.js

@@ -5,10 +5,12 @@ import {
   cutGbzRegion,
   featuresOnBackbone,
   figureSvg,
+  filterSamples,
   forceLayout,
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   graphBackbone,
   haplotypeIndexBeside,
   layoutModeByValue,
@@ -16,9 +18,10 @@ import {
   loadGraph,
   openGbz,
   parseRegion,
+  placeRowGenes,
   refNameBinding,
   walkRows
-} from "../chunks/chunk-7KQ2IWLP.js";
+} from "../chunks/chunk-NUCLM4VR.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -172,13 +175,30 @@ async function renderSpec(spec, base) {
     },
     engine
   )).result;
-  const stripRows = spec.walkStrip ? walkRows(graph, source.region) : void 0;
+  const bars = spec.walkStrip ? walkRows(graph, source.region) : void 0;
+  const stripRows = bars && {
+    ...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

@@ -58,6 +58,7 @@ import {
   facetSettingOf,
   featuresOnBackbone,
   figureSvg,
+  filterSamples,
   fitTransform,
   forceLayout,
   formatBp,
@@ -66,6 +67,7 @@ import {
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   getNodeColor,
   graphBackbone,
   haplotypeWanted,
@@ -136,7 +138,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-7KQ2IWLP.js";
+} from "./chunks/chunk-NUCLM4VR.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -1854,6 +1856,7 @@ export {
   facetSettingOf,
   featuresOnBackbone,
   figureSvg,
+  filterSamples,
   findHoveredEdge,
   findHoveredNode,
   fitTransform,
@@ -1864,6 +1867,7 @@ export {
   genesFromBed,
   genesFromGff3Lines,
   genesFromText,
+  genesOnRow,
   getDpr,
   graphBackbone,
   haplotypeWanted,

package/dist/types/cli/figure.d.ts

@@ -13,6 +13,7 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
     bubbleSpread?: BubbleSpread;
     walks?: (string | WalkLayer)[];
     walkStrip?: boolean;
+    walkRowSamples?: string[];
     genes?: {
         file: string;
         index?: string;

package/dist/types/index.d.ts

@@ -54,9 +54,9 @@ export type { BubbleHalo } from './bubbles/bubbleHalos.js';
 export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble, } from './bubbles/classifyBubble.js';
 export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
-export { walkRows } from './layout/walkRows.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 {
@@ -74,6 +75,7 @@ export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => nu
 export type KeySwatch = {
     kind: 'bar';
     fill: string;
+    ramp?: true;
 } | {
     kind: 'gap';
     fill: string;
@@ -108,7 +110,7 @@ export type WalkRowsWithCalls = Omit<WalkRows, 'reference' | 'rows'> & {
     })[];
 };
 export declare const DISAGREES = "#c62828";
-export declare function walkRowsKeyTree(entries: KeyEntry[], x: number, y: number): {
+export declare function walkRowsKeyTree(entries: KeyEntry[], x: number, y: number, idPrefix?: string): {
     width: number;
     tree: El;
 };

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

@@ -30,6 +30,10 @@ export interface WalkRows {
     reference: WalkRow;
     rows: WalkRow[];
 }
+export declare function filterSamples<R extends {
+    sample: string;
+    label: string;
+}>(rows: R[], samples: string[] | undefined): R[];
 export declare function walkRows(graph: Graph, region?: {
     start: number;
     end: number;

package/dist/types/referenceRampCss.d.ts

@@ -11,4 +11,8 @@ export declare function rampStops({ start, bp, reversed }: {
     start: number;
     end: number;
 }): number[];
+export declare const RAMP_GRADIENT_STOPS: {
+    offset: number;
+    color: string;
+}[];
 export declare const RAMP_GRADIENT_CSS: string;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.5.0";
+export declare const version = "4.7.0";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.5.0",
+  "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": {