@jbrowse/bandage-core 8.1.0 → 8.2.0

package/dist/chunks/{chunk-MP7LXLWV.js → chunk-3C5UXR2U.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-SZNZ2T6D.js";
+} from "./chunk-MAUEPAMG.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-T4SQ5QGM.js → chunk-3FXPFVKJ.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "8.1.0";
+var version = "8.2.0";
 
 export {
   version

package/dist/chunks/{chunk-3PYY7OIP.js → chunk-CF62U3QS.js}

@@ -14,7 +14,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-DYYIHN3P.js → chunk-DE4UFDUZ.js}

@@ -8,12 +8,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-O2ANJQVH.js";
+} from "./chunk-WDTXW7T2.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-V3MD3IZB.js";
+} from "./chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
 } from "./chunk-2WNBVB55.js";
@@ -42,14 +42,14 @@ import {
 } from "./chunk-HBEKUQO4.js";
 import {
   version
-} from "./chunk-T4SQ5QGM.js";
+} from "./chunk-3FXPFVKJ.js";
 import {
   axisScaleOf
 } from "./chunk-TL4B342F.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-MP7LXLWV.js";
+} from "./chunk-3C5UXR2U.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";

package/dist/chunks/{chunk-SZNZ2T6D.js → chunk-MAUEPAMG.js}

@@ -53,12 +53,16 @@ function sliceBetween(steps, span, region, flanked = true) {
   if (!region || !flanked) {
     return { ids: steps, complete: true, from: -1, to: -1 };
   }
+  const spanAt = (i) => {
+    const id = steps[i];
+    return typeof id === "string" ? span.get(id) : void 0;
+  };
   let i0 = -1;
   let i1 = -1;
   let bestEnd = -Infinity;
   let bestStart = Infinity;
-  steps.forEach((id, i) => {
-    const s = typeof id === "string" ? span.get(id) : void 0;
+  steps.forEach((_, i) => {
+    const s = spanAt(i);
     if (s) {
       if (s.end <= region.start && s.end > bestEnd) {
         bestEnd = s.end;
@@ -70,15 +74,38 @@ function sliceBetween(steps, span, region, flanked = true) {
       }
     }
   });
-  if (i0 < 0 || i1 < 0) {
+  if (i0 >= 0 && i1 >= 0) {
+    const ids2 = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
+    return {
+      ids: i0 < i1 ? ids2 : ids2.reverse(),
+      complete: true,
+      from: i0,
+      to: i1
+    };
+  }
+  const flank = i0 >= 0 ? i0 : i1;
+  let near = -1;
+  for (let d = 1; flank >= 0 && near < 0 && d < steps.length; d++) {
+    near = [flank - d, flank + d].find((j) => spanAt(j) !== void 0) ?? -1;
+  }
+  if (near < 0) {
     return { ids: steps, complete: false, from: -1, to: -1 };
   }
-  const ids = steps.slice(Math.min(i0, i1) + 1, Math.max(i0, i1));
+  const forward = near > flank === spanAt(near).start > spanAt(flank).start;
+  const after = forward === (flank === i0);
+  const ids = after ? steps.slice(flank + 1) : steps.slice(0, flank).reverse();
+  const last = ids.length > 0 ? ids.length - 1 : -1;
+  const end = last < 0 ? spanAt(flank) : spanAt(after ? flank + 1 + last : 0);
+  const stop = {
+    contigEnds: end !== void 0,
+    shortBp: !end ? 0 : Math.max(0, region.start - end.end, end.start - region.end)
+  };
   return {
-    ids: i0 < i1 ? ids : ids.reverse(),
-    complete: true,
-    from: i0,
-    to: i1
+    ids,
+    complete: false,
+    from: flank,
+    to: after ? steps.length : -1,
+    stop
   };
 }
 function filterSamples(rows, samples) {
@@ -117,7 +144,7 @@ function walkRows(graph, region, unit) {
   const rowOf = (pieces) => {
     const path = pieces[0];
     const ordered = [...pieces].sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
-    const { ids, complete, from, to } = sliceBetween(
+    const { ids, complete, from, to, stop } = sliceBetween(
       stepsOf(ordered, lengthOf),
       span,
       cut,
@@ -177,6 +204,7 @@ function walkRows(graph, region, unit) {
       offReferenceBp,
       gapBp,
       complete,
+      stop,
       runs,
       axis
     };

package/dist/chunks/{chunk-V3MD3IZB.js → chunk-MIW3HYPE.js}

@@ -34,15 +34,24 @@ function units(bp, unit) {
   return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
 }
 function walkRowReadout(row, reference, unit, call) {
-  const { bp, gapBp, complete } = row;
+  const { bp, gapBp, complete, stop } = row;
   if (!reference) {
     return `${kb(bp)}${units(bp, unit)}`;
   }
-  const delta = bp - reference.bp;
-  const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
   const outside = gapBp > 0 ? ` \xB7 ${kb(gapBp)} outside the cut` : "";
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
-  return `${kb(bp)}${units(bp, unit)}${against}${outside}${complete ? "" : " \xB7 partial walk"}${called}`;
+  if (complete) {
+    const delta = bp - reference.bp;
+    const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
+    return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;
+  }
+  const region = unit ? "repeat" : "window";
+  if (stop?.contigEnds && bp === 0) {
+    const where = stop.shortBp > 0 ? `${kb(stop.shortBp)} before` : "at";
+    return `contig ends ${where} the ${region}${called}`;
+  }
+  const why = !stop ? "partial walk" : stop.contigEnds ? `contig ends inside the ${region}` : "does not rejoin the reference within the cut";
+  return `\u2265 ${kb(bp)}${units(bp, unit)} \xB7 ${why}${outside}${called}`;
 }
 function readoutPlacement(text, endX, width) {
   const x = endX + 6;

package/dist/chunks/{chunk-O2ANJQVH.js → chunk-WDTXW7T2.js}

@@ -2,7 +2,7 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-V3MD3IZB.js";
+} from "./chunk-MIW3HYPE.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/cli/figure.js

@@ -7,7 +7,7 @@ import {
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-3PYY7OIP.js";
+} from "../chunks/chunk-CF62U3QS.js";
 import "../chunks/chunk-W2I4DOL4.js";
 import "../chunks/chunk-TEDQJPMI.js";
 import "../chunks/chunk-LOEA5IHZ.js";
@@ -35,14 +35,14 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-DYYIHN3P.js";
+} from "../chunks/chunk-DE4UFDUZ.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-O2ANJQVH.js";
+import "../chunks/chunk-WDTXW7T2.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-2WNBVB55.js";
 import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-3S3YVOJ7.js";
@@ -53,13 +53,13 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-T4SQ5QGM.js";
+import "../chunks/chunk-3FXPFVKJ.js";
 import "../chunks/chunk-TL4B342F.js";
-import "../chunks/chunk-MP7LXLWV.js";
+import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import {

package/dist/figure.js

@@ -1,10 +1,10 @@
 import {
   figureSvg
-} from "./chunks/chunk-DYYIHN3P.js";
+} from "./chunks/chunk-DE4UFDUZ.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-O2ANJQVH.js";
-import "./chunks/chunk-V3MD3IZB.js";
+import "./chunks/chunk-WDTXW7T2.js";
+import "./chunks/chunk-MIW3HYPE.js";
 import "./chunks/chunk-2WNBVB55.js";
 import "./chunks/chunk-4BYTEJGW.js";
 import "./chunks/chunk-3S3YVOJ7.js";
@@ -15,10 +15,10 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-6ZNQJ5ZD.js";
 import "./chunks/chunk-HBEKUQO4.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-T4SQ5QGM.js";
+import "./chunks/chunk-3FXPFVKJ.js";
 import "./chunks/chunk-TL4B342F.js";
-import "./chunks/chunk-MP7LXLWV.js";
-import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-3C5UXR2U.js";
+import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-RAKOB6IV.js";

package/dist/index.js

@@ -69,7 +69,7 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-3PYY7OIP.js";
+} from "./chunks/chunk-CF62U3QS.js";
 import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.js";
 import "./chunks/chunk-LOEA5IHZ.js";
@@ -112,7 +112,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-DYYIHN3P.js";
+} from "./chunks/chunk-DE4UFDUZ.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -130,7 +130,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-O2ANJQVH.js";
+} from "./chunks/chunk-WDTXW7T2.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -157,7 +157,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-V3MD3IZB.js";
+} from "./chunks/chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
 } from "./chunks/chunk-2WNBVB55.js";
@@ -204,7 +204,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-T4SQ5QGM.js";
+} from "./chunks/chunk-3FXPFVKJ.js";
 import {
   axisScaleOf,
   contains,
@@ -216,11 +216,11 @@ import {
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunks/chunk-MP7LXLWV.js";
+} from "./chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
-} from "./chunks/chunk-SZNZ2T6D.js";
+} from "./chunks/chunk-MAUEPAMG.js";
 import {
   NODE_WIDTHS,
   maxNodeWidthPx,

package/dist/layout/walkRowDraw.js

@@ -26,7 +26,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";

package/dist/layout/walkRowLayout.js

@@ -2,8 +2,8 @@ import {
   walkRowLabels,
   walkRowLayout,
   walkRowsExtent
-} from "../chunks/chunk-MP7LXLWV.js";
-import "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-3C5UXR2U.js";
+import "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/layout/walkRows.js

@@ -1,7 +1,7 @@
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-SZNZ2T6D.js";
+} from "../chunks/chunk-MAUEPAMG.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";

package/dist/layout/walkStrip.js

@@ -9,10 +9,10 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-O2ANJQVH.js";
+} from "../chunks/chunk-WDTXW7T2.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-V3MD3IZB.js";
+} from "../chunks/chunk-MIW3HYPE.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";

package/dist/layoutModes.js

@@ -4,7 +4,7 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-3PYY7OIP.js";
+} from "./chunks/chunk-CF62U3QS.js";
 import "./chunks/chunk-W2I4DOL4.js";
 import "./chunks/chunk-TEDQJPMI.js";
 import "./chunks/chunk-LOEA5IHZ.js";
@@ -13,8 +13,8 @@ import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-RVS2QCOX.js";
 import "./chunks/chunk-HNQPEMYE.js";
-import "./chunks/chunk-MP7LXLWV.js";
-import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-3C5UXR2U.js";
+import "./chunks/chunk-MAUEPAMG.js";
 import "./chunks/chunk-7GBL7SJY.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/dist/types/index.d.ts

@@ -68,7 +68,7 @@ export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble
 export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
 export { filterSamples, walkRows } from './layout/walkRows.js';
-export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
+export type { WalkAxis, WalkRow, WalkRows, WalkRun, WalkStop, } from './layout/walkRows.js';
 export { BAR_PX as WALK_BAR_PX, CALL_TICK as WALK_CALL_TICK, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, UNBACKED_TICK as WALK_UNBACKED_TICK, alongRow, callTickInk, coalesceRuns, genesOnRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowPitch, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
 export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, RowPitch, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
 export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';

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

@@ -14,7 +14,7 @@ export interface ReadoutCall {
     spanningReads?: number;
     agrees?: boolean;
 }
-export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
+export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'>, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
 export declare function readoutPlacement(text: string, endX: number, width: number): {
     x: number;
     anchor: "start";

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

@@ -12,6 +12,10 @@ export interface WalkAxis {
     start: number;
     reversed: boolean;
 }
+export interface WalkStop {
+    contigEnds: boolean;
+    shortBp: number;
+}
 export interface WalkRow {
     name: string;
     label: string;
@@ -21,6 +25,7 @@ export interface WalkRow {
     offReferenceBp: number;
     gapBp: number;
     complete: boolean;
+    stop?: WalkStop;
     runs: WalkRun[];
     axis?: WalkAxis;
 }

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "8.1.0";
+export declare const version = "8.2.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-T4SQ5QGM.js";
+} from "./chunks/chunk-3FXPFVKJ.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "8.1.0",
+  "version": "8.2.0",
   "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": {