@jbrowse/bandage-core 11.3.0 → 11.5.0

package/dist/bubbles/superbubbles.js

@@ -1,12 +1,12 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-2Q22S52W.js";
-import "../chunks/chunk-RFG42VIO.js";
-import "../chunks/chunk-PNMJFFNB.js";
+} from "../chunks/chunk-2E25TX4G.js";
 import "../chunks/chunk-E4ZM4OOJ.js";
+import "../chunks/chunk-RFG42VIO.js";
 import "../chunks/chunk-A4JDEUAI.js";
 import "../chunks/chunk-FX4RDMDN.js";
+import "../chunks/chunk-PNMJFFNB.js";
 import "../chunks/chunk-UAFATXYA.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";

package/dist/chunks/{chunk-T35BSLW5.js → chunk-3BCVMZUT.js}

@@ -4,27 +4,27 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-DR24UTRS.js";
-import {
-  walkKey
-} from "./chunk-D4ZFRBB4.js";
+} from "./chunk-VQ7474EH.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-JOWKKQAL.js";
+import {
+  walkKey
+} from "./chunk-D4ZFRBB4.js";
 import {
   walkRowsExtent
-} from "./chunk-TZLEHZVC.js";
+} from "./chunk-FWSERUJV.js";
 import {
   pathLegend,
   walkLabelsOf
 } from "./chunk-3GP3KT5L.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-EFD753MS.js";
+} from "./chunk-K5LDBMLX.js";
 import {
   drawingBounds
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 import {
   referenceLabel
 } from "./chunk-234NFZS4.js";

package/dist/chunks/{chunk-3HGYGISG.js → chunk-3U3C4PRK.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-M75QPZNJ.js";
+} from "./chunk-64FCX424.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

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

@@ -3,7 +3,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-3LZ334X4.js";
+} from "./chunk-RK3HRRCW.js";
 import {
   sampleRowLayout
 } from "./chunk-GJU6BJJA.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-TZLEHZVC.js";
+} from "./chunk-FWSERUJV.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-M75QPZNJ.js → chunk-64FCX424.js}

@@ -1,7 +1,7 @@
 import {
   tableNodeIds,
   tablePath
-} from "./chunk-B5ARSBOH.js";
+} from "./chunk-NJGYLYU7.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";
@@ -69,8 +69,8 @@ function graphPieces(graph) {
     heads,
     from,
     to,
-    steps,
-    lengths,
+    steps: Int32Array.from(steps),
+    lengths: Int32Array.from(lengths),
     names,
     reference: referenceWalkName(graph)
   };
@@ -92,8 +92,8 @@ function tablePieces(tables, referencePath, visits) {
   }
   return {
     heads,
-    from: kept.map((p) => w.offsets[p]),
-    to: kept.map((p) => w.offsets[p + 1]),
+    from: Int32Array.from(kept, (p) => w.offsets[p]),
+    to: Int32Array.from(kept, (p) => w.offsets[p + 1]),
     steps: w.steps,
     lengths: n.lengths,
     // a visit names its node as the Graph does, which costs a pass over the
@@ -120,24 +120,35 @@ var Columns = class {
   get length() {
     return this.values[0].length;
   }
-  push(...row) {
-    row.forEach((v, i) => this.values[i].push(v));
+  push(a, b, c, d, e) {
+    const v = this.values;
+    v[0].push(a);
+    v[1].push(b);
+    v[2].push(c);
+    v[3].push(d);
+    if (e !== void 0) {
+      v[4].push(e);
+    }
   }
   endRow() {
     this.offsets.push(this.length);
   }
   // the rows in `order`, column i in the array `make[i]` makes
   reorder(order, make) {
-    const columns = make.map((m) => m(this.length));
     const offsets = new Uint32Array(order.length + 1);
-    let at = 0;
     order.forEach((row, i) => {
-      for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++, at++) {
-        columns.forEach((column, c) => {
-          column[at] = this.values[c][k];
-        });
+      offsets[i + 1] = offsets[i] + this.offsets[row + 1] - this.offsets[row];
+    });
+    const columns = make.map((m, c) => {
+      const from = this.values[c];
+      const out = m(this.length);
+      let at = 0;
+      for (const row of order) {
+        for (let k = this.offsets[row]; k < this.offsets[row + 1]; k++) {
+          out[at++] = from[k];
+        }
       }
-      offsets[i + 1] = at;
+      return out;
     });
     return { offsets, columns };
   }
@@ -173,7 +184,7 @@ function walkRowRuns(source, region, o = {}) {
   const cut = region && region.end > region.start ? region : void 0;
   for (const piece of referencePieces) {
     let pos = startOf(piece) ?? 0;
-    for (let s = from[piece]; s < to[piece]; s++) {
+    for (let s = from[piece], stop = to[piece]; s < stop; s++) {
       const node = all[s];
       const len = lengthOf(node);
       if (Number.isNaN(spanStart[node])) {
@@ -241,7 +252,7 @@ function walkRowRuns(source, region, o = {}) {
         stepStart[length++] = end;
       }
       let pos = start2 ?? 0;
-      for (let s = from[piece]; s < to[piece]; s++) {
+      for (let s = from[piece], stop2 = to[piece]; s < stop2; s++) {
         const node = all[s];
         steps[length] = node;
         stepStart[length++] = pos;
@@ -298,8 +309,8 @@ function walkRowRuns(source, region, o = {}) {
       let bestEnd = -Infinity;
       let bestStart = Infinity;
       for (let i = 0; i < length; i++) {
-        if (onReference(i)) {
-          const id = steps[i];
+        const id = steps[i];
+        if (id >= 0 && !Number.isNaN(spanStart[id])) {
           if (spanEnd[id] <= cut.start && spanEnd[id] > bestEnd) {
             bestEnd = spanEnd[id];
             i0 = i;

package/dist/chunks/{chunk-XVS52NMZ.js → chunk-7EDGWT67.js}

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

package/dist/chunks/{chunk-PNM6Z3IE.js → chunk-A32ZKSHN.js}

@@ -3,14 +3,14 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-XZ6PQBU6.js";
+} from "./chunk-TRGKMLXT.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM,
   longestBar
-} from "./chunk-TZLEHZVC.js";
+} from "./chunk-FWSERUJV.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-BXLLMWC3.js → chunk-AKLSY4GD.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-3UST3ZQE.js → chunk-EGBBIXTG.js}

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

package/dist/chunks/{chunk-TZLEHZVC.js → chunk-FWSERUJV.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-JDZ5GTZT.js";
+} from "./chunk-IOWLTUEB.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-TABI4JEU.js → chunk-HN3WHMPJ.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-JOWKKQAL.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-JDZ5GTZT.js → chunk-IOWLTUEB.js}

@@ -1,7 +1,7 @@
 import {
   walkRowRuns,
   walkRowsOf
-} from "./chunk-M75QPZNJ.js";
+} from "./chunk-64FCX424.js";
 
 // src/layout/walkRows.ts
 function filterSamples(rows, samples) {

package/dist/chunks/{chunk-TUQKGAK3.js → chunk-J3JODFDF.js}

@@ -28,7 +28,7 @@ function parseRegion(text) {
   const m = /^\s*([^:\s]+):([\d,]+)-([\d,]+)\s*$/.exec(text);
   if (!m) {
     throw new Error(
-      `"${text}" is not a region like chr6:160,614,798-160,647,758`
+      `"${text}" is not a 0-based region like chr6:160,614,797-160,647,758`
     );
   }
   const n = (s) => Number(s.replaceAll(",", ""));

package/dist/chunks/chunk-JOLLU34X.js

@@ -0,0 +1,21 @@
+// src/locus.ts
+var LOCUS = /^\s*([^:\s]+):\s*([\d,]+)(?:\s*(?:-|\.\.)\s*([\d,]+))?\s*$/;
+function parseLocus(text) {
+  const m = LOCUS.exec(text);
+  if (!m) {
+    return void 0;
+  }
+  const n = (s) => Number(s.replaceAll(",", ""));
+  const start = n(m[2]) - 1;
+  const end = m[3] ? n(m[3]) : start + 1;
+  return start >= 0 && end > start ? { refName: m[1], start, end } : void 0;
+}
+var grouped = (n) => String(n).replace(/\B(?=(\d{3})+(?!\d))/g, ",");
+function formatLocus(r) {
+  return `${r.refName}:${grouped(r.start + 1)}-${grouped(r.end)}`;
+}
+
+export {
+  parseLocus,
+  formatLocus
+};

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

@@ -35,6 +35,9 @@ import {
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";
+import {
+  isBackbone
+} from "./chunk-RJWPJCIB.js";
 
 // src/renderer/GeometryBuilder.ts
 var EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);
@@ -262,6 +265,10 @@ function hashColor(str, alpha) {
 var REFERENCE_RAMP_ALT_RGB = [60, 65, 72];
 var REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);
 var REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(", ")})`;
+function rampFraction(node, ramp) {
+  const mid = ramp.midpoints.get(node.id);
+  return isBackbone(node) && mid !== void 0 ? (mid - ramp.start) / ramp.span : void 0;
+}
 function computeReferenceRamp(graph, domain) {
   const midpoints = referenceMidpoints(graph);
   if (domain && domain.end > domain.start) {
@@ -339,20 +346,15 @@ function getNodeColor(node, nodeIndex, colorScheme, range) {
         range.maxRank > 1 ? (node.stable.rank - 1) / (range.maxRank - 1) : 0
       );
     // Position on the reference, the one quantity both panels of a
-    // graph-over-linear figure can state. A node with no reference position at
-    // all — nothing anchored, or an allele whose flanks fell outside the cut —
-    // is grey rather than a hue it has not earned.
+    // graph-over-linear figure can state, so only the backbone takes a hue
     case "reference-position": {
       const ramp = range.referenceRamp;
-      const mid = ramp?.midpoints.get(node.id);
-      if (ramp === void 0 || mid === void 0) {
+      if (ramp === void 0) {
         return packAbgr(160, 160, 160, 255);
       }
-      if (node.stable !== void 0 && node.stable.rank > 0) {
-        return REFERENCE_RAMP_ALT_COLOR;
-      }
-      return packHsl(
-        rampHueAt((mid - ramp.start) / ramp.span),
+      const t = rampFraction(node, ramp);
+      return t === void 0 ? REFERENCE_RAMP_ALT_COLOR : packHsl(
+        rampHueAt(t),
         REFERENCE_RAMP_SATURATION,
         REFERENCE_RAMP_LIGHTNESS
       );
@@ -687,6 +689,7 @@ export {
   hslToRgb,
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_ALT_CSS,
+  rampFraction,
   computeReferenceRamp,
   computeColorSchemeRange,
   getNodeColor,

package/dist/chunks/{chunk-EFD753MS.js → chunk-K5LDBMLX.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

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

@@ -3,25 +3,25 @@ import {
 } from "./chunk-JMABOQWL.js";
 import {
   layoutModeByValue
-} from "./chunk-TEXAKEJX.js";
+} from "./chunk-5F4D35U5.js";
 import {
   parseRegion
-} from "./chunk-TUQKGAK3.js";
+} from "./chunk-J3JODFDF.js";
 import {
   genePins
 } from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-XEWPWCML.js";
+} from "./chunk-WLR4KJVI.js";
 import {
   axisScaleOf
-} from "./chunk-CE6ZIKJX.js";
+} from "./chunk-XKZ56L5A.js";
 import {
   figureScene
-} from "./chunk-T35BSLW5.js";
+} from "./chunk-3BCVMZUT.js";
 import {
   encodingStops
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-HN3WHMPJ.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -30,13 +30,13 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-EFD753MS.js";
+} from "./chunk-K5LDBMLX.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";

package/dist/chunks/{chunk-B5ARSBOH.js → chunk-NJGYLYU7.js}

@@ -55,7 +55,7 @@ function namesByList(lists, names, listCount, pathNames) {
     return out;
   });
 }
-function tableNodeIds({ nodes: n, links: l, walks: w }) {
+function tableNodeIds({ nodes: n, links: l, walks: w }, traversals) {
   const canonical = new Uint8Array(n.names.length);
   const claim = (node, reversed) => {
     if (canonical[node] === 0) {
@@ -68,7 +68,11 @@ function tableNodeIds({ nodes: n, links: l, walks: w }) {
   }
   const stepCount = w.offsets[w.names.length] ?? 0;
   for (let s = 0; s < stepCount; s++) {
-    claim(w.steps[s], w.reversed[s]);
+    const node = w.steps[s];
+    claim(node, w.reversed[s]);
+    if (traversals) {
+      traversals[node]++;
+    }
   }
   return n.names.map(
     (segment, i) => `${segment}${canonical[i] === 2 ? "-" : "+"}`
@@ -84,10 +88,7 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
     }
   }
   const traversals = new Int32Array(count);
-  for (const node of w.steps.subarray(0, w.offsets[w.names.length])) {
-    traversals[node]++;
-  }
-  const ids = tableNodeIds({ nodes: n, links: l, walks: w });
+  const ids = tableNodeIds({ nodes: n, links: l, walks: w }, traversals);
   const nodes = [];
   for (let i = 0; i < declared; i++) {
     const ref = n.refs[i];

package/dist/chunks/{chunk-RNNYRNDU.js → chunk-PQBALYSO.js}

@@ -1,19 +1,19 @@
+import {
+  stripGeneGaps,
+  walkStripFrame,
+  walkStripLabelsTree
+} from "./chunk-A32ZKSHN.js";
 import {
   Canvas2DRenderer
 } from "./chunk-EJRJAAN7.js";
 import {
   svgCanvas
 } from "./chunk-V4YML3GR.js";
-import {
-  stripGeneGaps,
-  walkStripFrame,
-  walkStripLabelsTree
-} from "./chunk-PNM6Z3IE.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-XZ6PQBU6.js";
+} from "./chunk-TRGKMLXT.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -34,32 +34,32 @@ import {
 } from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-XEWPWCML.js";
+} from "./chunk-WLR4KJVI.js";
 import {
   axisScaleOf
-} from "./chunk-CE6ZIKJX.js";
+} from "./chunk-XKZ56L5A.js";
 import {
   figureScene
-} from "./chunk-T35BSLW5.js";
+} from "./chunk-3BCVMZUT.js";
 import {
   encodingStops
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-HN3WHMPJ.js";
 import {
   rangeText
 } from "./chunk-D4ZFRBB4.js";
 import {
   walkRowLabels
-} from "./chunk-TZLEHZVC.js";
+} from "./chunk-FWSERUJV.js";
 import {
   nodeInk
 } from "./chunk-CRCD3ODN.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-EFD753MS.js";
+} from "./chunk-K5LDBMLX.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-3LZ334X4.js → chunk-RK3HRRCW.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-M75QPZNJ.js";
+} from "./chunk-64FCX424.js";
 import {
   pathCssColor,
   pathGreyCssColor

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

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-JOWKKQAL.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-TJOOHTJ6.js → chunk-VD4MLYEK.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-3LZ334X4.js";
+} from "./chunk-RK3HRRCW.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-DR24UTRS.js → chunk-VQ7474EH.js}

@@ -1,7 +1,10 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-HN3WHMPJ.js";
+import {
+  rampFraction
+} from "./chunk-JOWKKQAL.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";
@@ -114,8 +117,7 @@ function laneColors(byId, walk, encoding, ramp) {
   const colors = /* @__PURE__ */ new Map();
   for (const [id, progress] of walk.progress) {
     const node = byId.get(id);
-    const mid = ramp?.midpoints.get(id);
-    const t = encoding.field === "progress" ? progress : ramp && mid !== void 0 && !(node?.stable && node.stable.rank > 0) ? (mid - ramp.start) / ramp.span : void 0;
+    const t = encoding.field === "progress" ? progress : ramp && node ? rampFraction(node, ramp) : void 0;
     colors.set(id, encodedColor(encoding, t));
   }
   return colors;

package/dist/chunks/{chunk-7O7EGTYG.js → chunk-WC6HX6GJ.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-3LZ334X4.js";
+} from "./chunk-RK3HRRCW.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-REOWLPH4.js → chunk-WG5D2H7X.js}

@@ -1,12 +1,12 @@
+import {
+  smoothChain
+} from "./chunk-OPPVSPEF.js";
 import {
   orientToReference
 } from "./chunk-3PZSBNLI.js";
 import {
   seededNodes
 } from "./chunk-CKUVEHSS.js";
-import {
-  smoothChain
-} from "./chunk-OPPVSPEF.js";
 import {
   routeNodes,
   takeRoutes,
@@ -20,7 +20,7 @@ import {
 } from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
-} from "./chunk-B5ARSBOH.js";
+} from "./chunk-NJGYLYU7.js";
 import {
   anchorGraph
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-XEWPWCML.js → chunk-WLR4KJVI.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.3.0";
+var version = "11.5.0";
 
 export {
   version

package/dist/chunks/{chunk-CE6ZIKJX.js → chunk-XKZ56L5A.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-WG5D2H7X.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {