@jbrowse/bandage-core 4.0.29 → 4.0.30

package/dist/chunks/{chunk-QN464POI.js → chunk-P7UDDVHK.js}

@@ -1946,16 +1946,32 @@ function sampleOf(path) {
 function labelOf(path) {
   return path.haplotype !== void 0 && path.sample !== void 0 ? `${path.sample}#${path.haplotype}` : sampleOf(path);
 }
-function sliceBetween(nodeIds, span, region, flanked = true) {
+function stepsOf(pieces, lengthOf) {
+  const steps = [];
+  let end;
+  for (const piece of pieces) {
+    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {
+      steps.push(piece.start - end);
+    }
+    steps.push(...piece.nodeIds);
+    const bp = piece.nodeIds.reduce(
+      (sum, id) => sum + (lengthOf.get(id) ?? 0),
+      0
+    );
+    end = piece.start === void 0 ? void 0 : piece.start + bp;
+  }
+  return steps;
+}
+function sliceBetween(steps, span, region, flanked = true) {
   if (!region || !flanked) {
-    return { ids: nodeIds, complete: true };
+    return { ids: steps, complete: true };
   }
   let i0 = -1;
   let i1 = -1;
   let bestEnd = -Infinity;
   let bestStart = Infinity;
-  nodeIds.forEach((id, i) => {
-    const s = span.get(id);
+  steps.forEach((id, i) => {
+    const s = typeof id === "string" ? span.get(id) : void 0;
     if (s) {
       if (s.end <= region.start && s.end > bestEnd) {
         bestEnd = s.end;
@@ -1968,9 +1984,9 @@ function sliceBetween(nodeIds, span, region, flanked = true) {
     }
   });
   if (i0 < 0 || i1 < 0) {
-    return { ids: nodeIds, complete: false };
+    return { ids: steps, complete: false };
   }
-  const ids = nodeIds.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
+  const ids = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
   return { ids: i0 < i1 ? ids : ids.reverse(), complete: true };
 }
 function walkRows(graph, region, unit) {
@@ -1982,6 +1998,10 @@ function walkRows(graph, region, unit) {
   if (!first || others.length === 0) {
     return void 0;
   }
+  const walks = /* @__PURE__ */ new Map();
+  for (const path of others) {
+    walks.set(path.name, [...walks.get(path.name) ?? [], path]);
+  }
   const lengthOf = new Map(graph.nodes.map((n2) => [n2.id, n2.length]));
   const referenceStart = first.start ?? 0;
   const cut = region && region.end > region.start ? region : void 0;
@@ -1997,20 +2017,35 @@ function walkRows(graph, region, unit) {
     }
   }
   const flanked = cut === void 0 || [...span.values()].some((s) => s.end <= cut.start) && [...span.values()].some((s) => s.start >= cut.end);
-  const rowOf = (path) => {
-    const { ids, complete } = sliceBetween(path.nodeIds, span, cut, flanked);
+  const rowOf = (pieces) => {
+    const path = pieces[0];
+    const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
+    const { ids, complete } = sliceBetween(
+      stepsOf(ordered, lengthOf),
+      span,
+      cut,
+      flanked
+    );
     const runs = [];
     let bp = 0;
     let offReferenceBp = 0;
+    let gapBp = 0;
     let step = 0;
     for (const id of ids) {
+      if (typeof id === "number") {
+        runs.push({ start: bp, bp: id, onReference: false, gap: true });
+        bp += id;
+        gapBp += id;
+        step = 0;
+        continue;
+      }
       const len = lengthOf.get(id) ?? 0;
       const s = span.get(id);
       const last = runs.at(-1);
       const at = last?.referenceStart;
       const forward = s && at !== void 0 && step >= 0 && at + last.bp === s.start;
       const backward = s && at !== void 0 && step <= 0 && s.end === at;
-      if (!s && last && !last.onReference) {
+      if (!s && last && !last.onReference && !last.gap) {
         last.bp += len;
       } else if (forward || backward) {
         last.bp += len;
@@ -2040,6 +2075,7 @@ function walkRows(graph, region, unit) {
       haplotype: path.haplotype,
       bp,
       offReferenceBp,
+      gapBp,
       complete,
       runs
     };
@@ -2048,11 +2084,8 @@ function walkRows(graph, region, unit) {
   return {
     origin,
     unit,
-    reference: rowOf({
-      ...first,
-      nodeIds: referencePieces2.flatMap((piece) => piece.nodeIds)
-    }),
-    rows: others.map(rowOf).sort(
+    reference: rowOf(referencePieces2),
+    rows: [...walks.values()].map(rowOf).sort(
       (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)
     )
   };
@@ -4349,8 +4382,11 @@ function walkKey(walk, reference) {
   const { field } = walk.encoding;
   const own = walk.range ? rangeText(walk.range.contig, walk.range.start, walk.range.end) : void 0;
   const scale = field === "progress" ? own : field === "reference" && reference ? rangeText(reference.name, reference.start, reference.end) : void 0;
+  const spanned = walk.range ? walk.range.end - walk.range.start : walk.bp;
+  const outside = spanned - walk.bp;
   return {
-    delta: walk.referenceBp === void 0 || walk.bp === walk.referenceBp ? "" : ` ${walk.bp > walk.referenceBp ? "+" : "\u2212"}${formatBp(Math.abs(walk.bp - walk.referenceBp))}`,
+    delta: walk.referenceBp === void 0 || spanned === walk.referenceBp ? "" : ` ${spanned > walk.referenceBp ? "+" : "\u2212"}${formatBp(Math.abs(spanned - walk.referenceBp))}`,
+    outside: outside > 0 ? `, ${formatBp(outside)} outside the cut` : "",
     reversed: walk.reversedBp > 0 ? `, ${formatBp(walk.reversedBp)} reversed` : "",
     shades: field !== "walk",
     scale,
@@ -4788,7 +4824,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.0.29";
+var version = "4.0.30";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -4866,7 +4902,7 @@ function walkKeySvg(id, x, y, walk, label, reference) {
     y,
     encodingStops(walk.encoding),
     label,
-    key.delta + key.reversed,
+    key.delta + key.outside + key.reversed,
     key.scale
   );
 }
@@ -5402,7 +5438,7 @@ function parseWalk(line) {
     end: +fields[5]
   };
 }
-var stepsOf = (walk) => walk.fields[6].match(/[<>][^<>]+/g) ?? [];
+var stepsOf2 = (walk) => walk.fields[6].match(/[<>][^<>]+/g) ?? [];
 function segmentLengths(lines) {
   const lengths = /* @__PURE__ */ new Map();
   for (const line of lines) {
@@ -5421,7 +5457,7 @@ function extend(a, b, lengths) {
   if (b.end <= a.end) {
     return a;
   }
-  const steps = stepsOf(b);
+  const steps = stepsOf2(b);
   let pos = b.start;
   for (const [i, step] of steps.entries()) {
     if (pos === a.end) {
@@ -5455,7 +5491,7 @@ function joinPieces(pieces, lengths, startsPath) {
 }
 var flip2 = (sign) => sign === "+" ? "-" : "+";
 function* stepLinks(walk) {
-  const steps = stepsOf(walk).map((step) => ({
+  const steps = stepsOf2(walk).map((step) => ({
     id: step.slice(1),
     sign: step.startsWith(">") ? "+" : "-"
   }));

package/dist/cli/figure.js

@@ -17,7 +17,7 @@ import {
   openGbz,
   parseRegion,
   refNameBinding
-} from "../chunks/chunk-QN464POI.js";
+} from "../chunks/chunk-P7UDDVHK.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";

package/dist/index.js

@@ -101,7 +101,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-QN464POI.js";
+} from "./chunks/chunk-P7UDDVHK.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";

package/dist/types/layout/walkRows.d.ts

@@ -5,6 +5,7 @@ export interface WalkRun {
     onReference: boolean;
     referenceStart?: number;
     reversed?: true;
+    gap?: true;
 }
 export interface WalkRow {
     name: string;
@@ -13,6 +14,7 @@ export interface WalkRow {
     haplotype?: number;
     bp: number;
     offReferenceBp: number;
+    gapBp: number;
     complete: boolean;
     runs: WalkRun[];
 }

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.0.29";
+export declare const version = "4.0.30";

package/dist/types/walkKey.d.ts

@@ -6,6 +6,7 @@ export declare function walkKey(walk: LiftedWalk, reference?: {
     end: number;
 }): {
     delta: string;
+    outside: string;
     reversed: string;
     shades: boolean;
     scale: string | undefined;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.29",
+  "version": "4.0.30",
   "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": {
@@ -31,7 +31,7 @@
     "dist"
   ],
   "dependencies": {
-    "@gmod/gbz-base": "^4.1.0",
+    "@gmod/gbz-base": "^5.0.0",
     "@gmod/tabix": "^3.9.0",
     "@gmod/tubemap-core": "^0.1.0",
     "@jbrowse/core": "5.0.0-beta.9",