@jbrowse/bandage-core 10.3.0 → 11.0.0

package/dist/chunks/chunk-EIY2SKD3.js

@@ -0,0 +1,164 @@
+// src/gfa/walkStops.ts
+var START_STOP_TAG = "ws";
+var END_STOP_TAG = "we";
+var STOP_KINDS = ["elsewhere", "break", "end"];
+var GAP_CAUSE_TEXT = {
+  missing: "not in the graph",
+  elsewhere: "on nodes filed elsewhere",
+  unknown: "gap, cause unknown"
+};
+var OUTSIDE_TEXT = "outside the extracted subgraph";
+function gapParts(bp, after, before) {
+  if (!after && !before) {
+    return [{ bp }];
+  }
+  const left = Math.min(after?.trimmed ?? 0, bp);
+  const right = Math.min(before?.trimmed ?? 0, bp - left);
+  let rest = bp - left - right;
+  const lead = after?.kind === "break" ? Math.min(after.bp, rest) : 0;
+  rest -= lead;
+  const trail = before?.kind === "break" ? Math.min(before.bp, rest) : 0;
+  rest -= trail;
+  const elsewhere = [after, before].find((s) => s?.kind === "elsewhere");
+  const parts = [
+    { bp: left },
+    { bp: lead, cause: "missing" },
+    elsewhere?.kind === "elsewhere" ? { bp: rest, cause: "elsewhere", chunk: elsewhere.chunk } : { bp: rest, cause: "unknown" },
+    { bp: trail, cause: "missing" },
+    { bp: right }
+  ];
+  return parts.filter((part) => part.bp > 0);
+}
+function stopAt(table, i) {
+  const bp = table.bp[i];
+  const ref = table.chunkRefs[i];
+  return stopOf(
+    table.kindNames[table.kinds[i]],
+    Number.isNaN(bp) ? void 0 : bp,
+    table.trimmed[i],
+    ref < 0 ? void 0 : { refName: table.chunkRefNames[ref], start: table.chunkStarts[i] }
+  );
+}
+function stopOf(kind, bp, trimmed, chunk) {
+  const cut = trimmed > 0 ? { trimmed } : {};
+  if (kind === "elsewhere" && chunk) {
+    return { kind, chunk, ...bp === void 0 ? {} : { bp }, ...cut };
+  }
+  if (kind === "break" && bp !== void 0) {
+    return { kind, bp, ...chunk ? { chunk } : {}, ...cut };
+  }
+  return kind === "end" ? { kind, ...cut } : void 0;
+}
+function stopTag(stop) {
+  const parts = [stop.kind];
+  if ("bp" in stop && stop.bp !== void 0) {
+    parts.push(`bp=${stop.bp}`);
+  }
+  if (stop.trimmed) {
+    parts.push(`trimmed=${stop.trimmed}`);
+  }
+  if ("chunk" in stop && stop.chunk) {
+    parts.push(`chunk=${stop.chunk.refName}:${stop.chunk.start}`);
+  }
+  return parts.join(",");
+}
+function parseStopTag(value) {
+  const [kind, ...fields] = value.split(",");
+  let bp;
+  let trimmed = 0;
+  let chunk;
+  for (const field of fields) {
+    if (field.startsWith("bp=")) {
+      bp = +field.slice(3);
+    } else if (field.startsWith("trimmed=")) {
+      trimmed = +field.slice(8);
+    } else if (field.startsWith("chunk=")) {
+      const at = field.lastIndexOf(":");
+      chunk = { refName: field.slice(6, at), start: +field.slice(at + 1) };
+    }
+  }
+  return stopOf(kind, bp, trimmed, chunk);
+}
+function stopFields(before, after) {
+  return {
+    ...before ? { before } : {},
+    ...after ? { after } : {}
+  };
+}
+function walkStopFields(tags) {
+  const before = tags[START_STOP_TAG];
+  const after = tags[END_STOP_TAG];
+  return stopFields(
+    typeof before === "string" ? parseStopTag(before) : void 0,
+    typeof after === "string" ? parseStopTag(after) : void 0
+  );
+}
+function walkStopTags(walks, p) {
+  const tags = [];
+  for (const [tag, table] of [
+    [START_STOP_TAG, walks.before],
+    [END_STOP_TAG, walks.after]
+  ]) {
+    const stop = table && stopAt(table, p);
+    if (stop) {
+      tags.push(`	${tag}:Z:${stopTag(stop)}`);
+    }
+  }
+  return tags.join("");
+}
+var StopColumns = class {
+  constructor() {
+    this.kinds = [];
+    this.bp = [];
+    this.trimmed = [];
+    this.chunkRefs = [];
+    this.chunkStarts = [];
+    this.chunkRefNames = [];
+    this.refIndex = /* @__PURE__ */ new Map();
+  }
+  push(stop) {
+    this.kinds.push(STOP_KINDS.indexOf(stop.kind));
+    this.bp.push("bp" in stop && stop.bp !== void 0 ? stop.bp : NaN);
+    this.trimmed.push(stop.trimmed ?? 0);
+    const chunk = "chunk" in stop ? stop.chunk : void 0;
+    if (chunk) {
+      let ref = this.refIndex.get(chunk.refName);
+      if (ref === void 0) {
+        ref = this.chunkRefNames.length;
+        this.refIndex.set(chunk.refName, ref);
+        this.chunkRefNames.push(chunk.refName);
+      }
+      this.chunkRefs.push(ref);
+      this.chunkStarts.push(chunk.start);
+    } else {
+      this.chunkRefs.push(-1);
+      this.chunkStarts.push(NaN);
+    }
+  }
+  table() {
+    return {
+      kinds: Uint8Array.from(this.kinds),
+      kindNames: [...STOP_KINDS],
+      bp: Float64Array.from(this.bp),
+      trimmed: Float64Array.from(this.trimmed),
+      chunkRefs: Int32Array.from(this.chunkRefs),
+      chunkStarts: Float64Array.from(this.chunkStarts),
+      chunkRefNames: this.chunkRefNames
+    };
+  }
+};
+
+export {
+  START_STOP_TAG,
+  END_STOP_TAG,
+  GAP_CAUSE_TEXT,
+  OUTSIDE_TEXT,
+  gapParts,
+  stopAt,
+  stopTag,
+  parseStopTag,
+  stopFields,
+  walkStopFields,
+  walkStopTags,
+  StopColumns
+};

package/dist/chunks/{chunk-A55OZVYX.js → chunk-EY2ZGSCP.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-ZNJ4JAPT.js";
+} from "./chunk-PK5QQOMN.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   PathVisitsBuilder
 } from "./chunk-ZPZ7GNBT.js";

package/dist/chunks/{chunk-RWKP7UO4.js → chunk-FFHJGWDK.js}

@@ -4,7 +4,10 @@ import {
 import {
   pathOrigin,
   surveyPaths
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
+import {
+  walkStopFields
+} from "./chunk-EIY2SKD3.js";
 
 // src/gfa/gfaConverter.ts
 function surveySegments(gfaGraph, pathSteps) {
@@ -152,7 +155,8 @@ function convertGFAToGraph(gfaGraph, name = "Imported GFA") {
       start: walkStart(walk),
       sample: walk.sample,
       haplotype: walk.haplotype,
-      contig: walk.contig
+      contig: walk.contig,
+      ...walkStopFields(walk.tags)
     });
     recordPathEdges(nodeIds2, name2);
   }

package/dist/chunks/{chunk-KWHWNOTY.js → chunk-KDU4EF66.js}

@@ -14,19 +14,19 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-RWKP7UO4.js";
+} from "./chunk-FFHJGWDK.js";
 import {
   parseGFA
 } from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
-} from "./chunk-DBLV7PGG.js";
+} from "./chunk-3XSRT7RQ.js";
 import {
   anchorGraph
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   gfaTables
-} from "./chunk-Z6XZWPXK.js";
+} from "./chunk-DZR37KXT.js";
 import {
   mergeRuns,
   splitRuns

package/dist/chunks/{chunk-65ILXEIN.js → chunk-L5IETLWP.js}

@@ -1,18 +1,18 @@
-import {
-  tubeMapMismatches
-} from "./chunk-BX4AUMZE.js";
 import {
   MAX_GAP_PX
 } from "./chunk-MYDHU2UV.js";
+import {
+  tubeMapMismatches
+} from "./chunk-BX4AUMZE.js";
 import {
   readColor
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-5YILQTHE.js";
+} from "./chunk-CIDSF47D.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-GIHTHYXY.js → chunk-NMWQUFPF.js}

@@ -6,7 +6,7 @@ import {
 } from "./chunk-234NFZS4.js";
 import {
   gfaTables
-} from "./chunk-Z6XZWPXK.js";
+} from "./chunk-DZR37KXT.js";
 import {
   panSNMatchesPrefix,
   panSNSample

package/dist/chunks/{chunk-QQCOVMMT.js → chunk-OLKXMZ6J.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-5YILQTHE.js";
+} from "./chunk-CIDSF47D.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-ZNJ4JAPT.js → chunk-PK5QQOMN.js}

@@ -5,14 +5,14 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-5YILQTHE.js";
+} from "./chunk-CIDSF47D.js";
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-IYALCKNB.js";
+} from "./chunk-3GP3KT5L.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   ownStrand,
   strandSides

package/dist/chunks/{chunk-PPDE4IVT.js → chunk-PNMJFFNB.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

package/dist/chunks/{chunk-WJ4TIAVA.js → chunk-RNYPCQZ3.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-KWHWNOTY.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-2XEQR54X.js → chunk-SWCULW6S.js}

@@ -16,7 +16,7 @@ import {
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-IYALCKNB.js";
+} from "./chunk-3GP3KT5L.js";
 import {
   meanDepth,
   nodeWidthPx

package/dist/chunks/{chunk-SHKGYGM4.js → chunk-TEF3NBG3.js}

@@ -3,17 +3,17 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-SZHQK6GL.js";
+} from "./chunk-XZ6PQBU6.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM,
   longestBar
-} from "./chunk-QQCOVMMT.js";
+} from "./chunk-OLKXMZ6J.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-M5NPD55W.js → chunk-TUQKGAK3.js}

@@ -6,7 +6,7 @@ import {
   haplotypeWanted,
   referencePathQuery,
   referenceSamplesOf
-} from "./chunk-GIHTHYXY.js";
+} from "./chunk-NMWQUFPF.js";
 import {
   panSNSample
 } from "./chunk-4XWZNPQ2.js";

package/dist/chunks/{chunk-ZPBEUOBM.js → chunk-W6EXQDV5.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-KWHWNOTY.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-7XR26JST.js → chunk-XVS52NMZ.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-2XEQR54X.js";
+} from "./chunk-SWCULW6S.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-SZHQK6GL.js → chunk-XZ6PQBU6.js}

@@ -3,27 +3,37 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-2XEQR54X.js";
+} from "./chunk-SWCULW6S.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
 } from "./chunk-GQZVR5DW.js";
+import {
+  GAP_CAUSE_TEXT,
+  OUTSIDE_TEXT
+} from "./chunk-EIY2SKD3.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
+import {
+  panSNContig
+} from "./chunk-4XWZNPQ2.js";
 
 // src/layout/walkRowDraw.ts
 var ON_REFERENCE = "#2f8fd6";
 var OFF_REFERENCE = "#8e3fbf";
 var OUTSIDE_CUT = "#bdbdbd";
+var MISSING_INK = "#8a8a8a";
+var UNKNOWN_GAP = "#e2e2e2";
 var GENE_INK = "#1c1c22";
 var BAR_PX = 12;
 var GAP_PX = 4;
+var MISSING_PX = 1;
 var LABELLED_ROW_PX = 12;
 var MIN_TILED_BAR_PX = 6;
 var MIN_TILE_PX = 3;
@@ -37,12 +47,36 @@ function signedLength(delta) {
 function units(bp, unit) {
   return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
 }
+var near = ({ refName, start }) => `${panSNContig(refName)}:${start < 1e6 ? `${Math.round(start / 1e3)} kb` : `${(start / 1e6).toFixed(1)} Mb`}`;
+function gapsText(gapBp, runs) {
+  const gaps = (runs ?? []).filter((r) => r.gap);
+  if (gapBp <= 0) {
+    return "";
+  }
+  if (!gaps.some((g) => g.cause)) {
+    return ` \xB7 ${kb(gapBp)} ${OUTSIDE_TEXT}`;
+  }
+  const bpOf = (cause) => gaps.filter((g) => g.cause === cause).reduce((sum, g) => sum + g.bp, 0);
+  const places = [
+    ...new Set(gaps.flatMap((g) => g.chunk ? [near(g.chunk)] : []))
+  ];
+  const parts = [
+    [bpOf("missing"), GAP_CAUSE_TEXT.missing],
+    [
+      bpOf("elsewhere"),
+      `on nodes filed near ${places[0]}${places.length > 1 ? ` and ${places.length - 1} more place${places.length > 2 ? "s" : ""}` : ""}`
+    ],
+    [bpOf("unknown"), GAP_CAUSE_TEXT.unknown],
+    [bpOf(void 0), OUTSIDE_TEXT]
+  ];
+  return parts.filter(([bp]) => bp > 0).map(([bp, text]) => ` \xB7 ${kb(bp)} ${text}`).join("");
+}
 function walkRowReadout(row, reference, unit, call) {
   const { bp, gapBp, complete, stop } = row;
   if (!reference) {
     return `${kb(bp)}${units(bp, unit)}`;
   }
-  const outside = gapBp > 0 ? ` \xB7 ${kb(gapBp)} outside the cut` : "";
+  const outside = gapsText(gapBp, row.runs);
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
   if (complete) {
     const delta = bp - reference.bp;
@@ -54,7 +88,7 @@ function walkRowReadout(row, reference, unit, call) {
     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";
+  const why = !stop ? "partial walk" : stop.contigEnds ? `contig ends inside the ${region}` : "does not rejoin the reference within the extracted subgraph";
   return `\u2265 ${kb(bp)}${units(bp, unit)} \xB7 ${why}${outside}${called}`;
 }
 function readoutPlacement(text, endX, width) {
@@ -72,9 +106,12 @@ function unitTicks(bp, unit, pxPerBp) {
   }
   return ticks;
 }
+function gapStyle(cause) {
+  return cause === "missing" ? { fill: MISSING_INK, px: MISSING_PX, label: GAP_CAUSE_TEXT.missing } : cause === "unknown" ? { fill: UNKNOWN_GAP, px: GAP_PX, label: GAP_CAUSE_TEXT.unknown } : { fill: OUTSIDE_CUT, px: GAP_PX, label: OUTSIDE_TEXT };
+}
 function runPaint(run, ramp) {
   if (run.gap) {
-    return { fill: OUTSIDE_CUT };
+    return { fill: gapStyle(run.cause).fill };
   }
   if (!ramp) {
     return { fill: run.onReference ? ON_REFERENCE : OFF_REFERENCE };
@@ -180,11 +217,15 @@ function walkRowsKey(bars, o = {}) {
       label: `off ${bars.reference.label}'s path`
     }
   ];
-  if ([bars.reference, ...bars.rows].some((row) => row.gapBp > 0)) {
-    entries.push({
-      swatch: { kind: "gap", fill: OUTSIDE_CUT },
-      label: "walked outside the cut"
-    });
+  const gaps = [bars.reference, ...bars.rows].flatMap(
+    (row) => row.runs.filter((run) => run.gap)
+  );
+  const labels = new Set(gaps.map((run) => gapStyle(run.cause).label));
+  for (const cause of [void 0, "missing", "unknown"]) {
+    const { fill, px, label } = gapStyle(cause);
+    if (labels.has(label)) {
+      entries.push({ swatch: { kind: "gap", fill, px }, label });
+    }
   }
   if (o.genes?.crowded) {
     entries.push({
@@ -248,9 +289,9 @@ function walkRowsKeyTree(entries, x, y, idPrefix = "walk-key") {
       "stroke-width": 1.5
     }) : el("rect", {
       x: at,
-      y: e.swatch.kind === "gap" ? 7 : 5,
+      y: e.swatch.kind === "gap" ? 9 - e.swatch.px / 2 : 5,
       width: 18,
-      height: e.swatch.kind === "gap" ? GAP_PX : 8,
+      height: e.swatch.kind === "gap" ? e.swatch.px : 8,
       rx: 2,
       fill: ramp ? `url(#${rampId})` : e.swatch.fill
     });
@@ -399,9 +440,10 @@ function walkRowsTree(bars, frame, o = {}) {
     if (y < -barPx || y > frame.height + barPx) {
       return void 0;
     }
-    const runs = coalesceRuns(row.runs, frame.scaleX).flatMap((run) => {
+    const drawn = frame.bars === false ? [] : row.runs;
+    const runs = coalesceRuns(drawn, frame.scaleX).flatMap((run) => {
       const paint = runPaint(run, o.ramp);
-      const h = run.gap ? Math.min(GAP_PX, barPx) : barPx;
+      const h = run.gap ? Math.min(gapStyle(run.cause).px, barPx) : barPx;
       const id = `${prefix}-${i}-${run.start}`;
       const rect = el("rect", {
         x: along(run.start),
@@ -486,13 +528,17 @@ export {
   ON_REFERENCE,
   OFF_REFERENCE,
   OUTSIDE_CUT,
+  MISSING_INK,
+  UNKNOWN_GAP,
   GENE_INK,
   BAR_PX,
   GAP_PX,
+  MISSING_PX,
   LABELLED_ROW_PX,
   walkRowReadout,
   readoutPlacement,
   unitTicks,
+  gapStyle,
   runPaint,
   alongRow,
   rowSpan,

package/dist/cli/figure.js

@@ -7,13 +7,13 @@ import {
 } from "../chunks/chunk-G6UIYQZR.js";
 import {
   figureSvg
-} from "../chunks/chunk-7JGLJK44.js";
+} from "../chunks/chunk-5LTZVKZQ.js";
 import "../chunks/chunk-V4YML3GR.js";
-import "../chunks/chunk-SHKGYGM4.js";
+import "../chunks/chunk-TEF3NBG3.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-SZHQK6GL.js";
+} from "../chunks/chunk-XZ6PQBU6.js";
 import "../chunks/chunk-EJRJAAN7.js";
 import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-JSUCGZ6K.js";
@@ -25,17 +25,17 @@ import "../chunks/chunk-H2H4Y3TV.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-AMX4OQAW.js";
+} from "../chunks/chunk-CTZRIDMY.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
 } from "../chunks/chunk-JMABOQWL.js";
 import {
   LAYOUT_MODES
-} from "../chunks/chunk-MD5VPXXT.js";
-import "../chunks/chunk-GJU6BJJA.js";
-import "../chunks/chunk-ZNJ4JAPT.js";
+} from "../chunks/chunk-EDWU7OM4.js";
+import "../chunks/chunk-PK5QQOMN.js";
 import "../chunks/chunk-A7H753BA.js";
+import "../chunks/chunk-GJU6BJJA.js";
 import "../chunks/chunk-GJLZ2MKE.js";
 import "../chunks/chunk-MYLAJDKB.js";
 import "../chunks/chunk-C44YRP5F.js";
@@ -47,45 +47,46 @@ import {
   haplotypeIndexBeside,
   openGbz,
   parseRegion
-} from "../chunks/chunk-M5NPD55W.js";
-import "../chunks/chunk-GIHTHYXY.js";
+} from "../chunks/chunk-TUQKGAK3.js";
+import "../chunks/chunk-NMWQUFPF.js";
 import "../chunks/chunk-HNWJ4B7S.js";
-import "../chunks/chunk-PTQPTDZH.js";
-import "../chunks/chunk-WONB6LMC.js";
-import "../chunks/chunk-XUT4HXVE.js";
+import "../chunks/chunk-6OP4HPXG.js";
+import "../chunks/chunk-AI5PTOSV.js";
+import "../chunks/chunk-CZT33FZG.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-BVYR7IFN.js";
-import "../chunks/chunk-V7J6U4XC.js";
-import "../chunks/chunk-CGFPFBT2.js";
-import "../chunks/chunk-2XEQR54X.js";
+import "../chunks/chunk-C3NT37C3.js";
+import "../chunks/chunk-DO62DG26.js";
+import "../chunks/chunk-D4ZFRBB4.js";
+import "../chunks/chunk-SWCULW6S.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";
-import "../chunks/chunk-QQCOVMMT.js";
+import "../chunks/chunk-OLKXMZ6J.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-5YILQTHE.js";
-import "../chunks/chunk-IYALCKNB.js";
+} from "../chunks/chunk-CIDSF47D.js";
+import "../chunks/chunk-3GP3KT5L.js";
 import "../chunks/chunk-CRCD3ODN.js";
-import "../chunks/chunk-ZPBEUOBM.js";
-import "../chunks/chunk-KWHWNOTY.js";
+import "../chunks/chunk-W6EXQDV5.js";
+import "../chunks/chunk-KDU4EF66.js";
 import "../chunks/chunk-3PZSBNLI.js";
 import "../chunks/chunk-CKUVEHSS.js";
 import "../chunks/chunk-OPPVSPEF.js";
 import "../chunks/chunk-VPE4AYP7.js";
-import "../chunks/chunk-RWKP7UO4.js";
+import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-DBLV7PGG.js";
-import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-3XSRT7RQ.js";
+import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import {
   featuresOnBackbone,
   graphBackbone,
   refNameBinding
 } from "../chunks/chunk-234NFZS4.js";
-import "../chunks/chunk-Z6XZWPXK.js";
+import "../chunks/chunk-DZR37KXT.js";
+import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-PFRQBCGC.js";
 import "../chunks/chunk-HMXCN6PG.js";

package/dist/cli/fold.js

@@ -10,18 +10,19 @@ import {
 } from "../chunks/chunk-SOMZGDVS.js";
 import {
   loadGraph
-} from "../chunks/chunk-KWHWNOTY.js";
+} from "../chunks/chunk-KDU4EF66.js";
 import "../chunks/chunk-3PZSBNLI.js";
 import "../chunks/chunk-CKUVEHSS.js";
 import "../chunks/chunk-OPPVSPEF.js";
 import "../chunks/chunk-VPE4AYP7.js";
-import "../chunks/chunk-RWKP7UO4.js";
+import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-DBLV7PGG.js";
-import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-3XSRT7RQ.js";
+import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
-import "../chunks/chunk-Z6XZWPXK.js";
+import "../chunks/chunk-DZR37KXT.js";
+import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BZFOFC4D.js";
 import "../chunks/chunk-HKYXWZQS.js";