@jbrowse/bandage-core 10.2.4 → 10.2.6

package/dist/chunks/{chunk-XAWLIU54.js → chunk-FB5RKZQY.js}

@@ -3,13 +3,13 @@ import {
 } from "./chunk-JMABOQWL.js";
 import {
   layoutModeByValue
-} from "./chunk-WL6ZKUVC.js";
+} from "./chunk-TKIJ5535.js";
 import {
   parseRegion
 } from "./chunk-VQWHMWLF.js";
 import {
   version
-} from "./chunk-2CHS5LMM.js";
+} from "./chunk-YYMW5XOF.js";
 import {
   axisScaleOf
 } from "./chunk-BS4UZ44I.js";
@@ -18,7 +18,7 @@ import {
 } from "./chunk-4ETPXDO6.js";
 import {
   figureScene
-} from "./chunk-D5D36ZF6.js";
+} from "./chunk-HFVGGB3U.js";
 import {
   abgrAlpha,
   abgrBlue,

package/dist/chunks/{chunk-D5D36ZF6.js → chunk-HFVGGB3U.js}

@@ -11,7 +11,7 @@ import {
 } from "./chunk-A4PFFC4Q.js";
 import {
   walkRowsExtent
-} from "./chunk-54POIBVC.js";
+} from "./chunk-L2HDM2R3.js";
 import {
   pathLegend,
   walkLabelsOf

package/dist/chunks/{chunk-54POIBVC.js → chunk-L2HDM2R3.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-RIPAA7OK.js";
+} from "./chunk-LKW2TP4N.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-RIPAA7OK.js → chunk-LKW2TP4N.js}

@@ -152,8 +152,13 @@ function filterSamples(rows, samples) {
 }
 function walkRows(graph, region, unit) {
   const paths = graph.paths ?? [];
-  const isReference = (p) => pathOrigin(p.name).name === graph.referencePath;
-  const referencePieces = paths.some(isReference) ? paths.filter(isReference).sort((a, b) => (a.start ?? 0) - (b.start ?? 0)) : paths.slice(0, 1);
+  const nameOf = (p) => pathOrigin(p.name).name;
+  const rankZero = new Set(
+    graph.nodes.flatMap((n) => n.stable?.rank === 0 ? [n.stable.refName] : [])
+  );
+  const names = paths.map(nameOf);
+  const referenceName = graph.referencePath !== void 0 && names.includes(graph.referencePath) ? graph.referencePath : names.find((n) => rankZero.has(n)) ?? names[0];
+  const referencePieces = paths.filter((p) => nameOf(p) === referenceName).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
   const first = referencePieces[0];
   const others = paths.filter((p) => !referencePieces.includes(p));
   if (!first || others.length === 0) {

package/dist/chunks/{chunk-WL6ZKUVC.js → chunk-TKIJ5535.js}

@@ -15,7 +15,7 @@ import {
 } from "./chunk-CM6LO6OC.js";
 import {
   walkRowLayout
-} from "./chunk-54POIBVC.js";
+} from "./chunk-L2HDM2R3.js";
 import {
   isBackbone,
   isOffReference
@@ -52,7 +52,7 @@ var LAYOUT_MODES = [
   {
     value: "walkrows",
     label: "Walk rows",
-    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.",
+    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 a reference and two or more walks.",
     run: walkRowLayout,
     cutMargins: false,
     wholeWalks: true,
@@ -96,7 +96,7 @@ var LAYOUT_MODES = [
   {
     value: "force",
     label: FORCE_LAYOUT_LABEL,
-    description: "OGDF FMMM, via the external Bandage engine.",
+    description: "OGDF FMMM (wasm) or stress, whichever engine is chosen.",
     run: () => void 0,
     cutMargins: false,
     wholeWalks: false,

package/dist/chunks/{chunk-BAETMD3J.js → chunk-WBSWROE6.js}

@@ -8,7 +8,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM
-} from "./chunk-54POIBVC.js";
+} from "./chunk-L2HDM2R3.js";
 import {
   pathOrigin
 } from "./chunk-M6LK4GII.js";

package/dist/chunks/{chunk-GINYTQ43.js → chunk-XBHMXTOR.js}

@@ -5,7 +5,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-BAETMD3J.js";
+} from "./chunk-WBSWROE6.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
@@ -34,7 +34,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-2CHS5LMM.js";
+} from "./chunk-YYMW5XOF.js";
 import {
   axisScaleOf
 } from "./chunk-BS4UZ44I.js";
@@ -44,13 +44,13 @@ import {
 } from "./chunk-4ETPXDO6.js";
 import {
   figureScene
-} from "./chunk-D5D36ZF6.js";
+} from "./chunk-HFVGGB3U.js";
 import {
   encodingStops
 } from "./chunk-VQC7KELB.js";
 import {
   walkRowLabels
-} from "./chunk-54POIBVC.js";
+} from "./chunk-L2HDM2R3.js";
 import {
   nodeInk
 } from "./chunk-JBCZIBFC.js";

package/dist/chunks/{chunk-2CHS5LMM.js → chunk-YYMW5XOF.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.2.4";
+var version = "10.2.6";
 
 export {
   version

package/dist/cli/figure.js

@@ -7,9 +7,9 @@ import {
 } from "../chunks/chunk-G6UIYQZR.js";
 import {
   figureSvg
-} from "../chunks/chunk-GINYTQ43.js";
+} from "../chunks/chunk-XBHMXTOR.js";
 import "../chunks/chunk-RUCH6ZFL.js";
-import "../chunks/chunk-BAETMD3J.js";
+import "../chunks/chunk-WBSWROE6.js";
 import {
   genesOnRow,
   placeRowGenes
@@ -26,14 +26,14 @@ import "../chunks/chunk-H2H4Y3TV.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-XAWLIU54.js";
+} from "../chunks/chunk-FB5RKZQY.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
 } from "../chunks/chunk-JMABOQWL.js";
 import {
   LAYOUT_MODES
-} from "../chunks/chunk-WL6ZKUVC.js";
+} from "../chunks/chunk-TKIJ5535.js";
 import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-XI3ZUTWF.js";
 import "../chunks/chunk-CWFNEKST.js";
@@ -51,21 +51,21 @@ import {
 } from "../chunks/chunk-VQWHMWLF.js";
 import "../chunks/chunk-Q7LYHGGQ.js";
 import "../chunks/chunk-WSIFAZU7.js";
-import "../chunks/chunk-2CHS5LMM.js";
+import "../chunks/chunk-YYMW5XOF.js";
 import "../chunks/chunk-BS4UZ44I.js";
 import "../chunks/chunk-4ETPXDO6.js";
-import "../chunks/chunk-D5D36ZF6.js";
+import "../chunks/chunk-HFVGGB3U.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-CU6P5RUG.js";
 import "../chunks/chunk-VQC7KELB.js";
 import "../chunks/chunk-A4PFFC4Q.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-ZY2AFL4Y.js";
-import "../chunks/chunk-54POIBVC.js";
+import "../chunks/chunk-L2HDM2R3.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-RIPAA7OK.js";
+} from "../chunks/chunk-LKW2TP4N.js";
 import "../chunks/chunk-3XSM4OZU.js";
 import "../chunks/chunk-JBCZIBFC.js";
 import "../chunks/chunk-HNCXR2VS.js";

package/dist/figure.js

@@ -1,8 +1,8 @@
 import {
   figureSvg
-} from "./chunks/chunk-GINYTQ43.js";
+} from "./chunks/chunk-XBHMXTOR.js";
 import "./chunks/chunk-RUCH6ZFL.js";
-import "./chunks/chunk-BAETMD3J.js";
+import "./chunks/chunk-WBSWROE6.js";
 import "./chunks/chunk-EFQLEGWM.js";
 import "./chunks/chunk-QLWI2PZ3.js";
 import "./chunks/chunk-RBCE2OQH.js";
@@ -13,18 +13,18 @@ import "./chunks/chunk-KC7T5RWG.js";
 import "./chunks/chunk-4HWM3FNK.js";
 import "./chunks/chunk-KBEP7VYK.js";
 import "./chunks/chunk-H2H4Y3TV.js";
-import "./chunks/chunk-2CHS5LMM.js";
+import "./chunks/chunk-YYMW5XOF.js";
 import "./chunks/chunk-BS4UZ44I.js";
 import "./chunks/chunk-4ETPXDO6.js";
-import "./chunks/chunk-D5D36ZF6.js";
+import "./chunks/chunk-HFVGGB3U.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-CU6P5RUG.js";
 import "./chunks/chunk-VQC7KELB.js";
 import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-ZY2AFL4Y.js";
-import "./chunks/chunk-54POIBVC.js";
-import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-L2HDM2R3.js";
+import "./chunks/chunk-LKW2TP4N.js";
 import "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-HNCXR2VS.js";

package/dist/figureData.js

@@ -3,9 +3,9 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-XAWLIU54.js";
+} from "./chunks/chunk-FB5RKZQY.js";
 import "./chunks/chunk-JMABOQWL.js";
-import "./chunks/chunk-WL6ZKUVC.js";
+import "./chunks/chunk-TKIJ5535.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-XI3ZUTWF.js";
 import "./chunks/chunk-CWFNEKST.js";
@@ -17,18 +17,18 @@ import "./chunks/chunk-RVS2QCOX.js";
 import "./chunks/chunk-VQWHMWLF.js";
 import "./chunks/chunk-Q7LYHGGQ.js";
 import "./chunks/chunk-WSIFAZU7.js";
-import "./chunks/chunk-2CHS5LMM.js";
+import "./chunks/chunk-YYMW5XOF.js";
 import "./chunks/chunk-BS4UZ44I.js";
 import "./chunks/chunk-4ETPXDO6.js";
-import "./chunks/chunk-D5D36ZF6.js";
+import "./chunks/chunk-HFVGGB3U.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-CU6P5RUG.js";
 import "./chunks/chunk-VQC7KELB.js";
 import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-ZY2AFL4Y.js";
-import "./chunks/chunk-54POIBVC.js";
-import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-L2HDM2R3.js";
+import "./chunks/chunk-LKW2TP4N.js";
 import "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-HNCXR2VS.js";

package/dist/figureScene.js

@@ -1,14 +1,14 @@
 import {
   figureScene
-} from "./chunks/chunk-D5D36ZF6.js";
+} from "./chunks/chunk-HFVGGB3U.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-CU6P5RUG.js";
 import "./chunks/chunk-VQC7KELB.js";
 import "./chunks/chunk-A4PFFC4Q.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-ZY2AFL4Y.js";
-import "./chunks/chunk-54POIBVC.js";
-import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-L2HDM2R3.js";
+import "./chunks/chunk-LKW2TP4N.js";
 import "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-JBCZIBFC.js";
 import "./chunks/chunk-HNCXR2VS.js";

package/dist/index.js

@@ -83,7 +83,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-GINYTQ43.js";
+} from "./chunks/chunk-XBHMXTOR.js";
 import {
   svgCanvas
 } from "./chunks/chunk-RUCH6ZFL.js";
@@ -98,7 +98,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-BAETMD3J.js";
+} from "./chunks/chunk-WBSWROE6.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -164,7 +164,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-XAWLIU54.js";
+} from "./chunks/chunk-FB5RKZQY.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -174,7 +174,7 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-WL6ZKUVC.js";
+} from "./chunks/chunk-TKIJ5535.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-XI3ZUTWF.js";
 import "./chunks/chunk-CWFNEKST.js";
@@ -201,7 +201,7 @@ import {
 import "./chunks/chunk-WSIFAZU7.js";
 import {
   version
-} from "./chunks/chunk-2CHS5LMM.js";
+} from "./chunks/chunk-YYMW5XOF.js";
 import {
   axisScaleOf,
   contains,
@@ -215,7 +215,7 @@ import {
   walkKey,
   walkPosition
 } from "./chunks/chunk-4ETPXDO6.js";
-import "./chunks/chunk-D5D36ZF6.js";
+import "./chunks/chunk-HFVGGB3U.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -242,11 +242,11 @@ import "./chunks/chunk-ZY2AFL4Y.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunks/chunk-54POIBVC.js";
+} from "./chunks/chunk-L2HDM2R3.js";
 import {
   filterSamples,
   walkRows
-} from "./chunks/chunk-RIPAA7OK.js";
+} from "./chunks/chunk-LKW2TP4N.js";
 import {
   pathColorsLegible,
   pathLegend,

package/dist/layout/walkRowLayout.js

@@ -3,8 +3,8 @@ import {
   walkRowLabels,
   walkRowLayout,
   walkRowsExtent
-} from "../chunks/chunk-54POIBVC.js";
-import "../chunks/chunk-RIPAA7OK.js";
+} from "../chunks/chunk-L2HDM2R3.js";
+import "../chunks/chunk-LKW2TP4N.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";

package/dist/layout/walkRows.js

@@ -1,7 +1,7 @@
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-RIPAA7OK.js";
+} from "../chunks/chunk-LKW2TP4N.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";

package/dist/layout/walkStrip.js

@@ -9,7 +9,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-BAETMD3J.js";
+} from "../chunks/chunk-WBSWROE6.js";
 import {
   LABELLED_ROW_PX
 } from "../chunks/chunk-EFQLEGWM.js";
@@ -18,8 +18,8 @@ import "../chunks/chunk-H2H4Y3TV.js";
 import "../chunks/chunk-A4PFFC4Q.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-ZY2AFL4Y.js";
-import "../chunks/chunk-54POIBVC.js";
-import "../chunks/chunk-RIPAA7OK.js";
+import "../chunks/chunk-L2HDM2R3.js";
+import "../chunks/chunk-LKW2TP4N.js";
 import "../chunks/chunk-3XSM4OZU.js";
 import "../chunks/chunk-JBCZIBFC.js";
 import "../chunks/chunk-M6LK4GII.js";

package/dist/layoutModes.js

@@ -4,7 +4,7 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-WL6ZKUVC.js";
+} from "./chunks/chunk-TKIJ5535.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-XI3ZUTWF.js";
 import "./chunks/chunk-CWFNEKST.js";
@@ -13,8 +13,8 @@ import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-CM6LO6OC.js";
 import "./chunks/chunk-RVS2QCOX.js";
-import "./chunks/chunk-54POIBVC.js";
-import "./chunks/chunk-RIPAA7OK.js";
+import "./chunks/chunk-L2HDM2R3.js";
+import "./chunks/chunk-LKW2TP4N.js";
 import "./chunks/chunk-3XSM4OZU.js";
 import "./chunks/chunk-M6LK4GII.js";
 import "./chunks/chunk-RAEABQNW.js";

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, 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 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 a reference and two or more walks.";
     readonly run: typeof walkRowLayout;
     readonly cutMargins: false;
     readonly wholeWalks: true;
@@ -82,7 +82,7 @@ export declare const LAYOUT_MODES: readonly [{
 }, {
     readonly value: "force";
     readonly label: "Force-directed layout";
-    readonly description: "OGDF FMMM, via the external Bandage engine.";
+    readonly description: "OGDF FMMM (wasm) or stress, whichever engine is chosen.";
     readonly run: () => undefined;
     readonly cutMargins: false;
     readonly wholeWalks: false;
@@ -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, 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 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 a reference and two or more walks.";
     readonly run: typeof walkRowLayout;
     readonly cutMargins: false;
     readonly wholeWalks: true;
@@ -156,7 +156,7 @@ export declare function layoutModeByValue(value: string): {
 } | {
     readonly value: "force";
     readonly label: "Force-directed layout";
-    readonly description: "OGDF FMMM, via the external Bandage engine.";
+    readonly description: "OGDF FMMM (wasm) or stress, whichever engine is chosen.";
     readonly run: () => undefined;
     readonly cutMargins: false;
     readonly wholeWalks: false;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "10.2.4";
+export declare const version = "10.2.6";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-2CHS5LMM.js";
+} from "./chunks/chunk-YYMW5XOF.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.2.4",
+  "version": "10.2.6",
   "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": {