@jbrowse/bandage-core 9.0.0 → 9.2.0

package/dist/index.js

@@ -1,42 +1,48 @@
 import {
   wheelZoomFactor
 } from "./chunks/chunk-TDQLINVI.js";
+import {
+  tubeMapNodeColors
+} from "./chunks/chunk-A4MYLGKG.js";
+import {
+  connectorAt,
+  drawLitConnector,
+  drawTubeMapConnectors,
+  tubeMapConnectors
+} from "./chunks/chunk-2ZT7ZF7A.js";
 import {
   drawTubeMap,
+  drawTubeMapHighlight,
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "./chunks/chunk-LLP3FXPM.js";
+} from "./chunks/chunk-75HR3756.js";
+import "./chunks/chunk-XXT2JCAC.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
 } from "./chunks/chunk-VZQ4FKLR.js";
-import {
-  drawTubeMapGenes,
-  tubeMapGenes
-} from "./chunks/chunk-WEDZ76AK.js";
-import "./chunks/chunk-XXT2JCAC.js";
-import {
-  tubeMapNodeColors
-} from "./chunks/chunk-FFFQNQUI.js";
 import {
   referenceKnots,
   warpX
 } from "./chunks/chunk-KQFOCDFY.js";
+import {
+  drawTubeMapGenes,
+  tubeMapGenes
+} from "./chunks/chunk-WEDZ76AK.js";
 import {
   drawTubeMapRuler,
   referenceBoxes,
   rulerBoxes,
   tubeX
 } from "./chunks/chunk-BPRXQ2SS.js";
-import {
-  connectorAt,
-  drawTubeMapConnectors,
-  tubeMapConnectors
-} from "./chunks/chunk-YOYLCLIG.js";
 import {
   createForceLayoutCache
-} from "./chunks/chunk-SKKYLBRA.js";
+} from "./chunks/chunk-BV64PQ2C.js";
+import {
+  graphBubbles,
+  superbubblesFromGraph
+} from "./chunks/chunk-ZDJDM77V.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -48,32 +54,40 @@ import {
 } from "./chunks/chunk-BXEPA4KS.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-ISEI2FH3.js";
-import {
-  bubblesFromGraph
-} from "./chunks/chunk-4S47XRYA.js";
+} from "./chunks/chunk-2AWUWGAD.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "./chunks/chunk-WOO7QYKB.js";
-import "./chunks/chunk-MFKORG3F.js";
+} from "./chunks/chunk-XKWD2RY3.js";
+import {
+  bubblesFromGraph
+} from "./chunks/chunk-GOZYKNQ2.js";
+import "./chunks/chunk-FX4RDMDN.js";
 import {
   REFERENCE_STRIP_ZONE_PX,
   drawReferenceStrip,
   referenceStripBlocks,
   stripBlockAt
-} from "./chunks/chunk-W253V6RR.js";
+} from "./chunks/chunk-CVYDR2OP.js";
+import {
+  LAYOUT_ENGINES,
+  layoutEngine
+} from "./chunks/chunk-6EJIU6IA.js";
+import {
+  stressLayout
+} from "./chunks/chunk-UNOE2NDN.js";
+import "./chunks/chunk-LYJ4US66.js";
 import {
   FORCE_LAYOUT_LABEL,
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-WNUZP3WQ.js";
+} from "./chunks/chunk-M7SRZJ32.js";
+import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-INJ2UVOT.js";
 import "./chunks/chunk-CWFNEKST.js";
-import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";
@@ -82,6 +96,9 @@ import "./chunks/chunk-HNQPEMYE.js";
 import {
   LAYOUT_QUALITIES
 } from "./chunks/chunk-K5SIJGAE.js";
+import {
+  loadBandage
+} from "./chunks/chunk-7XHHVYG7.js";
 import {
   HPRC_GBZ,
   cutGbzRegion,
@@ -100,26 +117,9 @@ import {
   edgeHoverText,
   regionLabel
 } from "./chunks/chunk-AZFVORTC.js";
-import {
-  LAYOUT_ENGINES,
-  layoutEngine
-} from "./chunks/chunk-6EJIU6IA.js";
-import {
-  stressLayout
-} from "./chunks/chunk-UNOE2NDN.js";
-import "./chunks/chunk-LYJ4US66.js";
-import {
-  loadBandage
-} from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-TLQ7F2ZT.js";
-import {
-  layoutGeometryInputs
-} from "./chunks/chunk-LOCJN3BZ.js";
-import {
-  svgCanvas
-} from "./chunks/chunk-47DYCZOK.js";
+} from "./chunks/chunk-HOOVOF2Y.js";
 import {
   WALK_STRIP_CEILING_PX,
   cutsWholeWalks,
@@ -131,7 +131,19 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-WDTXW7T2.js";
+} from "./chunks/chunk-UD5FOCI2.js";
+import {
+  Canvas2DRenderer
+} from "./chunks/chunk-WBCOREDZ.js";
+import {
+  getDpr
+} from "./chunks/chunk-4BYTEJGW.js";
+import {
+  layoutGeometryInputs
+} from "./chunks/chunk-LOCJN3BZ.js";
+import {
+  svgCanvas
+} from "./chunks/chunk-47DYCZOK.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -158,26 +170,28 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-MIW3HYPE.js";
-import {
-  Canvas2DRenderer
-} from "./chunks/chunk-2WNBVB55.js";
+} from "./chunks/chunk-GFRPX6M2.js";
 import {
-  getDpr
-} from "./chunks/chunk-4BYTEJGW.js";
+  genePins
+} from "./chunks/chunk-BUBZ32IC.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
 } from "./chunks/chunk-3S3YVOJ7.js";
 import {
-  genePins
-} from "./chunks/chunk-BUBZ32IC.js";
+  axisScaleOf,
+  contains,
+  padded,
+  screenToLayout,
+  viewportOf,
+  zoomAbout
+} from "./chunks/chunk-XKM5OHQQ.js";
 import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-MBB7ATM6.js";
+} from "./chunks/chunk-LFKMASER.js";
 import {
   WALK_FIELDS,
   WALK_SCHEMES,
@@ -185,7 +199,7 @@ import {
   encodingSwatchCss,
   resolveEncoding,
   schemeCss
-} from "./chunks/chunk-DPV2CUIE.js";
+} from "./chunks/chunk-XPT66H6H.js";
 import {
   rangeText,
   walkKey,
@@ -196,24 +210,16 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-6ZNQJ5ZD.js";
+} from "./chunks/chunk-OXTR3BVF.js";
 import {
   REFERENCE_RAMP_MAX_HUE,
   buildGeometry,
   computeReferenceRamp
-} from "./chunks/chunk-HBEKUQO4.js";
+} from "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-AMS3MAFP.js";
-import {
-  axisScaleOf,
-  contains,
-  padded,
-  screenToLayout,
-  viewportOf,
-  zoomAbout
-} from "./chunks/chunk-TL4B342F.js";
+} from "./chunks/chunk-FM6XRXPX.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -222,6 +228,11 @@ import {
   filterSamples,
   walkRows
 } from "./chunks/chunk-MAUEPAMG.js";
+import {
+  pathColorsLegible,
+  pathLegend,
+  walkLabelsOf
+} from "./chunks/chunk-7GBL7SJY.js";
 import {
   NODE_WIDTHS,
   maxNodeWidthPx,
@@ -229,11 +240,6 @@ import {
   nodeInk,
   nodeWidthPx
 } from "./chunks/chunk-PBENCR5L.js";
-import {
-  pathColorsLegible,
-  pathLegend,
-  walkLabelsOf
-} from "./chunks/chunk-7GBL7SJY.js";
 import {
   WELL_KNOWN_SAMPLES,
   assemblyWalk,
@@ -284,7 +290,7 @@ import {
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-6VBDMZBZ.js";
+} from "./chunks/chunk-BLRJ6IGK.js";
 import {
   ENGINE_DEFAULTS,
   FIT_PADDING,
@@ -297,16 +303,17 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
-import "./chunks/chunk-QYBZZI5H.js";
-import "./chunks/chunk-CDLPYR5O.js";
 import {
   graphFromTables,
   graphTablesGFA
 } from "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import {
@@ -315,7 +322,6 @@ import {
   panSNSample
 } from "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import {
   BUBBLE_SPREADS
 } from "./chunks/chunk-UVBGRJQX.js";
@@ -394,10 +400,12 @@ export {
   cutsWholeWalks,
   deletionDrawing,
   deletionEdges,
+  drawLitConnector,
   drawReferenceStrip,
   drawTubeMap,
   drawTubeMapConnectors,
   drawTubeMapGenes,
+  drawTubeMapHighlight,
   drawTubeMapRuler,
   drawingBounds,
   edgeHoverText,
@@ -430,6 +438,7 @@ export {
   genesOnRow,
   getDpr,
   graphBackbone,
+  graphBubbles,
   graphFromTables,
   graphTablesGFA,
   haplotypeWanted,
@@ -485,6 +494,7 @@ export {
   stripGeneGaps,
   stripMarks,
   stripRowAt,
+  superbubblesFromGraph,
   svgCanvas,
   tubeMapConnectors,
   tubeMapFrame,

package/dist/layout/forceCache.js

@@ -1,18 +1,18 @@
 import {
   createForceLayoutCache
-} from "../chunks/chunk-SKKYLBRA.js";
-import "../chunks/chunk-5OIVTEF7.js";
+} from "../chunks/chunk-BV64PQ2C.js";
+import "../chunks/chunk-ZGRYFUXE.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-OCMBULGN.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-UVBGRJQX.js";
 import "../chunks/chunk-6JEWNXCQ.js";
 import "../chunks/chunk-N6FECAXP.js";

package/dist/layout/trimToWindow.js

@@ -94,6 +94,19 @@ function trimVisits(visits, paths, spans, nameOf) {
   });
   return out;
 }
+function clipToWindow(graph, window, reachBp) {
+  const nodes = graph.nodes.map((node) => {
+    if (!isBackbone(node)) {
+      return node;
+    }
+    const from = node.stable.start;
+    const to = from + node.length;
+    const [start, end] = overlapsWindow(node, window) ? [Math.max(from, window.start), Math.min(to, window.end)] : to <= window.start ? [Math.max(from, to - reachBp), to] : [from, Math.min(to, from + reachBp)];
+    return start === from && end === to ? node : { ...node, length: end - start, stable: { ...node.stable, start } };
+  });
+  return nodes.some((node, i) => node !== graph.nodes[i]) ? { ...graph, nodes } : graph;
+}
 export {
+  clipToWindow,
   trimToWindow
 };

package/dist/layout/walkRowDraw.js

@@ -26,12 +26,12 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-MIW3HYPE.js";
-import "../chunks/chunk-6ZNQJ5ZD.js";
-import "../chunks/chunk-HBEKUQO4.js";
+} from "../chunks/chunk-GFRPX6M2.js";
+import "../chunks/chunk-OXTR3BVF.js";
+import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";

package/dist/layout/walkStrip.js

@@ -9,15 +9,15 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-WDTXW7T2.js";
+} from "../chunks/chunk-UD5FOCI2.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-MIW3HYPE.js";
-import "../chunks/chunk-6ZNQJ5ZD.js";
-import "../chunks/chunk-HBEKUQO4.js";
+} from "../chunks/chunk-GFRPX6M2.js";
+import "../chunks/chunk-OXTR3BVF.js";
+import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";

package/dist/layoutModes.js

@@ -4,10 +4,10 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-WNUZP3WQ.js";
+} from "./chunks/chunk-M7SRZJ32.js";
+import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-INJ2UVOT.js";
 import "./chunks/chunk-CWFNEKST.js";
-import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
 import "./chunks/chunk-C44YRP5F.js";

package/dist/pipeline.js

@@ -11,18 +11,18 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/referenceRampCss.js

@@ -4,11 +4,11 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-6ZNQJ5ZD.js";
-import "./chunks/chunk-HBEKUQO4.js";
+} from "./chunks/chunk-OXTR3BVF.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/dist/referenceStrip.js

@@ -7,11 +7,11 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-W253V6RR.js";
-import "./chunks/chunk-HBEKUQO4.js";
+} from "./chunks/chunk-CVYDR2OP.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-WFB5TXRA.js";
 import "./chunks/chunk-3ZZSX5HN.js";
 import "./chunks/chunk-AB35TJST.js";

package/dist/renderer/Canvas2DRenderer.js

@@ -1,7 +1,7 @@
 import {
   Canvas2DRenderer,
   arrowheadOutline
-} from "../chunks/chunk-2WNBVB55.js";
+} from "../chunks/chunk-WBCOREDZ.js";
 import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-G2FD7S3C.js";
 export {

package/dist/renderer/GeometryBuilder.js

@@ -11,10 +11,10 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-HBEKUQO4.js";
+} from "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";

package/dist/renderer/recordingCanvas.js

@@ -4,6 +4,7 @@ function recordingCanvas() {
   const fills = [];
   const lineWidths = [];
   const points = [];
+  let clears = 0;
   const at = (x, y) => {
     points.push({ x, y });
   };
@@ -27,6 +28,9 @@ function recordingCanvas() {
     },
     fillRect: () => {
     },
+    clearRect: () => {
+      clears++;
+    },
     stroke: () => {
       strokes.push(ctx.strokeStyle);
       lineWidths.push(ctx.lineWidth);
@@ -37,7 +41,14 @@ function recordingCanvas() {
   };
   const canvas = document.createElement("canvas");
   canvas.getContext = () => ctx;
-  return { canvas, strokes, fills, lineWidths, points };
+  return {
+    canvas,
+    strokes,
+    fills,
+    lineWidths,
+    points,
+    clears: () => clears
+  };
 }
 export {
   recordingCanvas

package/dist/tubeMap/connectors.js

@@ -1,10 +1,12 @@
 import {
   connectorAt,
+  drawLitConnector,
   drawTubeMapConnectors,
   tubeMapConnectors
-} from "../chunks/chunk-YOYLCLIG.js";
+} from "../chunks/chunk-2ZT7ZF7A.js";
 export {
   connectorAt,
+  drawLitConnector,
   drawTubeMapConnectors,
   tubeMapConnectors
 };

package/dist/tubeMap/draw.js

@@ -1,5 +1,6 @@
 import {
   drawTubeMap,
+  drawTubeMapHighlight,
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,
@@ -7,12 +8,13 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-LLP3FXPM.js";
+} from "../chunks/chunk-75HR3756.js";
 import "../chunks/chunk-XXT2JCAC.js";
 import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   drawTubeMap,
+  drawTubeMapHighlight,
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,

package/dist/tubeMap/nodeColors.js

@@ -1,10 +1,10 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-FFFQNQUI.js";
-import "../chunks/chunk-HBEKUQO4.js";
+} from "../chunks/chunk-A4MYLGKG.js";
+import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-WFB5TXRA.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";

package/dist/types/bubbles/bubbleHalos.d.ts

@@ -17,4 +17,6 @@ export interface RouteLabel {
     at: NodeSegment;
     text: string;
 }
+export declare const WHOLE_FRACTION = 0.9;
+export declare function coversGraph(members: number, nodes: number): boolean;
 export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, walkLabel?: (name: string) => string, repeats?: readonly RepeatSpan[]): BubbleHalo[];

package/dist/types/bubbles/bubbleLine.d.ts

@@ -12,6 +12,8 @@ export interface MinigraphBubble {
     longestAllele: string | undefined;
     partial?: boolean;
     routes?: BubbleRoute[];
+    key?: string;
+    offReference?: true;
 }
 export interface BubbleRoute {
     steps: string[];
@@ -20,6 +22,7 @@ export interface BubbleRoute {
 }
 export declare function parseBubbleLine(line: string): MinigraphBubble;
 export declare function sameBubble(a: MinigraphBubble, b: MinigraphBubble): boolean;
+export declare function bubbleKey(b: MinigraphBubble): string;
 export declare function bubbleLabel(bubble: MinigraphBubble): string;
 export declare const SATURATED_PATH_COUNT = 2147483647;
 export declare function bubbleDescription(bubble: MinigraphBubble): string;

package/dist/types/bubbles/bubblesFromGraph.d.ts

@@ -1,3 +1,13 @@
-import type { MinigraphBubble } from './bubbleLine.js';
-import type { Graph } from '../types.js';
+import type { BubbleRoute, MinigraphBubble } from './bubbleLine.js';
+import type { Graph, GraphNode } from '../types.js';
+export interface Routes {
+    min: number;
+    max: number;
+    n: number;
+}
 export declare function bubblesFromGraph(graph: Graph): MinigraphBubble[];
+export declare function walkIndexOf(graph: Graph): Map<string, number>[] | undefined;
+export declare function walkRoutes(graph: Graph, byId: Map<string, GraphNode>, walkIndex: Map<string, number>[], startId: string, endId: string): (Routes & {
+    left: number;
+    routes: BubbleRoute[];
+}) | undefined;

package/dist/types/bubbles/superbubbles.d.ts

@@ -0,0 +1,5 @@
+import type { MinigraphBubble } from './bubbleLine.js';
+import type { Graph } from '../types.js';
+export declare const MAX_SUPERBUBBLES = 50;
+export declare function superbubblesFromGraph(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];
+export declare function graphBubbles(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];

package/dist/types/cli/fold.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/types/foldVariants.d.ts

@@ -0,0 +1,2 @@
+import type { Graph } from './types.js';
+export declare function foldVariants(graph: Graph, belowBp: number): Graph;

package/dist/types/gfa/writeRgfa.d.ts

@@ -0,0 +1,2 @@
+import type { Graph } from '../types.js';
+export declare function writeRgfa(graph: Graph): string;