@jbrowse/bandage-core 10.2.7 → 10.3.0

package/dist/tubeMap/bundle.js

@@ -1,20 +1,24 @@
 import {
   bundleRoutes
-} from "../chunks/chunk-5GMFEPWR.js";
-import "../chunks/chunk-XI3ZUTWF.js";
-import "../chunks/chunk-CWFNEKST.js";
+} from "../chunks/chunk-TCOLHD7N.js";
+import "../chunks/chunk-ZNJ4JAPT.js";
+import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-3XSM4OZU.js";
-import "../chunks/chunk-M6LK4GII.js";
-import "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-5YILQTHE.js";
+import "../chunks/chunk-IYALCKNB.js";
+import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 export {
   bundleRoutes
 };

package/dist/tubeMap/coarsen.js

@@ -1,351 +1,26 @@
 import {
-  pathSteps
-} from "../chunks/chunk-XI3ZUTWF.js";
-import "../chunks/chunk-CWFNEKST.js";
+  coarsenTubeMap,
+  lastAtMost
+} from "../chunks/chunk-A55OZVYX.js";
+import "../chunks/chunk-ZNJ4JAPT.js";
+import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-3XSM4OZU.js";
-import {
-  pathOrigin
-} from "../chunks/chunk-M6LK4GII.js";
-import {
-  PathVisitsBuilder
-} from "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-5YILQTHE.js";
+import "../chunks/chunk-IYALCKNB.js";
+import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import {
-  isBackbone
-} from "../chunks/chunk-FYQWPEEY.js";
-
-// src/tubeMap/coarsen.ts
-function readWalk(path, steps) {
-  const runs = [];
-  const open = () => ({ a: -Infinity, b: Infinity, detour: [], bp: 0 });
-  const gaps = [open()];
-  for (const { node, strand } of steps) {
-    const gap = gaps.at(-1);
-    const last = runs.at(-1);
-    if (isBackbone(node)) {
-      const start = node.stable.start;
-      const end = start + node.length;
-      const inverted = strand !== (node.stable.strand ?? "+");
-      const joins = last !== void 0 && gap.detour.length === 0;
-      if (joins && !last.inverted && !inverted && last.end === start) {
-        last.end = end;
-      } else if (joins && last.inverted && inverted && last.start === end) {
-        last.start = start;
-      } else {
-        runs.push({ start, end, inverted });
-        gaps.push(open());
-      }
-    } else {
-      gap.detour.push({ node, strand });
-      gap.bp += node.length;
-    }
-  }
-  runs.forEach((run, i) => {
-    gaps[i].b = run.start;
-    gaps[i + 1].a = run.end;
-  });
-  return { path, runs, gaps };
-}
-function isSmall(gap, sigma) {
-  return Number.isFinite(gap.a) && Number.isFinite(gap.b) && gap.b >= gap.a && Math.max(gap.b - gap.a, gap.bp) < sigma;
-}
-function strictlyInside(cuts, a, b) {
-  let lo = 0;
-  let hi = cuts.length;
-  while (lo < hi) {
-    const mid = lo + hi >> 1;
-    if (cuts[mid] <= a) {
-      lo = mid + 1;
-    } else {
-      hi = mid;
-    }
-  }
-  return lo < cuts.length && cuts[lo] < b;
-}
-function referenceGaps(backbone) {
-  const cuts = /* @__PURE__ */ new Map();
-  for (let i = 1; i < backbone.length; i++) {
-    const prev = backbone[i - 1];
-    const node = backbone[i];
-    const end = prev.stable.start + prev.length;
-    if (end !== node.stable.start) {
-      cuts.set(end, "reference-gap");
-      cuts.set(node.stable.start, "reference-gap");
-    }
-  }
-  return cuts;
-}
-function findCuts(walks, sigma, cuts) {
-  const cut = (bp, cause) => {
-    if (Number.isFinite(bp) && !cuts.has(bp)) {
-      cuts.set(bp, cause);
-    }
-  };
-  for (const { runs, gaps } of walks) {
-    const first = runs[0];
-    const last = runs.at(-1);
-    if (first && last) {
-      cut(first.start, "walk-end");
-      cut(last.end, "walk-end");
-    }
-    for (const run of runs) {
-      if (run.inverted && run.end - run.start >= sigma) {
-        cut(run.start, "inversion");
-        cut(run.end, "inversion");
-      }
-    }
-    for (const gap of gaps) {
-      if (gap.b < gap.a) {
-        cut(gap.a, "backward");
-        cut(gap.b, "backward");
-      } else if (!isSmall(gap, sigma)) {
-        cut(gap.a, "variant");
-        cut(gap.b, "variant");
-      }
-    }
-  }
-  const spans = walks.flatMap(({ runs, gaps }) => [
-    ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),
-    ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])
-  ]);
-  for (let changed = true; changed; ) {
-    changed = false;
-    const sorted = [...cuts.keys()].sort((x, y) => x - y);
-    for (const [a, b] of spans) {
-      if (strictlyInside(sorted, a, b)) {
-        changed ||= !cuts.has(a) || !cuts.has(b);
-        cut(a, "overlap");
-        cut(b, "overlap");
-      }
-    }
-  }
-  return cuts;
-}
-function mergeReference(backbone, cuts) {
-  const merged = [];
-  let group = [];
-  const close = () => {
-    const first = group[0];
-    const last = group.at(-1);
-    if (first && last) {
-      const bp0 = first.stable.start;
-      const bp1 = last.stable.start + last.length;
-      const name = `${bp0}-${bp1}`;
-      merged.push({
-        node: {
-          id: `${name}+`,
-          name,
-          length: bp1 - bp0,
-          depth: 0,
-          stable: {
-            refName: first.stable.refName,
-            start: bp0,
-            rank: 0,
-            strand: "+"
-          }
-        },
-        members: group
-      });
-    }
-    group = [];
-  };
-  for (const node of backbone) {
-    if (cuts.has(node.stable.start)) {
-      close();
-    }
-    group.push(node);
-  }
-  close();
-  return merged;
-}
-function coarsenTubeMap(graph, sigma) {
-  const backbone = graph.nodes.filter(isBackbone).sort((a, b) => a.stable.start - b.stable.start);
-  const paths = graph.paths ?? [];
-  if (backbone.length === 0 || paths.length === 0) {
-    return void 0;
-  }
-  const stepsOf = pathSteps(graph);
-  const walks = paths.map((p, i) => readWalk(p, stepsOf[i]));
-  const cuts = findCuts(walks, sigma, referenceGaps(backbone));
-  const sortedCuts = [...cuts.keys()].sort((x, y) => x - y);
-  const merged = mergeReference(backbone, cuts);
-  const starts = merged.map((m) => m.node.stable.start);
-  const mergedAt = (bp) => {
-    let lo = 0;
-    let hi = starts.length - 1;
-    while (lo < hi) {
-      const mid = lo + hi + 1 >> 1;
-      if (starts[mid] <= bp) {
-        lo = mid;
-      } else {
-        hi = mid - 1;
-      }
-    }
-    return lo;
-  };
-  const members = /* @__PURE__ */ new Map();
-  const coarseOf = /* @__PURE__ */ new Map();
-  for (const m of merged) {
-    members.set(
-      m.node.id,
-      m.members.map((n) => n.id)
-    );
-    for (const n of m.members) {
-      coarseOf.set(n.id, m.node.id);
-    }
-  }
-  const routes = /* @__PURE__ */ new Map();
-  const routeFor = (gap) => {
-    const key = `${gap.a}	${gap.b}	${gap.detour.map((s) => s.node.id + s.strand).join(",")}`;
-    let node = routes.get(key);
-    if (!node) {
-      const name = `r${routes.size}`;
-      node = {
-        id: `${name}+`,
-        name,
-        length: gap.bp,
-        depth: 0,
-        stable: {
-          refName: backbone[0].stable.refName,
-          start: Number.isFinite(gap.a) ? gap.a : gap.b,
-          rank: 1,
-          strand: "+"
-        }
-      };
-      routes.set(key, node);
-      members.set(
-        node.id,
-        gap.detour.map((s) => s.node.id)
-      );
-      for (const s of gap.detour) {
-        if (!coarseOf.has(s.node.id)) {
-          coarseOf.set(s.node.id, node.id);
-        }
-      }
-    }
-    return node;
-  };
-  const deviations = /* @__PURE__ */ new Map();
-  const coarsePaths = [];
-  const pathVisits = new PathVisitsBuilder();
-  const edges = /* @__PURE__ */ new Map();
-  const depth = /* @__PURE__ */ new Map();
-  for (const { path, runs, gaps } of walks) {
-    const steps = [];
-    const devs = [];
-    let continuing = false;
-    const append = (node, strand) => {
-      const last = steps.at(-1);
-      if (!(continuing && last?.node === node && last.strand === strand)) {
-        steps.push({ node, strand });
-      }
-      continuing = true;
-    };
-    const structural = (gap) => {
-      continuing = false;
-      if (gap.detour.length > 0) {
-        append(routeFor(gap), "+");
-        continuing = false;
-      }
-    };
-    const fold = (gap) => {
-      if (gap.bp > 0 || gap.b > gap.a) {
-        devs.push({ start: gap.a, end: gap.b, bp: gap.bp });
-      }
-      const home = merged[mergedAt(gap.b > gap.a ? gap.a : gap.a - 1)];
-      for (const s of gap.detour) {
-        if (!coarseOf.has(s.node.id)) {
-          coarseOf.set(s.node.id, home.node.id);
-          members.get(home.node.id).push(s.node.id);
-        }
-      }
-    };
-    runs.forEach((run, i) => {
-      const gap = gaps[i];
-      if (isSmall(gap, sigma) && !strictlyInside(sortedCuts, gap.a, gap.b)) {
-        fold(gap);
-      } else {
-        structural(gap);
-      }
-      const i0 = mergedAt(run.start);
-      const i1 = mergedAt(run.end - 1);
-      const small = run.end - run.start < sigma;
-      if (run.inverted && !small) {
-        continuing = false;
-        for (let j = i1; j >= i0; j--) {
-          append(merged[j].node, "-");
-        }
-        continuing = false;
-      } else {
-        if (run.inverted) {
-          devs.push({
-            start: run.start,
-            end: run.end,
-            bp: run.end - run.start,
-            inverted: true
-          });
-        }
-        for (let j = i0; j <= i1; j++) {
-          append(merged[j].node, "+");
-        }
-      }
-    });
-    structural(gaps.at(-1));
-    const visitName = pathOrigin(path.name).name;
-    let pos = 0;
-    steps.forEach(({ node, strand }, i) => {
-      depth.set(node.id, (depth.get(node.id) ?? 0) + 1);
-      pathVisits.add(
-        node.name,
-        visitName,
-        path.sample ?? visitName,
-        pos,
-        strand === "-"
-      );
-      pos += node.length;
-      const next = steps[i + 1];
-      if (next) {
-        const key = `${node.id}${strand}	${next.node.id}${next.strand}`;
-        const edge = edges.get(key);
-        if (edge) {
-          edge.pathIds.push(path.name);
-        } else {
-          edges.set(key, {
-            from: node.id,
-            to: next.node.id,
-            fromStrand: strand,
-            toStrand: next.strand,
-            pathIds: [path.name]
-          });
-        }
-      }
-    });
-    coarsePaths.push({ ...path, nodeIds: steps.map((s) => s.node.id) });
-    deviations.set(path.name, devs);
-  }
-  const nodes = [...merged.map((m) => m.node), ...routes.values()].filter((n) => depth.has(n.id)).map((n) => ({ ...n, depth: depth.get(n.id) }));
-  return {
-    graph: {
-      ...graph,
-      nodes,
-      edges: [...edges.values()],
-      paths: coarsePaths,
-      pathVisits: pathVisits.build(),
-      reads: void 0
-    },
-    members,
-    coarseOf,
-    deviations,
-    cuts
-  };
-}
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 export {
-  coarsenTubeMap
+  coarsenTubeMap,
+  lastAtMost
 };

package/dist/tubeMap/deviations.js

@@ -1,36 +1,68 @@
 import {
+  lastAtMost
+} from "../chunks/chunk-A55OZVYX.js";
+import {
+  boxX,
   referenceBoxes
-} from "../chunks/chunk-XMW266WS.js";
-import "../chunks/chunk-PTABFYQ7.js";
+} from "../chunks/chunk-HSVFCA2J.js";
+import "../chunks/chunk-ZNJ4JAPT.js";
+import "../chunks/chunk-A7H753BA.js";
+import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-5YILQTHE.js";
+import "../chunks/chunk-IYALCKNB.js";
+import {
+  pathOrigin
+} from "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import {
+  pushTo
+} from "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 
 // src/tubeMap/deviations.ts
 function boxAt(boxes, bp, visited) {
-  let lo = 0;
-  let hi = boxes.length - 1;
-  while (lo < hi) {
-    const mid = lo + hi + 1 >> 1;
-    if (boxes[mid].bp0 <= bp) {
-      lo = mid;
-    } else {
-      hi = mid - 1;
-    }
-  }
+  const lo = lastAtMost(boxes, (box) => box.bp0, bp);
   return [boxes[lo], boxes[lo - 1]].find(
     (box) => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1
   );
 }
+function deviationsByPath(graph, deviations) {
+  const byWalk = /* @__PURE__ */ new Map();
+  for (const [name, devs] of deviations) {
+    for (const d of devs) {
+      pushTo(byWalk, pathOrigin(name).name, d);
+    }
+  }
+  const byPath = /* @__PURE__ */ new Map();
+  for (const path of graph.paths ?? []) {
+    if (path.members) {
+      const union = /* @__PURE__ */ new Map();
+      for (const d of path.members.flatMap((m) => byWalk.get(m) ?? [])) {
+        union.set(`${d.start}-${d.end}`, d);
+      }
+      byPath.set(path.name, [...union.values()]);
+    } else {
+      byPath.set(path.name, deviations.get(path.name) ?? []);
+    }
+  }
+  return byPath;
+}
 function deviationMarks(drawing, deviations) {
-  const { layout } = drawing;
+  const { graph, layout } = drawing;
   const boxes = [...referenceBoxes(drawing).values()].flat().sort((a, b) => a.bp0 - b.bp0);
+  const byPath = deviationsByPath(graph, deviations);
   const marks = [];
   for (const track of layout.tracks) {
-    const devs = track.name ? deviations.get(track.name) : void 0;
+    const devs = track.name ? byPath.get(track.name) : void 0;
     if (devs?.length) {
       const visited = /* @__PURE__ */ new Map();
       for (const segment of track.path) {
@@ -41,12 +73,10 @@ function deviationMarks(drawing, deviations) {
       for (const d of devs) {
         const box = boxAt(boxes, d.start, visited);
         if (box) {
-          const { bp0, bp1, x0, x1, index } = box;
-          const at = (bp) => x0 + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * (x1 - x0);
           marks.push({
-            x0: at(d.start),
-            x1: at(d.end),
-            y: visited.get(index),
+            x0: boxX(box, d.start),
+            x1: boxX(box, d.end),
+            y: visited.get(box.index),
             height: track.width
           });
         }

package/dist/tubeMap/draw.js

@@ -8,15 +8,18 @@ import {
   tubeMapMismatchAt,
   tubeMapPicture,
   tubeMapTrackAt
-} from "../chunks/chunk-B6IW3IRE.js";
-import "../chunks/chunk-XXT2JCAC.js";
-import "../chunks/chunk-HK5Y2YWV.js";
-import "../chunks/chunk-CWFNEKST.js";
+} from "../chunks/chunk-65ILXEIN.js";
+import "../chunks/chunk-BX4AUMZE.js";
+import "../chunks/chunk-MYDHU2UV.js";
+import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
-import "../chunks/chunk-M6LK4GII.js";
-import "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-5YILQTHE.js";
+import "../chunks/chunk-LGJBB5BP.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 {
   drawTubeMap,
   drawTubeMapHighlight,

package/dist/tubeMap/frame.js

@@ -1,8 +1,9 @@
 import {
   tubeMapFrame,
   tubeMapNodeAt
-} from "../chunks/chunk-2CMYNW3E.js";
-import "../chunks/chunk-HK5Y2YWV.js";
+} from "../chunks/chunk-SI3BB4DO.js";
+import "../chunks/chunk-MYDHU2UV.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
   tubeMapFrame,
   tubeMapNodeAt

package/dist/tubeMap/genes.js

@@ -3,15 +3,18 @@ import {
   drawTubeMapGenes,
   tubeMapGeneRows,
   tubeMapGenes
-} from "../chunks/chunk-4DRQTBBE.js";
-import "../chunks/chunk-XMW266WS.js";
-import "../chunks/chunk-PTABFYQ7.js";
+} from "../chunks/chunk-6EOB6ANX.js";
+import "../chunks/chunk-HSVFCA2J.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
   GENE_ROW_PX,
   drawTubeMapGenes,

package/dist/tubeMap/mismatches.js

@@ -1,6 +1,6 @@
 import {
   tubeMapMismatches
-} from "../chunks/chunk-XXT2JCAC.js";
+} from "../chunks/chunk-BX4AUMZE.js";
 export {
   tubeMapMismatches
 };

package/dist/tubeMap/nodeColors.js

@@ -1,22 +1,26 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-T2PCSAFY.js";
-import "../chunks/chunk-A4PFFC4Q.js";
+} from "../chunks/chunk-7XR26JST.js";
+import "../chunks/chunk-2XEQR54X.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-ZY2AFL4Y.js";
-import "../chunks/chunk-3XSM4OZU.js";
-import "../chunks/chunk-JBCZIBFC.js";
-import "../chunks/chunk-M6LK4GII.js";
-import "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-GQZVR5DW.js";
+import "../chunks/chunk-WA5WNP6V.js";
+import "../chunks/chunk-IYALCKNB.js";
+import "../chunks/chunk-CRCD3ODN.js";
+import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-VX656OAZ.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 export {
   tubeMapNodeColors
 };

package/dist/tubeMap/reads.js

@@ -5,7 +5,7 @@ import {
   readColor,
   stepName,
   tubeMapReads
-} from "../chunks/chunk-CWFNEKST.js";
+} from "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   FORWARD_READ_COLORS,

package/dist/tubeMap/warp.js

@@ -2,7 +2,8 @@ import {
   MAX_GAP_PX,
   referenceKnots,
   warpX
-} from "../chunks/chunk-HK5Y2YWV.js";
+} from "../chunks/chunk-MYDHU2UV.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
   MAX_GAP_PX,
   referenceKnots,

package/dist/types/alleleProjection/projectAlleles.d.ts

@@ -1,4 +1,5 @@
 import type { Graph } from '../types.js';
+export { parsePanSN } from '../pansn.js';
 export interface ProjectedAllele {
     start: number;
     refSpan: number;
@@ -6,8 +7,4 @@ export interface ProjectedAllele {
     nodeOffsets: number[];
     pathLength: number;
 }
-export declare function parsePanSN(refName: string): {
-    sample: string;
-    haplotype: number | undefined;
-};
 export declare function projectAlleles(graph: Graph): ProjectedAllele[];

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

@@ -12,7 +12,5 @@ export interface BubbleHalo {
     whole: boolean;
     tick: boolean;
 }
-export declare const WHOLE_FRACTION = 0.9;
 export declare function coversGraph(members: number, nodes: number): boolean;
-export declare const SMALL_VARIANT_BP = 50;
 export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, repeats?: readonly RepeatSpan[]): BubbleHalo[];