@jbrowse/bandage-core 10.3.1 → 11.0.0

package/dist/chunks/{chunk-KMBE2Q42.js → chunk-KDU4EF66.js}

@@ -14,19 +14,19 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-NZTYV3JL.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-B5X2RLJG.js";
 import {
   gfaTables
-} from "./chunk-Z6XZWPXK.js";
+} from "./chunk-DZR37KXT.js";
 import {
   mergeRuns,
   splitRuns

package/dist/chunks/{chunk-WYJQIC75.js → chunk-L5IETLWP.js}

@@ -1,15 +1,15 @@
-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-OOIOX36I.js";
+} from "./chunk-CIDSF47D.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.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-A2TJ5UX6.js → chunk-OLKXMZ6J.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-OOIOX36I.js";
+} from "./chunk-CIDSF47D.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-FW2R7UDZ.js → chunk-PK5QQOMN.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-OOIOX36I.js";
+} from "./chunk-CIDSF47D.js";
 import {
   pathCssColor,
   pathGreyCssColor

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

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-SFP3E4RI.js → chunk-TEF3NBG3.js}

@@ -3,14 +3,14 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-ZJBOM73S.js";
+} from "./chunk-XZ6PQBU6.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM,
   longestBar
-} from "./chunk-A2TJ5UX6.js";
+} from "./chunk-OLKXMZ6J.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.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-D7WIYPG3.js → chunk-W6EXQDV5.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-ZJBOM73S.js → chunk-XZ6PQBU6.js}

@@ -10,20 +10,30 @@ import {
   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-EWLXU3UG.js";
+} from "../chunks/chunk-5LTZVKZQ.js";
 import "../chunks/chunk-V4YML3GR.js";
-import "../chunks/chunk-SFP3E4RI.js";
+import "../chunks/chunk-TEF3NBG3.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-ZJBOM73S.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-CHNESV7L.js";
+} from "../chunks/chunk-CTZRIDMY.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
 } from "../chunks/chunk-JMABOQWL.js";
 import {
   LAYOUT_MODES
-} from "../chunks/chunk-AZ4EEF6Q.js";
-import "../chunks/chunk-GJU6BJJA.js";
-import "../chunks/chunk-FW2R7UDZ.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";
@@ -47,37 +47,37 @@ 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-AQCOIE5R.js";
-import "../chunks/chunk-BKEZLETL.js";
-import "../chunks/chunk-QH2MIXBA.js";
+import "../chunks/chunk-6OP4HPXG.js";
+import "../chunks/chunk-AI5PTOSV.js";
+import "../chunks/chunk-CZT33FZG.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-YZQI35UJ.js";
+import "../chunks/chunk-C3NT37C3.js";
 import "../chunks/chunk-DO62DG26.js";
-import "../chunks/chunk-CGFPFBT2.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-A2TJ5UX6.js";
+import "../chunks/chunk-OLKXMZ6J.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-OOIOX36I.js";
+} from "../chunks/chunk-CIDSF47D.js";
 import "../chunks/chunk-3GP3KT5L.js";
 import "../chunks/chunk-CRCD3ODN.js";
-import "../chunks/chunk-D7WIYPG3.js";
-import "../chunks/chunk-KMBE2Q42.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-NZTYV3JL.js";
+import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-DBLV7PGG.js";
+import "../chunks/chunk-3XSRT7RQ.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import {
@@ -85,7 +85,8 @@ import {
   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-KMBE2Q42.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-NZTYV3JL.js";
+import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-DBLV7PGG.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";

package/dist/figure.js

@@ -1,9 +1,9 @@
 import {
   figureSvg
-} from "./chunks/chunk-EWLXU3UG.js";
+} from "./chunks/chunk-5LTZVKZQ.js";
 import "./chunks/chunk-V4YML3GR.js";
-import "./chunks/chunk-SFP3E4RI.js";
-import "./chunks/chunk-ZJBOM73S.js";
+import "./chunks/chunk-TEF3NBG3.js";
+import "./chunks/chunk-XZ6PQBU6.js";
 import "./chunks/chunk-EJRJAAN7.js";
 import "./chunks/chunk-RBCE2OQH.js";
 import "./chunks/chunk-JSUCGZ6K.js";
@@ -12,35 +12,36 @@ import "./chunks/chunk-PSCSZSVK.js";
 import "./chunks/chunk-OMUPUB4J.js";
 import "./chunks/chunk-3VCKBSML.js";
 import "./chunks/chunk-H2H4Y3TV.js";
-import "./chunks/chunk-AQCOIE5R.js";
-import "./chunks/chunk-BKEZLETL.js";
-import "./chunks/chunk-QH2MIXBA.js";
+import "./chunks/chunk-6OP4HPXG.js";
+import "./chunks/chunk-AI5PTOSV.js";
+import "./chunks/chunk-CZT33FZG.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-YZQI35UJ.js";
+import "./chunks/chunk-C3NT37C3.js";
 import "./chunks/chunk-DO62DG26.js";
-import "./chunks/chunk-CGFPFBT2.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-A2TJ5UX6.js";
-import "./chunks/chunk-OOIOX36I.js";
+import "./chunks/chunk-OLKXMZ6J.js";
+import "./chunks/chunk-CIDSF47D.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-D7WIYPG3.js";
-import "./chunks/chunk-KMBE2Q42.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-NZTYV3JL.js";
+import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-DBLV7PGG.js";
+import "./chunks/chunk-3XSRT7RQ.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./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/figureData.js

@@ -3,49 +3,50 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-CHNESV7L.js";
+} from "./chunks/chunk-CTZRIDMY.js";
 import "./chunks/chunk-JMABOQWL.js";
-import "./chunks/chunk-AZ4EEF6Q.js";
-import "./chunks/chunk-GJU6BJJA.js";
-import "./chunks/chunk-FW2R7UDZ.js";
+import "./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";
 import "./chunks/chunk-UAFATXYA.js";
 import "./chunks/chunk-3GLG3ZLE.js";
-import "./chunks/chunk-M5NPD55W.js";
-import "./chunks/chunk-GIHTHYXY.js";
+import "./chunks/chunk-TUQKGAK3.js";
+import "./chunks/chunk-NMWQUFPF.js";
 import "./chunks/chunk-HNWJ4B7S.js";
-import "./chunks/chunk-AQCOIE5R.js";
-import "./chunks/chunk-BKEZLETL.js";
-import "./chunks/chunk-QH2MIXBA.js";
+import "./chunks/chunk-6OP4HPXG.js";
+import "./chunks/chunk-AI5PTOSV.js";
+import "./chunks/chunk-CZT33FZG.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-YZQI35UJ.js";
+import "./chunks/chunk-C3NT37C3.js";
 import "./chunks/chunk-DO62DG26.js";
-import "./chunks/chunk-CGFPFBT2.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-A2TJ5UX6.js";
-import "./chunks/chunk-OOIOX36I.js";
+import "./chunks/chunk-OLKXMZ6J.js";
+import "./chunks/chunk-CIDSF47D.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-D7WIYPG3.js";
-import "./chunks/chunk-KMBE2Q42.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-NZTYV3JL.js";
+import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-DBLV7PGG.js";
+import "./chunks/chunk-3XSRT7RQ.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./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/figureScene.js

@@ -1,32 +1,33 @@
 import {
   figureScene
-} from "./chunks/chunk-QH2MIXBA.js";
+} from "./chunks/chunk-CZT33FZG.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-YZQI35UJ.js";
+import "./chunks/chunk-C3NT37C3.js";
 import "./chunks/chunk-DO62DG26.js";
-import "./chunks/chunk-CGFPFBT2.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-A2TJ5UX6.js";
-import "./chunks/chunk-OOIOX36I.js";
+import "./chunks/chunk-OLKXMZ6J.js";
+import "./chunks/chunk-CIDSF47D.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-D7WIYPG3.js";
-import "./chunks/chunk-KMBE2Q42.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-NZTYV3JL.js";
+import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-DBLV7PGG.js";
+import "./chunks/chunk-3XSRT7RQ.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./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/figureSettings.js

@@ -1,19 +1,20 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-D7WIYPG3.js";
-import "./chunks/chunk-KMBE2Q42.js";
+} from "./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-NZTYV3JL.js";
+import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-DBLV7PGG.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";

package/dist/gbzCut.js

@@ -5,11 +5,12 @@ 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-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-BSOZW3FC.js";
 import "./chunks/chunk-RJWPJCIB.js";

package/dist/gbzWindow.js

@@ -12,10 +12,11 @@ import {
   referencePathQuery,
   referenceSamplesOf,
   resolveReferenceSample
-} from "./chunks/chunk-GIHTHYXY.js";
+} from "./chunks/chunk-NMWQUFPF.js";
 import "./chunks/chunk-HNWJ4B7S.js";
 import "./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-BSOZW3FC.js";
 import "./chunks/chunk-RJWPJCIB.js";

package/dist/gfa/gfaConverter.js

@@ -1,9 +1,10 @@
 import {
   convertGFAToGraph
-} from "../chunks/chunk-NZTYV3JL.js";
+} from "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.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";