@jbrowse/bandage-core 11.3.0 → 11.4.0

package/dist/chunks/{chunk-3UST3ZQE.js → chunk-6VVGFQ7S.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-XSF4RQRP.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

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

@@ -8,12 +8,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-PNM6Z3IE.js";
+} from "./chunk-I4BYUNJN.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-XZ6PQBU6.js";
+} from "./chunk-VIQL7GZ4.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -34,16 +34,16 @@ import {
 } from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-XEWPWCML.js";
+} from "./chunk-QM7KEWWT.js";
 import {
   axisScaleOf
 } from "./chunk-CE6ZIKJX.js";
 import {
   figureScene
-} from "./chunk-T35BSLW5.js";
+} from "./chunk-JQ52XYD2.js";
 import {
   encodingStops
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-GM7M25NW.js";
 import {
   rangeText
 } from "./chunk-D4ZFRBB4.js";

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

@@ -1,13 +1,16 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-GM7M25NW.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";
 import {
   gapParts
 } from "./chunk-EIY2SKD3.js";
+import {
+  isBackbone
+} from "./chunk-RJWPJCIB.js";
 import {
   panSNContig
 } from "./chunk-4XWZNPQ2.js";
@@ -115,7 +118,7 @@ function laneColors(byId, walk, encoding, ramp) {
   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 && mid !== void 0 && node && isBackbone(node) ? (mid - ramp.start) / ramp.span : void 0;
     colors.set(id, encodedColor(encoding, t));
   }
   return colors;

package/dist/chunks/{chunk-XVS52NMZ.js → chunk-G3I4TCEZ.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-XSF4RQRP.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-TABI4JEU.js → chunk-GM7M25NW.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-XSF4RQRP.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-PNM6Z3IE.js → chunk-I4BYUNJN.js}

@@ -3,7 +3,7 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-XZ6PQBU6.js";
+} from "./chunk-VIQL7GZ4.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";

package/dist/chunks/{chunk-T35BSLW5.js → chunk-JQ52XYD2.js}

@@ -4,14 +4,14 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-DR24UTRS.js";
+} from "./chunk-FRTYQQDI.js";
 import {
   walkKey
 } from "./chunk-D4ZFRBB4.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-XSF4RQRP.js";
 import {
   walkRowsExtent
 } from "./chunk-TZLEHZVC.js";

package/dist/chunks/{chunk-SLDCKMIP.js → chunk-N7G5ROIV.js}

@@ -12,16 +12,16 @@ import {
 } from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-XEWPWCML.js";
+} from "./chunk-QM7KEWWT.js";
 import {
   axisScaleOf
 } from "./chunk-CE6ZIKJX.js";
 import {
   figureScene
-} from "./chunk-T35BSLW5.js";
+} from "./chunk-JQ52XYD2.js";
 import {
   encodingStops
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-GM7M25NW.js";
 import {
   abgrAlpha,
   abgrBlue,

package/dist/chunks/{chunk-XEWPWCML.js → chunk-QM7KEWWT.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.3.0";
+var version = "11.4.0";
 
 export {
   version

package/dist/chunks/{chunk-XZ6PQBU6.js → chunk-VIQL7GZ4.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-SWCULW6S.js";
+} from "./chunk-XSF4RQRP.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-SWCULW6S.js → chunk-XSF4RQRP.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);
@@ -339,16 +342,14 @@ 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) {
+      const mid = ramp.midpoints.get(node.id);
+      if (!isBackbone(node) || mid === void 0) {
         return REFERENCE_RAMP_ALT_COLOR;
       }
       return packHsl(

package/dist/cli/figure.js

@@ -8,15 +8,15 @@ import {
 import "../chunks/chunk-G6UIYQZR.js";
 import {
   figureSvg
-} from "../chunks/chunk-RNNYRNDU.js";
+} from "../chunks/chunk-6YJESZND.js";
 import "../chunks/chunk-EJRJAAN7.js";
 import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-V4YML3GR.js";
-import "../chunks/chunk-PNM6Z3IE.js";
+import "../chunks/chunk-I4BYUNJN.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-XZ6PQBU6.js";
+} from "../chunks/chunk-VIQL7GZ4.js";
 import "../chunks/chunk-JSUCGZ6K.js";
 import "../chunks/chunk-PSCSZSVK.js";
 import "../chunks/chunk-OMUPUB4J.js";
@@ -25,7 +25,7 @@ import "../chunks/chunk-H2H4Y3TV.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-SLDCKMIP.js";
+} from "../chunks/chunk-N7G5ROIV.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
@@ -51,14 +51,14 @@ import {
 import "../chunks/chunk-NMWQUFPF.js";
 import "../chunks/chunk-HNWJ4B7S.js";
 import "../chunks/chunk-77EGQQJU.js";
-import "../chunks/chunk-XEWPWCML.js";
+import "../chunks/chunk-QM7KEWWT.js";
 import "../chunks/chunk-CE6ZIKJX.js";
-import "../chunks/chunk-T35BSLW5.js";
+import "../chunks/chunk-JQ52XYD2.js";
 import "../chunks/chunk-LOCJN3BZ.js";
-import "../chunks/chunk-DR24UTRS.js";
-import "../chunks/chunk-TABI4JEU.js";
+import "../chunks/chunk-FRTYQQDI.js";
+import "../chunks/chunk-GM7M25NW.js";
 import "../chunks/chunk-D4ZFRBB4.js";
-import "../chunks/chunk-SWCULW6S.js";
+import "../chunks/chunk-XSF4RQRP.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

package/dist/figure.js

@@ -1,25 +1,25 @@
 import {
   figureSvg
-} from "./chunks/chunk-RNNYRNDU.js";
+} from "./chunks/chunk-6YJESZND.js";
 import "./chunks/chunk-EJRJAAN7.js";
 import "./chunks/chunk-RBCE2OQH.js";
 import "./chunks/chunk-V4YML3GR.js";
-import "./chunks/chunk-PNM6Z3IE.js";
-import "./chunks/chunk-XZ6PQBU6.js";
+import "./chunks/chunk-I4BYUNJN.js";
+import "./chunks/chunk-VIQL7GZ4.js";
 import "./chunks/chunk-JSUCGZ6K.js";
 import "./chunks/chunk-PSCSZSVK.js";
 import "./chunks/chunk-OMUPUB4J.js";
 import "./chunks/chunk-3VCKBSML.js";
 import "./chunks/chunk-H2H4Y3TV.js";
 import "./chunks/chunk-77EGQQJU.js";
-import "./chunks/chunk-XEWPWCML.js";
+import "./chunks/chunk-QM7KEWWT.js";
 import "./chunks/chunk-CE6ZIKJX.js";
-import "./chunks/chunk-T35BSLW5.js";
+import "./chunks/chunk-JQ52XYD2.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-DR24UTRS.js";
-import "./chunks/chunk-TABI4JEU.js";
+import "./chunks/chunk-FRTYQQDI.js";
+import "./chunks/chunk-GM7M25NW.js";
 import "./chunks/chunk-D4ZFRBB4.js";
-import "./chunks/chunk-SWCULW6S.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/figureData.js

@@ -3,7 +3,7 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-SLDCKMIP.js";
+} from "./chunks/chunk-N7G5ROIV.js";
 import "./chunks/chunk-JMABOQWL.js";
 import "./chunks/chunk-TEXAKEJX.js";
 import "./chunks/chunk-3LZ334X4.js";
@@ -18,14 +18,14 @@ import "./chunks/chunk-TUQKGAK3.js";
 import "./chunks/chunk-NMWQUFPF.js";
 import "./chunks/chunk-HNWJ4B7S.js";
 import "./chunks/chunk-77EGQQJU.js";
-import "./chunks/chunk-XEWPWCML.js";
+import "./chunks/chunk-QM7KEWWT.js";
 import "./chunks/chunk-CE6ZIKJX.js";
-import "./chunks/chunk-T35BSLW5.js";
+import "./chunks/chunk-JQ52XYD2.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-DR24UTRS.js";
-import "./chunks/chunk-TABI4JEU.js";
+import "./chunks/chunk-FRTYQQDI.js";
+import "./chunks/chunk-GM7M25NW.js";
 import "./chunks/chunk-D4ZFRBB4.js";
-import "./chunks/chunk-SWCULW6S.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/figureScene.js

@@ -1,11 +1,11 @@
 import {
   figureScene
-} from "./chunks/chunk-T35BSLW5.js";
+} from "./chunks/chunk-JQ52XYD2.js";
 import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-DR24UTRS.js";
-import "./chunks/chunk-TABI4JEU.js";
+import "./chunks/chunk-FRTYQQDI.js";
+import "./chunks/chunk-GM7M25NW.js";
 import "./chunks/chunk-D4ZFRBB4.js";
-import "./chunks/chunk-SWCULW6S.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/index.js

@@ -3,7 +3,7 @@ import {
 } from "./chunks/chunk-TDQLINVI.js";
 import {
   tubeMapNodeColors
-} from "./chunks/chunk-XVS52NMZ.js";
+} from "./chunks/chunk-G3I4TCEZ.js";
 import {
   bundleRoutes
 } from "./chunks/chunk-TJOOHTJ6.js";
@@ -82,7 +82,7 @@ import {
   drawReferenceStrip,
   referenceStripBlocks,
   stripBlockAt
-} from "./chunks/chunk-3UST3ZQE.js";
+} from "./chunks/chunk-6VVGFQ7S.js";
 import {
   LAYOUT_QUALITIES
 } from "./chunks/chunk-K5SIJGAE.js";
@@ -92,7 +92,7 @@ import {
 } from "./chunks/chunk-AZFVORTC.js";
 import {
   figureSvg
-} from "./chunks/chunk-RNNYRNDU.js";
+} from "./chunks/chunk-6YJESZND.js";
 import {
   Canvas2DRenderer
 } from "./chunks/chunk-EJRJAAN7.js";
@@ -113,7 +113,7 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunks/chunk-PNM6Z3IE.js";
+} from "./chunks/chunk-I4BYUNJN.js";
 import {
   BAR_PX,
   CALL_TICK,
@@ -141,7 +141,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunks/chunk-XZ6PQBU6.js";
+} from "./chunks/chunk-VIQL7GZ4.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -165,7 +165,7 @@ import {
 import {
   figureData,
   gfaFigureData
-} from "./chunks/chunk-SLDCKMIP.js";
+} from "./chunks/chunk-N7G5ROIV.js";
 import {
   LAYOUT_ENGINES,
   layoutEngine
@@ -205,7 +205,7 @@ import {
 } from "./chunks/chunk-77EGQQJU.js";
 import {
   version
-} from "./chunks/chunk-XEWPWCML.js";
+} from "./chunks/chunk-QM7KEWWT.js";
 import {
   axisScaleOf,
   contains,
@@ -214,7 +214,7 @@ import {
   viewportOf,
   zoomAbout
 } from "./chunks/chunk-CE6ZIKJX.js";
-import "./chunks/chunk-T35BSLW5.js";
+import "./chunks/chunk-JQ52XYD2.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -222,7 +222,7 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-DR24UTRS.js";
+} from "./chunks/chunk-FRTYQQDI.js";
 import {
   WALK_FIELDS,
   WALK_SCHEMES,
@@ -230,7 +230,7 @@ import {
   encodingSwatchCss,
   resolveEncoding,
   schemeCss
-} from "./chunks/chunk-TABI4JEU.js";
+} from "./chunks/chunk-GM7M25NW.js";
 import {
   rangeText,
   walkKey,
@@ -239,7 +239,7 @@ import {
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   RAMP_GRADIENT_CSS,

package/dist/layout/walkRowDraw.js

@@ -29,9 +29,9 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "../chunks/chunk-XZ6PQBU6.js";
+} from "../chunks/chunk-VIQL7GZ4.js";
 import "../chunks/chunk-H2H4Y3TV.js";
-import "../chunks/chunk-SWCULW6S.js";
+import "../chunks/chunk-XSF4RQRP.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

package/dist/layout/walkStrip.js

@@ -9,12 +9,12 @@ import {
   walkStripApplies,
   walkStripFrame,
   walkStripLabelsTree
-} from "../chunks/chunk-PNM6Z3IE.js";
+} from "../chunks/chunk-I4BYUNJN.js";
 import {
   LABELLED_ROW_PX
-} from "../chunks/chunk-XZ6PQBU6.js";
+} from "../chunks/chunk-VIQL7GZ4.js";
 import "../chunks/chunk-H2H4Y3TV.js";
-import "../chunks/chunk-SWCULW6S.js";
+import "../chunks/chunk-XSF4RQRP.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

package/dist/referenceStrip.js

@@ -7,8 +7,8 @@ import {
   stripBlockAt,
   stripOverhang,
   stripPixels
-} from "./chunks/chunk-3UST3ZQE.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-6VVGFQ7S.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/renderer/GeometryBuilder.js

@@ -10,7 +10,7 @@ import {
   endTangent,
   getNodeColor,
   hslToRgb
-} from "../chunks/chunk-SWCULW6S.js";
+} from "../chunks/chunk-XSF4RQRP.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import {
   REFERENCE_RAMP_MAX_HUE

package/dist/tubeMap/nodeColors.js

@@ -1,7 +1,7 @@
 import {
   tubeMapNodeColors
-} from "../chunks/chunk-XVS52NMZ.js";
-import "../chunks/chunk-SWCULW6S.js";
+} from "../chunks/chunk-G3I4TCEZ.js";
+import "../chunks/chunk-XSF4RQRP.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "11.3.0";
+export declare const version = "11.4.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-XEWPWCML.js";
+} from "./chunks/chunk-QM7KEWWT.js";
 export {
   version
 };

package/dist/walkEncoding.js

@@ -9,8 +9,8 @@ import {
   schemeColor,
   schemeCss,
   schemeRgb
-} from "./chunks/chunk-TABI4JEU.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-GM7M25NW.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/dist/walkHighlight.js

@@ -2,9 +2,9 @@ import {
   facetLifts,
   walkHighlight,
   walkLift
-} from "./chunks/chunk-DR24UTRS.js";
-import "./chunks/chunk-TABI4JEU.js";
-import "./chunks/chunk-SWCULW6S.js";
+} from "./chunks/chunk-FRTYQQDI.js";
+import "./chunks/chunk-GM7M25NW.js";
+import "./chunks/chunk-XSF4RQRP.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "11.3.0",
+  "version": "11.4.0",
   "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": {