@jbrowse/bandage-core 11.11.0 → 11.11.1

package/dist/chunks/{chunk-F47LKG5B.js → chunk-27QSY2OI.js}

@@ -10,8 +10,12 @@ import {
   gapParts
 } from "./chunk-LG2UK4MB.js";
 import {
-  pathOrigin
+  pathOrigin,
+  referenceVisitStarts
 } from "./chunk-3YBP46PB.js";
+import {
+  isBackbone
+} from "./chunk-RJWPJCIB.js";
 import {
   panSNContig
 } from "./chunk-2JL2JVZ2.js";
@@ -132,20 +136,60 @@ function highlightOf(graph, name, { byId, edgeAt }) {
     unknownBp
   };
 }
-function laneColors(byId, walk, encoding, ramp) {
+function laneColors(graph, byId, walk, encoding, ramp) {
+  const places = encoding.field === "progress" || !ramp ? void 0 : referencePlaces(graph, byId, walk, ramp);
   const colors = /* @__PURE__ */ new Map();
   const passColors = /* @__PURE__ */ new Map();
   for (const [id, progress] of walk.passProgress) {
-    const node = byId.get(id);
-    const atNode = ramp && node ? rampFraction(node, ramp) : void 0;
+    const at = places?.get(id);
     const each = progress.map(
-      (t) => encodedColor(encoding, encoding.field === "progress" ? t : atNode)
+      (t, pass) => encodedColor(encoding, places ? at?.[pass] : t)
     );
     colors.set(id, each[0]);
     passColors.set(id, each);
   }
   return { colors, passColors };
 }
+function referencePlaces(graph, byId, walk, ramp) {
+  const startsOf = referenceVisitStarts(graph);
+  const places = /* @__PURE__ */ new Map();
+  for (const piece of walk.route) {
+    let cursor = Number.NaN;
+    let last = Number.NaN;
+    for (const id of piece) {
+      const node = byId.get(id);
+      let t = node && rampFraction(node, ramp);
+      if (node && t !== void 0 && isBackbone(node)) {
+        const starts = startsOf(node);
+        const len = node.length;
+        let at = starts[0];
+        if (starts.length > 1 && !Number.isNaN(cursor)) {
+          let gap = Infinity;
+          for (const start of starts) {
+            const g = Math.min(
+              Math.abs(start - cursor),
+              Math.abs(start + len - cursor)
+            );
+            if (g < gap) {
+              at = start;
+              gap = g;
+            }
+          }
+          t = (at + len / 2 - ramp.start) / ramp.span;
+        }
+        cursor = at + len === last ? at : at + len;
+        last = at;
+      }
+      const seen = places.get(id);
+      if (seen) {
+        seen.push(t);
+      } else {
+        places.set(id, [t]);
+      }
+    }
+  }
+  return places;
+}
 function reversedNodes(graph, byId, walk) {
   const reversed = /* @__PURE__ */ new Set();
   let bp = 0;
@@ -198,7 +242,7 @@ function walkLift(graph, layers, ramp) {
     return {
       ...walk,
       encoding,
-      ...laneColors(index.byId, walk, encoding, ramp),
+      ...laneColors(graph, index.byId, walk, encoding, ramp),
       reversed,
       reversedBp: bp
     };
@@ -220,7 +264,7 @@ function facetLifts(graph, lift, layers, ramp) {
         {
           ...walk,
           encoding,
-          ...laneColors(byId, walk, encoding, ramp)
+          ...laneColors(graph, byId, walk, encoding, ramp)
         }
       ],
       ramp

package/dist/chunks/{chunk-7553WCL3.js → chunk-4CK2SN7U.js}

@@ -12,13 +12,13 @@ import {
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-N4QOWBRR.js";
+} from "./chunk-OWNGPF73.js";
 import {
   axisScaleOf
 } from "./chunk-3DHGSHC3.js";
 import {
   figureScene
-} from "./chunk-R36RBFNH.js";
+} from "./chunk-U2UPDVH4.js";
 import {
   encodingStops
 } from "./chunk-EB4Q35QD.js";

package/dist/chunks/{chunk-JPT44REW.js → chunk-LF7V3QSH.js}

@@ -30,13 +30,13 @@ import {
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-N4QOWBRR.js";
+} from "./chunk-OWNGPF73.js";
 import {
   axisScaleOf
 } from "./chunk-3DHGSHC3.js";
 import {
   figureScene
-} from "./chunk-R36RBFNH.js";
+} from "./chunk-U2UPDVH4.js";
 import {
   encodingStops
 } from "./chunk-EB4Q35QD.js";

package/dist/chunks/{chunk-N4QOWBRR.js → chunk-OWNGPF73.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.11.0";
+var version = "11.11.1";
 
 export {
   version

package/dist/chunks/{chunk-R36RBFNH.js → chunk-U2UPDVH4.js}

@@ -4,7 +4,7 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-F47LKG5B.js";
+} from "./chunk-27QSY2OI.js";
 import {
   buildGeometry,
   computeReferenceRamp

package/dist/cli/figure.js

@@ -9,7 +9,7 @@ import "../chunks/chunk-EQDQ7P4Y.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-7553WCL3.js";
+} from "../chunks/chunk-4CK2SN7U.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
@@ -36,7 +36,7 @@ import "../chunks/chunk-ZKSC7QVE.js";
 import "../chunks/chunk-HNWJ4B7S.js";
 import {
   figureSvg
-} from "../chunks/chunk-JPT44REW.js";
+} from "../chunks/chunk-LF7V3QSH.js";
 import "../chunks/chunk-V4YML3GR.js";
 import "../chunks/chunk-KYTV5EAZ.js";
 import "../chunks/chunk-4DMSPNYV.js";
@@ -50,11 +50,11 @@ import "../chunks/chunk-TQ26XEFL.js";
 import "../chunks/chunk-4JDO7ZLN.js";
 import "../chunks/chunk-7YSIP3O2.js";
 import "../chunks/chunk-HEYIAMTC.js";
-import "../chunks/chunk-N4QOWBRR.js";
+import "../chunks/chunk-OWNGPF73.js";
 import "../chunks/chunk-3DHGSHC3.js";
-import "../chunks/chunk-R36RBFNH.js";
+import "../chunks/chunk-U2UPDVH4.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-F47LKG5B.js";
+import "../chunks/chunk-27QSY2OI.js";
 import "../chunks/chunk-EB4Q35QD.js";
 import "../chunks/chunk-GXCMBPC6.js";
 import "../chunks/chunk-4KBZ7WPP.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-JPT44REW.js";
+} from "./chunks/chunk-LF7V3QSH.js";
 import "./chunks/chunk-V4YML3GR.js";
 import "./chunks/chunk-KYTV5EAZ.js";
 import "./chunks/chunk-4DMSPNYV.js";
@@ -11,11 +11,11 @@ import "./chunks/chunk-TQ26XEFL.js";
 import "./chunks/chunk-4JDO7ZLN.js";
 import "./chunks/chunk-7YSIP3O2.js";
 import "./chunks/chunk-HEYIAMTC.js";
-import "./chunks/chunk-N4QOWBRR.js";
+import "./chunks/chunk-OWNGPF73.js";
 import "./chunks/chunk-3DHGSHC3.js";
-import "./chunks/chunk-R36RBFNH.js";
+import "./chunks/chunk-U2UPDVH4.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-F47LKG5B.js";
+import "./chunks/chunk-27QSY2OI.js";
 import "./chunks/chunk-EB4Q35QD.js";
 import "./chunks/chunk-GXCMBPC6.js";
 import "./chunks/chunk-4KBZ7WPP.js";

package/dist/figureData.js

@@ -3,7 +3,7 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-7553WCL3.js";
+} from "./chunks/chunk-4CK2SN7U.js";
 import "./chunks/chunk-CO6RGQAD.js";
 import "./chunks/chunk-WE7CLY2E.js";
 import "./chunks/chunk-XR2HMGAS.js";
@@ -18,11 +18,11 @@ import "./chunks/chunk-FNDNSDKW.js";
 import "./chunks/chunk-ZKSC7QVE.js";
 import "./chunks/chunk-HNWJ4B7S.js";
 import "./chunks/chunk-HEYIAMTC.js";
-import "./chunks/chunk-N4QOWBRR.js";
+import "./chunks/chunk-OWNGPF73.js";
 import "./chunks/chunk-3DHGSHC3.js";
-import "./chunks/chunk-R36RBFNH.js";
+import "./chunks/chunk-U2UPDVH4.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-F47LKG5B.js";
+import "./chunks/chunk-27QSY2OI.js";
 import "./chunks/chunk-EB4Q35QD.js";
 import "./chunks/chunk-GXCMBPC6.js";
 import "./chunks/chunk-4KBZ7WPP.js";

package/dist/figureScene.js

@@ -1,8 +1,8 @@
 import {
   figureScene
-} from "./chunks/chunk-R36RBFNH.js";
+} from "./chunks/chunk-U2UPDVH4.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-F47LKG5B.js";
+import "./chunks/chunk-27QSY2OI.js";
 import "./chunks/chunk-EB4Q35QD.js";
 import "./chunks/chunk-GXCMBPC6.js";
 import "./chunks/chunk-4KBZ7WPP.js";

package/dist/index.js

@@ -97,7 +97,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-7553WCL3.js";
+} from "./chunks/chunk-4CK2SN7U.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -134,7 +134,7 @@ import {
 import "./chunks/chunk-HNWJ4B7S.js";
 import {
   figureSvg
-} from "./chunks/chunk-JPT44REW.js";
+} from "./chunks/chunk-LF7V3QSH.js";
 import {
   svgCanvas
 } from "./chunks/chunk-V4YML3GR.js";
@@ -205,7 +205,7 @@ import {
 } from "./chunks/chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunks/chunk-N4QOWBRR.js";
+} from "./chunks/chunk-OWNGPF73.js";
 import {
   axisScaleOf,
   contains,
@@ -214,7 +214,7 @@ import {
   viewportOf,
   zoomAbout
 } from "./chunks/chunk-3DHGSHC3.js";
-import "./chunks/chunk-R36RBFNH.js";
+import "./chunks/chunk-U2UPDVH4.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -222,7 +222,7 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-F47LKG5B.js";
+} from "./chunks/chunk-27QSY2OI.js";
 import {
   WALK_FIELDS,
   WALK_SCHEMES,

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "11.11.0";
+export declare const version = "11.11.1";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-N4QOWBRR.js";
+} from "./chunks/chunk-OWNGPF73.js";
 export {
   version
 };

package/dist/walkHighlight.js

@@ -2,7 +2,7 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-F47LKG5B.js";
+} from "./chunks/chunk-27QSY2OI.js";
 import "./chunks/chunk-EB4Q35QD.js";
 import "./chunks/chunk-GXCMBPC6.js";
 import "./chunks/chunk-4KBZ7WPP.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "11.11.0",
+  "version": "11.11.1",
   "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": {