@jbrowse/bandage-core 11.5.0 → 11.6.1

package/dist/chunks/{chunk-RK3HRRCW.js → chunk-NXBW6KY6.js}

@@ -1,22 +1,21 @@
 import {
-  canonicalStrand,
   stepName,
   tubeMapReads
-} from "./chunk-A7H753BA.js";
+} from "./chunk-SDI6BVG7.js";
 import {
   referenceWalkName
-} from "./chunk-64FCX424.js";
+} from "./chunk-D3E7AXBB.js";
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-3GP3KT5L.js";
+} from "./chunk-BW2NMXRV.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   ownStrand,
   strandSides
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";
@@ -39,7 +38,7 @@ function pathSteps(graph) {
       }
       const at = visits && next ? next(visits.slot(node.name), walk) : -1;
       return [
-        { node, strand: at >= 0 ? visits.strand(at) : canonicalStrand(node) }
+        { node, strand: at >= 0 ? visits.strand(at) : ownStrand(node.id) }
       ];
     });
   });

package/dist/chunks/{chunk-WC6HX6GJ.js → chunk-OUM54ZSQ.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-NXBW6KY6.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   PathVisitsBuilder
 } from "./chunk-ZPZ7GNBT.js";

package/dist/chunks/{chunk-WA5WNP6V.js → chunk-OYCQVJYY.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-HMXCN6PG.js";
 import {
   edgeCurvesOf
-} from "./chunk-CGMSKIEO.js";
+} from "./chunk-DV5B5UU7.js";
 
 // src/util/edgeCurves.ts
 var cache = weakMemo();

package/dist/chunks/{chunk-FWSERUJV.js → chunk-P5PBJONQ.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-IOWLTUEB.js";
+} from "./chunk-MEVTV4FI.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-JOLLU34X.js → chunk-PQIFYQVI.js}

@@ -1,5 +1,5 @@
 // src/locus.ts
-var LOCUS = /^\s*([^:\s]+):\s*([\d,]+)(?:\s*(?:-|\.\.)\s*([\d,]+))?\s*$/;
+var LOCUS = /^\s*(\S+?):\s*([\d,]+)(?:\s*(?:-|\.\.)\s*([\d,]+))?\s*$/;
 function parseLocus(text) {
   const m = LOCUS.exec(text);
   if (!m) {

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

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JOWKKQAL.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-5F4D35U5.js → chunk-QD35GH4C.js}

@@ -3,10 +3,10 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-NXBW6KY6.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-P5PBJONQ.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-XKZ56L5A.js → chunk-RLCYVZ4B.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-7OTWJQGA.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

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

@@ -2,10 +2,10 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-A32ZKSHN.js";
+} from "./chunk-4WXFQOYV.js";
 import {
   Canvas2DRenderer
-} from "./chunk-EJRJAAN7.js";
+} from "./chunk-4DMSPNYV.js";
 import {
   svgCanvas
 } from "./chunk-V4YML3GR.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-TRGKMLXT.js";
+} from "./chunk-MXLYBDOX.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,45 +21,45 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-PSCSZSVK.js";
+} from "./chunk-KA4F3N55.js";
 import {
   nodesUnderBox
-} from "./chunk-OMUPUB4J.js";
+} from "./chunk-56L6R6D2.js";
 import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
 import {
   genePins
-} from "./chunk-77EGQQJU.js";
+} from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-WLR4KJVI.js";
+} from "./chunk-TXTSE44S.js";
 import {
   axisScaleOf
-} from "./chunk-XKZ56L5A.js";
+} from "./chunk-RLCYVZ4B.js";
 import {
   figureScene
-} from "./chunk-3BCVMZUT.js";
+} from "./chunk-BVWMVWLJ.js";
 import {
   encodingStops
-} from "./chunk-HN3WHMPJ.js";
+} from "./chunk-2XEAITWM.js";
 import {
   rangeText
-} from "./chunk-D4ZFRBB4.js";
+} from "./chunk-JGQQAUVL.js";
 import {
   walkRowLabels
-} from "./chunk-FWSERUJV.js";
+} from "./chunk-P5PBJONQ.js";
 import {
   nodeInk
-} from "./chunk-CRCD3ODN.js";
+} from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-K5LDBMLX.js";
+} from "./chunk-3FWNQNF7.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-7OTWJQGA.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -72,7 +72,7 @@ import {
   FACET_PAD_PX,
   FACET_TITLE_PX,
   facetGrid
-} from "./chunk-TGUFT6KK.js";
+} from "./chunk-BLUEFYIR.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';

package/dist/chunks/{chunk-A7H753BA.js → chunk-SDI6BVG7.js}

@@ -1,13 +1,13 @@
 import {
   parseCs
-} from "./chunk-C44YRP5F.js";
+} from "./chunk-5OJZV6YT.js";
+import {
+  ownStrand
+} from "./chunk-VACK24HF.js";
 
 // src/tubeMap/reads.ts
-function canonicalStrand(node) {
-  return node.id.endsWith("-") ? "-" : "+";
-}
 function stepName(node, strand) {
-  return strand === canonicalStrand(node) ? node.id : `-${node.id}`;
+  return strand === ownStrand(node.id) ? node.id : `-${node.id}`;
 }
 function stepStarts(lengths, total) {
   const starts = lengths.map(() => void 0);
@@ -137,7 +137,6 @@ function readColor(read) {
 }
 
 export {
-  canonicalStrand,
   stepName,
   tubeMapReads,
   FORWARD_READ_COLORS,

package/dist/chunks/{chunk-A4JDEUAI.js → chunk-SNF2MIEF.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-NMWQUFPF.js → chunk-SVVFWTG4.js}

@@ -3,14 +3,14 @@ import {
 } from "./chunk-HNWJ4B7S.js";
 import {
   wellKnownSample
-} from "./chunk-234NFZS4.js";
+} from "./chunk-5ORP7EFJ.js";
 import {
   gfaTables
 } from "./chunk-DZR37KXT.js";
 import {
   panSNMatchesPrefix,
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/gbzWindow.ts
 import { isReverse, nodeId } from "@gmod/gbz-base";

package/dist/chunks/{chunk-PFRQBCGC.js → chunk-T3H5ELLA.js}

@@ -7,15 +7,15 @@ import {
 } from "./chunk-AB35TJST.js";
 import {
   polylineMidpoint
-} from "./chunk-BZFOFC4D.js";
+} from "./chunk-2VMKQKVO.js";
 import {
   edgeCurvesOf
-} from "./chunk-CGMSKIEO.js";
+} from "./chunk-DV5B5UU7.js";
 import {
   curveBounds,
   curveMidpoint,
   polylinePx
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 
 // src/graphLabels.ts
 var MIN_DELETION_LABEL_PX = 26;
@@ -55,7 +55,7 @@ function groupDigits(n) {
   return String(n).replace(/\B(?=(\d{3})+$)/g, ",");
 }
 function formatBp(bp) {
-  const [value, unit] = bp >= 1e6 ? [bp / 1e6, "Mb"] : bp >= 1e3 ? [bp / 1e3, "kb"] : [];
+  const [value, unit] = bp >= 999500 ? [bp / 1e6, "Mb"] : bp >= 1e3 ? [bp / 1e3, "kb"] : [];
   if (value === void 0) {
     return `${bp} bp`;
   }

package/dist/chunks/{chunk-WLR4KJVI.js → chunk-TXTSE44S.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.5.0";
+var version = "11.6.1";
 
 export {
   version

package/dist/chunks/{chunk-UBQSRCWR.js → chunk-VACK24HF.js}

@@ -71,16 +71,56 @@ function curveTangentAt(c, t) {
     y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)
   };
 }
-function dashCurves(curves, dashWorld) {
+var VISIBLE_SAMPLES = 32;
+function visibleStretches(curves, lengths, bounds, yToX) {
+  const stretches = [];
+  let start = 0;
+  curves.forEach((c, k) => {
+    const length = lengths[k];
+    const pad = length / VISIBLE_SAMPLES;
+    let last = curvePointAt(c, 0);
+    for (let i = 1; i <= VISIBLE_SAMPLES; i++) {
+      const next = curvePointAt(c, i / VISIBLE_SAMPLES);
+      if (Math.max(last.x, next.x) + pad >= bounds.minX && Math.min(last.x, next.x) - pad <= bounds.maxX && Math.max(last.y, next.y) + pad / yToX >= bounds.minY && Math.min(last.y, next.y) - pad / yToX <= bounds.maxY) {
+        const from = start + length * (i - 1) / VISIBLE_SAMPLES;
+        const to = start + length * i / VISIBLE_SAMPLES;
+        const prev = stretches.at(-1);
+        if (prev && prev[1] >= from) {
+          prev[1] = to;
+        } else {
+          stretches.push([from, to]);
+        }
+      }
+      last = next;
+    }
+    start += length;
+  });
+  return stretches;
+}
+function dashCurves(curves, dashWorld, yToX = 1, bounds) {
   const lengths = curves.map(
-    (c) => Math.hypot(c.cx0 - c.x0, c.cy0 - c.y0) + Math.hypot(c.cx1 - c.cx0, c.cy1 - c.cy0) + Math.hypot(c.x1 - c.cx1, c.y1 - c.cy1)
+    (c) => Math.hypot(c.cx0 - c.x0, (c.cy0 - c.y0) * yToX) + Math.hypot(c.cx1 - c.cx0, (c.cy1 - c.cy0) * yToX) + Math.hypot(c.x1 - c.cx1, (c.y1 - c.cy1) * yToX)
   );
   const total = lengths.reduce((a, b) => a + b, 0);
-  const spans = Math.max(3, Math.round(total / dashWorld) | 1);
+  const periods = Math.round(total / dashWorld);
+  const spans = Math.max(3, periods % 2 ? periods : periods + 1);
+  const stretches = bounds ? visibleStretches(curves, lengths, bounds, yToX) : void 0;
+  let seen = 0;
   const out = [];
   for (let i = 0; i < spans; i += 2) {
     const from = i / spans * total;
     const to = (i + 1) / spans * total;
+    if (stretches) {
+      while (seen < stretches.length && stretches[seen][1] < from) {
+        seen++;
+      }
+      if (seen === stretches.length) {
+        break;
+      }
+      if (stretches[seen][0] > to) {
+        continue;
+      }
+    }
     const dash = [];
     let start = 0;
     curves.forEach((c, k) => {

package/dist/chunks/{chunk-HSVFCA2J.js → chunk-VO6FKNZE.js}

@@ -1,6 +1,6 @@
 import {
   formatBp
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-NJGYLYU7.js → chunk-W2YAW36J.js}

@@ -9,7 +9,7 @@ import {
 import {
   panSNFields,
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/gfa/graphTables.ts
 function pLineName(name, start, end) {

package/dist/chunks/{chunk-VD4MLYEK.js → chunk-WI6SUU5B.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-NXBW6KY6.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-GJU6BJJA.js → chunk-XR2HMGAS.js}

@@ -12,7 +12,7 @@ import {
 } from "./chunk-RJWPJCIB.js";
 import {
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/layout/sampleRowLayout.ts
 function contributingSamples(graph, keep) {

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

@@ -1,27 +1,27 @@
 import {
   layoutEngine
-} from "./chunk-JMABOQWL.js";
+} from "./chunk-CO6RGQAD.js";
 import {
   layoutModeByValue
-} from "./chunk-5F4D35U5.js";
+} from "./chunk-QD35GH4C.js";
 import {
   parseRegion
-} from "./chunk-J3JODFDF.js";
+} from "./chunk-5WB7O7IT.js";
 import {
   genePins
-} from "./chunk-77EGQQJU.js";
+} from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-WLR4KJVI.js";
+} from "./chunk-TXTSE44S.js";
 import {
   axisScaleOf
-} from "./chunk-XKZ56L5A.js";
+} from "./chunk-RLCYVZ4B.js";
 import {
   figureScene
-} from "./chunk-3BCVMZUT.js";
+} from "./chunk-BVWMVWLJ.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-3FWNQNF7.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-7OTWJQGA.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-7EDGWT67.js → chunk-YEYQFNFQ.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JOWKKQAL.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-UFUSPK2A.js → chunk-YYIU7P73.js}

@@ -186,7 +186,10 @@ function walkRowBlocks(rows, join = ribbonJoin(rows)) {
       if (setKey.has(id)) {
         const root = find(id);
         total.set(root, (total.get(root) ?? 0) + bp);
-        least.set(root, [least.get(root) ?? id, id].sort()[0]);
+        const lowest = least.get(root);
+        if (lowest === void 0 || id < lowest) {
+          least.set(root, id);
+        }
       }
     }
   }

package/dist/chunks/{chunk-CRCD3ODN.js → chunk-ZANALBSX.js}

@@ -37,13 +37,20 @@ function nodeWidthPx(node, contigThickness, nodeWidth, mean) {
 function maxNodeWidthPx(contigThickness, nodeWidth) {
   return contigThickness * (nodeWidth === "depth" ? MAX_FACTOR : 1);
 }
-function nodeInk(graph, nodeById, contigThickness, nodeWidth) {
+var MIN_WALK_LANE_PX = 4;
+function walkLaneWidthPx(width, lanes) {
+  return Math.max(width / lanes, MIN_WALK_LANE_PX);
+}
+function nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {
   const mean = graph ? meanDepth(graph) : 0;
+  const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;
   return {
-    maxHalfWidthPx: maxNodeWidthPx(contigThickness, nodeWidth) / 2,
+    maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),
     halfWidthPx: (id) => {
       const node = nodeById?.get(id);
-      return node ? nodeWidthPx(node, contigThickness, nodeWidth, mean) / 2 : contigThickness / 2;
+      return reach(
+        node ? nodeWidthPx(node, contigThickness, nodeWidth, mean) : contigThickness
+      );
     }
   };
 }
@@ -53,5 +60,6 @@ export {
   meanDepth,
   nodeWidthPx,
   maxNodeWidthPx,
+  walkLaneWidthPx,
   nodeInk
 };