@jbrowse/bandage-core 11.4.0 → 11.6.1

package/dist/chunks/{chunk-PSCSZSVK.js → chunk-KA4F3N55.js}

@@ -1,10 +1,10 @@
 import {
   nodesUnderBox
-} from "./chunk-OMUPUB4J.js";
+} from "./chunk-56L6R6D2.js";
 import {
   graphLabels,
   rowLabelBox
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -25,7 +25,7 @@ function geneCoverageNote(pin) {
   if (pin.covered >= 0.98) {
     return void 0;
   }
-  const [per, unit] = length >= 1e6 ? [1e6, "Mb"] : length >= 1e3 ? [1e3, "kb"] : [1, "bp"];
+  const [per, unit] = length >= 999500 ? [1e6, "Mb"] : length >= 1e3 ? [1e3, "kb"] : [1, "bp"];
   const amount = (bp) => +(bp / per).toFixed(per === 1 ? 0 : 1);
   return `${amount(pin.covered * length)} of ${amount(length)} ${unit}`;
 }
@@ -114,7 +114,7 @@ function layoutLabels(m) {
     frame,
     take
   );
-  const ticks = m.bubbleHalos.filter((h) => h.tick && !h.whole).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);
+  const ticks = m.bubbleHalos.filter((h) => h.tick).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);
   const genes = placeLabels(
     geneLabelCandidates(
       m.genePins,

package/dist/chunks/{chunk-SOMZGDVS.js → chunk-KJDERUQF.js}

@@ -1,6 +1,6 @@
 import {
   ownStrand
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-E4ZM4OOJ.js → chunk-KZMSSPS6.js}

@@ -1,10 +1,10 @@
 import {
   bubbleSegmentIds,
   classifyBubble
-} from "./chunk-A4JDEUAI.js";
+} from "./chunk-SNF2MIEF.js";
 import {
   svgPath
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";

package/dist/chunks/{chunk-JDZ5GTZT.js → chunk-MEVTV4FI.js}

@@ -1,7 +1,7 @@
 import {
   walkRowRuns,
   walkRowsOf
-} from "./chunk-M75QPZNJ.js";
+} from "./chunk-D3E7AXBB.js";
 
 // src/layout/walkRows.ts
 function filterSamples(rows, samples) {

package/dist/chunks/{chunk-PNMJFFNB.js → chunk-MHZTTLBU.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

package/dist/chunks/{chunk-VIQL7GZ4.js → chunk-MXLYBDOX.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-XSF4RQRP.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,
@@ -22,7 +22,7 @@ import {
 } from "./chunk-CPMHA4W5.js";
 import {
   panSNContig
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/layout/walkRowDraw.ts
 var ON_REFERENCE = "#2f8fd6";
@@ -49,10 +49,10 @@ function units(bp, unit) {
 }
 var near = ({ refName, start }) => `${panSNContig(refName)}:${start < 1e6 ? `${Math.round(start / 1e3)} kb` : `${(start / 1e6).toFixed(1)} Mb`}`;
 function gapsText(gapBp, runs) {
-  const gaps = (runs ?? []).filter((r) => r.gap);
   if (gapBp <= 0) {
     return "";
   }
+  const gaps = (runs ?? []).filter((r) => r.gap);
   if (!gaps.some((g) => g.cause)) {
     return ` \xB7 ${kb(gapBp)} ${OUTSIDE_TEXT}`;
   }
@@ -477,14 +477,15 @@ function walkRowsTree(bars, frame, o = {}) {
       })
     ) : [];
     const { call } = row;
-    const text = walkRowReadout(
-      row,
-      i === 0 ? void 0 : reference,
-      unit,
-      call
-    );
-    const at = readoutPlacement(text, along(row.bp), frame.width);
-    const readouts = frame.readouts ?? true;
+    const readout = frame.readouts ?? true ? {
+      text: walkRowReadout(
+        row,
+        i === 0 ? void 0 : reference,
+        unit,
+        call
+      )
+    } : void 0;
+    const at = readout && readoutPlacement(readout.text, along(row.bp), frame.width);
     return el(
       "g",
       {
@@ -504,7 +505,7 @@ function walkRowsTree(bars, frame, o = {}) {
         height: barPx + 2 * overhang,
         fill: callTickInk(call)
       }),
-      readouts && el(
+      readout && at && el(
         "text",
         {
           x: at.x,
@@ -517,7 +518,7 @@ function walkRowsTree(bars, frame, o = {}) {
           "paint-order": "stroke",
           "text-anchor": at.anchor
         },
-        text
+        readout.text
       )
     );
   };

package/dist/chunks/{chunk-3LZ334X4.js → chunk-NXBW6KY6.js}

@@ -1,22 +1,21 @@
 import {
-  canonicalStrand,
   stepName,
   tubeMapReads
-} from "./chunk-A7H753BA.js";
+} from "./chunk-SDI6BVG7.js";
 import {
   referenceWalkName
-} from "./chunk-M75QPZNJ.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-7O7EGTYG.js → chunk-OUM54ZSQ.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-3LZ334X4.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-TZLEHZVC.js → chunk-P5PBJONQ.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-JDZ5GTZT.js";
+} from "./chunk-MEVTV4FI.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/chunk-PQIFYQVI.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-6VVGFQ7S.js → chunk-QCOVHLJO.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-XSF4RQRP.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

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

@@ -3,10 +3,10 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-3LZ334X4.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-TZLEHZVC.js";
+} from "./chunk-P5PBJONQ.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-CE6ZIKJX.js → chunk-RLCYVZ4B.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-REOWLPH4.js";
+} from "./chunk-7OTWJQGA.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-6YJESZND.js → chunk-ROLACYCO.js}

@@ -1,19 +1,19 @@
+import {
+  stripGeneGaps,
+  walkStripFrame,
+  walkStripLabelsTree
+} from "./chunk-4WXFQOYV.js";
 import {
   Canvas2DRenderer
-} from "./chunk-EJRJAAN7.js";
+} from "./chunk-4DMSPNYV.js";
 import {
   svgCanvas
 } from "./chunk-V4YML3GR.js";
-import {
-  stripGeneGaps,
-  walkStripFrame,
-  walkStripLabelsTree
-} from "./chunk-I4BYUNJN.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-VIQL7GZ4.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-QM7KEWWT.js";
+} from "./chunk-TXTSE44S.js";
 import {
   axisScaleOf
-} from "./chunk-CE6ZIKJX.js";
+} from "./chunk-RLCYVZ4B.js";
 import {
   figureScene
-} from "./chunk-JQ52XYD2.js";
+} from "./chunk-BVWMVWLJ.js";
 import {
   encodingStops
-} from "./chunk-GM7M25NW.js";
+} from "./chunk-2XEAITWM.js";
 import {
   rangeText
-} from "./chunk-D4ZFRBB4.js";
+} from "./chunk-JGQQAUVL.js";
 import {
   walkRowLabels
-} from "./chunk-TZLEHZVC.js";
+} from "./chunk-P5PBJONQ.js";
 import {
   nodeInk
-} from "./chunk-CRCD3ODN.js";
+} from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-EFD753MS.js";
+} from "./chunk-3FWNQNF7.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-REOWLPH4.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-QM7KEWWT.js → chunk-TXTSE44S.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.4.0";
+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-B5ARSBOH.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) {
@@ -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-TJOOHTJ6.js → chunk-WI6SUU5B.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-3LZ334X4.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) {