@jbrowse/bandage-core 11.3.0 → 11.5.0

package/dist/layout/walkRowDraw.js

@@ -29,9 +29,9 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-XZ6PQBU6.js";
+} from "../chunks/chunk-TRGKMLXT.js";
 import "../chunks/chunk-H2H4Y3TV.js";
-import "../chunks/chunk-SWCULW6S.js";
+import "../chunks/chunk-JOWKKQAL.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

package/dist/layout/walkRowLayout.js

@@ -5,10 +5,10 @@ import {
   walkRowLayout,
   walkRowLayoutOf,
   walkRowsExtent
-} from "../chunks/chunk-TZLEHZVC.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
-import "../chunks/chunk-B5ARSBOH.js";
+} from "../chunks/chunk-FWSERUJV.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/layout/walkRowRuns.js

@@ -3,8 +3,8 @@ import {
   runAt,
   walkRowRuns,
   walkRowsOf
-} from "../chunks/chunk-M75QPZNJ.js";
-import "../chunks/chunk-B5ARSBOH.js";
+} from "../chunks/chunk-64FCX424.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/layout/walkRows.js

@@ -1,11 +1,11 @@
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-JDZ5GTZT.js";
+} from "../chunks/chunk-IOWLTUEB.js";
 import {
   referenceWalkName
-} from "../chunks/chunk-M75QPZNJ.js";
-import "../chunks/chunk-B5ARSBOH.js";
+} from "../chunks/chunk-64FCX424.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/layout/walkStrip.js

@@ -9,21 +9,21 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-PNM6Z3IE.js";
+} from "../chunks/chunk-A32ZKSHN.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-XZ6PQBU6.js";
+} from "../chunks/chunk-TRGKMLXT.js";
 import "../chunks/chunk-H2H4Y3TV.js";
-import "../chunks/chunk-SWCULW6S.js";
+import "../chunks/chunk-JOWKKQAL.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";
-import "../chunks/chunk-TZLEHZVC.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-FWSERUJV.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
 import "../chunks/chunk-3GP3KT5L.js";
 import "../chunks/chunk-CRCD3ODN.js";
-import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-EIY2SKD3.js";

package/dist/layoutModes.js

@@ -4,8 +4,8 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-TEXAKEJX.js";
-import "./chunks/chunk-3LZ334X4.js";
+} from "./chunks/chunk-5F4D35U5.js";
+import "./chunks/chunk-RK3HRRCW.js";
 import "./chunks/chunk-A7H753BA.js";
 import "./chunks/chunk-GJU6BJJA.js";
 import "./chunks/chunk-GJLZ2MKE.js";
@@ -13,11 +13,11 @@ import "./chunks/chunk-MYLAJDKB.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-UAFATXYA.js";
 import "./chunks/chunk-3GLG3ZLE.js";
-import "./chunks/chunk-TZLEHZVC.js";
-import "./chunks/chunk-JDZ5GTZT.js";
-import "./chunks/chunk-M75QPZNJ.js";
+import "./chunks/chunk-FWSERUJV.js";
+import "./chunks/chunk-IOWLTUEB.js";
+import "./chunks/chunk-64FCX424.js";
 import "./chunks/chunk-3GP3KT5L.js";
-import "./chunks/chunk-B5ARSBOH.js";
+import "./chunks/chunk-NJGYLYU7.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-EIY2SKD3.js";

package/dist/locus.js

@@ -0,0 +1,8 @@
+import {
+  formatLocus,
+  parseLocus
+} from "./chunks/chunk-JOLLU34X.js";
+export {
+  formatLocus,
+  parseLocus
+};

package/dist/pipeline.js

@@ -11,15 +11,15 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-REOWLPH4.js";
+} from "./chunks/chunk-WG5D2H7X.js";
+import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
-import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-B5ARSBOH.js";
+import "./chunks/chunk-NJGYLYU7.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-DZR37KXT.js";

package/dist/referenceStrip.js

@@ -7,8 +7,8 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-3UST3ZQE.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-EGBBIXTG.js";
+import "./chunks/chunk-JOWKKQAL.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/renderer/GeometryBuilder.js

@@ -9,8 +9,9 @@ import {
   computeReferenceRamp,
   endTangent,
   getNodeColor,
-  hslToRgb
-} from "../chunks/chunk-SWCULW6S.js";
+  hslToRgb,
+  rampFraction
+} from "../chunks/chunk-JOWKKQAL.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import {
   REFERENCE_RAMP_MAX_HUE
@@ -44,5 +45,6 @@ export {
   computeReferenceRamp,
   endTangent,
   getNodeColor,
-  hslToRgb
+  hslToRgb,
+  rampFraction
 };

package/dist/tubeMap/bundle.js

@@ -1,13 +1,13 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-TJOOHTJ6.js";
-import "../chunks/chunk-3LZ334X4.js";
+} from "../chunks/chunk-VD4MLYEK.js";
+import "../chunks/chunk-RK3HRRCW.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
 import "../chunks/chunk-3GP3KT5L.js";
-import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/tubeMap/coarsen.js

@@ -1,14 +1,14 @@
 import {
   coarsenTubeMap,
   lastAtMost
-} from "../chunks/chunk-7O7EGTYG.js";
-import "../chunks/chunk-3LZ334X4.js";
+} from "../chunks/chunk-WC6HX6GJ.js";
+import "../chunks/chunk-RK3HRRCW.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
 import "../chunks/chunk-3GP3KT5L.js";
-import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/tubeMap/deviations.js

@@ -1,17 +1,17 @@
 import {
   lastAtMost
-} from "../chunks/chunk-7O7EGTYG.js";
+} from "../chunks/chunk-WC6HX6GJ.js";
 import {
   boxX,
   referenceBoxes
 } from "../chunks/chunk-HSVFCA2J.js";
-import "../chunks/chunk-3LZ334X4.js";
+import "../chunks/chunk-RK3HRRCW.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
 import "../chunks/chunk-3GP3KT5L.js";
-import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import {
   pathOrigin
 } from "../chunks/chunk-B5X2RLJG.js";

package/dist/tubeMap/draw.js

@@ -8,14 +8,14 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-3HGYGISG.js";
+} from "../chunks/chunk-3U3C4PRK.js";
 import "../chunks/chunk-BX4AUMZE.js";
 import "../chunks/chunk-MYDHU2UV.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-JDZ5GTZT.js";
-import "../chunks/chunk-M75QPZNJ.js";
-import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-IOWLTUEB.js";
+import "../chunks/chunk-64FCX424.js";
+import "../chunks/chunk-NJGYLYU7.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/tubeMap/nodeColors.js

@@ -1,7 +1,7 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-XVS52NMZ.js";
-import "../chunks/chunk-SWCULW6S.js";
+} from "../chunks/chunk-7EDGWT67.js";
+import "../chunks/chunk-JOWKKQAL.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

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

@@ -38,9 +38,10 @@ export declare function tablePath(w: GraphTables['walks'], p: number): Omit<Grap
 };
 /**
  * Each segment's Graph node id: its name and its one drawn orientation, first
- * claimed by a link and else by a walk
+ * claimed by a link and else by a walk. Counts each segment's walk steps into
+ * `traversals` when given one.
  */
-export declare function tableNodeIds({ nodes: n, links: l, walks: w }: GraphTables): string[];
+export declare function tableNodeIds({ nodes: n, links: l, walks: w }: GraphTables, traversals?: Int32Array): string[];
 /**
  * The Graph `convertGFAToGraph` builds from `graphTablesGFA(tables)`, deep
  * equal, built by index: a step costs a few array reads and its visit, where

package/dist/types/index.d.ts

@@ -56,6 +56,7 @@ export { genesFromBed, genesFromGff3Lines, genesFromText, mergeOverlappingByName
 export { backboneGenes } from './genes/backboneGenes.js';
 export type { BackboneGenes, GeneSource, IndexedGeneFile, } from './genes/backboneGenes.js';
 export { HPRC_GBZ, cutGbzRegion, openGbz, parseRegion } from './gbzCut.js';
+export { formatLocus, parseLocus } from './locus.js';
 export type { GbzSource } from './gbzCut.js';
 export { version } from './version.js';
 export type { FigureOptions } from './figure.js';

package/dist/types/locus.d.ts

@@ -0,0 +1,10 @@
+export declare function parseLocus(text: string): {
+    refName: string;
+    start: number;
+    end: number;
+} | undefined;
+export declare function formatLocus(r: {
+    refName: string;
+    start: number;
+    end: number;
+}): string;

package/dist/types/renderer/GeometryBuilder.d.ts

@@ -42,6 +42,7 @@ export interface ReferenceRamp {
     span: number;
     midpoints: Map<string, number>;
 }
+export declare function rampFraction(node: GraphNode, ramp: ReferenceRamp): number | undefined;
 export interface ColorSchemeRange {
     minDepth: number;
     maxDepth: number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "11.3.0";
+export declare const version = "11.5.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-XEWPWCML.js";
+} from "./chunks/chunk-WLR4KJVI.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,16 +5,16 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-CE6ZIKJX.js";
-import "./chunks/chunk-REOWLPH4.js";
+} from "./chunks/chunk-XKZ56L5A.js";
+import "./chunks/chunk-WG5D2H7X.js";
+import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
-import "./chunks/chunk-OPPVSPEF.js";
 import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-B5ARSBOH.js";
+import "./chunks/chunk-NJGYLYU7.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-DZR37KXT.js";

package/dist/walkEncoding.js

@@ -9,8 +9,8 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-TABI4JEU.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-HN3WHMPJ.js";
+import "./chunks/chunk-JOWKKQAL.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/walkHighlight.js

@@ -2,9 +2,9 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-DR24UTRS.js";
-import "./chunks/chunk-TABI4JEU.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-VQ7474EH.js";
+import "./chunks/chunk-HN3WHMPJ.js";
+import "./chunks/chunk-JOWKKQAL.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "11.3.0",
+  "version": "11.5.0",
   "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": {

package/dist/chunks/{chunk-2Q22S52W.js → chunk-2E25TX4G.js}

@@ -1,3 +1,6 @@
+import {
+  coversGraph
+} from "./chunk-E4ZM4OOJ.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -5,15 +8,12 @@ import {
   walkIndexOf,
   walkRoutes
 } from "./chunk-RFG42VIO.js";
-import {
-  bubbleSubgraph
-} from "./chunk-PNMJFFNB.js";
-import {
-  coversGraph
-} from "./chunk-E4ZM4OOJ.js";
 import {
   bubbleSegmentIds
 } from "./chunk-A4JDEUAI.js";
+import {
+  bubbleSubgraph
+} from "./chunk-PNMJFFNB.js";
 import {
   strandSides
 } from "./chunk-UBQSRCWR.js";