@jbrowse/bandage-core 11.5.0 → 11.7.0

package/dist/chunks/{chunk-77EGQQJU.js → chunk-BFUS3ENH.js}

@@ -1,9 +1,9 @@
 import {
   polylineSlice
-} from "./chunk-BZFOFC4D.js";
+} from "./chunk-2VMKQKVO.js";
 import {
   svgPath
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   firstNodeAtOrAfter,
   isAnchored

package/dist/chunks/{chunk-TGUFT6KK.js → chunk-BLUEFYIR.js}

@@ -1,6 +1,6 @@
 import {
   panSNFields
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/facetGrid.ts
 var FACET_GAP_PX = 8;
@@ -43,6 +43,9 @@ function facetGrid({
     return tile(Math.max(1, Math.min(count, Math.round(columns))));
   }
   let best = tile(1);
+  if (pixelRows) {
+    return best;
+  }
   for (let across = 2; across <= count; across++) {
     const grid = tile(across);
     if (grid.scale > best.scale) {

package/dist/chunks/{chunk-3GP3KT5L.js → chunk-BW2NMXRV.js}

@@ -1,12 +1,12 @@
-import {
-  pathOrigin
-} from "./chunk-B5X2RLJG.js";
 import {
   groupDigits
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
+import {
+  pathOrigin
+} from "./chunk-3YBP46PB.js";
 import {
   isGenericSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/pathColors.ts
 function nameHue(name) {

package/dist/chunks/{chunk-IOWLTUEB.js → chunk-BXE3SBBN.js}

@@ -1,7 +1,7 @@
 import {
   walkRowRuns,
   walkRowsOf
-} from "./chunk-64FCX424.js";
+} from "./chunk-G7SG4XMK.js";
 
 // src/layout/walkRows.ts
 function filterSamples(rows, samples) {

package/dist/chunks/{chunk-2E25TX4G.js → chunk-C6E6HXP5.js}

@@ -1,6 +1,6 @@
 import {
   coversGraph
-} from "./chunk-E4ZM4OOJ.js";
+} from "./chunk-KZMSSPS6.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -10,13 +10,13 @@ import {
 } from "./chunk-RFG42VIO.js";
 import {
   bubbleSegmentIds
-} from "./chunk-A4JDEUAI.js";
+} from "./chunk-SNF2MIEF.js";
 import {
   bubbleSubgraph
-} from "./chunk-PNMJFFNB.js";
+} from "./chunk-MHZTTLBU.js";
 import {
   strandSides
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-5I3K4R2G.js → chunk-CFXXFHRK.js}

@@ -57,7 +57,8 @@ function parseGFA(file) {
   };
   for (const rawLine of file.split("\n")) {
     const line = rawLine.endsWith("\r") ? rawLine.slice(0, -1) : rawLine;
-    const type = line.split("	", 1)[0];
+    const tab = line.indexOf("	");
+    const type = tab === -1 ? line : line.slice(0, tab);
     if (type === "H") {
       const [, ...rest] = line.split("	");
       graph.header.push(parseTags(rest));

package/dist/chunks/{chunk-JMABOQWL.js → chunk-CO6RGQAD.js}

@@ -18,13 +18,8 @@ function isLayoutEngineKind(value) {
   return LAYOUT_ENGINE_VALUES.includes(value);
 }
 var layoutEngine = async (request) => {
-  if (request.options.engine === "stress") {
-    const start2 = performance.now();
-    const result2 = stressLayout(request);
-    return { result: result2, duration: performance.now() - start2 };
-  }
   const start = performance.now();
-  const result = await fmmmLayout(request);
+  const result = request.options.engine === "stress" ? stressLayout(request) : await fmmmLayout(request);
   return { result, duration: performance.now() - start };
 };
 

package/dist/chunks/{chunk-5F4D35U5.js → chunk-DD5EZG3T.js}

@@ -3,10 +3,10 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-SIA75TEG.js";
 import {
   sampleRowLayout
-} from "./chunk-GJU6BJJA.js";
+} from "./chunk-XR2HMGAS.js";
 import {
   anchoredLayout
 } from "./chunk-GJLZ2MKE.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-FWSERUJV.js";
+} from "./chunk-SENPGW4O.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-AKLSY4GD.js → chunk-DTEXQ65J.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-VQ7474EH.js → chunk-DUREQSOJ.js}

@@ -1,24 +1,25 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-HN3WHMPJ.js";
+} from "./chunk-2XEAITWM.js";
 import {
   rampFraction
-} from "./chunk-JOWKKQAL.js";
-import {
-  pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   gapParts
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
+import {
+  pathOrigin
+} from "./chunk-3YBP46PB.js";
 import {
   panSNContig
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/walkHighlight.ts
 var isReference = (graph, name) => !!graph.referencePath && pathOrigin(name).name === graph.referencePath;
 function piecesOf(graph, name) {
-  return (graph.paths ?? []).filter((p) => p.name === name).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
+  const origin = pathOrigin(name).name;
+  return (graph.paths ?? []).filter((p) => pathOrigin(p.name).name === origin).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
 }
 var nodesById = (graph) => new Map(graph.nodes.map((n) => [n.id, n]));
 function graphIndex(graph) {

package/dist/chunks/{chunk-CGMSKIEO.js → chunk-DV5B5UU7.js}

@@ -1,9 +1,12 @@
+import {
+  referenceVisitStarts
+} from "./chunk-3YBP46PB.js";
 import {
   computeEdgeCurves,
   edgeJoinOf,
   routedEdgeCurves,
   strandSides
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";
@@ -11,6 +14,9 @@ import {
   firstNodeAtOrAfter,
   isBackbone
 } from "./chunk-RJWPJCIB.js";
+import {
+  partitionPoint
+} from "./chunk-HOAIOEI7.js";
 
 // src/deletionEdges.ts
 var MIN_DELETION_BP = 1;
@@ -70,22 +76,63 @@ function skipsBetween(edge, from, to, forwards) {
   const arrivesLeft = toStrand === (to.stable.strand ?? "+");
   return forwards ? leavesRight && arrivesLeft : !leavesRight && !arrivesLeft;
 }
+function skippedSpan(edge, from, to, startsOf) {
+  let best;
+  for (const a of startsOf(from)) {
+    for (const b of startsOf(to)) {
+      const forwards = a <= b;
+      const span = forwards ? { start: a + from.length, end: b } : { start: b + to.length, end: a };
+      if (skipsBetween(edge, from, to, forwards) && (!best || Math.abs(span.end - span.start) < Math.abs(best.end - best.start))) {
+        best = span;
+      }
+    }
+  }
+  return best;
+}
+var COPY_SWITCH_SHARE = 0.01;
+function repeatCopies(backbone, startsOf) {
+  const bySequence = /* @__PURE__ */ new Map();
+  for (const [refName, nodes] of backbone) {
+    const copies = nodes.flatMap((node) => {
+      const starts = startsOf(node);
+      return starts.slice(1).map((next, i) => ({
+        at: starts[i],
+        copy: next - starts[i]
+      }));
+    });
+    if (copies.length) {
+      bySequence.set(
+        refName,
+        copies.sort((a, b) => a.at - b.at)
+      );
+    }
+  }
+  return bySequence;
+}
+function switchesCopy(copies, start, bp) {
+  if (!copies) {
+    return false;
+  }
+  const i = partitionPoint(copies.length, (k) => copies[k].at < start);
+  const near = [copies[i - 1], copies[i]].filter((c) => c !== void 0).sort((a, b) => Math.abs(a.at - start) - Math.abs(b.at - start))[0];
+  return near !== void 0 && Math.abs(near.at - start) <= near.copy && Math.abs(bp - near.copy) <= near.copy * COPY_SWITCH_SHARE;
+}
 function deletionEdges(graph) {
   const byId = new Map(graph.nodes.map((n) => [n.id, n]));
   const backbone = backboneBySequence(graph);
+  const startsOf = referenceVisitStarts(graph);
+  const copies = repeatCopies(backbone, startsOf);
   const found = [];
   for (let edgeIndex = 0; edgeIndex < graph.edges.length; edgeIndex++) {
     const edge = graph.edges[edgeIndex];
     const from = byId.get(edge.from);
     const to = byId.get(edge.to);
     if (from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {
-      const forwards = from.stable.start <= to.stable.start;
-      const [left, right] = forwards ? [from, to] : [to, from];
-      const start = left.stable.start + left.length;
-      const end = right.stable.start;
-      const bp = end - start;
-      if (bp >= MIN_DELETION_BP && skipsBetween(edge, from, to, forwards)) {
-        const refName = left.stable.refName;
+      const span = skippedSpan(edge, from, to, startsOf);
+      const refName = from.stable.refName;
+      const bp = span ? span.end - span.start : 0;
+      if (span && bp >= MIN_DELETION_BP && !switchesCopy(copies.get(refName), span.start, bp)) {
+        const { start, end } = span;
         found.push({
           edgeIndex,
           from: edge.from,

package/dist/chunks/{chunk-KOJKFNCW.js → chunk-EH5JZETS.js}

@@ -1,27 +1,27 @@
 import {
   layoutEngine
-} from "./chunk-JMABOQWL.js";
+} from "./chunk-CO6RGQAD.js";
 import {
   layoutModeByValue
-} from "./chunk-5F4D35U5.js";
+} from "./chunk-DD5EZG3T.js";
 import {
   parseRegion
-} from "./chunk-J3JODFDF.js";
+} from "./chunk-FNDNSDKW.js";
 import {
   genePins
-} from "./chunk-77EGQQJU.js";
+} from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-WLR4KJVI.js";
+} from "./chunk-ZHZRAYEM.js";
 import {
   axisScaleOf
-} from "./chunk-XKZ56L5A.js";
+} from "./chunk-5ZQKQ24Z.js";
 import {
   figureScene
-} from "./chunk-3BCVMZUT.js";
+} from "./chunk-WWIUC4N4.js";
 import {
   encodingStops
-} from "./chunk-HN3WHMPJ.js";
+} from "./chunk-2XEAITWM.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -30,13 +30,16 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-K5LDBMLX.js";
+} from "./chunk-NTKWT6XL.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
+import {
+  referenceVisitStarts
+} from "./chunk-3YBP46PB.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";
@@ -68,6 +71,7 @@ function figureData(graph, layout, o = {}) {
   const {
     bounds,
     colorScheme,
+    referenceRamp,
     drawnDeletions,
     lift,
     facets,
@@ -225,6 +229,7 @@ function figureData(graph, layout, o = {}) {
       }
     }
   }
+  const startsOf = referenceVisitStarts(graph);
   return {
     meta: {
       generator: `@jbrowse/bandage-core@${version}`,
@@ -234,7 +239,13 @@ function figureData(graph, layout, o = {}) {
       pixelRows,
       referenceAxis: layout.referenceAxis ?? false,
       colorScheme,
-      referenceName: referenceName ?? null
+      referenceName: referenceName ?? null,
+      // the reference bp the position hues run between, hue 0 to 300
+      referenceRamp: referenceRamp ? {
+        start: referenceRamp.start,
+        end: referenceRamp.start + referenceRamp.span
+      } : null,
+      deletions: drawnDeletions.shown.length
     },
     panels: {
       panel: panels.map((p) => p.name),
@@ -253,7 +264,10 @@ function figureData(graph, layout, o = {}) {
       name: graph.nodes.map((n) => n.name),
       length: graph.nodes.map((n) => n.length),
       depth: graph.nodes.map((n) => n.depth),
-      backbone: graph.nodes.map((n) => isBackbone(n))
+      backbone: graph.nodes.map((n) => isBackbone(n)),
+      referenceVisits: graph.nodes.map(
+        (n) => isBackbone(n) ? startsOf(n).length : 0
+      )
     },
     rowLabels: {
       label: (layout.rowLabels ?? []).map((r) => r.label),

package/dist/chunks/{chunk-G6UIYQZR.js → chunk-EQDQ7P4Y.js}

@@ -136,13 +136,14 @@ function mergeOverlappingByName(genes) {
   }
   return out;
 }
+var BED_HEADER = /^(#|track\s|browser\s)/;
 function genesFromBed(text) {
   const rows = [];
   for (const line of text.split("\n")) {
     const cols = line.replace(/\r$/, "").split("	");
     const start = Number(cols[1]);
     const end = Number(cols[2]);
-    if (/^(#|track|browser)/.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {
+    if (BED_HEADER.test(line) || cols.length < 3 || !Number.isInteger(start) || !(end > start)) {
       continue;
     }
     const refName = cols[0];
@@ -165,7 +166,7 @@ function genesFromBed(text) {
   return mergeOverlappingByName(rows);
 }
 function sniffedFormat(text) {
-  const first = text.split("\n", 1e3).find((l) => l.trim() !== "" && !/^(#|track|browser)/.test(l));
+  const first = text.split("\n", 1e3).find((l) => l.trim() !== "" && !BED_HEADER.test(l));
   const cols = first?.split("	") ?? [];
   return /^\d+$/.test(cols[1] ?? "") && /^\d+$/.test(cols[2] ?? "") ? "bed" : "gff3";
 }

package/dist/chunks/{chunk-J3JODFDF.js → chunk-FNDNSDKW.js}

@@ -6,10 +6,10 @@ import {
   haplotypeWanted,
   referencePathQuery,
   referenceSamplesOf
-} from "./chunk-NMWQUFPF.js";
+} from "./chunk-ZKSC7QVE.js";
 import {
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/gbzCut.ts
 import { GBZBase } from "@gmod/gbz-base";
@@ -25,7 +25,7 @@ function haplotypeIndexBeside(db) {
   return GBZ_DB.test(db) ? db.replace(GBZ_DB, ".haplotype-index.db") : void 0;
 }
 function parseRegion(text) {
-  const m = /^\s*([^:\s]+):([\d,]+)-([\d,]+)\s*$/.exec(text);
+  const m = /^\s*(\S+?):([\d,]+)-([\d,]+)\s*$/.exec(text);
   if (!m) {
     throw new Error(
       `"${text}" is not a 0-based region like chr6:160,614,797-160,647,758`

package/dist/chunks/{chunk-64FCX424.js → chunk-G7SG4XMK.js}

@@ -1,26 +1,32 @@
 import {
   tableNodeIds,
   tablePath
-} from "./chunk-NJGYLYU7.js";
-import {
-  pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-7L7MN2OM.js";
 import {
   gapParts
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
+import {
+  pathOrigin
+} from "./chunk-3YBP46PB.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";
 import {
   panSNContig,
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/layout/walkRowRuns.ts
 var RUN_ON_REFERENCE = 1;
 var RUN_REVERSED = 2;
 var RUN_GAP = 4;
-var GAP_CAUSES = [void 0, "missing", "elsewhere", "unknown"];
+var GAP_CAUSES = [
+  void 0,
+  "missing",
+  "elsewhere",
+  "unknown",
+  "abridged"
+];
 var CAUSE_SHIFT = 3;
 var causeFlags = (cause) => GAP_CAUSES.indexOf(cause) << CAUSE_SHIFT;
 function referenceOf(names, referencePath, rankZero) {
@@ -179,6 +185,7 @@ function walkRowRuns(source, region, o = {}) {
   const walks = groupBy(others, nameOf);
   const spanStart = new Float64Array(names.length).fill(Number.NaN);
   const spanEnd = new Float64Array(names.length);
+  const revisits = /* @__PURE__ */ new Map();
   let reachesBefore = false;
   let reachesAfter = false;
   const cut = region && region.end > region.start ? region : void 0;
@@ -187,7 +194,14 @@ function walkRowRuns(source, region, o = {}) {
     for (let s = from[piece], stop = to[piece]; s < stop; s++) {
       const node = all[s];
       const len = lengthOf(node);
-      if (Number.isNaN(spanStart[node])) {
+      if (!Number.isNaN(spanStart[node])) {
+        const starts = revisits.get(node);
+        if (starts) {
+          starts.push(pos);
+        } else {
+          revisits.set(node, [spanStart[node], pos]);
+        }
+      } else {
         spanStart[node] = pos;
         spanEnd[node] = pos + len;
         if (cut) {
@@ -222,8 +236,10 @@ function walkRowRuns(source, region, o = {}) {
     const head = heads[pieces[0]];
     const ordered = [...pieces].sort(byStart);
     let count = ordered.length - 1;
+    let abridgedSteps = 0;
     for (const piece of ordered) {
-      count += to[piece] - from[piece];
+      count += to[piece] - from[piece] + (heads[piece].abridged ? 1 : 0);
+      abridgedSteps += heads[piece].abridged?.steps ?? 0;
     }
     if (count > steps.length) {
       steps = new Int32Array(count * 2);
@@ -252,8 +268,16 @@ function walkRowRuns(source, region, o = {}) {
         stepStart[length++] = end;
       }
       let pos = start2 ?? 0;
+      const abridged = heads[piece].abridged;
       for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {
         const node = all[s];
+        const bp3 = abridged ? abridged.bp - (pos - (start2 ?? 0)) - lengthOf(node) : 0;
+        if (bp3 > 0 && s === stop2 - 1 && s > from[piece]) {
+          partsAt.set(length, [{ bp: bp3, cause: "abridged" }]);
+          steps[length] = -bp3;
+          stepStart[length++] = pos;
+          pos += bp3;
+        }
         steps[length] = node;
         stepStart[length++] = pos;
         pos += lengthOf(node);
@@ -345,6 +369,27 @@ function walkRowRuns(source, region, o = {}) {
     let last = -1;
     let lastFlags = 0;
     let lastRef = Number.NaN;
+    let cursor = Number.NaN;
+    const placeOf = (id) => {
+      const starts = revisits.get(id);
+      if (!starts || Number.isNaN(cursor)) {
+        return spanStart[id];
+      }
+      const len = lengthOf(id);
+      let best = starts[0];
+      let bestGap = Infinity;
+      for (const start2 of starts) {
+        const gap = Math.min(
+          Math.abs(start2 - cursor),
+          Math.abs(start2 + len - cursor)
+        );
+        if (gap < bestGap) {
+          best = start2;
+          bestGap = gap;
+        }
+      }
+      return best;
+    };
     const [, runBp, runRef, runFlags] = runs.values;
     for (let k = lo; k < hi; k++) {
       const index = backward ? hi - 1 - (k - lo) : k;
@@ -369,12 +414,12 @@ function walkRowRuns(source, region, o = {}) {
         continue;
       }
       const len = lengthOf(id);
-      const at = spanStart[id];
+      const at = placeOf(id);
       const on = !Number.isNaN(at);
       visits?.push(id, bp2, len, on ? 1 : 0);
       const placed = last >= 0 && !Number.isNaN(lastRef);
       const forward = on && placed && step >= 0 && lastRef + (runBp[last] ?? 0) === at;
-      const back = on && placed && step <= 0 && spanEnd[id] === lastRef;
+      const back = on && placed && step <= 0 && at + len === lastRef;
       if (!on && last >= 0 && !(lastFlags & (RUN_ON_REFERENCE | RUN_GAP))) {
         runBp[last] += len;
       } else if (forward || back) {
@@ -394,7 +439,9 @@ function walkRowRuns(source, region, o = {}) {
         step = 0;
       }
       bp2 += len;
-      if (!on) {
+      if (on) {
+        cursor = step < 0 ? at : at + len;
+      } else {
         offReferenceBp += len;
       }
     }
@@ -410,7 +457,8 @@ function walkRowRuns(source, region, o = {}) {
       gapBp,
       complete,
       stop,
-      axis
+      axis,
+      ...abridgedSteps > 0 ? { abridgedSteps } : {}
     };
   };
   const referenceRow = rowOf(referencePieces);
@@ -462,7 +510,7 @@ function runAt(t, k) {
   };
   if (f & RUN_GAP) {
     run.gap = true;
-    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 3];
+    const cause = GAP_CAUSES[f >> CAUSE_SHIFT & 7];
     if (cause) {
       run.cause = cause;
     }

package/dist/chunks/{chunk-6EOB6ANX.js → chunk-GZ36HNPJ.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-HSVFCA2J.js";
+} from "./chunk-VO6FKNZE.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-A32ZKSHN.js → chunk-HELOUO6K.js}

@@ -3,20 +3,20 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-TRGKMLXT.js";
+} from "./chunk-A7Q7RTWX.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM,
   longestBar
-} from "./chunk-FWSERUJV.js";
-import {
-  pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-SENPGW4O.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
+import {
+  pathOrigin
+} from "./chunk-3YBP46PB.js";
 import {
   partitionPoint
 } from "./chunk-HOAIOEI7.js";