@jbrowse/bandage-core 6.0.3 → 6.1.0

package/dist/chunks/chunk-4BYTEJGW.js

@@ -0,0 +1,44 @@
+// src/renderer/canvas.ts
+var MAX_DPR = 2;
+var MAX_CANVAS_DIM_PX = 8192;
+function getDpr() {
+  return typeof devicePixelRatio === "undefined" ? 1 : Math.min(devicePixelRatio, MAX_DPR);
+}
+var warnedCanvasClamp = false;
+function backingPx(cssSize, dpr, axis) {
+  const value = Math.round(cssSize * dpr);
+  if (value > MAX_CANVAS_DIM_PX) {
+    if (!warnedCanvasClamp) {
+      warnedCanvasClamp = true;
+      console.warn(
+        `Canvas ${axis} ${value}px exceeds the safe limit ${MAX_CANVAS_DIM_PX}px and was clamped`
+      );
+    }
+    return MAX_CANVAS_DIM_PX;
+  }
+  return value;
+}
+function syncCanvasSize(canvas, width, height) {
+  const dpr = getDpr();
+  const pw = backingPx(width, dpr, "width");
+  const ph = backingPx(height, dpr, "height");
+  if (canvas.width !== pw || canvas.height !== ph) {
+    canvas.width = pw;
+    canvas.height = ph;
+  }
+  const cssWidth = `${width}px`;
+  const cssHeight = `${height}px`;
+  if (canvas.style.width !== cssWidth) {
+    canvas.style.width = cssWidth;
+  }
+  if (canvas.style.height !== cssHeight) {
+    canvas.style.height = cssHeight;
+  }
+}
+
+export {
+  MAX_DPR,
+  MAX_CANVAS_DIM_PX,
+  getDpr,
+  syncCanvasSize
+};

package/dist/chunks/{chunk-IO2PCPZI.js → chunk-6UACM7VU.js}

@@ -11,10 +11,11 @@ import {
   parseGFA
 } from "./chunk-CDLPYR5O.js";
 import {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "./chunk-MI35EUIE.js";
+} from "./chunk-C6USNTTP.js";
 import {
   anchorGraph
 } from "./chunk-ST2IBUAN.js";
@@ -79,12 +80,14 @@ function engineRequest(graph, scaling, settings) {
 }
 function engineKey(graph, settings) {
   const anchored = graph.nodes.some(isBackbone);
-  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${anchored}|${graph.referencePath ?? ""}`;
+  return `${settings.quality}|${settings.linearLayout}|${settings.bubbleSpread}|${settings.spacing ?? 1}|${settings.componentSeparation ?? 1}|${settings.showDeletionEdges !== false}|${anchored}|${graph.referencePath ?? ""}`;
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);
-  const deletions = deletionEdges(graph);
-  const routed = withDeletionRoutes(graph, deletions);
+  const found = deletionEdges(graph);
+  const dropped = settings.showDeletionEdges === false ? closableDeletions(graph, found) : /* @__PURE__ */ new Set();
+  const deletions = found.filter((d) => !dropped.has(d.edgeIndex));
+  const routed = withDeletionRoutes(graph, deletions, dropped);
   const merged = mergeRuns(routed.graph, routed.ids);
   const runs = {
     ...merged.graph,

package/dist/chunks/{chunk-MQJUG2D2.js → chunk-AMHZMY6E.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-IO2PCPZI.js";
+} from "./chunk-6UACM7VU.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-MI35EUIE.js → chunk-C6USNTTP.js}

@@ -1,13 +1,16 @@
 // src/layout/deletionRoutes.ts
 var ROUTE_ID = "\0deletion:";
 var ROUTE_FRACTION = 0.5;
-function withDeletionRoutes(graph, deletions) {
+function withDeletionRoutes(graph, deletions, dropped = /* @__PURE__ */ new Set()) {
   const routes = new Map(
     deletions.map((d) => [d.edgeIndex, `${ROUTE_ID}${d.edgeIndex}`])
   );
   const edges = [];
   graph.edges.forEach((edge, ei) => {
     const id = routes.get(ei);
+    if (dropped.has(ei)) {
+      return;
+    }
     if (id === void 0) {
       edges.push(edge);
     } else {
@@ -36,6 +39,14 @@ function withDeletionRoutes(graph, deletions) {
     ids: new Set(routes.values())
   };
 }
+function closableDeletions(graph, deletions) {
+  const lengths = new Map(graph.nodes.map((n) => [n.id, n.length]));
+  return new Set(
+    deletions.filter(
+      (d) => d.bypassed.reduce((sum, id) => sum + (lengths.get(id) ?? 0), 0) >= d.bp
+    ).map((d) => d.edgeIndex)
+  );
+}
 function routeNodes(graph, deletions, routes, drawnOf, opts) {
   const lengths = new Map(graph.nodes.map((n) => [n.id, n.length]));
   return deletions.map((d) => {
@@ -71,6 +82,7 @@ function takeRoutes(positions, routes) {
 
 export {
   withDeletionRoutes,
+  closableDeletions,
   routeNodes,
   takeRoutes
 };

package/dist/chunks/{chunk-D3M7SBKL.js → chunk-CH3DLBUT.js}

@@ -1,29 +1,37 @@
 import {
-  brightenAbgr
-} from "./chunk-MNUSQCLG.js";
-
-// src/renderer/Canvas2DRenderer.ts
+  syncCanvasSize
+} from "./chunk-4BYTEJGW.js";
 import {
   abgrToCssRgba,
+  brightenAbgr,
   normalizedRgbToCssRgba
-} from "@jbrowse/core/util/colorBits";
-import { syncCanvasSize } from "@jbrowse/render-core/canvas2dUtils";
-import { Canvas2DRenderingBackendBase } from "@jbrowse/render-core/renderingBackendBase";
-var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
-  constructor() {
-    super(...arguments);
+} from "./chunk-UMNCCYBN.js";
+
+// src/renderer/Canvas2DRenderer.ts
+var Canvas2DRenderer = class {
+  constructor(canvas) {
     this.transform = null;
     this.batch = null;
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;
     this.highlightFactor = 1;
+    const ctx = canvas.getContext("2d");
+    if (!ctx) {
+      throw new Error("Canvas 2D context not available");
+    }
+    this.canvas = canvas;
+    this.ctx = ctx;
+  }
+  setErrorHandler(_handler) {
+  }
+  releaseOffscreenTargets() {
   }
-  // render-core's, not a local `width * devicePixelRatio`: it clamps the
-  // backing store at MAX_CANVAS_DIM_PX, reads the ratio through `getDpr()` so
-  // this agrees with the transform the model builds, and writes the css size
+  // Not a local `width * devicePixelRatio`: syncCanvasSize clamps the backing
+  // store at MAX_CANVAS_DIM_PX, reads the ratio through `getDpr()` so this
+  // agrees with the transform the model builds, and writes the css size
   // independently of the backing size.
   resize(width, height) {
-    syncCanvasSize(this.ctx.canvas, width, height);
+    syncCanvasSize(this.canvas, width, height);
   }
   uploadGeometry(batch) {
     this.batch = batch;
@@ -159,7 +167,6 @@ var Canvas2DRenderer = class extends Canvas2DRenderingBackendBase {
     }
   }
   dispose() {
-    super.dispose();
     this.batch = null;
     this.nodeHighlights = /* @__PURE__ */ new Map();
     this.highlightedEdge = null;

package/dist/chunks/{chunk-5XQDMQXU.js → chunk-KKU6JRJC.js}

@@ -5,15 +5,15 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-ROF2R3RF.js";
+} from "./chunk-V5BPIOLS.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-6SXMCK6I.js";
+} from "./chunk-PJESIRDU.js";
 import {
   Canvas2DRenderer
-} from "./chunk-D3M7SBKL.js";
+} from "./chunk-CH3DLBUT.js";
 import {
   genePins
 } from "./chunk-BUBZ32IC.js";
@@ -24,17 +24,17 @@ import {
 } from "./chunk-3S3YVOJ7.js";
 import {
   version
-} from "./chunk-LLJUG2H7.js";
+} from "./chunk-LPFN4POU.js";
 import {
   axisScaleOf
-} from "./chunk-MQJUG2D2.js";
+} from "./chunk-AMHZMY6E.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-GGQRADFS.js";
+} from "./chunk-ZKGM7VLA.js";
 import {
   encodingStops
-} from "./chunk-WFX3MAKA.js";
+} from "./chunk-X4VVPLI5.js";
 import {
   rangeText,
   walkKey
@@ -43,11 +43,11 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-IO2PCPZI.js";
+} from "./chunk-6UACM7VU.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
 import {
   geneLabelCandidates
 } from "./chunk-DKOB2OPC.js";

package/dist/chunks/{chunk-LLJUG2H7.js → chunk-LPFN4POU.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "6.0.3";
+var version = "6.1.0";
 
 export {
   version

package/dist/chunks/{chunk-6SXMCK6I.js → chunk-PJESIRDU.js}

@@ -3,10 +3,10 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-CJ2EE4AF.js";
+} from "./chunk-ZHCDYSA5.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-PCZ4PTYC.js → chunk-RX5CSWJW.js}

@@ -1,6 +1,8 @@
 import {
-  fadeAbgr
-} from "./chunk-MNUSQCLG.js";
+  abgrToCssRgba,
+  fadeAbgr,
+  packAbgr
+} from "./chunk-UMNCCYBN.js";
 import {
   baseEdgeCurves
 } from "./chunk-Y3IOTZJA.js";
@@ -26,7 +28,6 @@ import {
 } from "./chunk-2CVHXFK7.js";
 
 // src/renderer/GeometryBuilder.ts
-import { abgrToCssRgba, packAbgr } from "@jbrowse/core/util/colorBits";
 var EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);
 var EDGE_PATH_FALLBACK_COLOR = packAbgr(136, 136, 136, 217);
 var EDGE_DELETION_COLOR = packAbgr(24, 24, 28, 240);

package/dist/chunks/{chunk-EK4HGYO7.js → chunk-SMQ545MU.js}

@@ -2,13 +2,15 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  abgrToCssRgba
+} from "./chunk-UMNCCYBN.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
 
 // src/referenceStrip.ts
-import { abgrToCssRgba } from "@jbrowse/core/util/colorBits";
 var REFERENCE_STRIP_PX = 12;
 var REFERENCE_STRIP_ZONE_PX = REFERENCE_STRIP_PX + 8;
 var OVERHANG_PX = 8;

package/dist/chunks/chunk-UMNCCYBN.js

@@ -0,0 +1,50 @@
+// src/renderer/colorBits.ts
+function packAbgr(r, g, b, a) {
+  return (a << 24 | b << 16 | g << 8 | r) >>> 0;
+}
+function abgrRed(c) {
+  return c & 255;
+}
+function abgrGreen(c) {
+  return c >>> 8 & 255;
+}
+function abgrBlue(c) {
+  return c >>> 16 & 255;
+}
+function abgrAlpha(c) {
+  return c >>> 24 & 255;
+}
+function abgrToCssRgba(c) {
+  return `rgba(${abgrRed(c)},${abgrGreen(c)},${abgrBlue(c)},${abgrAlpha(c) / 255})`;
+}
+function normalizedRgbToCssRgba(c, alpha) {
+  return `rgba(${Math.round(c[0] * 255)},${Math.round(c[1] * 255)},${Math.round(c[2] * 255)},${alpha})`;
+}
+function fadeAbgr(c, alpha) {
+  return packAbgr(
+    abgrRed(c),
+    abgrGreen(c),
+    abgrBlue(c),
+    Math.round(abgrAlpha(c) * alpha)
+  );
+}
+function brightenAbgr(c, factor) {
+  return packAbgr(
+    Math.min(255, Math.round(abgrRed(c) * factor)),
+    Math.min(255, Math.round(abgrGreen(c) * factor)),
+    Math.min(255, Math.round(abgrBlue(c) * factor)),
+    abgrAlpha(c)
+  );
+}
+
+export {
+  packAbgr,
+  abgrRed,
+  abgrGreen,
+  abgrBlue,
+  abgrAlpha,
+  abgrToCssRgba,
+  normalizedRgbToCssRgba,
+  fadeAbgr,
+  brightenAbgr
+};

package/dist/chunks/{chunk-ROF2R3RF.js → chunk-V5BPIOLS.js}

@@ -1,7 +1,7 @@
 import {
   alongRow,
   boxesGenes
-} from "./chunk-6SXMCK6I.js";
+} from "./chunk-PJESIRDU.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-WFX3MAKA.js → chunk-X4VVPLI5.js}

@@ -2,10 +2,12 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  packAbgr
+} from "./chunk-UMNCCYBN.js";
 
 // src/walkEncoding.ts
-import { packAbgr } from "@jbrowse/core/util/colorBits";
 var WALK_FIELDS = [
   { value: "progress", label: "Progress along the walk" },
   { value: "walk", label: "One colour for the walk" },

package/dist/chunks/{chunk-CJ2EE4AF.js → chunk-ZHCDYSA5.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_MAX_HUE
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
 
 // src/referenceRampCss.ts
 function rampHueCss(hue) {

package/dist/chunks/{chunk-GGQRADFS.js → chunk-ZKGM7VLA.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-WFX3MAKA.js";
+} from "./chunk-X4VVPLI5.js";
 import {
   pathOrigin
 } from "./chunk-ST2IBUAN.js";

package/dist/chunks/{chunk-EPZORFTI.js → chunk-ZZA2AFB4.js}

@@ -1,10 +1,12 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-PCZ4PTYC.js";
+} from "./chunk-RX5CSWJW.js";
+import {
+  abgrToCssRgba
+} from "./chunk-UMNCCYBN.js";
 
 // src/tubeMap/nodeColors.ts
-import { abgrToCssRgba } from "@jbrowse/core/util/colorBits";
 function tubeMapNodeColors(graph, colorScheme, referenceRamp) {
   if (colorScheme === "uniform" || colorScheme === "grey") {
     return void 0;

package/dist/cli/figure.js

@@ -21,34 +21,35 @@ import {
 } from "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-5XQDMQXU.js";
+} from "../chunks/chunk-KKU6JRJC.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-ROF2R3RF.js";
+import "../chunks/chunk-V5BPIOLS.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-6SXMCK6I.js";
-import "../chunks/chunk-D3M7SBKL.js";
+} from "../chunks/chunk-PJESIRDU.js";
+import "../chunks/chunk-CH3DLBUT.js";
+import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-BUBZ32IC.js";
 import "../chunks/chunk-3S3YVOJ7.js";
-import "../chunks/chunk-LLJUG2H7.js";
-import "../chunks/chunk-MQJUG2D2.js";
-import "../chunks/chunk-GGQRADFS.js";
-import "../chunks/chunk-WFX3MAKA.js";
+import "../chunks/chunk-LPFN4POU.js";
+import "../chunks/chunk-AMHZMY6E.js";
+import "../chunks/chunk-ZKGM7VLA.js";
+import "../chunks/chunk-X4VVPLI5.js";
 import "../chunks/chunk-GOY6REMT.js";
 import {
   forceLayout,
   loadGraph
-} from "../chunks/chunk-IO2PCPZI.js";
+} from "../chunks/chunk-6UACM7VU.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
 import "../chunks/chunk-72N5DJHZ.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-MI35EUIE.js";
-import "../chunks/chunk-CJ2EE4AF.js";
-import "../chunks/chunk-PCZ4PTYC.js";
-import "../chunks/chunk-MNUSQCLG.js";
+import "../chunks/chunk-C6USNTTP.js";
+import "../chunks/chunk-ZHCDYSA5.js";
+import "../chunks/chunk-RX5CSWJW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-DKOB2OPC.js";
 import "../chunks/chunk-YMSSF2RK.js";
 import "../chunks/chunk-MREQ7GIA.js";
@@ -240,7 +241,8 @@ async function renderSpec(spec, base) {
       linearLayout: false,
       bubbleSpread: spec.bubbleSpread ?? "auto",
       spacing: spec.spacing,
-      componentSeparation: spec.componentSeparation
+      componentSeparation: spec.componentSeparation,
+      showDeletionEdges: !!spec.showDeletionEdges
     },
     engine
   )).result;

package/dist/figure.js

@@ -1,27 +1,28 @@
 import {
   figureSvg
-} from "./chunks/chunk-5XQDMQXU.js";
+} from "./chunks/chunk-KKU6JRJC.js";
 import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-ROF2R3RF.js";
-import "./chunks/chunk-6SXMCK6I.js";
-import "./chunks/chunk-D3M7SBKL.js";
+import "./chunks/chunk-V5BPIOLS.js";
+import "./chunks/chunk-PJESIRDU.js";
+import "./chunks/chunk-CH3DLBUT.js";
+import "./chunks/chunk-4BYTEJGW.js";
 import "./chunks/chunk-BUBZ32IC.js";
 import "./chunks/chunk-3S3YVOJ7.js";
-import "./chunks/chunk-LLJUG2H7.js";
-import "./chunks/chunk-MQJUG2D2.js";
-import "./chunks/chunk-GGQRADFS.js";
-import "./chunks/chunk-WFX3MAKA.js";
+import "./chunks/chunk-LPFN4POU.js";
+import "./chunks/chunk-AMHZMY6E.js";
+import "./chunks/chunk-ZKGM7VLA.js";
+import "./chunks/chunk-X4VVPLI5.js";
 import "./chunks/chunk-GOY6REMT.js";
-import "./chunks/chunk-IO2PCPZI.js";
+import "./chunks/chunk-6UACM7VU.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
-import "./chunks/chunk-CJ2EE4AF.js";
-import "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+import "./chunks/chunk-C6USNTTP.js";
+import "./chunks/chunk-ZHCDYSA5.js";
+import "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-DKOB2OPC.js";
 import "./chunks/chunk-YMSSF2RK.js";
 import "./chunks/chunk-MREQ7GIA.js";

package/dist/index.js

@@ -1,6 +1,10 @@
 import {
   wheelZoomFactor
 } from "./chunks/chunk-TDQLINVI.js";
+import {
+  drawTubeMap,
+  tubeMapPicture
+} from "./chunks/chunk-CR7EGAFE.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
@@ -9,9 +13,10 @@ import {
   drawTubeMapGenes,
   tubeMapGenes
 } from "./chunks/chunk-CTSBC2O6.js";
+import "./chunks/chunk-EJ5OZTCK.js";
 import {
   tubeMapNodeColors
-} from "./chunks/chunk-EPZORFTI.js";
+} from "./chunks/chunk-ZZA2AFB4.js";
 import {
   referenceKnots,
   warpX
@@ -28,11 +33,6 @@ import {
   referenceNodes,
   tubeMapConnectors
 } from "./chunks/chunk-GQ2AOHU4.js";
-import {
-  drawTubeMap,
-  tubeMapPicture
-} from "./chunks/chunk-CR7EGAFE.js";
-import "./chunks/chunk-EJ5OZTCK.js";
 import {
   bubbleHalos
 } from "./chunks/chunk-ISEI2FH3.js";
@@ -60,7 +60,7 @@ import {
   drawReferenceStrip,
   referenceStripBlocks,
   stripBlockAt
-} from "./chunks/chunk-EK4HGYO7.js";
+} from "./chunks/chunk-SMQ545MU.js";
 import {
   FORCE_LAYOUT_LABEL,
   LAYOUT_MODES,
@@ -80,7 +80,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-5XQDMQXU.js";
+} from "./chunks/chunk-KKU6JRJC.js";
 import {
   svgCanvas
 } from "./chunks/chunk-47DYCZOK.js";
@@ -94,7 +94,7 @@ import {
   walkMarksTree,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-ROF2R3RF.js";
+} from "./chunks/chunk-V5BPIOLS.js";
 import {
   BAR_PX,
   DISAGREES,
@@ -116,10 +116,13 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-6SXMCK6I.js";
+} from "./chunks/chunk-PJESIRDU.js";
 import {
   Canvas2DRenderer
-} from "./chunks/chunk-D3M7SBKL.js";
+} from "./chunks/chunk-CH3DLBUT.js";
+import {
+  getDpr
+} from "./chunks/chunk-4BYTEJGW.js";
 import {
   genePins
 } from "./chunks/chunk-BUBZ32IC.js";
@@ -130,7 +133,7 @@ import {
 } from "./chunks/chunk-3S3YVOJ7.js";
 import {
   version
-} from "./chunks/chunk-LLJUG2H7.js";
+} from "./chunks/chunk-LPFN4POU.js";
 import {
   axisScaleOf,
   contains,
@@ -138,12 +141,12 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-MQJUG2D2.js";
+} from "./chunks/chunk-AMHZMY6E.js";
 import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-GGQRADFS.js";
+} from "./chunks/chunk-ZKGM7VLA.js";
 import {
   WALK_FIELDS,
   WALK_SCHEMES,
@@ -151,7 +154,7 @@ import {
   encodingSwatchCss,
   resolveEncoding,
   schemeCss
-} from "./chunks/chunk-WFX3MAKA.js";
+} from "./chunks/chunk-X4VVPLI5.js";
 import {
   rangeText,
   walkKey,
@@ -167,25 +170,25 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-6UACM7VU.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-C6USNTTP.js";
 import {
   RAMP_GRADIENT_CSS,
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-CJ2EE4AF.js";
+} from "./chunks/chunk-ZHCDYSA5.js";
 import {
   REFERENCE_RAMP_MAX_HUE,
   buildGeometry,
   computeReferenceRamp
-} from "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+} from "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import {
   HALO_FACTOR,
   LEGEND_INSET_PX,
@@ -284,9 +287,6 @@ import {
   panSNSample
 } from "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-FYQWPEEY.js";
-
-// src/index.ts
-import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,

package/dist/layout/deletionRoutes.js

@@ -1,9 +1,11 @@
 import {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes
-} from "../chunks/chunk-MI35EUIE.js";
+} from "../chunks/chunk-C6USNTTP.js";
 export {
+  closableDeletions,
   routeNodes,
   takeRoutes,
   withDeletionRoutes

package/dist/layout/walkRowDraw.js

@@ -21,10 +21,10 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-6SXMCK6I.js";
-import "../chunks/chunk-CJ2EE4AF.js";
-import "../chunks/chunk-PCZ4PTYC.js";
-import "../chunks/chunk-MNUSQCLG.js";
+} from "../chunks/chunk-PJESIRDU.js";
+import "../chunks/chunk-ZHCDYSA5.js";
+import "../chunks/chunk-RX5CSWJW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-Y3IOTZJA.js";
 import "../chunks/chunk-X5L37W4J.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/layout/walkStrip.js

@@ -8,11 +8,11 @@ import {
   walkMarksTree,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-ROF2R3RF.js";
-import "../chunks/chunk-6SXMCK6I.js";
-import "../chunks/chunk-CJ2EE4AF.js";
-import "../chunks/chunk-PCZ4PTYC.js";
-import "../chunks/chunk-MNUSQCLG.js";
+} from "../chunks/chunk-V5BPIOLS.js";
+import "../chunks/chunk-PJESIRDU.js";
+import "../chunks/chunk-ZHCDYSA5.js";
+import "../chunks/chunk-RX5CSWJW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-Y3IOTZJA.js";
 import "../chunks/chunk-X5L37W4J.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/pipeline.js

@@ -9,13 +9,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-6UACM7VU.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-C6USNTTP.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/dist/referenceRampCss.js

@@ -4,9 +4,9 @@ import {
   rampHue,
   rampHueCss,
   rampStops
-} from "./chunks/chunk-CJ2EE4AF.js";
-import "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+} from "./chunks/chunk-ZHCDYSA5.js";
+import "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-Y3IOTZJA.js";
 import "./chunks/chunk-X5L37W4J.js";
 import "./chunks/chunk-ST2IBUAN.js";

package/dist/referenceStrip.js

@@ -7,9 +7,9 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-EK4HGYO7.js";
-import "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+} from "./chunks/chunk-SMQ545MU.js";
+import "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-Y3IOTZJA.js";
 import "./chunks/chunk-X5L37W4J.js";
 import "./chunks/chunk-ST2IBUAN.js";

package/dist/renderer/Canvas2DRenderer.js

@@ -1,8 +1,9 @@
 import {
   Canvas2DRenderer,
   arrowheadOutline
-} from "../chunks/chunk-D3M7SBKL.js";
-import "../chunks/chunk-MNUSQCLG.js";
+} from "../chunks/chunk-CH3DLBUT.js";
+import "../chunks/chunk-4BYTEJGW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 export {
   Canvas2DRenderer,
   arrowheadOutline

package/dist/renderer/GeometryBuilder.js

@@ -11,8 +11,8 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-PCZ4PTYC.js";
-import "../chunks/chunk-MNUSQCLG.js";
+} from "../chunks/chunk-RX5CSWJW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-Y3IOTZJA.js";
 import "../chunks/chunk-X5L37W4J.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/renderer/canvas.js

@@ -0,0 +1,12 @@
+import {
+  MAX_CANVAS_DIM_PX,
+  MAX_DPR,
+  getDpr,
+  syncCanvasSize
+} from "../chunks/chunk-4BYTEJGW.js";
+export {
+  MAX_CANVAS_DIM_PX,
+  MAX_DPR,
+  getDpr,
+  syncCanvasSize
+};

package/dist/renderer/colorBits.js

@@ -1,8 +1,22 @@
 import {
+  abgrAlpha,
+  abgrBlue,
+  abgrGreen,
+  abgrRed,
+  abgrToCssRgba,
   brightenAbgr,
-  fadeAbgr
-} from "../chunks/chunk-MNUSQCLG.js";
+  fadeAbgr,
+  normalizedRgbToCssRgba,
+  packAbgr
+} from "../chunks/chunk-UMNCCYBN.js";
 export {
+  abgrAlpha,
+  abgrBlue,
+  abgrGreen,
+  abgrRed,
+  abgrToCssRgba,
   brightenAbgr,
-  fadeAbgr
+  fadeAbgr,
+  normalizedRgbToCssRgba,
+  packAbgr
 };

package/dist/tubeMap/nodeColors.js

@@ -1,8 +1,8 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-EPZORFTI.js";
-import "../chunks/chunk-PCZ4PTYC.js";
-import "../chunks/chunk-MNUSQCLG.js";
+} from "../chunks/chunk-ZZA2AFB4.js";
+import "../chunks/chunk-RX5CSWJW.js";
+import "../chunks/chunk-UMNCCYBN.js";
 import "../chunks/chunk-Y3IOTZJA.js";
 import "../chunks/chunk-X5L37W4J.js";
 import "../chunks/chunk-ST2IBUAN.js";

package/dist/types/index.d.ts

@@ -10,7 +10,7 @@ export { BUBBLE_SPREADS } from './bubbleSpreads.js';
 export type { BubbleSpread } from './bubbleSpreads.js';
 export { REFERENCE_RAMP_MAX_HUE, buildGeometry, computeReferenceRamp, } from './renderer/GeometryBuilder.js';
 export { Canvas2DRenderer } from './renderer/Canvas2DRenderer.js';
-export { getDpr } from '@jbrowse/render-core/canvas2dUtils';
+export { getDpr } from './renderer/canvas.js';
 export type { Renderer } from './renderer/types.js';
 export { findHoveredEdge, findHoveredNode } from './util/hitDetection.js';
 export type { NodeInk } from './util/hitDetection.js';

package/dist/types/layout/deletionRoutes.d.ts

@@ -2,7 +2,7 @@ import type { BandageScaleOpts } from './drawnScale.js';
 import type { DeletionEdge } from '../deletionEdges.js';
 import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
 export type DeletionRoutes = Record<number, NodeSegment[]>;
-export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[]): {
+export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[], dropped?: Set<number>): {
     graph: {
         nodes: {
             id: string;
@@ -22,6 +22,7 @@ export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge
     routes: Map<number, string>;
     ids: Set<string>;
 };
+export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
 export declare function routeNodes(graph: Graph, deletions: DeletionEdge[], routes: Map<number, string>, drawnOf: (bp: number) => number, opts: BandageScaleOpts): GraphNode[];
 export declare function takeRoutes(positions: Record<string, NodeSegment[]>, routes: Map<number, string>): {
     nodePositions: {

package/dist/types/pansn.d.ts

@@ -1,9 +1,12 @@
-import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+interface ConfAdapter {
+    getConf(slot: any): unknown;
+}
 export declare function panSNSample(refName: string): string;
 export declare function isGenericSample(sample: string): boolean;
 export declare function panSNHaplotype(refName: string): string | undefined;
 export declare function panSNContig(refName: string): string;
 export declare function panSNMatchesPrefix(refName: string, prefix: string | undefined): boolean;
-export declare function resolvePanSNPrefix(adapter: BaseFeatureDataAdapter, name: string): string;
-export declare function resolvePanSNPrefix(adapter: BaseFeatureDataAdapter, name: string | undefined): string | undefined;
-export declare function assemblyByPanSNPrefix(adapter: BaseFeatureDataAdapter): Record<string, string>;
+export declare function resolvePanSNPrefix(adapter: ConfAdapter, name: string): string;
+export declare function resolvePanSNPrefix(adapter: ConfAdapter, name: string | undefined): string | undefined;
+export declare function assemblyByPanSNPrefix(adapter: ConfAdapter): Record<string, string>;
+export {};

package/dist/types/pipeline.d.ts

@@ -29,6 +29,7 @@ export interface EngineSettings {
     bubbleSpread: BubbleSpread;
     spacing?: number;
     componentSeparation?: number;
+    showDeletionEdges?: boolean;
 }
 export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;

package/dist/types/renderer/Canvas2DRenderer.d.ts

@@ -1,11 +1,15 @@
-import { Canvas2DRenderingBackendBase } from '@jbrowse/render-core/renderingBackendBase';
 import type { Arrowhead, RenderBatch, Renderer, TransformUniform } from './types.js';
-export declare class Canvas2DRenderer extends Canvas2DRenderingBackendBase implements Renderer {
+export declare class Canvas2DRenderer implements Renderer {
+    readonly canvas: HTMLCanvasElement;
+    readonly ctx: CanvasRenderingContext2D;
     private transform;
     private batch;
     private nodeHighlights;
     private highlightedEdge;
     private highlightFactor;
+    constructor(canvas: HTMLCanvasElement);
+    setErrorHandler(_handler: (error: Error) => void): void;
+    releaseOffscreenTargets(): void;
     resize(width: number, height: number): void;
     uploadGeometry(batch: RenderBatch): void;
     setNodeHighlights(factors: ReadonlyMap<string, number>): void;

package/dist/types/renderer/canvas.d.ts

@@ -0,0 +1,4 @@
+export declare const MAX_DPR = 2;
+export declare const MAX_CANVAS_DIM_PX = 8192;
+export declare function getDpr(): number;
+export declare function syncCanvasSize(canvas: HTMLCanvasElement, width: number, height: number): void;

package/dist/types/renderer/colorBits.d.ts

@@ -1,2 +1,9 @@
+export declare function packAbgr(r: number, g: number, b: number, a: number): number;
+export declare function abgrRed(c: number): number;
+export declare function abgrGreen(c: number): number;
+export declare function abgrBlue(c: number): number;
+export declare function abgrAlpha(c: number): number;
+export declare function abgrToCssRgba(c: number): string;
+export declare function normalizedRgbToCssRgba(c: readonly [number, number, number], alpha: number): string;
 export declare function fadeAbgr(c: number, alpha: number): number;
 export declare function brightenAbgr(c: number, factor: number): number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "6.0.3";
+export declare const version = "6.1.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-LLJUG2H7.js";
+} from "./chunks/chunk-LPFN4POU.js";
 export {
   version
 };

package/dist/viewport.js

@@ -5,14 +5,14 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-MQJUG2D2.js";
-import "./chunks/chunk-IO2PCPZI.js";
+} from "./chunks/chunk-AMHZMY6E.js";
+import "./chunks/chunk-6UACM7VU.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
 import "./chunks/chunk-72N5DJHZ.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-MI35EUIE.js";
+import "./chunks/chunk-C6USNTTP.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-TAMCZHLW.js";

package/dist/walkEncoding.js

@@ -9,9 +9,9 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-WFX3MAKA.js";
-import "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+} from "./chunks/chunk-X4VVPLI5.js";
+import "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-Y3IOTZJA.js";
 import "./chunks/chunk-X5L37W4J.js";
 import "./chunks/chunk-ST2IBUAN.js";

package/dist/walkHighlight.js

@@ -2,10 +2,10 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-GGQRADFS.js";
-import "./chunks/chunk-WFX3MAKA.js";
-import "./chunks/chunk-PCZ4PTYC.js";
-import "./chunks/chunk-MNUSQCLG.js";
+} from "./chunks/chunk-ZKGM7VLA.js";
+import "./chunks/chunk-X4VVPLI5.js";
+import "./chunks/chunk-RX5CSWJW.js";
+import "./chunks/chunk-UMNCCYBN.js";
 import "./chunks/chunk-Y3IOTZJA.js";
 import "./chunks/chunk-X5L37W4J.js";
 import "./chunks/chunk-ST2IBUAN.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "6.0.3",
+  "version": "6.1.0",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {
@@ -36,9 +36,7 @@
   "dependencies": {
     "@gmod/gbz-base": "^7.0.0",
     "@gmod/tabix": "^3.9.1",
-    "@gmod/tubemap-core": "^0.1.0",
-    "@jbrowse/core": "5.0.0-beta.11",
-    "@jbrowse/render-core": "5.0.0-beta.11"
+    "@gmod/tubemap-core": "^0.1.0"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",

package/dist/chunks/chunk-MNUSQCLG.js

@@ -1,29 +0,0 @@
-// src/renderer/colorBits.ts
-import {
-  abgrAlpha,
-  abgrBlue,
-  abgrGreen,
-  abgrRed,
-  packAbgr
-} from "@jbrowse/core/util/colorBits";
-function fadeAbgr(c, alpha) {
-  return packAbgr(
-    abgrRed(c),
-    abgrGreen(c),
-    abgrBlue(c),
-    Math.round(abgrAlpha(c) * alpha)
-  );
-}
-function brightenAbgr(c, factor) {
-  return packAbgr(
-    Math.min(255, Math.round(abgrRed(c) * factor)),
-    Math.min(255, Math.round(abgrGreen(c) * factor)),
-    Math.min(255, Math.round(abgrBlue(c) * factor)),
-    abgrAlpha(c)
-  );
-}
-
-export {
-  fadeAbgr,
-  brightenAbgr
-};