@jbrowse/bandage-core 8.0.1 → 8.0.2

package/dist/chunks/{chunk-4UBWXZVX.js → chunk-AO2VAMA4.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-WZATPZNH.js";
+} from "./chunk-XRPU24OP.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-MRZ7CFBN.js → chunk-H5ABLOPB.js}

@@ -42,10 +42,10 @@ import {
 } from "./chunk-HBEKUQO4.js";
 import {
   version
-} from "./chunk-V5W5E3UN.js";
+} from "./chunk-XNE4UNSJ.js";
 import {
   axisScaleOf
-} from "./chunk-4UBWXZVX.js";
+} from "./chunk-AO2VAMA4.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -91,7 +91,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-WZATPZNH.js";
+} from "./chunk-XRPU24OP.js";
 import {
   deletionDrawing,
   deletionEdges

package/dist/chunks/{chunk-72N5DJHZ.js → chunk-OCMBULGN.js}

@@ -16,8 +16,11 @@ function surveySegments(gfaGraph) {
     }
   }
   function traverse(id, strand) {
-    claim(id, strand);
-    traversals.set(id, (traversals.get(id) ?? 0) + 1);
+    const seen = traversals.get(id);
+    if (seen === void 0) {
+      claim(id, strand);
+    }
+    traversals.set(id, (seen ?? 0) + 1);
   }
   for (const link of gfaGraph.links) {
     claim(link.source, link.strand1 === "-" ? "-" : "+");
@@ -36,6 +39,7 @@ function surveySegments(gfaGraph) {
   return { canonical, traversals };
 }
 var walkStart = (w) => w.start === -1 ? 0 : w.start;
+var stranded = (s) => s.strand === "+" || s.strand === "-";
 function anchorablePaths(gfaGraph) {
   return [
     ...gfaGraph.paths.map((p) => ({
@@ -48,7 +52,7 @@ function anchorablePaths(gfaGraph) {
     ...gfaGraph.walks.map((w) => ({
       name: `${w.sample}#${w.haplotype}#${w.contig}`,
       start: walkStart(w),
-      steps: w.segments.map((s) => ({
+      steps: w.segments.every(stranded) ? w.segments : w.segments.map((s) => ({
         id: s.id,
         strand: s.strand === "-" ? "-" : "+"
       }))
@@ -82,7 +86,15 @@ function convertGFAToGraph(gfaGraph, name = "Imported GFA") {
   const nodes = [];
   const edges = [];
   const { canonical, traversals } = surveySegments(gfaGraph);
-  const nodeId = (segmentId) => `${segmentId}${canonical.get(segmentId) ?? "+"}`;
+  const nodeIds = /* @__PURE__ */ new Map();
+  const nodeId = (segmentId) => {
+    let id = nodeIds.get(segmentId);
+    if (id === void 0) {
+      id = `${segmentId}${canonical.get(segmentId) ?? "+"}`;
+      nodeIds.set(segmentId, id);
+    }
+    return id;
+  };
   for (const gfaNode of gfaGraph.nodes) {
     const depth = statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1);
     nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? "+", depth));
@@ -96,45 +108,58 @@ function convertGFAToGraph(gfaGraph, name = "Imported GFA") {
     });
   }
   const paths = [];
-  const edgeToPathsMap = /* @__PURE__ */ new Map();
-  const edgeKey = (a, b) => [a, b].sort().join("--");
-  function recordPathEdges(nodeIds, name2) {
-    for (let i = 0; i < nodeIds.length - 1; i++) {
-      const key = edgeKey(nodeIds[i], nodeIds[i + 1]);
-      if (!edgeToPathsMap.has(key)) {
-        edgeToPathsMap.set(key, /* @__PURE__ */ new Set());
-      }
-      edgeToPathsMap.get(key).add(name2);
+  const pathsByPair = /* @__PURE__ */ new Map();
+  const pairPaths = (a, b) => pathsByPair.get(a)?.get(b);
+  function addPair(a, b, set) {
+    let to = pathsByPair.get(a);
+    if (!to) {
+      to = /* @__PURE__ */ new Map();
+      pathsByPair.set(a, to);
+    }
+    to.set(b, set);
+  }
+  const edgePaths = edges.map((edge) => {
+    let set = pairPaths(edge.from, edge.to);
+    if (!set) {
+      set = /* @__PURE__ */ new Set();
+      addPair(edge.from, edge.to, set);
+      addPair(edge.to, edge.from, set);
+    }
+    return set;
+  });
+  function recordPathEdges(nodeIds2, name2) {
+    for (let i = 0; i < nodeIds2.length - 1; i++) {
+      pairPaths(nodeIds2[i], nodeIds2[i + 1])?.add(name2);
     }
   }
   for (const gfaPath of gfaGraph.paths) {
-    const nodeIds = gfaPath.path.split(",").map((segment) => nodeId(segment.slice(0, -1)));
+    const nodeIds2 = gfaPath.path.split(",").map((segment) => nodeId(segment.slice(0, -1)));
     paths.push({
       name: gfaPath.name,
-      nodeIds,
+      nodeIds: nodeIds2,
       start: pathOrigin(gfaPath.name).start
     });
-    recordPathEdges(nodeIds, gfaPath.name);
+    recordPathEdges(nodeIds2, gfaPath.name);
   }
   for (const walk of gfaGraph.walks) {
-    const nodeIds = walk.segments.map((seg) => nodeId(seg.id));
+    const nodeIds2 = walk.segments.map((seg) => nodeId(seg.id));
     const name2 = `${walk.sample}#${walk.haplotype}#${walk.contig}`;
     paths.push({
       name: name2,
-      nodeIds,
+      nodeIds: nodeIds2,
       start: walkStart(walk),
       sample: walk.sample,
       haplotype: walk.haplotype,
       contig: walk.contig
     });
-    recordPathEdges(nodeIds, name2);
+    recordPathEdges(nodeIds2, name2);
   }
-  for (const edge of edges) {
-    const pathIds = edgeToPathsMap.get(edgeKey(edge.from, edge.to));
-    if (pathIds && pathIds.size > 0) {
+  edges.forEach((edge, i) => {
+    const pathIds = edgePaths[i];
+    if (pathIds.size > 0) {
       edge.pathIds = [...pathIds];
     }
-  }
+  });
   const lengths = new Map(gfaGraph.nodes.map((n) => [n.id, n.length]));
   const anchoring = gfaGraph.paths.length > 0 || gfaGraph.walks.length > 0 ? surveyPaths(anchorablePaths(gfaGraph), (id) => lengths.get(id) ?? 0) : void 0;
   return {

package/dist/chunks/{chunk-XVSBZ4ZW.js → chunk-WBFYKGXL.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-WZATPZNH.js";
+} from "./chunk-XRPU24OP.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-H5S2ONCJ.js → chunk-WC3Y3TD2.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-WZATPZNH.js";
+} from "./chunk-XRPU24OP.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-V5W5E3UN.js → chunk-XNE4UNSJ.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "8.0.1";
+var version = "8.0.2";
 
 export {
   version

package/dist/chunks/{chunk-WZATPZNH.js → chunk-XRPU24OP.js}

@@ -6,7 +6,7 @@ import {
 } from "./chunk-PUG7LXDF.js";
 import {
   convertGFAToGraph
-} from "./chunk-72N5DJHZ.js";
+} from "./chunk-OCMBULGN.js";
 import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";

package/dist/cli/figure.js

@@ -35,7 +35,7 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-MRZ7CFBN.js";
+} from "../chunks/chunk-H5ABLOPB.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-O2ANJQVH.js";
@@ -53,8 +53,8 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-V5W5E3UN.js";
-import "../chunks/chunk-4UBWXZVX.js";
+import "../chunks/chunk-XNE4UNSJ.js";
+import "../chunks/chunk-AO2VAMA4.js";
 import "../chunks/chunk-MP7LXLWV.js";
 import {
   filterSamples,
@@ -80,10 +80,10 @@ import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-WZATPZNH.js";
+} from "../chunks/chunk-XRPU24OP.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-PUG7LXDF.js";
-import "../chunks/chunk-72N5DJHZ.js";
+import "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
 import "../chunks/chunk-ES2N6V56.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-MRZ7CFBN.js";
+} from "./chunks/chunk-H5ABLOPB.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-O2ANJQVH.js";
@@ -15,8 +15,8 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-6ZNQJ5ZD.js";
 import "./chunks/chunk-HBEKUQO4.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-V5W5E3UN.js";
-import "./chunks/chunk-4UBWXZVX.js";
+import "./chunks/chunk-XNE4UNSJ.js";
+import "./chunks/chunk-AO2VAMA4.js";
 import "./chunks/chunk-MP7LXLWV.js";
 import "./chunks/chunk-SZNZ2T6D.js";
 import "./chunks/chunk-PBENCR5L.js";
@@ -31,10 +31,10 @@ import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-JKJWSY4V.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-XV4P5KEQ.js";
-import "./chunks/chunk-WZATPZNH.js";
+import "./chunks/chunk-XRPU24OP.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";

package/dist/figureSettings.js

@@ -1,11 +1,11 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-H5S2ONCJ.js";
-import "./chunks/chunk-WZATPZNH.js";
+} from "./chunks/chunk-WC3Y3TD2.js";
+import "./chunks/chunk-XRPU24OP.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";

package/dist/gfa/gfaConverter.js

@@ -1,6 +1,6 @@
 import {
   convertGFAToGraph
-} from "../chunks/chunk-72N5DJHZ.js";
+} from "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/index.js

@@ -35,7 +35,7 @@ import {
 } from "./chunks/chunk-GQ2AOHU4.js";
 import {
   createForceLayoutCache
-} from "./chunks/chunk-XVSBZ4ZW.js";
+} from "./chunks/chunk-WBFYKGXL.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -112,7 +112,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-MRZ7CFBN.js";
+} from "./chunks/chunk-H5ABLOPB.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -204,7 +204,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-V5W5E3UN.js";
+} from "./chunks/chunk-XNE4UNSJ.js";
 import {
   axisScaleOf,
   contains,
@@ -212,7 +212,7 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-4UBWXZVX.js";
+} from "./chunks/chunk-AO2VAMA4.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -283,7 +283,7 @@ import {
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-H5S2ONCJ.js";
+} from "./chunks/chunk-WC3Y3TD2.js";
 import {
   ENGINE_DEFAULTS,
   FIT_PADDING,
@@ -296,10 +296,10 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-WZATPZNH.js";
+} from "./chunks/chunk-XRPU24OP.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";

package/dist/layout/forceCache.js

@@ -1,10 +1,10 @@
 import {
   createForceLayoutCache
-} from "../chunks/chunk-XVSBZ4ZW.js";
-import "../chunks/chunk-WZATPZNH.js";
+} from "../chunks/chunk-WBFYKGXL.js";
+import "../chunks/chunk-XRPU24OP.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-PUG7LXDF.js";
-import "../chunks/chunk-72N5DJHZ.js";
+import "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
 import "../chunks/chunk-ES2N6V56.js";

package/dist/pipeline.js

@@ -11,10 +11,10 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-WZATPZNH.js";
+} from "./chunks/chunk-XRPU24OP.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "8.0.1";
+export declare const version = "8.0.2";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-V5W5E3UN.js";
+} from "./chunks/chunk-XNE4UNSJ.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,11 +5,11 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-4UBWXZVX.js";
-import "./chunks/chunk-WZATPZNH.js";
+} from "./chunks/chunk-AO2VAMA4.js";
+import "./chunks/chunk-XRPU24OP.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-PUG7LXDF.js";
-import "./chunks/chunk-72N5DJHZ.js";
+import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "8.0.1",
+  "version": "8.0.2",
   "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": {