@jbrowse/bandage-core 10.3.1 → 11.1.0

package/dist/chunks/{chunk-EWLXU3UG.js → chunk-JFHYG25O.js}

@@ -5,12 +5,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-SFP3E4RI.js";
+} from "./chunk-IZ6Y5D23.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-ZJBOM73S.js";
+} from "./chunk-XZ6PQBU6.js";
 import {
   Canvas2DRenderer
 } from "./chunk-EJRJAAN7.js";
@@ -19,9 +19,6 @@ import {
   exonOutlineTree,
   exonStretches
 } from "./chunk-JSUCGZ6K.js";
-import {
-  genePins
-} from "./chunk-BS6HPYCZ.js";
 import {
   geneLabelCandidates
 } from "./chunk-PSCSZSVK.js";
@@ -32,34 +29,37 @@ import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
+import {
+  genePins
+} from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-AQCOIE5R.js";
+} from "./chunk-Y3FDMDNT.js";
 import {
   axisScaleOf
-} from "./chunk-BKEZLETL.js";
+} from "./chunk-AI5PTOSV.js";
 import {
   figureScene
-} from "./chunk-QH2MIXBA.js";
+} from "./chunk-IVOK5V3H.js";
 import {
   encodingStops
-} from "./chunk-DO62DG26.js";
+} from "./chunk-TABI4JEU.js";
 import {
   rangeText
-} from "./chunk-CGFPFBT2.js";
+} from "./chunk-D4ZFRBB4.js";
 import {
   walkRowLabels
-} from "./chunk-A2TJ5UX6.js";
+} from "./chunk-YHJ5JLBI.js";
 import {
   nodeInk
 } from "./chunk-CRCD3ODN.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-D7WIYPG3.js";
+} from "./chunk-W6EXQDV5.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-KMBE2Q42.js → chunk-KDU4EF66.js}

@@ -14,19 +14,19 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-NZTYV3JL.js";
+} from "./chunk-FFHJGWDK.js";
 import {
   parseGFA
 } from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
-} from "./chunk-DBLV7PGG.js";
+} from "./chunk-3XSRT7RQ.js";
 import {
   anchorGraph
 } from "./chunk-B5X2RLJG.js";
 import {
   gfaTables
-} from "./chunk-Z6XZWPXK.js";
+} from "./chunk-DZR37KXT.js";
 import {
   mergeRuns,
   splitRuns

package/dist/chunks/{chunk-FW2R7UDZ.js → chunk-LMH5KVJZ.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-OOIOX36I.js";
+} from "./chunk-DEDD7TFJ.js";
 import {
   pathCssColor,
   pathGreyCssColor

package/dist/chunks/{chunk-AZ4EEF6Q.js → chunk-NGUM77EP.js}

@@ -1,12 +1,12 @@
-import {
-  sampleRowLayout
-} from "./chunk-GJU6BJJA.js";
 import {
   hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-FW2R7UDZ.js";
+} from "./chunk-LMH5KVJZ.js";
+import {
+  sampleRowLayout
+} from "./chunk-GJU6BJJA.js";
 import {
   anchoredLayout
 } from "./chunk-GJLZ2MKE.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-A2TJ5UX6.js";
+} from "./chunk-YHJ5JLBI.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-GIHTHYXY.js → chunk-NMWQUFPF.js}

@@ -6,7 +6,7 @@ import {
 } from "./chunk-234NFZS4.js";
 import {
   gfaTables
-} from "./chunk-Z6XZWPXK.js";
+} from "./chunk-DZR37KXT.js";
 import {
   panSNMatchesPrefix,
   panSNSample

package/dist/chunks/{chunk-CHNESV7L.js → chunk-OI4YVAMM.js}

@@ -3,19 +3,25 @@ import {
 } from "./chunk-JMABOQWL.js";
 import {
   layoutModeByValue
-} from "./chunk-AZ4EEF6Q.js";
+} from "./chunk-NGUM77EP.js";
 import {
   parseRegion
-} from "./chunk-M5NPD55W.js";
+} from "./chunk-TUQKGAK3.js";
+import {
+  genePins
+} from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-AQCOIE5R.js";
+} from "./chunk-Y3FDMDNT.js";
 import {
   axisScaleOf
-} from "./chunk-BKEZLETL.js";
+} from "./chunk-AI5PTOSV.js";
 import {
   figureScene
-} from "./chunk-QH2MIXBA.js";
+} from "./chunk-IVOK5V3H.js";
+import {
+  encodingStops
+} from "./chunk-TABI4JEU.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -24,13 +30,13 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-D7WIYPG3.js";
+} from "./chunk-W6EXQDV5.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";
@@ -76,21 +82,58 @@ function figureData(graph, layout, o = {}) {
   }
   const axis = axisScaleOf(fit.scale, pixelRows);
   const panels = [];
+  const keys = columns(["panel", "walk", "note", "scale", "stops"]);
+  const pushKey = (walk, panel) => {
+    const key = keyText(walk);
+    keys.push({
+      panel,
+      walk: labelOf(walk.name),
+      note: key.note,
+      scale: key.scale ?? "",
+      stops: encodingStops(walk.encoding).map((s) => cssHex(s.abgr)).join(",")
+    });
+    return key;
+  };
   if (facets) {
     const ordered = facets.panels.map((panel, i) => ({ panel, cell: facets.place.cells[i] })).sort((a, b) => a.cell - b.cell);
     for (const { panel } of ordered) {
       const walk = panel.walks[0];
-      const key = keyText(walk);
+      const name = labelOf(walk.name);
+      const key = pushKey(walk, name);
       panels.push({
         highlight: panel,
-        name: labelOf(walk.name),
+        name,
         key: key.note,
         range: key.scale ?? ""
       });
     }
   } else {
+    for (const walk of lift?.walks ?? []) {
+      pushKey(walk, "");
+    }
     panels.push({ highlight: lift, name: "", key: "", range: "" });
   }
+  const pins = columns(["gene", "x", "y", "covered", "bp"]);
+  const exons = columns(["gene", "node", "stretch", "x", "y"]);
+  let stretch = 0;
+  for (const pin of o.genes?.length ? genePins(graph, o.genes, layout.nodePositions) : []) {
+    const gene = pin.gene.name;
+    pins.push({
+      gene,
+      x: pin.at.x,
+      y: pin.at.y,
+      covered: pin.covered,
+      bp: pin.gene.end - pin.gene.start
+    });
+    for (const { nodeId, stretches } of pin.exonsByNode) {
+      for (const points of stretches) {
+        stretch++;
+        for (const { x, y } of points) {
+          exons.push({ gene, node: nodeId, stretch, x, y });
+        }
+      }
+    }
+  }
   const nodes = columns([
     "panel",
     "node",
@@ -198,6 +241,10 @@ function figureData(graph, layout, o = {}) {
       key: panels.map((p) => p.key),
       range: panels.map((p) => p.range)
     },
+    keys: keys.out,
+    pins: pins.out,
+    exons: exons.out,
+    walkNames: [...new Set((graph.paths ?? []).map((p) => p.name))],
     nodes: nodes.out,
     edges: edges.out,
     arrows: arrows.out,

package/dist/chunks/{chunk-R2PJKD3Y.js → chunk-RETNT73O.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-FW2R7UDZ.js";
+} from "./chunk-LMH5KVJZ.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-OXRUPNSV.js → chunk-RNYPCQZ3.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-DO62DG26.js → chunk-TABI4JEU.js}

@@ -88,10 +88,12 @@ function encodedColor({ field, scheme }, t) {
 }
 var NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;
 function encodingStops({ field, scheme }) {
-  return field === "walk" ? [{ offset: 0, color: schemeCss(scheme, BASE_T) }] : Array.from({ length: 7 }, (_, i) => ({
-    offset: i / 6,
-    color: schemeCss(scheme, i / 6)
-  }));
+  const stop = (offset, t) => ({
+    offset,
+    color: schemeCss(scheme, t),
+    abgr: schemeColor(scheme, t)
+  });
+  return field === "walk" ? [stop(0, BASE_T)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, i / 6));
 }
 function encodingSwatchCss(encoding) {
   const stops = encodingStops(encoding);

package/dist/chunks/{chunk-M5NPD55W.js → chunk-TUQKGAK3.js}

@@ -6,7 +6,7 @@ import {
   haplotypeWanted,
   referencePathQuery,
   referenceSamplesOf
-} from "./chunk-GIHTHYXY.js";
+} from "./chunk-NMWQUFPF.js";
 import {
   panSNSample
 } from "./chunk-4XWZNPQ2.js";

package/dist/chunks/{chunk-MWOVW4AH.js → chunk-V5MAL7LU.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-FW2R7UDZ.js";
+} from "./chunk-LMH5KVJZ.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-D7WIYPG3.js → chunk-W6EXQDV5.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-KMBE2Q42.js";
+} from "./chunk-KDU4EF66.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-ZJBOM73S.js → chunk-XZ6PQBU6.js}

@@ -10,20 +10,30 @@ import {
   rampHueCss,
   rampStops
 } from "./chunk-GQZVR5DW.js";
+import {
+  GAP_CAUSE_TEXT,
+  OUTSIDE_TEXT
+} from "./chunk-EIY2SKD3.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
+import {
+  panSNContig
+} from "./chunk-4XWZNPQ2.js";
 
 // src/layout/walkRowDraw.ts
 var ON_REFERENCE = "#2f8fd6";
 var OFF_REFERENCE = "#8e3fbf";
 var OUTSIDE_CUT = "#bdbdbd";
+var MISSING_INK = "#8a8a8a";
+var UNKNOWN_GAP = "#e2e2e2";
 var GENE_INK = "#1c1c22";
 var BAR_PX = 12;
 var GAP_PX = 4;
+var MISSING_PX = 1;
 var LABELLED_ROW_PX = 12;
 var MIN_TILED_BAR_PX = 6;
 var MIN_TILE_PX = 3;
@@ -37,12 +47,36 @@ function signedLength(delta) {
 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);
+  if (gapBp <= 0) {
+    return "";
+  }
+  if (!gaps.some((g) => g.cause)) {
+    return ` \xB7 ${kb(gapBp)} ${OUTSIDE_TEXT}`;
+  }
+  const bpOf = (cause) => gaps.filter((g) => g.cause === cause).reduce((sum, g) => sum + g.bp, 0);
+  const places = [
+    ...new Set(gaps.flatMap((g) => g.chunk ? [near(g.chunk)] : []))
+  ];
+  const parts = [
+    [bpOf("missing"), GAP_CAUSE_TEXT.missing],
+    [
+      bpOf("elsewhere"),
+      `on nodes filed near ${places[0]}${places.length > 1 ? ` and ${places.length - 1} more place${places.length > 2 ? "s" : ""}` : ""}`
+    ],
+    [bpOf("unknown"), GAP_CAUSE_TEXT.unknown],
+    [bpOf(void 0), OUTSIDE_TEXT]
+  ];
+  return parts.filter(([bp]) => bp > 0).map(([bp, text]) => ` \xB7 ${kb(bp)} ${text}`).join("");
+}
 function walkRowReadout(row, reference, unit, call) {
   const { bp, gapBp, complete, stop } = row;
   if (!reference) {
     return `${kb(bp)}${units(bp, unit)}`;
   }
-  const outside = gapBp > 0 ? ` \xB7 ${kb(gapBp)} outside the cut` : "";
+  const outside = gapsText(gapBp, row.runs);
   const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
   if (complete) {
     const delta = bp - reference.bp;
@@ -54,7 +88,7 @@ function walkRowReadout(row, reference, unit, call) {
     const where = stop.shortBp > 0 ? `${kb(stop.shortBp)} before` : "at";
     return `contig ends ${where} the ${region}${called}`;
   }
-  const why = !stop ? "partial walk" : stop.contigEnds ? `contig ends inside the ${region}` : "does not rejoin the reference within the cut";
+  const why = !stop ? "partial walk" : stop.contigEnds ? `contig ends inside the ${region}` : "does not rejoin the reference within the extracted subgraph";
   return `\u2265 ${kb(bp)}${units(bp, unit)} \xB7 ${why}${outside}${called}`;
 }
 function readoutPlacement(text, endX, width) {
@@ -72,9 +106,12 @@ 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 };
+}
 function runPaint(run, ramp) {
   if (run.gap) {
-    return { fill: OUTSIDE_CUT };
+    return { fill: gapStyle(run.cause).fill };
   }
   if (!ramp) {
     return { fill: run.onReference ? ON_REFERENCE : OFF_REFERENCE };
@@ -180,11 +217,15 @@ function walkRowsKey(bars, o = {}) {
       label: `off ${bars.reference.label}'s path`
     }
   ];
-  if ([bars.reference, ...bars.rows].some((row) => row.gapBp > 0)) {
-    entries.push({
-      swatch: { kind: "gap", fill: OUTSIDE_CUT },
-      label: "walked outside the cut"
-    });
+  const gaps = [bars.reference, ...bars.rows].flatMap(
+    (row) => row.runs.filter((run) => run.gap)
+  );
+  const labels = new Set(gaps.map((run) => gapStyle(run.cause).label));
+  for (const cause of [void 0, "missing", "unknown"]) {
+    const { fill, px, label } = gapStyle(cause);
+    if (labels.has(label)) {
+      entries.push({ swatch: { kind: "gap", fill, px }, label });
+    }
   }
   if (o.genes?.crowded) {
     entries.push({
@@ -248,9 +289,9 @@ function walkRowsKeyTree(entries, x, y, idPrefix = "walk-key") {
       "stroke-width": 1.5
     }) : el("rect", {
       x: at,
-      y: e.swatch.kind === "gap" ? 7 : 5,
+      y: e.swatch.kind === "gap" ? 9 - e.swatch.px / 2 : 5,
       width: 18,
-      height: e.swatch.kind === "gap" ? GAP_PX : 8,
+      height: e.swatch.kind === "gap" ? e.swatch.px : 8,
       rx: 2,
       fill: ramp ? `url(#${rampId})` : e.swatch.fill
     });
@@ -399,9 +440,10 @@ function walkRowsTree(bars, frame, o = {}) {
     if (y < -barPx || y > frame.height + barPx) {
       return void 0;
     }
-    const runs = coalesceRuns(row.runs, frame.scaleX).flatMap((run) => {
+    const drawn = frame.bars === false ? [] : row.runs;
+    const runs = coalesceRuns(drawn, frame.scaleX).flatMap((run) => {
       const paint = runPaint(run, o.ramp);
-      const h = run.gap ? Math.min(GAP_PX, barPx) : barPx;
+      const h = run.gap ? Math.min(gapStyle(run.cause).px, barPx) : barPx;
       const id = `${prefix}-${i}-${run.start}`;
       const rect = el("rect", {
         x: along(run.start),
@@ -486,13 +528,17 @@ export {
   ON_REFERENCE,
   OFF_REFERENCE,
   OUTSIDE_CUT,
+  MISSING_INK,
+  UNKNOWN_GAP,
   GENE_INK,
   BAR_PX,
   GAP_PX,
+  MISSING_PX,
   LABELLED_ROW_PX,
   walkRowReadout,
   readoutPlacement,
   unitTicks,
+  gapStyle,
   runPaint,
   alongRow,
   rowSpan,

package/dist/chunks/{chunk-AQCOIE5R.js → chunk-Y3FDMDNT.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.3.1";
+var version = "11.1.0";
 
 export {
   version

package/dist/chunks/{chunk-A2TJ5UX6.js → chunk-YHJ5JLBI.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-OOIOX36I.js";
+} from "./chunk-DEDD7TFJ.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-WYJQIC75.js → chunk-ZUL52ZX2.js}

@@ -1,15 +1,15 @@
-import {
-  tubeMapMismatches
-} from "./chunk-BX4AUMZE.js";
 import {
   MAX_GAP_PX
 } from "./chunk-MYDHU2UV.js";
+import {
+  tubeMapMismatches
+} from "./chunk-BX4AUMZE.js";
 import {
   readColor
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-OOIOX36I.js";
+} from "./chunk-DEDD7TFJ.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";