@jbrowse/bandage-core 10.1.0 → 10.2.0

package/dist/chunks/{chunk-YPYWYPHX.js → chunk-AFP3NWSL.js}

@@ -10,7 +10,7 @@ function foldVariants(graph, belowBp) {
   if (!(belowBp > 0) || graph.paths?.length || !graph.nodes.some((node) => isBackbone(node))) {
     return graph;
   }
-  const { nodes, edges } = graph;
+  const { nodes, edges } = readForward(graph);
   const index = new Map(nodes.map((node, i) => [node.id, i]));
   const sides = edges.map(forwardSides);
   const links = linksAt(nodes.length, edges, sides, index);
@@ -47,7 +47,34 @@ function foldVariants(graph, belowBp) {
     const skip = skipped(nodes[a], sides[k].from, nodes[b], sides[k].to);
     return kept[a] && kept[b] && !(skip > 0 && skip < belowBp);
   });
-  return mergeAlleleRuns({ ...graph, edges: keptEdges }, kept, allele);
+  return mergeAlleleRuns({ ...graph, nodes, edges: keptEdges }, kept, allele);
+}
+function readForward({ nodes, edges }) {
+  const reversed = new Set(
+    nodes.filter((node) => node.stable?.strand === "-").map((node) => node.id)
+  );
+  if (reversed.size === 0) {
+    return { nodes, edges };
+  }
+  const read = (id, strand) => {
+    const own = strand ?? ownStrand(id);
+    return reversed.has(id) ? complement(own) : own;
+  };
+  return {
+    nodes: nodes.map(
+      (node) => reversed.has(node.id) ? { ...node, stable: { ...node.stable, strand: "+" } } : node
+    ),
+    edges: edges.map(
+      (edge) => reversed.has(edge.from) || reversed.has(edge.to) ? {
+        ...edge,
+        fromStrand: read(edge.from, edge.fromStrand),
+        toStrand: read(edge.to, edge.toStrand)
+      } : edge
+    )
+  };
+}
+function complement(strand) {
+  return strand === "+" ? "-" : "+";
 }
 function forwardSides(edge) {
   return {
@@ -61,8 +88,9 @@ function linksAt(count, edges, sides, index) {
     const a = index.get(edge.from);
     const b = index.get(edge.to);
     if (a !== void 0 && b !== void 0) {
-      links[a].push({ other: b, side: sides[k].from });
-      links[b].push({ other: a, side: sides[k].to });
+      const { from, to } = sides[k];
+      links[a].push({ other: b, side: from, otherSide: to });
+      links[b].push({ other: a, side: to, otherSide: from });
     }
   });
   return links;
@@ -74,11 +102,11 @@ function onOneSequence(a, b) {
 }
 function continues(a, aSide, b, bSide) {
   const pair = onOneSequence(a, b);
-  if (!pair || aSide === bSide) {
+  if (!pair) {
     return false;
   }
   const [sa, sb] = pair;
-  return sa.start + a.length === sb.start || sb.start + b.length === sa.start;
+  return aSide === "e" && bSide === "s" && sa.start + a.length === sb.start || bSide === "e" && aSide === "s" && sb.start + b.length === sa.start;
 }
 function skipped(a, aSide, b, bSide) {
   const pair = onOneSequence(a, b);
@@ -86,10 +114,10 @@ function skipped(a, aSide, b, bSide) {
     return 0;
   }
   const [sa, sb] = pair;
-  return Math.max(
-    sb.start - (sa.start + a.length),
-    sa.start - (sb.start + b.length)
-  );
+  return Math.abs(position(sb, b, bSide) - position(sa, a, aSide));
+}
+function position({ start }, node, side) {
+  return side === "s" ? start : start + node.length;
 }
 function alleleOf(nodes, edges, sides, index) {
   const parent = nodes.map((_, i) => i);
@@ -132,13 +160,14 @@ function alleleContent(group, nodes, links, allele) {
   let oneSequence = true;
   for (const i of group) {
     length += nodes[i].length;
-    for (const { other } of links[i]) {
+    for (const { other, otherSide } of links[i]) {
       const node = nodes[other];
       if (allele[other] !== allele[i] && isBackbone(node)) {
         refName ??= node.stable.refName;
         oneSequence &&= node.stable.refName === refName;
-        lo = Math.min(lo, node.stable.start + node.length);
-        hi = Math.max(hi, node.stable.start);
+        const at = position(node.stable, node, otherSide);
+        lo = Math.min(lo, at);
+        hi = Math.max(hi, at);
       }
     }
   }

package/dist/chunks/{chunk-VIERZJO2.js → chunk-CPVZGVDL.js}

@@ -1,6 +1,6 @@
 import {
   layoutEngine
-} from "./chunk-FLUQODT2.js";
+} from "./chunk-DT2GGH4D.js";
 import {
   layoutModeByValue
 } from "./chunk-4R6QNG23.js";
@@ -12,7 +12,7 @@ import {
 } from "./chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunk-MZIOBJZB.js";
+} from "./chunk-M3NPTHSE.js";
 import {
   axisScaleOf
 } from "./chunk-L5WF4ZPS.js";

package/dist/chunks/{chunk-FLUQODT2.js → chunk-DT2GGH4D.js}

@@ -13,7 +13,7 @@ var LAYOUT_ENGINES = [
   {
     value: "stress",
     label: "Stress",
-    description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring."
+    description: "Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference."
   }
 ];
 var LAYOUT_ENGINE_VALUES = LAYOUT_ENGINES.map((e) => e.value);

package/dist/chunks/{chunk-CFPER2S2.js → chunk-EDR4CGCQ.js}

@@ -36,7 +36,7 @@ import {
 } from "./chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunk-MZIOBJZB.js";
+} from "./chunk-M3NPTHSE.js";
 import {
   axisScaleOf
 } from "./chunk-L5WF4ZPS.js";

package/dist/chunks/{chunk-MZIOBJZB.js → chunk-M3NPTHSE.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.1.0";
+var version = "10.2.0";
 
 export {
   version

package/dist/cli/figure.js

@@ -6,7 +6,7 @@ import {
 } from "../chunks/chunk-BXEPA4KS.js";
 import {
   figureSvg
-} from "../chunks/chunk-CFPER2S2.js";
+} from "../chunks/chunk-EDR4CGCQ.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-RPDXZLCG.js";
 import "../chunks/chunk-WBCOREDZ.js";
@@ -26,7 +26,7 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "../chunks/chunk-FLUQODT2.js";
+} from "../chunks/chunk-DT2GGH4D.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
@@ -50,7 +50,7 @@ import {
 import "../chunks/chunk-Q7LYHGGQ.js";
 import "../chunks/chunk-WSIFAZU7.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-MZIOBJZB.js";
+import "../chunks/chunk-M3NPTHSE.js";
 import "../chunks/chunk-L5WF4ZPS.js";
 import "../chunks/chunk-R456ME6J.js";
 import "../chunks/chunk-ALDGONEI.js";

package/dist/cli/fold.js

@@ -4,7 +4,7 @@ import {
 } from "../chunks/chunk-B4YH42OP.js";
 import {
   foldVariants
-} from "../chunks/chunk-YPYWYPHX.js";
+} from "../chunks/chunk-AFP3NWSL.js";
 import {
   loadGraph
 } from "../chunks/chunk-XTCNEKO5.js";

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-CFPER2S2.js";
+} from "./chunks/chunk-EDR4CGCQ.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-RPDXZLCG.js";
 import "./chunks/chunk-WBCOREDZ.js";
@@ -14,7 +14,7 @@ import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-MZIOBJZB.js";
+import "./chunks/chunk-M3NPTHSE.js";
 import "./chunks/chunk-L5WF4ZPS.js";
 import "./chunks/chunk-R456ME6J.js";
 import "./chunks/chunk-ALDGONEI.js";

package/dist/figureData.js

@@ -1,8 +1,8 @@
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-VIERZJO2.js";
-import "./chunks/chunk-FLUQODT2.js";
+} from "./chunks/chunk-CPVZGVDL.js";
+import "./chunks/chunk-DT2GGH4D.js";
 import "./chunks/chunk-4R6QNG23.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-DK5P2YOL.js";
@@ -17,7 +17,7 @@ import "./chunks/chunk-FLFBYSJO.js";
 import "./chunks/chunk-Q7LYHGGQ.js";
 import "./chunks/chunk-WSIFAZU7.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-MZIOBJZB.js";
+import "./chunks/chunk-M3NPTHSE.js";
 import "./chunks/chunk-L5WF4ZPS.js";
 import "./chunks/chunk-R456ME6J.js";
 import "./chunks/chunk-ALDGONEI.js";

package/dist/foldVariants.js

@@ -1,6 +1,6 @@
 import {
   foldVariants
-} from "./chunks/chunk-YPYWYPHX.js";
+} from "./chunks/chunk-AFP3NWSL.js";
 import "./chunks/chunk-2CVHXFK7.js";
 import "./chunks/chunk-CPMHA4W5.js";
 import "./chunks/chunk-FYQWPEEY.js";

package/dist/index.js

@@ -87,7 +87,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-CFPER2S2.js";
+} from "./chunks/chunk-EDR4CGCQ.js";
 import {
   svgCanvas
 } from "./chunks/chunk-47DYCZOK.js";
@@ -168,11 +168,11 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-VIERZJO2.js";
+} from "./chunks/chunk-CPVZGVDL.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
-} from "./chunks/chunk-FLUQODT2.js";
+} from "./chunks/chunk-DT2GGH4D.js";
 import {
   FORCE_LAYOUT_LABEL,
   LAYOUT_MODES,
@@ -211,7 +211,7 @@ import {
 } from "./chunks/chunk-LOCJN3BZ.js";
 import {
   version
-} from "./chunks/chunk-MZIOBJZB.js";
+} from "./chunks/chunk-M3NPTHSE.js";
 import {
   axisScaleOf,
   contains,

package/dist/layoutEngines.js

@@ -3,7 +3,7 @@ import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind,
   layoutEngine
-} from "./chunks/chunk-FLUQODT2.js";
+} from "./chunks/chunk-DT2GGH4D.js";
 import "./chunks/chunk-7XHHVYG7.js";
 export {
   LAYOUT_ENGINES,

package/dist/types/layoutEngines.d.ts

@@ -6,7 +6,7 @@ export declare const LAYOUT_ENGINES: readonly [{
 }, {
     readonly value: "stress";
     readonly label: "Stress";
-    readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
+    readonly description: "Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference.";
 }];
 export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];
 export declare const LAYOUT_ENGINE_VALUES: ("fmmm" | "stress")[];

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "10.1.0";
+export declare const version = "10.2.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-MZIOBJZB.js";
+} from "./chunks/chunk-M3NPTHSE.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "10.1.0",
+  "version": "10.2.0",
   "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": {