@jbrowse/bandage-core 11.5.0 → 11.7.0

package/dist/alleleProjection/projectAlleles.js

@@ -7,7 +7,7 @@ import "../chunks/chunk-RJWPJCIB.js";
 import "../chunks/chunk-HOAIOEI7.js";
 import {
   parsePanSN
-} from "../chunks/chunk-4XWZNPQ2.js";
+} from "../chunks/chunk-2JL2JVZ2.js";
 export {
   parsePanSN,
   projectAlleles

package/dist/bubbles/bubbleHalos.js

@@ -1,19 +1,22 @@
 import {
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-E4ZM4OOJ.js";
-import "../chunks/chunk-A4JDEUAI.js";
+} from "../chunks/chunk-KZMSSPS6.js";
+import "../chunks/chunk-SNF2MIEF.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-T3H5ELLA.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-BZFOFC4D.js";
-import "../chunks/chunk-CGMSKIEO.js";
-import "../chunks/chunk-UBQSRCWR.js";
+import "../chunks/chunk-2VMKQKVO.js";
+import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-3YBP46PB.js";
+import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";
 import "../chunks/chunk-RJWPJCIB.js";
 import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-2JL2JVZ2.js";
 export {
   bubbleHalos,
   coversGraph

package/dist/bubbles/classifyBubble.js

@@ -3,18 +3,21 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-A4JDEUAI.js";
+} from "../chunks/chunk-SNF2MIEF.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-T3H5ELLA.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-BZFOFC4D.js";
-import "../chunks/chunk-CGMSKIEO.js";
-import "../chunks/chunk-UBQSRCWR.js";
+import "../chunks/chunk-2VMKQKVO.js";
+import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-3YBP46PB.js";
+import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";
 import "../chunks/chunk-RJWPJCIB.js";
 import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-2JL2JVZ2.js";
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,

package/dist/bubbles/popBubble.js

@@ -1,12 +1,12 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-PNMJFFNB.js";
-import "../chunks/chunk-B5X2RLJG.js";
+} from "../chunks/chunk-MHZTTLBU.js";
+import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";
 import "../chunks/chunk-RJWPJCIB.js";
 import "../chunks/chunk-HOAIOEI7.js";
-import "../chunks/chunk-4XWZNPQ2.js";
+import "../chunks/chunk-2JL2JVZ2.js";
 export {
   bubbleSubgraph
 };

package/dist/bubbles/superbubbles.js

@@ -1,27 +1,27 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-2E25TX4G.js";
-import "../chunks/chunk-E4ZM4OOJ.js";
+} from "../chunks/chunk-C6E6HXP5.js";
+import "../chunks/chunk-KZMSSPS6.js";
 import "../chunks/chunk-RFG42VIO.js";
-import "../chunks/chunk-A4JDEUAI.js";
+import "../chunks/chunk-SNF2MIEF.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-PNMJFFNB.js";
+import "../chunks/chunk-MHZTTLBU.js";
 import "../chunks/chunk-UAFATXYA.js";
-import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
-import "../chunks/chunk-ZPZ7GNBT.js";
-import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-T3H5ELLA.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-BZFOFC4D.js";
-import "../chunks/chunk-CGMSKIEO.js";
-import "../chunks/chunk-UBQSRCWR.js";
+import "../chunks/chunk-2VMKQKVO.js";
+import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-3YBP46PB.js";
+import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";
 import "../chunks/chunk-RJWPJCIB.js";
 import "../chunks/chunk-HOAIOEI7.js";
-import "../chunks/chunk-4XWZNPQ2.js";
+import "../chunks/chunk-2JL2JVZ2.js";
 export {
   graphBubbles,
   superbubblesFromGraph

package/dist/chunks/{chunk-4XWZNPQ2.js → chunk-2JL2JVZ2.js}

@@ -21,7 +21,7 @@ function panSNFields(name) {
 }
 function parsePanSN(refName) {
   const parts = refName.split(SEP);
-  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN;
+  const haplotype = parts.length >= 2 && parts[1] !== "" ? Number(parts[1]) : Number.NaN;
   return {
     sample: parts[0],
     haplotype: Number.isFinite(haplotype) ? haplotype : void 0

package/dist/chunks/{chunk-BZFOFC4D.js → chunk-2VMKQKVO.js}

@@ -1,7 +1,7 @@
 import {
   ownStrand,
   strandSides
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";
@@ -151,14 +151,24 @@ function arcPrefix(line) {
   }
   return arc;
 }
+function firstReaching(arc, s) {
+  let lo = 0;
+  let hi = arc.length;
+  while (lo < hi) {
+    const mid = lo + hi >> 1;
+    if (arc[mid] < s) {
+      lo = mid + 1;
+    } else {
+      hi = mid;
+    }
+  }
+  return lo;
+}
 function pointAt(line, arc, s) {
   if (s <= 0) {
     return { ...line[0] };
   }
-  let i = 1;
-  while (i < arc.length && arc[i] < s) {
-    i++;
-  }
+  const i = firstReaching(arc, s);
   if (i >= arc.length) {
     return { ...line.at(-1) };
   }
@@ -170,8 +180,8 @@ function pointAt(line, arc, s) {
 }
 function slice(line, arc, from, to) {
   const points = [pointAt(line, arc, from)];
-  for (let i = 0; i < line.length; i++) {
-    if (arc[i] > from && arc[i] < to) {
+  for (let i = firstReaching(arc, from); i < line.length && arc[i] < to; i++) {
+    if (arc[i] > from) {
       points.push({ ...line[i] });
     }
   }

package/dist/chunks/{chunk-HN3WHMPJ.js → chunk-2XEAITWM.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-JOWKKQAL.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";
@@ -61,18 +61,28 @@ function oklabToRgb([L, a, b]) {
     -0.0041960863 * l - 0.7034186147 * m + 1.707614701 * s
   ].map((c) => toGamma(Math.max(0, Math.min(1, c))) * 255);
 }
+var endsCache = /* @__PURE__ */ new Map();
+function oklabEnds(scheme) {
+  if (!endsCache.has(scheme)) {
+    const family = WALK_SCHEMES.find((s) => s.value === scheme);
+    endsCache.set(
+      scheme,
+      family && "ends" in family ? family.ends.map(oklab) : void 0
+    );
+  }
+  return endsCache.get(scheme);
+}
 function schemeRgb(scheme, t) {
   const x = Math.max(0, Math.min(1, t));
-  const family = WALK_SCHEMES.find((s) => s.value === scheme);
-  if (!family || !("ends" in family)) {
+  const ends = oklabEnds(scheme);
+  if (!ends) {
     return hslToRgb(
       rampHueAt(x),
       REFERENCE_RAMP_SATURATION,
       REFERENCE_RAMP_LIGHTNESS
     ).map((c) => c * 255);
   }
-  const from = oklab(family.ends[0]);
-  const to = oklab(family.ends[1]);
+  const [from, to] = ends;
   return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));
 }
 function schemeCss(scheme, t) {

package/dist/chunks/{chunk-7BTO7MZS.js → chunk-376YFQOY.js}

@@ -1,11 +1,11 @@
 import {
   genesFromText
-} from "./chunk-G6UIYQZR.js";
+} from "./chunk-EQDQ7P4Y.js";
 import {
   featuresOnBackbone,
   graphBackbone,
   refNameBinding
-} from "./chunk-234NFZS4.js";
+} from "./chunk-5ORP7EFJ.js";
 
 // src/genes/backboneGenes.ts
 async function backboneGenes(graph, source) {

package/dist/chunks/{chunk-B5X2RLJG.js → chunk-3YBP46PB.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-RJWPJCIB.js";
 import {
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/pathAnchoring.ts
 var RANGE_SUFFIX = /:(\d+)-\d+$/;
@@ -155,6 +155,30 @@ function trimOrigins(graph, kept) {
     } : o;
   });
 }
+function referenceVisitStarts(graph) {
+  const { pathVisits } = graph;
+  const cache = /* @__PURE__ */ new Map();
+  return (node) => {
+    let starts = cache.get(node.id);
+    if (!starts) {
+      starts = [];
+      const slot = pathVisits ? pathVisits.slot(node.name) : -1;
+      const p = slot >= 0 ? pathVisits.pathIndex(node.stable.refName) : -1;
+      if (p >= 0) {
+        for (let i = pathVisits.offsets[slot]; i < pathVisits.offsets[slot + 1]; i++) {
+          if (pathVisits.path[i] === p) {
+            starts.push(pathVisits.start[i]);
+          }
+        }
+      }
+      if (starts.length < 2) {
+        starts = [node.stable.start];
+      }
+      cache.set(node.id, starts);
+    }
+    return starts;
+  };
+}
 
 export {
   pathOrigin,
@@ -162,5 +186,6 @@ export {
   chooseReferencePath,
   anchorFromPaths,
   anchorGraph,
-  trimOrigins
+  trimOrigins,
+  referenceVisitStarts
 };

package/dist/chunks/{chunk-EJRJAAN7.js → chunk-4DMSPNYV.js}

@@ -17,6 +17,7 @@ var Canvas2DRenderer = class {
     this.highlightedEdge = null;
     this.highlightFactor = 1;
     this.fit = 1;
+    this.painted = null;
     const ctx = canvas.getContext("2d");
     if (!ctx) {
       throw new Error("Canvas 2D context not available");
@@ -37,13 +38,16 @@ var Canvas2DRenderer = class {
   uploadGeometry(batch) {
     this.batch = batch;
     this.highlightedEdge = null;
+    this.painted = null;
   }
   setNodeHighlights(factors) {
     this.nodeHighlights = factors;
+    this.painted = null;
   }
   setEdgeHighlight(edgeIndex, factor) {
     this.highlightedEdge = edgeIndex;
     this.highlightFactor = factor;
+    this.painted = null;
   }
   updateTransform(transform) {
     this.transform = transform;
@@ -70,46 +74,61 @@ var Canvas2DRenderer = class {
     if (clearColor[3] < 1) {
       ctx.clearRect(0, 0, width, height);
     }
-    ctx.fillStyle = normalizedRgbToCssRgba(
-      [clearColor[0], clearColor[1], clearColor[2]],
-      clearColor[3]
-    );
-    ctx.fillRect(0, 0, width, height);
+    if (clearColor[3] > 0) {
+      ctx.fillStyle = normalizedRgbToCssRgba(
+        [clearColor[0], clearColor[1], clearColor[2]],
+        clearColor[3]
+      );
+      ctx.fillRect(0, 0, width, height);
+    }
     const batch = this.batch;
     if (!batch) {
       return;
     }
     ctx.lineCap = "round";
     ctx.lineJoin = "round";
-    const factor = this.highlightFactor;
-    const edgeRun = this.edgeRun(batch.edgeCurveRuns);
-    for (const { color, items } of groupByPaint(batch.edgeCurves, (e, i) => ({
-      color: inRun(edgeRun, i) ? brightenAbgr(e.color, factor) : e.color,
-      weight: e.thickness,
-      last: inRun(edgeRun, i)
-    }))) {
+    const { edges, nodes, arrows } = this.paintedGroups(batch);
+    for (const { color, items } of edges) {
       this.strokeCurves(items, color, t);
     }
-    const lifted = this.liftedStrokes(batch);
-    for (const { color, items } of groupByPaint(batch.nodeStrokes, (s, i) => {
-      const f = lifted.get(i);
-      return {
-        color: f === void 0 ? s.color : brightenAbgr(s.color, f),
-        weight: s.thickness,
-        last: f !== void 0
-      };
-    })) {
+    for (const { color, items } of nodes) {
       this.strokeNodes(items, color, t);
     }
-    const arrowRun = this.edgeRun(batch.arrowRuns);
-    for (const { color, items } of groupByPaint(batch.arrows, (a, i) => ({
-      color: inRun(arrowRun, i) ? brightenAbgr(a.color, factor) : a.color,
-      weight: 0,
-      last: inRun(arrowRun, i)
-    }))) {
+    for (const { color, items } of arrows) {
       this.fillArrows(items, color, t);
     }
   }
+  // Grouping depends on the batch and the highlights, not on the transform, so
+  // a pan or zoom redraws from the groups it already has
+  paintedGroups(batch) {
+    if (this.painted) {
+      return this.painted;
+    }
+    const factor = this.highlightFactor;
+    const edgeRun = this.edgeRun(batch.edgeCurveRuns);
+    const arrowRun = this.edgeRun(batch.arrowRuns);
+    const lifted = this.liftedStrokes(batch);
+    return this.painted = {
+      edges: groupByPaint(batch.edgeCurves, (e, i) => ({
+        color: inRun(edgeRun, i) ? brightenAbgr(e.color, factor) : e.color,
+        weight: e.thickness,
+        last: inRun(edgeRun, i)
+      })),
+      nodes: groupByPaint(batch.nodeStrokes, (s, i) => {
+        const f = lifted.get(i);
+        return {
+          color: f === void 0 ? s.color : brightenAbgr(s.color, f),
+          weight: s.thickness,
+          last: f !== void 0
+        };
+      }),
+      arrows: groupByPaint(batch.arrows, (a, i) => ({
+        color: inRun(arrowRun, i) ? brightenAbgr(a.color, factor) : a.color,
+        weight: 0,
+        last: inRun(arrowRun, i)
+      }))
+    };
+  }
   // Only what the highlights lift, over a transparent clear, for a hover layer
   // stacked on a canvas that drew the batch without them: a pointer move then
   // repaints one node or edge rather than the whole drawing
@@ -226,6 +245,7 @@ var Canvas2DRenderer = class {
     this.batch = null;
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;
+    this.painted = null;
   }
 };
 var ARROW_NOTCH = 0.25;

package/dist/chunks/{chunk-OMUPUB4J.js → chunk-56L6R6D2.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-3VCKBSML.js";
+} from "./chunk-6YRSOL4K.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";
@@ -9,7 +9,7 @@ import {
   pathRibbonOffsets,
   translateCurves,
   yToXOf
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 
 // src/util/hitDetection.ts
 function distanceToSegment(px, py, x1, y1, x2, y2) {

package/dist/chunks/{chunk-C44YRP5F.js → chunk-5OJZV6YT.js}

@@ -10,7 +10,8 @@ function parseGafPath(column) {
   }
   return steps;
 }
-function parseGafLine(line) {
+function parseGafLine(text) {
+  const line = text.trimEnd();
   const columns = line.split("	");
   if (columns.length < 12 || line.startsWith("#")) {
     return void 0;
@@ -49,7 +50,7 @@ function parseGafLine(line) {
 function parseGaf(text) {
   const records = [];
   for (const line of text.split("\n")) {
-    const record = parseGafLine(line.trimEnd());
+    const record = parseGafLine(line);
     if (record) {
       records.push(record);
     }

package/dist/chunks/{chunk-234NFZS4.js → chunk-5ORP7EFJ.js}

@@ -9,7 +9,7 @@ import {
   panSNContig,
   panSNHaplotype,
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/reference.ts
 var WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([

package/dist/chunks/{chunk-XKZ56L5A.js → chunk-5ZQKQ24Z.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-VD4MLYEK.js → chunk-65YCFVS4.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-SIA75TEG.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-3VCKBSML.js → chunk-6YRSOL4K.js}

@@ -1,10 +1,10 @@
 import {
   baseEdgeCurves
-} from "./chunk-WA5WNP6V.js";
+} from "./chunk-OYCQVJYY.js";
 import {
   curveBounds,
   pathRibbonOffsets
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 
 // src/util/SpatialIndex.ts
 var FALLBACK_CELL_SIZE = 50;

package/dist/chunks/{chunk-NJGYLYU7.js → chunk-7L7MN2OM.js}

@@ -2,14 +2,14 @@ import {
   stopAt,
   stopFields,
   walkStopTags
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
 import {
   PathVisits
 } from "./chunk-ZPZ7GNBT.js";
 import {
   panSNFields,
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/gfa/graphTables.ts
 function pLineName(name, start, end) {
@@ -19,6 +19,8 @@ function tablePath(w, p) {
   const walkName = w.names[p];
   const fields = panSNFields(walkName);
   const start = w.starts[p];
+  const steps = w.abridgedSteps?.[p] ?? Number.NaN;
+  const abridged = Number.isNaN(steps) ? {} : { abridged: { steps, bp: w.abridgedBp?.[p] ?? 0 } };
   return fields ? {
     name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,
     start,
@@ -26,7 +28,8 @@ function tablePath(w, p) {
     ...stopFields(
       w.before && stopAt(w.before, p),
       w.after && stopAt(w.after, p)
-    )
+    ),
+    ...abridged
   } : { name: pLineName(walkName, start, w.ends[p]), start };
 }
 function namesByList(lists, names, listCount, pathNames) {

package/dist/chunks/{chunk-TRGKMLXT.js → chunk-A7Q7RTWX.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-JOWKKQAL.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,
@@ -13,7 +13,7 @@ import {
 import {
   GAP_CAUSE_TEXT,
   OUTSIDE_TEXT
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
@@ -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";
@@ -30,6 +30,7 @@ var OFF_REFERENCE = "#8e3fbf";
 var OUTSIDE_CUT = "#bdbdbd";
 var MISSING_INK = "#8a8a8a";
 var UNKNOWN_GAP = "#e2e2e2";
+var ABRIDGED_GAP = "#d9a441";
 var GENE_INK = "#1c1c22";
 var BAR_PX = 12;
 var GAP_PX = 4;
@@ -48,11 +49,14 @@ function units(bp, unit) {
   return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
 }
 var near = ({ refName, start }) => `${panSNContig(refName)}:${start < 1e6 ? `${Math.round(start / 1e3)} kb` : `${(start / 1e6).toFixed(1)} Mb`}`;
-function gapsText(gapBp, runs) {
-  const gaps = (runs ?? []).filter((r) => r.gap);
+function stepsText(steps) {
+  return steps < 1e3 ? `${steps}` : `${Math.round(steps / 1e3)} k`;
+}
+function gapsText(gapBp, runs, abridgedSteps = 0) {
   if (gapBp <= 0) {
     return "";
   }
+  const gaps = (runs ?? []).filter((r) => r.gap);
   if (!gaps.some((g) => g.cause)) {
     return ` \xB7 ${kb(gapBp)} ${OUTSIDE_TEXT}`;
   }
@@ -69,14 +73,15 @@ function gapsText(gapBp, runs) {
     [bpOf("unknown"), GAP_CAUSE_TEXT.unknown],
     [bpOf(void 0), OUTSIDE_TEXT]
   ];
-  return parts.filter(([bp]) => bp > 0).map(([bp, text]) => ` \xB7 ${kb(bp)} ${text}`).join("");
+  const abridged = bpOf("abridged");
+  return (abridged > 0 ? ` \xB7 ${stepsText(abridgedSteps)} steps, ${kb(abridged)} not loaded` : "") + parts.filter(([bp]) => bp > 0).map(([bp, text]) => ` \xB7 ${kb(bp)} ${text}`).join("");
 }
 function walkRowReadout(row, reference, unit, call) {
   const { bp, gapBp, complete, stop } = row;
   if (!reference) {
     return `${kb(bp)}${units(bp, unit)}`;
   }
-  const outside = gapsText(gapBp, row.runs);
+  const outside = gapsText(gapBp, row.runs, row.abridgedSteps);
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
   if (complete) {
     const delta = bp - reference.bp;
@@ -107,7 +112,7 @@ function unitTicks(bp, unit, pxPerBp) {
   return ticks;
 }
 function gapStyle(cause) {
-  return cause === "missing" ? { fill: MISSING_INK, px: MISSING_PX, label: GAP_CAUSE_TEXT.missing } : cause === "unknown" ? { fill: UNKNOWN_GAP, px: GAP_PX, label: GAP_CAUSE_TEXT.unknown } : { fill: OUTSIDE_CUT, px: GAP_PX, label: OUTSIDE_TEXT };
+  return cause === "missing" ? { fill: MISSING_INK, px: MISSING_PX, label: GAP_CAUSE_TEXT.missing } : cause === "unknown" ? { fill: UNKNOWN_GAP, px: GAP_PX, label: GAP_CAUSE_TEXT.unknown } : cause === "abridged" ? { fill: ABRIDGED_GAP, px: GAP_PX, label: GAP_CAUSE_TEXT.abridged } : { fill: OUTSIDE_CUT, px: GAP_PX, label: OUTSIDE_TEXT };
 }
 function runPaint(run, ramp) {
   if (run.gap) {
@@ -221,7 +226,7 @@ function walkRowsKey(bars, o = {}) {
     (row) => row.runs.filter((run) => run.gap)
   );
   const labels = new Set(gaps.map((run) => gapStyle(run.cause).label));
-  for (const cause of [void 0, "missing", "unknown"]) {
+  for (const cause of [void 0, "missing", "unknown", "abridged"]) {
     const { fill, px, label } = gapStyle(cause);
     if (labels.has(label)) {
       entries.push({ swatch: { kind: "gap", fill, px }, label });
@@ -477,14 +482,15 @@ 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 +510,7 @@ function walkRowsTree(bars, frame, o = {}) {
         height: barPx + 2 * overhang,
         fill: callTickInk(call)
       }),
-      readouts && el(
+      readout && at && el(
         "text",
         {
           x: at.x,
@@ -517,7 +523,7 @@ function walkRowsTree(bars, frame, o = {}) {
           "paint-order": "stroke",
           "text-anchor": at.anchor
         },
-        text
+        readout.text
       )
     );
   };
@@ -530,6 +536,7 @@ export {
   OUTSIDE_CUT,
   MISSING_INK,
   UNKNOWN_GAP,
+  ABRIDGED_GAP,
   GENE_INK,
   BAR_PX,
   GAP_PX,