@jbrowse/bandage-core 11.1.0 → 11.3.0

package/dist/index.js

@@ -1,6 +1,12 @@
 import {
   wheelZoomFactor
 } from "./chunks/chunk-TDQLINVI.js";
+import {
+  tubeMapNodeColors
+} from "./chunks/chunk-XVS52NMZ.js";
+import {
+  bundleRoutes
+} from "./chunks/chunk-TJOOHTJ6.js";
 import {
   connectorAt,
   drawLitConnector,
@@ -13,7 +19,8 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "./chunks/chunk-ZUL52ZX2.js";
+} from "./chunks/chunk-3HGYGISG.js";
+import "./chunks/chunk-BX4AUMZE.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
@@ -26,10 +33,6 @@ import {
   drawTubeMapGenes,
   tubeMapGenes
 } from "./chunks/chunk-6EOB6ANX.js";
-import "./chunks/chunk-BX4AUMZE.js";
-import {
-  tubeMapNodeColors
-} from "./chunks/chunk-XVS52NMZ.js";
 import {
   drawTubeMapRuler,
   referenceBoxes,
@@ -37,11 +40,14 @@ import {
   tubeX
 } from "./chunks/chunk-HSVFCA2J.js";
 import {
-  bundleRoutes
-} from "./chunks/chunk-RETNT73O.js";
+  ribbonJoin,
+  sharedRowOrder,
+  walkRowBlocks,
+  walkRowLinks
+} from "./chunks/chunk-UFUSPK2A.js";
 import {
   createForceLayoutCache
-} from "./chunks/chunk-RNYPCQZ3.js";
+} from "./chunks/chunk-BXLLMWC3.js";
 import {
   graphBubbles,
   superbubblesFromGraph
@@ -86,7 +92,13 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-JFHYG25O.js";
+} from "./chunks/chunk-RNNYRNDU.js";
+import {
+  Canvas2DRenderer
+} from "./chunks/chunk-EJRJAAN7.js";
+import {
+  getDpr
+} from "./chunks/chunk-RBCE2OQH.js";
 import {
   svgCanvas
 } from "./chunks/chunk-V4YML3GR.js";
@@ -101,7 +113,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-IZ6Y5D23.js";
+} from "./chunks/chunk-PNM6Z3IE.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -130,12 +142,6 @@ import {
   walkRowsKeyTree,
   walkRowsTree
 } from "./chunks/chunk-XZ6PQBU6.js";
-import {
-  Canvas2DRenderer
-} from "./chunks/chunk-EJRJAAN7.js";
-import {
-  getDpr
-} from "./chunks/chunk-RBCE2OQH.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -159,7 +165,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-OI4YVAMM.js";
+} from "./chunks/chunk-SLDCKMIP.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -169,8 +175,8 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-NGUM77EP.js";
-import "./chunks/chunk-LMH5KVJZ.js";
+} from "./chunks/chunk-TEXAKEJX.js";
+import "./chunks/chunk-3LZ334X4.js";
 import "./chunks/chunk-A7H753BA.js";
 import "./chunks/chunk-GJU6BJJA.js";
 import "./chunks/chunk-GJLZ2MKE.js";
@@ -199,7 +205,7 @@ import {
 } from "./chunks/chunk-77EGQQJU.js";
 import {
   version
-} from "./chunks/chunk-Y3FDMDNT.js";
+} from "./chunks/chunk-XEWPWCML.js";
 import {
   axisScaleOf,
   contains,
@@ -207,8 +213,8 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-AI5PTOSV.js";
-import "./chunks/chunk-IVOK5V3H.js";
+} from "./chunks/chunk-CE6ZIKJX.js";
+import "./chunks/chunk-T35BSLW5.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -245,12 +251,18 @@ import {
 import "./chunks/chunk-WA5WNP6V.js";
 import {
   walkRowLabels,
+  walkRowLayoutOf,
   walkRowsExtent
-} from "./chunks/chunk-YHJ5JLBI.js";
+} from "./chunks/chunk-TZLEHZVC.js";
 import {
   filterSamples,
   walkRows
-} from "./chunks/chunk-DEDD7TFJ.js";
+} from "./chunks/chunk-JDZ5GTZT.js";
+import {
+  runAt,
+  walkRowRuns,
+  walkRowsOf
+} from "./chunks/chunk-M75QPZNJ.js";
 import {
   pathColorsLegible,
   pathLegend,
@@ -266,7 +278,7 @@ import {
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-W6EXQDV5.js";
+} from "./chunks/chunk-EFD753MS.js";
 import {
   ENGINE_DEFAULTS,
   FIT_PADDING,
@@ -279,7 +291,7 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-KDU4EF66.js";
+} from "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -290,7 +302,7 @@ import "./chunks/chunk-5I3K4R2G.js";
 import {
   graphFromTables,
   graphTablesGFA
-} from "./chunks/chunk-3XSRT7RQ.js";
+} from "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import {
@@ -527,15 +539,18 @@ export {
   resolveColorScheme,
   resolveEncoding,
   resolveReferenceSample,
+  ribbonJoin,
   rowGeneBoxes,
   rowPitch,
   rowSpan,
   rulerBoxes,
+  runAt,
   runPaint,
   schemeCss,
   screenToLayout,
   segmentAt,
   serializeEl,
+  sharedRowOrder,
   stopTag,
   stressLayout,
   stripBlockAt,
@@ -562,12 +577,17 @@ export {
   walkLift,
   walkMarksTree,
   walkPosition,
+  walkRowBlocks,
   walkRowLabels,
+  walkRowLayoutOf,
+  walkRowLinks,
   walkRowReadout,
+  walkRowRuns,
   walkRows,
   walkRowsExtent,
   walkRowsKey,
   walkRowsKeyTree,
+  walkRowsOf,
   walkRowsTree,
   walkStripApplies,
   walkStripFrame,

package/dist/layout/forceCache.js

@@ -1,7 +1,7 @@
 import {
   createForceLayoutCache
-} from "../chunks/chunk-RNYPCQZ3.js";
-import "../chunks/chunk-KDU4EF66.js";
+} from "../chunks/chunk-BXLLMWC3.js";
+import "../chunks/chunk-REOWLPH4.js";
 import "../chunks/chunk-3PZSBNLI.js";
 import "../chunks/chunk-CKUVEHSS.js";
 import "../chunks/chunk-OPPVSPEF.js";
@@ -9,7 +9,7 @@ import "../chunks/chunk-VPE4AYP7.js";
 import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-3XSRT7RQ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-DZR37KXT.js";

package/dist/layout/tubeMapLayout.js

@@ -5,11 +5,13 @@ import {
   tubeMapLayout,
   tubeMapReferenceLayout,
   tubeMapTracks
-} from "../chunks/chunk-LMH5KVJZ.js";
+} from "../chunks/chunk-3LZ334X4.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/layout/walkRowLayout.js

@@ -3,9 +3,12 @@ import {
   longestBar,
   walkRowLabels,
   walkRowLayout,
+  walkRowLayoutOf,
   walkRowsExtent
-} from "../chunks/chunk-YHJ5JLBI.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+} from "../chunks/chunk-TZLEHZVC.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
@@ -19,5 +22,6 @@ export {
   longestBar,
   walkRowLabels,
   walkRowLayout,
+  walkRowLayoutOf,
   walkRowsExtent
 };

package/dist/layout/walkRowLinks.js

@@ -0,0 +1,12 @@
+import {
+  ribbonJoin,
+  sharedRowOrder,
+  walkRowBlocks,
+  walkRowLinks
+} from "../chunks/chunk-UFUSPK2A.js";
+export {
+  ribbonJoin,
+  sharedRowOrder,
+  walkRowBlocks,
+  walkRowLinks
+};

package/dist/layout/walkRowRuns.js

@@ -0,0 +1,20 @@
+import {
+  referenceWalkName,
+  runAt,
+  walkRowRuns,
+  walkRowsOf
+} from "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-B5ARSBOH.js";
+import "../chunks/chunk-B5X2RLJG.js";
+import "../chunks/chunk-EIY2SKD3.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
+export {
+  referenceWalkName,
+  runAt,
+  walkRowRuns,
+  walkRowsOf
+};

package/dist/layout/walkRows.js

@@ -1,8 +1,11 @@
 import {
   filterSamples,
-  referenceWalkName,
   walkRows
-} from "../chunks/chunk-DEDD7TFJ.js";
+} from "../chunks/chunk-JDZ5GTZT.js";
+import {
+  referenceWalkName
+} from "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/layout/walkStrip.js

@@ -9,7 +9,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-IZ6Y5D23.js";
+} from "../chunks/chunk-PNM6Z3IE.js";
 import {
   LABELLED_ROW_PX
 } from "../chunks/chunk-XZ6PQBU6.js";
@@ -18,10 +18,12 @@ import "../chunks/chunk-SWCULW6S.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";
-import "../chunks/chunk-YHJ5JLBI.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-TZLEHZVC.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
 import "../chunks/chunk-CRCD3ODN.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-EIY2SKD3.js";

package/dist/layoutModes.js

@@ -4,8 +4,8 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-NGUM77EP.js";
-import "./chunks/chunk-LMH5KVJZ.js";
+} from "./chunks/chunk-TEXAKEJX.js";
+import "./chunks/chunk-3LZ334X4.js";
 import "./chunks/chunk-A7H753BA.js";
 import "./chunks/chunk-GJU6BJJA.js";
 import "./chunks/chunk-GJLZ2MKE.js";
@@ -13,9 +13,11 @@ import "./chunks/chunk-MYLAJDKB.js";
 import "./chunks/chunk-C44YRP5F.js";
 import "./chunks/chunk-UAFATXYA.js";
 import "./chunks/chunk-3GLG3ZLE.js";
-import "./chunks/chunk-YHJ5JLBI.js";
-import "./chunks/chunk-DEDD7TFJ.js";
+import "./chunks/chunk-TZLEHZVC.js";
+import "./chunks/chunk-JDZ5GTZT.js";
+import "./chunks/chunk-M75QPZNJ.js";
 import "./chunks/chunk-3GP3KT5L.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-EIY2SKD3.js";

package/dist/pipeline.js

@@ -11,7 +11,7 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-KDU4EF66.js";
+} from "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -19,7 +19,7 @@ import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-3XSRT7RQ.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-DZR37KXT.js";

package/dist/tubeMap/bundle.js

@@ -1,11 +1,13 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-RETNT73O.js";
-import "../chunks/chunk-LMH5KVJZ.js";
+} from "../chunks/chunk-TJOOHTJ6.js";
+import "../chunks/chunk-3LZ334X4.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/tubeMap/coarsen.js

@@ -1,12 +1,14 @@
 import {
   coarsenTubeMap,
   lastAtMost
-} from "../chunks/chunk-V5MAL7LU.js";
-import "../chunks/chunk-LMH5KVJZ.js";
+} from "../chunks/chunk-7O7EGTYG.js";
+import "../chunks/chunk-3LZ334X4.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

package/dist/tubeMap/deviations.js

@@ -1,15 +1,17 @@
 import {
   lastAtMost
-} from "../chunks/chunk-V5MAL7LU.js";
+} from "../chunks/chunk-7O7EGTYG.js";
 import {
   boxX,
   referenceBoxes
 } from "../chunks/chunk-HSVFCA2J.js";
-import "../chunks/chunk-LMH5KVJZ.js";
+import "../chunks/chunk-3LZ334X4.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import {
   pathOrigin
 } from "../chunks/chunk-B5X2RLJG.js";

package/dist/tubeMap/draw.js

@@ -8,12 +8,14 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-ZUL52ZX2.js";
-import "../chunks/chunk-MYDHU2UV.js";
+} from "../chunks/chunk-3HGYGISG.js";
 import "../chunks/chunk-BX4AUMZE.js";
+import "../chunks/chunk-MYDHU2UV.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-DEDD7TFJ.js";
+import "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";

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

@@ -1,5 +1,5 @@
 import type { WalkStopTable } from './walkStops.js';
-import type { Graph } from '../types.js';
+import type { Graph, GraphPath } from '../types.js';
 /**
  * A graph as typed arrays, the shape a worker can hand across postMessage
  * without copying: what a GFA of S lines tagged LN/SN/SO/SR, L lines and W
@@ -32,6 +32,15 @@ export interface GraphTables {
         after?: WalkStopTable;
     };
 }
+/** The GraphPath `graphFromTables` builds of walk `p`, less its steps */
+export declare function tablePath(w: GraphTables['walks'], p: number): Omit<GraphPath, 'nodeIds'> & {
+    start: number;
+};
+/**
+ * Each segment's Graph node id: its name and its one drawn orientation, first
+ * claimed by a link and else by a walk
+ */
+export declare function tableNodeIds({ nodes: n, links: l, walks: w }: GraphTables): string[];
 /**
  * The Graph `convertGFAToGraph` builds from `graphTablesGFA(tables)`, deep
  * equal, built by index: a step costs a few array reads and its visit, where

package/dist/types/index.d.ts

@@ -74,6 +74,10 @@ 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 { runAt, walkRowRuns, walkRowsOf } from './layout/walkRowRuns.js';
+export type { WalkRowMeta, WalkRowRuns, WalkVisitColumns, } from './layout/walkRowRuns.js';
+export { ribbonJoin, sharedRowOrder, walkRowBlocks, walkRowLinks, } from './layout/walkRowLinks.js';
+export type { WalkRowBlock, WalkRowLink } from './layout/walkRowLinks.js';
 export type { WalkAxis, WalkRow, WalkRows, WalkRun, WalkStop, WalkVisit, } 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, gapStyle, 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';
@@ -82,7 +86,7 @@ export type { StripFrame, StripMark } from './layout/walkStrip.js';
 export { el, serializeEl } from './el.js';
 export type { El, ElAttrs } from './el.js';
 export { RAMP_GRADIENT_CSS, rampHue, rampHueCss, rampStops, } from './referenceRampCss.js';
-export { walkRowLabels, walkRowsExtent } from './layout/walkRowLayout.js';
+export { walkRowLabels, walkRowLayoutOf, walkRowsExtent, } from './layout/walkRowLayout.js';
 export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, geneCoverageNote, layoutLabels, } from './labelLayout.js';
 export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';

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

@@ -12,3 +12,7 @@ export declare function walkRowLayout(graph: Graph, region?: {
     start: number;
     end: number;
 }): LayoutResult | undefined;
+export declare function walkRowLayoutOf(graph: Graph, walks: WalkRows, region?: {
+    start: number;
+    end: number;
+}): LayoutResult | undefined;

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

@@ -0,0 +1,32 @@
+import type { WalkRow } from './walkRows.js';
+export interface WalkRowLink {
+    row: number;
+    a0: number;
+    a1: number;
+    b0: number;
+    b1: number;
+}
+export interface WalkRowBlock {
+    row: number;
+    start: number;
+    bp: number;
+    block: number;
+}
+export declare function ribbonJoin(rows: WalkRow[]): number;
+/**
+ * The first row, then each row after the one it shares the most sequence
+ * with, so neighbours share as much as they can. A row with no bar is passed
+ * over when comparing.
+ */
+export declare function sharedRowOrder(rows: WalkRow[]): number[];
+/** The ribbons between each two neighbouring rows that both have bars */
+export declare function walkRowLinks(rows: WalkRow[], join?: number): WalkRowLink[];
+/**
+ * Blocks of nodes off the reference's path that two or more rows walk: the
+ * nodes one set of rows walks, joined where a row walks them within `join` bp
+ * of each other. Blocks rank by bp over every visit, so a block has one rank
+ * in every row, set by neither the rows' order nor the build order that
+ * created its nodes. A block under 0.3% of the bp off the path is left out.
+ * Returns each row's stretches of each block.
+ */
+export declare function walkRowBlocks(rows: WalkRow[], join?: number): WalkRowBlock[];

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

@@ -0,0 +1,56 @@
+import type { WalkRow, WalkRows, WalkRun } from './walkRows.js';
+import type { GraphTables } from '../gfa/graphTables.js';
+import type { Graph, StopChunk } from '../types.js';
+export type WalkRowMeta = Omit<WalkRow, 'runs' | 'visits'>;
+/**
+ * Each row's visits, row i's at `offsets[i]` up to `offsets[i + 1]`: the
+ * node as an index into `names`, its bp offset from the bar's start, its bp,
+ * and 1 where the reference walk visits it anywhere in the cut
+ */
+export interface WalkVisitColumns {
+    offsets: Uint32Array;
+    node: Int32Array;
+    start: Float64Array;
+    bp: Float64Array;
+    onReference: Uint8Array;
+    names: ArrayLike<string>;
+}
+/**
+ * `walkRows` with each row's runs as typed arrays, which cross from a worker
+ * without an object per run. Row 0 is the reference; row i's runs are
+ * `offsets[i]` up to `offsets[i + 1]`.
+ */
+export interface WalkRowRuns {
+    origin: number;
+    rows: WalkRowMeta[];
+    offsets: Uint32Array;
+    start: Float64Array;
+    bp: Float64Array;
+    referenceStart: Float64Array;
+    flags: Uint8Array;
+    chunk: Int32Array;
+    chunks: StopChunk[];
+    visits?: WalkVisitColumns;
+}
+export declare function referenceWalkName(graph: Pick<Graph, 'nodes' | 'paths' | 'referencePath'>): string | undefined;
+/**
+ * The walk rows of a Graph, or of a cut's tables without the Graph of their
+ * steps, as `walkRows` reads them. Tables name their reference by
+ * `referencePath`, as loadGraph does.
+ *
+ * Each walk is cut at the nearest reference nodes IT visits on either side of
+ * the region, so a walk that skips one flanking node at a SNP is still
+ * measured between flanks rather than whole. A walk with one flank, whose
+ * contig ends inside the window, is the steps past that flank read in the
+ * reference's direction, a lower bound.
+ */
+export declare function walkRowRuns(source: Graph | GraphTables, region?: {
+    start: number;
+    end: number;
+}, o?: {
+    visits?: boolean;
+    referencePath?: string;
+}): WalkRowRuns | undefined;
+export declare function runAt(t: WalkRowRuns, k: number): WalkRun;
+/** The rows as `WalkRows`, an object per run, and per visit where it has them */
+export declare function walkRowsOf(t: WalkRowRuns, unit?: number): WalkRows;

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

@@ -1,5 +1,6 @@
 import type { GapCause } from '../gfa/walkStops.js';
 import type { Graph, StopChunk } from '../types.js';
+export { referenceWalkName } from './walkRowRuns.js';
 export interface WalkRun {
     start: number;
     bp: number;
@@ -22,6 +23,7 @@ export interface WalkStop {
 export interface WalkVisit {
     node: string;
     start: number;
+    bp: number;
     onReference: boolean;
 }
 export interface WalkRow {
@@ -35,7 +37,7 @@ export interface WalkRow {
     complete: boolean;
     stop?: WalkStop;
     runs: WalkRun[];
-    visits: WalkVisit[];
+    visits?: WalkVisit[];
     axis?: WalkAxis;
 }
 export interface WalkRows {
@@ -48,8 +50,9 @@ export declare function filterSamples<R extends {
     sample: string;
     label: string;
 }>(rows: R[], samples: string[] | undefined): R[];
-export declare function referenceWalkName(graph: Pick<Graph, 'nodes' | 'paths' | 'referencePath'>): string | undefined;
 export declare function walkRows(graph: Graph, region?: {
     start: number;
     end: number;
-}, unit?: number): WalkRows | undefined;
+}, unit?: number, o?: {
+    visits?: boolean;
+}): WalkRows | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "11.1.0";
+export declare const version = "11.3.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-Y3FDMDNT.js";
+} from "./chunks/chunk-XEWPWCML.js";
 export {
   version
 };