@jbrowse/bandage-core 9.8.0 → 9.9.0

package/dist/bubbles/popBubble.js

@@ -1,7 +1,7 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-VHW7FDHU.js";
-import "../chunks/chunk-ST2IBUAN.js";
+} from "../chunks/chunk-A6PSWTLX.js";
+import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/bubbles/superbubbles.js

@@ -1,14 +1,14 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-C55SC5AJ.js";
-import "../chunks/chunk-VHW7FDHU.js";
+} from "../chunks/chunk-ROQGMTFB.js";
+import "../chunks/chunk-A6PSWTLX.js";
 import "../chunks/chunk-EHUBJDDB.js";
 import "../chunks/chunk-XKWD2RY3.js";
 import "../chunks/chunk-CLOP7UVD.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-HNQPEMYE.js";
-import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-IGJCTPFB.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-75HR3756.js → chunk-2NROXCK3.js}

@@ -4,6 +4,9 @@ import {
 import {
   readColor
 } from "./chunk-CWFNEKST.js";
+import {
+  pathOrigin
+} from "./chunk-IGJCTPFB.js";
 
 // src/tubeMap/draw.ts
 import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";
@@ -53,9 +56,9 @@ function extentOf(commands) {
   }
   return { x0, x1 };
 }
-function shapeOf(d, color, id, haplotype) {
+function shapeOf(d, color, id, haplotype, reference) {
   const commands = parsePath(d);
-  return { commands, color, id, haplotype, ...extentOf(commands) };
+  return { commands, color, id, haplotype, reference, ...extentOf(commands) };
 }
 function trackColors(layout, pathColors) {
   return new Map(
@@ -65,30 +68,43 @@ function trackColors(layout, pathColors) {
     ])
   );
 }
-function layerOf(layout, type, colors) {
+function layerOf(layout, type, colors, referenceIds) {
   const { shapes } = layout;
   const haplotype = type === "haplotype";
   const colorOf = (s) => colors.get(s.id);
+  const isReference = (s) => haplotype && referenceIds.has(s.id);
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
     color: colorOf(r),
     id: r.id,
     haplotype,
+    reference: isReference(r),
     x0: r.xStart,
     x1: r.xEnd + 1,
     y0: r.yStart,
     y1: r.yEnd + 1
   }));
   const curves = curvePaths(shapes.curves, type).map(
-    (c) => shapeOf(c.path, colorOf(c), c.id, haplotype)
+    (c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c))
   );
-  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), c.id, haplotype));
+  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, colorOf(c), c.id, haplotype, isReference(c)));
   return { rects, shapes: [...curves, ...corners] };
 }
+function referenceTrackIds(graph) {
+  const ids = /* @__PURE__ */ new Set();
+  graph?.paths?.forEach((path, i) => {
+    if (pathOrigin(path.name).name === graph.referencePath) {
+      ids.add(i);
+    }
+  });
+  return ids;
+}
 function tubeMapPicture({
   layout,
-  pathColors
+  pathColors,
+  graph
 }) {
   const colors = trackColors(layout, pathColors);
+  const referenceIds = referenceTrackIds(graph);
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
@@ -99,8 +115,8 @@ function tubeMapPicture({
   return {
     bounds: layout.bounds,
     layers: [
-      layerOf(layout, "haplotype", colors),
-      layerOf(layout, "read", colors)
+      layerOf(layout, "haplotype", colors, referenceIds),
+      layerOf(layout, "read", colors, referenceIds)
     ],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
@@ -181,14 +197,29 @@ function drawTubeMap(ctx, picture, frame) {
   const colorOf = (item) => item.haplotype && frame.tubeColors?.[item.id] || item.color;
   ctx.globalAlpha = 1;
   for (const layer of picture.layers) {
-    fillByColor(ctx, layer.rects, visible, colorOf, (r) => {
-      const left = x(r.x0);
-      const top = y(r.y0);
-      ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);
-    });
-    fillByColor(ctx, layer.shapes, visible, colorOf, (s) => {
-      trace(ctx, s.commands, x, y);
-    });
+    for (const reference of [false, true]) {
+      const inPass = (item) => item.reference === reference;
+      fillByColor(
+        ctx,
+        layer.rects,
+        (r) => inPass(r) && visible(r),
+        colorOf,
+        (r) => {
+          const left = x(r.x0);
+          const top = y(r.y0);
+          ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);
+        }
+      );
+      fillByColor(
+        ctx,
+        layer.shapes,
+        (s) => inPass(s) && visible(s),
+        colorOf,
+        (s) => {
+          trace(ctx, s.commands, x, y);
+        }
+      );
+    }
   }
   const stroke = frame.darkMode ? "#d0d0d0" : "#000000";
   const fill = frame.darkMode ? "rgba(40,40,40,0.4)" : "rgba(255,255,255,0.4)";

package/dist/chunks/{chunk-MAUEPAMG.js → chunk-6PYZYBBF.js}

@@ -1,6 +1,6 @@
 import {
   pathOrigin
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 import {
   panSNContig,
   panSNSample

package/dist/chunks/{chunk-VHW7FDHU.js → chunk-A6PSWTLX.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

package/dist/chunks/{chunk-CG77WIFD.js → chunk-BEMPOHHG.js}

@@ -1,22 +1,22 @@
+import {
+  svgCanvas
+} from "./chunk-47DYCZOK.js";
 import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-QMJXHYVQ.js";
+} from "./chunk-MECWJY2R.js";
 import {
   Canvas2DRenderer
 } from "./chunk-WBCOREDZ.js";
 import {
   layoutGeometryInputs
 } from "./chunk-LOCJN3BZ.js";
-import {
-  svgCanvas
-} from "./chunk-47DYCZOK.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-EPREHMKU.js";
+} from "./chunk-P6O4RSOQ.js";
 import {
   genePins
 } from "./chunk-BUBZ32IC.js";
@@ -27,14 +27,14 @@ import {
 } from "./chunk-3S3YVOJ7.js";
 import {
   axisScaleOf
-} from "./chunk-XKM5OHQQ.js";
+} from "./chunk-ZBLKAWSD.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-3FVITQAJ.js";
+} from "./chunk-EE37PVQY.js";
 import {
   encodingStops
-} from "./chunk-AM3P3WWO.js";
+} from "./chunk-F5BYHLIN.js";
 import {
   rangeText,
   walkKey
@@ -42,18 +42,18 @@ import {
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-BOHK5BD3.js";
+} from "./chunk-F4BKWWLS.js";
 import {
   version
-} from "./chunk-JEF73V3A.js";
+} from "./chunk-UVZ56CZX.js";
 import {
   walkRowLabels,
   walkRowsExtent
-} from "./chunk-3C5UXR2U.js";
+} from "./chunk-TOVOJNT7.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-7GBL7SJY.js";
+} from "./chunk-EDASNMLY.js";
 import {
   nodeInk
 } from "./chunk-PBENCR5L.js";
@@ -91,7 +91,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-ZGRYFUXE.js";
+} from "./chunk-FPTI3WAV.js";
 import {
   deletionDrawing,
   deletionEdges

package/dist/chunks/{chunk-7GBL7SJY.js → chunk-EDASNMLY.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-3ZZSX5HN.js";
 import {
   pathOrigin
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 import {
   isGenericSample
 } from "./chunk-BPLIXMH7.js";

package/dist/chunks/{chunk-3FVITQAJ.js → chunk-EE37PVQY.js}

@@ -1,10 +1,10 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-AM3P3WWO.js";
+} from "./chunk-F5BYHLIN.js";
 import {
   pathOrigin
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 import {
   panSNContig
 } from "./chunk-BPLIXMH7.js";

package/dist/chunks/{chunk-BOHK5BD3.js → chunk-F4BKWWLS.js}

@@ -8,7 +8,7 @@ import {
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-7GBL7SJY.js";
+} from "./chunk-EDASNMLY.js";
 import {
   meanDepth,
   nodeWidthPx

package/dist/chunks/{chunk-AM3P3WWO.js → chunk-F5BYHLIN.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-BOHK5BD3.js";
+} from "./chunk-F4BKWWLS.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-ZGRYFUXE.js → chunk-FPTI3WAV.js}

@@ -6,7 +6,10 @@ import {
 } from "./chunk-IGVV37VI.js";
 import {
   convertGFAToGraph
-} from "./chunk-OCMBULGN.js";
+} from "./chunk-J7YKQ5YW.js";
+import {
+  gfaTables
+} from "./chunk-G45YY72K.js";
 import {
   graphFromTables
 } from "./chunk-OA7RIMZ2.js";
@@ -20,7 +23,7 @@ import {
 } from "./chunk-JVLURPFW.js";
 import {
   anchorGraph
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 import {
   mergeRuns,
   splitRuns
@@ -42,11 +45,15 @@ import {
 } from "./chunk-FYQWPEEY.js";
 
 // src/pipeline.ts
+function graphOf(source, name) {
+  if (typeof source !== "string") {
+    return graphFromTables(source, name);
+  }
+  const tables = gfaTables(source);
+  return tables ? graphFromTables(tables, name) : convertGFAToGraph(parseGFA(source), name);
+}
 function loadGraph(source, name, opts = {}) {
-  const graph = anchorGraph(
-    typeof source === "string" ? convertGFAToGraph(parseGFA(source), name) : graphFromTables(source, name),
-    opts.referencePath
-  );
+  const graph = anchorGraph(graphOf(source, name), opts.referencePath);
   if (graph.nodes.length === 0) {
     throw new Error(`No graph segments in ${name}`);
   }

package/dist/chunks/chunk-G45YY72K.js

@@ -0,0 +1,220 @@
+// src/gfa/gfaTables.ts
+var GT = 62;
+var LT = 60;
+var TAB = 9;
+var ZERO = 48;
+var NINE = 57;
+var TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;
+var UNTABLED_RECORD = /^[PEOUFG]\t/;
+var trimCR = (line) => line.endsWith("\r") ? line.slice(0, -1) : line;
+var Steps = class {
+  constructor() {
+    this.nodes = new Int32Array(1 << 16);
+    this.reversed = new Uint8Array(1 << 16);
+    this.length = 0;
+  }
+  push(node, reversed) {
+    if (this.length === this.nodes.length) {
+      const nodes = new Int32Array(this.length * 2);
+      nodes.set(this.nodes);
+      this.nodes = nodes;
+      const rev = new Uint8Array(this.length * 2);
+      rev.set(this.reversed);
+      this.reversed = rev;
+    }
+    this.nodes[this.length] = node;
+    this.reversed[this.length++] = reversed;
+  }
+};
+var SegmentIndex = class {
+  constructor() {
+    this.names = [];
+    this.byName = /* @__PURE__ */ new Map();
+    // ids that are plain decimal, so a walk step finds its segment without
+    // slicing a string out of the body
+    this.byNumber = /* @__PURE__ */ new Map();
+  }
+  has(name) {
+    return this.byName.has(name);
+  }
+  add(name) {
+    const i = this.names.length;
+    this.byName.set(name, i);
+    this.names.push(name);
+    const n = +name;
+    if (Number.isSafeInteger(n) && String(n) === name) {
+      this.byNumber.set(n, i);
+    }
+    return i;
+  }
+  of(name) {
+    return this.byName.get(name) ?? this.add(name);
+  }
+  ofNumber(n) {
+    return this.byNumber.get(n);
+  }
+};
+function readSegment(line) {
+  const [, name, sequence = "*", ...tags] = line.split("	");
+  if (!name || /^\d+$/.test(sequence)) {
+    return void 0;
+  }
+  let length = sequence === "*" ? 0 : sequence.length;
+  let refName;
+  let start;
+  let rank;
+  for (const tag of tags) {
+    if (!TABLE_TAG.test(tag)) {
+      return void 0;
+    }
+    const value = tag.slice(5);
+    const key = tag.slice(0, 2);
+    if (key === "LN") {
+      length = +value;
+    } else if (key === "SN") {
+      refName = value;
+    } else if (key === "SO") {
+      start = +value;
+    } else {
+      rank = +value;
+    }
+  }
+  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;
+  return { name, length, stable };
+}
+function readWalkBody(line, from, segments, steps) {
+  let reversed = 0;
+  let start = -1;
+  let value = 0;
+  let decimal = true;
+  const finish = (end) => {
+    if (start >= 0 && end > start) {
+      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;
+      steps.push(node ?? segments.of(line.slice(start, end)), reversed);
+    }
+  };
+  let i = from;
+  for (; i < line.length; i++) {
+    const ch = line.charCodeAt(i);
+    if (ch === GT || ch === LT) {
+      finish(i);
+      reversed = ch === LT ? 1 : 0;
+      start = i + 1;
+      value = 0;
+      decimal = true;
+    } else if (ch === TAB) {
+      break;
+    } else if (decimal && ch >= ZERO && ch <= NINE) {
+      value = value * 10 + ch - ZERO;
+    } else {
+      decimal = false;
+    }
+  }
+  finish(i);
+}
+function walkFields(line) {
+  const fields = [];
+  let at = 0;
+  while (fields.length < 6) {
+    const tab = line.indexOf("	", at);
+    if (tab === -1) {
+      return void 0;
+    }
+    fields.push(line.slice(at, tab));
+    at = tab + 1;
+  }
+  const [, sample, haplotype, contig, start, end] = fields;
+  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;
+}
+function gfaTables(text) {
+  const lines = text.split("\n");
+  const segments = new SegmentIndex();
+  const lengths = [];
+  const refs = [];
+  const starts = [];
+  const ranks = [];
+  const refNames = [];
+  const refIndex = /* @__PURE__ */ new Map();
+  for (const raw of lines) {
+    if (UNTABLED_RECORD.test(raw)) {
+      return void 0;
+    }
+    if (raw.startsWith("S	")) {
+      const s = readSegment(trimCR(raw));
+      if (!s || segments.has(s.name)) {
+        return void 0;
+      }
+      segments.add(s.name);
+      lengths.push(s.length);
+      let ref = -1;
+      if (s.stable) {
+        ref = refIndex.get(s.stable.refName) ?? refNames.length;
+        if (ref === refNames.length) {
+          refNames.push(s.stable.refName);
+          refIndex.set(s.stable.refName, ref);
+        }
+      }
+      refs.push(ref);
+      starts.push(s.stable?.start ?? 0);
+      ranks.push(s.stable?.rank ?? 0);
+    }
+  }
+  const from = [];
+  const to = [];
+  const strands = [];
+  const names = [];
+  const walkStarts = [];
+  const walkEnds = [];
+  const offsets = [0];
+  const steps = new Steps();
+  for (const raw of lines) {
+    if (raw.startsWith("L	")) {
+      const [, source, strand1, target, strand2] = trimCR(raw).split("	");
+      if (source && target && strand2) {
+        from.push(segments.of(source));
+        to.push(segments.of(target));
+        strands.push((strand1 === "-" ? 1 : 0) | (strand2 === "-" ? 2 : 0));
+      }
+    } else if (raw.startsWith("W	")) {
+      const line = trimCR(raw);
+      const w = walkFields(line);
+      if (w) {
+        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);
+        walkStarts.push(w.start === "*" ? 0 : +w.start);
+        walkEnds.push(w.end === "*" ? -1 : +w.end);
+        readWalkBody(line, w.body, segments, steps);
+        if (steps.length === offsets.at(-1)) {
+          return void 0;
+        }
+        offsets.push(steps.length);
+      }
+    }
+  }
+  return {
+    nodes: {
+      names: segments.names,
+      lengths: Int32Array.from(lengths),
+      refs: Int32Array.from(refs),
+      starts: Float64Array.from(starts),
+      ranks: Int32Array.from(ranks),
+      refNames
+    },
+    links: {
+      from: Int32Array.from(from),
+      to: Int32Array.from(to),
+      strands: Uint8Array.from(strands)
+    },
+    walks: {
+      names,
+      starts: Float64Array.from(walkStarts),
+      ends: Float64Array.from(walkEnds),
+      offsets: Int32Array.from(offsets),
+      steps: steps.nodes.slice(0, steps.length),
+      reversed: steps.reversed.slice(0, steps.length)
+    }
+  };
+}
+
+export {
+  gfaTables
+};

package/dist/chunks/{chunk-6N7H22SS.js → chunk-HOZI3FBG.js}

@@ -6,10 +6,10 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-7GBL7SJY.js";
+} from "./chunk-EDASNMLY.js";
 import {
   pathOrigin
-} from "./chunk-ST2IBUAN.js";
+} from "./chunk-IGJCTPFB.js";
 import {
   ownStrand,
   strandSides

package/dist/chunks/{chunk-ST2IBUAN.js → chunk-IGJCTPFB.js}

@@ -48,7 +48,7 @@ function chooseReferencePath(anchorPaths, preferred) {
   return named ?? anchorPaths[0];
 }
 var OFF_REFERENCE_RANK = 1;
-function anchorNode(node, visits, reference) {
+function anchorNode(node, visits, reference, samplesOf) {
   let anchored = node;
   if (visits && visits.length > 0) {
     const anchor = visits.find((v) => v.path === reference) ?? visits[0];
@@ -60,22 +60,47 @@ function anchorNode(node, visits, reference) {
         rank: anchor.path === reference ? REFERENCE_RANK : OFF_REFERENCE_RANK,
         strand: anchor.strand
       },
-      samples: [...new Set(visits.map((v) => v.sample))].sort()
+      samples: samplesOf(visits)
     };
   }
   return anchored;
 }
+function sampleSorter(paths) {
+  const sorted = [...new Set(paths.map((p) => p.sample))].sort();
+  const rank = new Map(sorted.map((sample, i) => [sample, i]));
+  const seen = new Uint8Array(sorted.length);
+  return (visits) => {
+    const ranks = [];
+    for (const { sample } of visits) {
+      const r = rank.get(sample);
+      if (r === void 0) {
+        ranks.forEach((r2) => seen[r2] = 0);
+        return [...new Set(visits.map((v) => v.sample))].sort();
+      }
+      if (seen[r] === 0) {
+        seen[r] = 1;
+        ranks.push(r);
+      }
+    }
+    ranks.forEach((r) => seen[r] = 0);
+    return Array.from(Int32Array.from(ranks).sort(), (r) => sorted[r]);
+  };
+}
 function anchorFromPaths(graph, preferred) {
   const { anchorPaths, pathVisits } = graph;
   const reference = anchorPaths && pathVisits ? chooseReferencePath(anchorPaths, preferred) : void 0;
-  return reference && pathVisits ? {
+  if (!reference || !anchorPaths || !pathVisits) {
+    return graph;
+  }
+  const samplesOf = sampleSorter(anchorPaths);
+  return {
     ...graph,
     nodes: graph.nodes.map(
-      (node) => anchorNode(node, pathVisits.get(node.name), reference.name)
+      (node) => anchorNode(node, pathVisits.get(node.name), reference.name, samplesOf)
     ),
     anchoredBy: "paths",
     referencePath: reference.name
-  } : graph;
+  };
 }
 function anchorGraph(graph, preferred) {
   return graph.anchoredBy === "tags" ? graph : anchorFromPaths(graph, preferred);

package/dist/chunks/{chunk-Z7UWHVOM.js → chunk-IJRNMO4D.js}

@@ -6,7 +6,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-6N7H22SS.js";
+} from "./chunk-HOZI3FBG.js";
 import {
   anchoredLayout
 } from "./chunk-L3O7AWLI.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-HNQPEMYE.js";
 import {
   walkRowLayout
-} from "./chunk-3C5UXR2U.js";
+} from "./chunk-TOVOJNT7.js";
 import {
   isBackbone,
   isOffReference