@jbrowse/bandage-core 11.14.0 → 11.16.0

package/dist/bubbles/bubbleHalos.js

@@ -1,14 +1,14 @@
 import {
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-SZYFZNCO.js";
-import "../chunks/chunk-NWEVR2OQ.js";
+} from "../chunks/chunk-RATN62M3.js";
+import "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/bubbles/classifyBubble.js

@@ -3,13 +3,13 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-NWEVR2OQ.js";
+} from "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/bubbles/superbubbles.js

@@ -1,19 +1,19 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-DOCI5O5R.js";
-import "../chunks/chunk-SZYFZNCO.js";
+} from "../chunks/chunk-G3R7LUOS.js";
+import "../chunks/chunk-RATN62M3.js";
 import "../chunks/chunk-V6WSDZPL.js";
-import "../chunks/chunk-NWEVR2OQ.js";
+import "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-MHZTTLBU.js";
 import "../chunks/chunk-Q7OFBTBW.js";
 import "../chunks/chunk-L4DBSRA2.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/chunks/{chunk-BDS5VZYZ.js → chunk-2BSGQKF3.js}

@@ -8,7 +8,7 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-2AVTTUP2.js → chunk-3KGUENAV.js}

@@ -39,7 +39,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   anchorGraph
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-TEFNVUGD.js → chunk-54CX2MCH.js}

@@ -6,7 +6,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-BDS5VZYZ.js";
+} from "./chunk-2BSGQKF3.js";
 import {
   anchoredLayout
 } from "./chunk-CNWAVRLF.js";

package/dist/chunks/{chunk-OYBYCF2O.js → chunk-5KQRVX4N.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-JUYPCLF4.js → chunk-72JZSR4B.js}

@@ -21,13 +21,13 @@ import {
 } from "./chunk-GQZVR5DW.js";
 import {
   baseEdgeCurves
-} from "./chunk-P2GJBFNA.js";
+} from "./chunk-AGUBPT45.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
   meanDepth,
   nodeWidthPx,

package/dist/chunks/{chunk-S6E3PMH7.js → chunk-7KVA7TFI.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-BDS5VZYZ.js";
+} from "./chunk-2BSGQKF3.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-EIMRD6L7.js → chunk-7UR5EXC2.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-P2GJBFNA.js → chunk-AGUBPT45.js}

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

package/dist/chunks/{chunk-QL673EK5.js → chunk-BMO5MVPB.js}

@@ -3,7 +3,7 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-OYBYCF2O.js";
+} from "./chunk-5KQRVX4N.js";
 import {
   READOUT_ROOM,
   longestBar

package/dist/chunks/{chunk-5SW3PTHO.js → chunk-CF2AXV5I.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-VQ353UDK.js → chunk-EHEIS3TE.js}

@@ -1,6 +1,6 @@
 import {
   groupDigits
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-AURNOR27.js → chunk-ENBFQH7Y.js}

@@ -10,7 +10,7 @@ import {
 } from "./chunk-HNNP5QUN.js";
 import {
   edgeCurvesOf
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   curveBounds,
   curveMidpoint,

package/dist/chunks/{chunk-XBX3HSC7.js → chunk-F3254CLY.js}

@@ -4,27 +4,27 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-WRSI6VK7.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   walkKey
-} from "./chunk-IZKM4NY7.js";
+} from "./chunk-OKH32P3Z.js";
 import {
   walkRowsExtent
 } from "./chunk-VCUOYVLC.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-CF2AXV5I.js";
 import {
   drawingBounds
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 import {
   referenceLabel
 } from "./chunk-5ORP7EFJ.js";
@@ -34,7 +34,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   facetCells,
   facetSettingOf

package/dist/chunks/{chunk-DOCI5O5R.js → chunk-G3R7LUOS.js}

@@ -1,6 +1,6 @@
 import {
   coversGraph
-} from "./chunk-SZYFZNCO.js";
+} from "./chunk-RATN62M3.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -10,7 +10,7 @@ import {
 } from "./chunk-V6WSDZPL.js";
 import {
   bubbleSegmentIds
-} from "./chunk-NWEVR2OQ.js";
+} from "./chunk-HYVIQS4D.js";
 import {
   bubbleSubgraph
 } from "./chunk-MHZTTLBU.js";

package/dist/chunks/{chunk-NWEVR2OQ.js → chunk-HYVIQS4D.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-EOB4Y3EM.js → chunk-JWXSEGEA.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-JUVIPVXX.js → chunk-KMYMAPQ3.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-CO6RGQAD.js";
 import {
   layoutModeByValue
-} from "./chunk-TEFNVUGD.js";
+} from "./chunk-54CX2MCH.js";
 import {
   parseRegion
 } from "./chunk-FNDNSDKW.js";
@@ -12,19 +12,19 @@ import {
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-FXUAVF4A.js";
+} from "./chunk-NIB2A2UZ.js";
 import {
   axisScaleOf
-} from "./chunk-OKPSS5PG.js";
+} from "./chunk-ZB5ADQYK.js";
 import {
   figureScene
-} from "./chunk-XBX3HSC7.js";
+} from "./chunk-F3254CLY.js";
 import {
   fadedKey
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-WRSI6VK7.js";
 import {
   encodingStops
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-JWXSEGEA.js";
 import {
   laneSlideAt,
   passesKey,
@@ -38,16 +38,19 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-CF2AXV5I.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 import {
   referencePositions
 } from "./chunk-L4DBSRA2.js";
+import {
+  deletionKey
+} from "./chunk-OMQWCVOJ.js";
 import {
   referenceVisitStarts
 } from "./chunk-3YBP46PB.js";
@@ -321,6 +324,7 @@ function figureData(graph, layout, o = {}) {
         end: referenceRamp.start + referenceRamp.span
       } : null,
       deletions: drawnDeletions.shown.length,
+      deletionKey: drawnDeletions.shown.length ? deletionKey(referenceName) : null,
       // what the key for the drawing a lift fades says
       fadedKey: lift ? fadedKey(
         graph,

package/dist/chunks/{chunk-FXUAVF4A.js → chunk-NIB2A2UZ.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.14.0";
+var version = "11.16.0";
 
 export {
   version

package/dist/chunks/{chunk-IZKM4NY7.js → chunk-OKH32P3Z.js}

@@ -5,7 +5,7 @@ import {
 import {
   formatBp,
   groupDigits
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-3GORESBG.js → chunk-OMQWCVOJ.js}

@@ -23,6 +23,7 @@ import {
 
 // src/deletionEdges.ts
 var MIN_DELETION_BP = 1;
+var deletionKey = (reference) => `skips ${reference ?? "the reference"} sequence (a deletion)`;
 function bypassedPoints(nodePositions, bypassed) {
   return bypassed.flatMap((id) => nodePositions[id] ?? []);
 }
@@ -204,6 +205,7 @@ function deletionDrawing(graph, deletions, show = true) {
 }
 
 export {
+  deletionKey,
   edgeCurvesOf,
   deletionEdges,
   closableDeletions,

package/dist/chunks/{chunk-4JDO7ZLN.js → chunk-QWLCHMNS.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-7YSIP3O2.js";
+} from "./chunk-WTWO2IPM.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";

package/dist/chunks/{chunk-SZYFZNCO.js → chunk-RATN62M3.js}

@@ -1,7 +1,7 @@
 import {
   bubbleSegmentIds,
   classifyBubble
-} from "./chunk-NWEVR2OQ.js";
+} from "./chunk-HYVIQS4D.js";
 import {
   svgPath
 } from "./chunk-JJV2GT2Z.js";

package/dist/chunks/{chunk-CLY6DKIU.js → chunk-SR6LCQ5U.js}

@@ -5,7 +5,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-QL673EK5.js";
+} from "./chunk-BMO5MVPB.js";
 import {
   Canvas2DRenderer
 } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-OYBYCF2O.js";
+} from "./chunk-5KQRVX4N.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,28 +21,28 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-TQ26XEFL.js";
+} from "./chunk-U6TXPLFJ.js";
 import {
   nodesUnderBox
-} from "./chunk-4JDO7ZLN.js";
+} from "./chunk-QWLCHMNS.js";
 import {
   genePins
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-FXUAVF4A.js";
+} from "./chunk-NIB2A2UZ.js";
 import {
   axisScaleOf
-} from "./chunk-OKPSS5PG.js";
+} from "./chunk-ZB5ADQYK.js";
 import {
   figureScene
-} from "./chunk-XBX3HSC7.js";
+} from "./chunk-F3254CLY.js";
 import {
   fadedKey
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-WRSI6VK7.js";
 import {
   encodingStops
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-JWXSEGEA.js";
 import {
   THREAD_PX,
   passesKey,
@@ -50,7 +50,7 @@ import {
 } from "./chunk-YUIKEUKY.js";
 import {
   rangeText
-} from "./chunk-IZKM4NY7.js";
+} from "./chunk-OKH32P3Z.js";
 import {
   walkRowLabels
 } from "./chunk-VCUOYVLC.js";
@@ -59,11 +59,11 @@ import {
 } from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-CF2AXV5I.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -71,6 +71,9 @@ import {
   occupancy,
   placeLabels
 } from "./chunk-AB35TJST.js";
+import {
+  deletionKey
+} from "./chunk-OMQWCVOJ.js";
 import {
   escapeAttr,
   serializeEl
@@ -91,6 +94,7 @@ var KEY_LINE_PX = 16;
 var KEY_TALL_PX = 32;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
+var DELETION_INK = "rgb(24,24,28)";
 var GENE_INK = "#1c1c22";
 function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   const bar = stops.length > 1 ? BAR_PX : SWATCH_PX;
@@ -113,6 +117,13 @@ function exonKeySvg(x, y) {
     markup: `<g transform="translate(${x} ${y})" ${FONT}><rect x="1" y="4" width="${SWATCH_PX - 2}" height="10" rx="4" fill="none" stroke="${EXON_COLOR}" stroke-width="2"/><text x="${SWATCH_PX + 5}" y="13">exon</text></g>`
   };
 }
+function deletionKeySvg(x, y, note, color) {
+  return {
+    width: SWATCH_PX + 5 + note.length * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
+    markup: `<g transform="translate(${x} ${y})" ${FONT}><line y1="9" y2="9" x2="${SWATCH_PX}" stroke="${color}" stroke-width="2" stroke-dasharray="4 3"/><text x="${SWATCH_PX + 5}" y="13">${note}</text></g>`
+  };
+}
 function passesKeySvg(x, y, note) {
   const lines = [6, 9, 12].map(
     (ly) => `<line y1="${ly}" y2="${ly}" x2="${SWATCH_PX}" stroke="#444" stroke-width="${THREAD_PX}"/>`
@@ -176,6 +187,7 @@ function figureSvg(graph, layout, o = {}) {
     labelOf,
     referenceName,
     keyText,
+    drawnDeletions,
     contigThickness,
     nodeWidth,
     geometry
@@ -363,6 +375,16 @@ function figureSvg(graph, layout, o = {}) {
         )
       );
     }
+    if (drawnDeletions.shown.length > 0) {
+      keys.push(
+        (x, y) => deletionKeySvg(
+          x,
+          y,
+          deletionKey(referenceName),
+          lift ? FADED : DELETION_INK
+        )
+      );
+    }
     if (pins.some((pin) => pin.exonsByNode.length > 0)) {
       keys.push((x, y) => exonKeySvg(x, y));
     }

package/dist/chunks/{chunk-RT4U3DH3.js → chunk-TICU3HMJ.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-I53QYITQ.js";
+} from "./chunk-TK2ANC2S.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-I53QYITQ.js → chunk-TK2ANC2S.js}

@@ -1,6 +1,6 @@
 import {
   formatBp
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-TQ26XEFL.js → chunk-U6TXPLFJ.js}

@@ -1,10 +1,10 @@
 import {
   nodesUnderBox
-} from "./chunk-4JDO7ZLN.js";
+} from "./chunk-QWLCHMNS.js";
 import {
   graphLabels,
   rowLabelBox
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-ZHCQOC67.js → chunk-U7JDTZSK.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-MB4UWYDG.js → chunk-WRSI6VK7.js}

@@ -2,10 +2,10 @@ import {
   encodedColor,
   resolveEncoding,
   splitFamilies
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-JWXSEGEA.js";
 import {
   rampFraction
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   gapParts
 } from "./chunk-LG2UK4MB.js";

package/dist/chunks/{chunk-7YSIP3O2.js → chunk-WTWO2IPM.js}

@@ -1,6 +1,6 @@
 import {
   baseEdgeCurves
-} from "./chunk-P2GJBFNA.js";
+} from "./chunk-AGUBPT45.js";
 import {
   curveBounds,
   pathRibbonOffsets

package/dist/chunks/{chunk-VNCHWWLG.js → chunk-Y5BPNRFM.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-BDS5VZYZ.js";
+} from "./chunk-2BSGQKF3.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-K4RGSISK.js → chunk-Z5T6EOPF.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-72JZSR4B.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-OKPSS5PG.js → chunk-ZB5ADQYK.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-3KGUENAV.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {