@jbrowse/bandage-core 6.0.0 → 6.0.2

package/dist/labelLayout.js

@@ -0,0 +1,24 @@
+import {
+  HALO_FACTOR,
+  LEGEND_INSET_PX,
+  geneCoverageNote,
+  geneLabelCandidates,
+  layoutLabels
+} from "./chunks/chunk-HB6PDCOU.js";
+import "./chunks/chunk-BJV2W4KZ.js";
+import "./chunks/chunk-LVZZH2NI.js";
+import "./chunks/chunk-6YRRNX2P.js";
+import "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  HALO_FACTOR,
+  LEGEND_INSET_PX,
+  geneCoverageNote,
+  geneLabelCandidates,
+  layoutLabels
+};

package/dist/layout/anchoredLayout.js

@@ -0,0 +1,11 @@
+import {
+  anchoredLayout
+} from "../chunks/chunk-L3O7AWLI.js";
+import "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-RVS2QCOX.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  anchoredLayout
+};

package/dist/layout/deletionRoutes.js

@@ -0,0 +1,10 @@
+import {
+  routeNodes,
+  takeRoutes,
+  withDeletionRoutes
+} from "../chunks/chunk-MI35EUIE.js";
+export {
+  routeNodes,
+  takeRoutes,
+  withDeletionRoutes
+};

package/dist/layout/drawnScale.js

@@ -0,0 +1,22 @@
+import {
+  MEAN_NODE_LENGTH,
+  PROPORTIONAL_LENGTH,
+  PROPORTIONAL_SPREAD,
+  bandageAutoScale,
+  drawnLengthFor,
+  drawnLengthOf,
+  drawnNodeLength,
+  isProportional,
+  layoutScaling
+} from "../chunks/chunk-6JEWNXCQ.js";
+export {
+  MEAN_NODE_LENGTH,
+  PROPORTIONAL_LENGTH,
+  PROPORTIONAL_SPREAD,
+  bandageAutoScale,
+  drawnLengthFor,
+  drawnLengthOf,
+  drawnNodeLength,
+  isProportional,
+  layoutScaling
+};

package/dist/layout/mergeRuns.js

@@ -0,0 +1,15 @@
+import {
+  mergeRuns,
+  polylineMidpoint,
+  polylineSlice,
+  splitRuns
+} from "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  mergeRuns,
+  polylineMidpoint,
+  polylineSlice,
+  splitRuns
+};

package/dist/layout/orderedLayout.js

@@ -0,0 +1,12 @@
+import {
+  layerGraph,
+  orderedLayout,
+  referenceOrder
+} from "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  layerGraph,
+  orderedLayout,
+  referenceOrder
+};

package/dist/layout/orientToReference.js

@@ -0,0 +1,7 @@
+import {
+  orientToReference
+} from "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  orientToReference
+};

package/dist/layout/placeOffReference.js

@@ -0,0 +1,9 @@
+import {
+  placeOffReference
+} from "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-RVS2QCOX.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  placeOffReference
+};

package/dist/layout/referenceSeeds.js

@@ -0,0 +1,11 @@
+import {
+  referenceSeeds,
+  seededNodes
+} from "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-6JEWNXCQ.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  referenceSeeds,
+  seededNodes
+};

package/dist/layout/rowSpacing.js

@@ -0,0 +1,6 @@
+import {
+  ROW_HEIGHT_PX
+} from "../chunks/chunk-CPMHA4W5.js";
+export {
+  ROW_HEIGHT_PX
+};

package/dist/layout/sampleRowLayout.js

@@ -0,0 +1,11 @@
+import {
+  sampleRowLayout
+} from "../chunks/chunk-LOEA5IHZ.js";
+import "../chunks/chunk-TZFWUT2C.js";
+import "../chunks/chunk-RVS2QCOX.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  sampleRowLayout
+};

package/dist/layout/trimToWindow.js

@@ -0,0 +1,99 @@
+import {
+  pathOrigin,
+  trimOrigins
+} from "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import {
+  isBackbone,
+  overlapsWindow
+} from "../chunks/chunk-FYQWPEEY.js";
+
+// src/layout/trimToWindow.ts
+function trimToWindow(graph, window) {
+  const inWindow = new Set(
+    graph.nodes.filter((n) => isBackbone(n) && overlapsWindow(n, window)).map((n) => n.id)
+  );
+  const paths = graph.paths ?? [];
+  if (inWindow.size === 0 || paths.length === 0) {
+    return graph;
+  }
+  const spans = paths.map((path) => {
+    let first = -1;
+    let last = -1;
+    path.nodeIds.forEach((id, i) => {
+      if (inWindow.has(id)) {
+        if (first < 0) {
+          first = i;
+        }
+        last = i;
+      }
+    });
+    return first < 0 ? void 0 : { first, last };
+  });
+  if (spans.every(
+    (span, i) => span?.first === 0 && span.last === paths[i].nodeIds.length - 1
+  )) {
+    return graph;
+  }
+  const kept = /* @__PURE__ */ new Set();
+  const trimmed = [];
+  const stretches = /* @__PURE__ */ new Map();
+  paths.forEach((path, i) => {
+    const span = spans[i];
+    if (span) {
+      const nodeIds = path.nodeIds.slice(span.first, span.last + 1);
+      for (const id of nodeIds) {
+        kept.add(id);
+      }
+      trimmed.push({ ...path, nodeIds });
+      stretches.set(path.name, { first: span.first, nodeIds });
+    }
+  });
+  return {
+    ...graph,
+    nodes: graph.nodes.filter((n) => kept.has(n.id)),
+    edges: graph.edges.filter((e) => kept.has(e.from) && kept.has(e.to)),
+    paths: trimmed,
+    pathVisits: graph.pathVisits && trimVisits(
+      graph.pathVisits,
+      paths,
+      spans,
+      new Map(graph.nodes.map((n) => [n.id, n.name]))
+    ),
+    anchorPaths: trimOrigins(graph, stretches)
+  };
+}
+function trimVisits(visits, paths, spans, nameOf) {
+  const cursor = /* @__PURE__ */ new Map();
+  const out = /* @__PURE__ */ new Map();
+  paths.forEach((path, p) => {
+    const origin = pathOrigin(path.name).name;
+    const span = spans[p];
+    path.nodeIds.forEach((id, i) => {
+      const segment = nameOf.get(id) ?? id;
+      const list = visits.get(segment);
+      if (!list) {
+        return;
+      }
+      const key = `${origin}	${segment}`;
+      let at = cursor.get(key) ?? 0;
+      while (at < list.length && list[at].path !== origin) {
+        at++;
+      }
+      const visit = list[at];
+      cursor.set(key, at + 1);
+      if (visit && span && i >= span.first && i <= span.last) {
+        const keptVisits = out.get(segment);
+        if (keptVisits) {
+          keptVisits.push(visit);
+        } else {
+          out.set(segment, [visit]);
+        }
+      }
+    });
+  });
+  return out;
+}
+export {
+  trimToWindow
+};

package/dist/layout/tubeMapLayout.js

@@ -0,0 +1,28 @@
+import {
+  hasTubeMapPaths,
+  tubeMapLayout,
+  tubeMapReferenceLayout,
+  tubeMapTracks,
+  tubeWidth,
+  visitStrands
+} from "../chunks/chunk-P7B3GDAY.js";
+import "../chunks/chunk-TEDQJPMI.js";
+import "../chunks/chunk-C44YRP5F.js";
+import "../chunks/chunk-7CHJKABZ.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-HCANBJDD.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-X32PABB7.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  hasTubeMapPaths,
+  tubeMapLayout,
+  tubeMapReferenceLayout,
+  tubeMapTracks,
+  tubeWidth,
+  visitStrands
+};

package/dist/layout/walkRowDraw.js

@@ -0,0 +1,65 @@
+import {
+  BAR_PX,
+  DISAGREES,
+  GAP_PX,
+  GENE_INK,
+  OFF_REFERENCE,
+  ON_REFERENCE,
+  OUTSIDE_CUT,
+  alongRow,
+  boxesGenes,
+  coalesceRuns,
+  genesOnRow,
+  kb,
+  placeRowGenes,
+  readoutPlacement,
+  rowGeneBoxes,
+  rowSpan,
+  runPaint,
+  unitTicks,
+  walkRowReadout,
+  walkRowsKey,
+  walkRowsKeyTree,
+  walkRowsTree
+} from "../chunks/chunk-QCYM44UL.js";
+import "../chunks/chunk-5QT6NPSO.js";
+import "../chunks/chunk-3WHKR5TY.js";
+import "../chunks/chunk-MNUSQCLG.js";
+import "../chunks/chunk-6YRRNX2P.js";
+import "../chunks/chunk-7CHJKABZ.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-HCANBJDD.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-X32PABB7.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-NNODIW4U.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  BAR_PX,
+  DISAGREES,
+  GAP_PX,
+  GENE_INK,
+  OFF_REFERENCE,
+  ON_REFERENCE,
+  OUTSIDE_CUT,
+  alongRow,
+  boxesGenes,
+  coalesceRuns,
+  genesOnRow,
+  kb,
+  placeRowGenes,
+  readoutPlacement,
+  rowGeneBoxes,
+  rowSpan,
+  runPaint,
+  unitTicks,
+  walkRowReadout,
+  walkRowsKey,
+  walkRowsKeyTree,
+  walkRowsTree
+};

package/dist/layout/walkRowLayout.js

@@ -0,0 +1,13 @@
+import {
+  walkRowLayout,
+  walkRowsExtent
+} from "../chunks/chunk-EZPBJPK6.js";
+import "../chunks/chunk-SZNZ2T6D.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  walkRowLayout,
+  walkRowsExtent
+};

package/dist/layout/walkRows.js

@@ -0,0 +1,11 @@
+import {
+  filterSamples,
+  walkRows
+} from "../chunks/chunk-SZNZ2T6D.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  filterSamples,
+  walkRows
+};

package/dist/layout/walkStrip.js

@@ -0,0 +1,40 @@
+import {
+  LABELLED_ROW_PX,
+  WALK_STRIP_CEILING_PX,
+  segmentAt,
+  stripGeneGaps,
+  stripMarks,
+  stripRowAt,
+  walkMarksTree,
+  walkStripFrame,
+  walkStripLabelsTree
+} from "../chunks/chunk-MHGHYHTL.js";
+import "../chunks/chunk-QCYM44UL.js";
+import "../chunks/chunk-5QT6NPSO.js";
+import "../chunks/chunk-3WHKR5TY.js";
+import "../chunks/chunk-MNUSQCLG.js";
+import "../chunks/chunk-6YRRNX2P.js";
+import "../chunks/chunk-7CHJKABZ.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-HCANBJDD.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-SDGM243E.js";
+import "../chunks/chunk-PBENCR5L.js";
+import "../chunks/chunk-X32PABB7.js";
+import "../chunks/chunk-3PLYZLYV.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-NNODIW4U.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-FYQWPEEY.js";
+export {
+  LABELLED_ROW_PX,
+  WALK_STRIP_CEILING_PX,
+  segmentAt,
+  stripGeneGaps,
+  stripMarks,
+  stripRowAt,
+  walkMarksTree,
+  walkStripFrame,
+  walkStripLabelsTree
+};

package/dist/layoutModes.js

@@ -0,0 +1,35 @@
+import {
+  FORCE_LAYOUT_LABEL,
+  LAYOUT_MODES,
+  LAYOUT_MODE_VALUES,
+  layoutModeByValue,
+  modeUsesLayoutEngine
+} from "./chunks/chunk-527AI7CP.js";
+import "./chunks/chunk-P7B3GDAY.js";
+import "./chunks/chunk-TEDQJPMI.js";
+import "./chunks/chunk-LOEA5IHZ.js";
+import "./chunks/chunk-L3O7AWLI.js";
+import "./chunks/chunk-TZFWUT2C.js";
+import "./chunks/chunk-HNQPEMYE.js";
+import "./chunks/chunk-C44YRP5F.js";
+import "./chunks/chunk-RVS2QCOX.js";
+import "./chunks/chunk-EZPBJPK6.js";
+import "./chunks/chunk-SZNZ2T6D.js";
+import "./chunks/chunk-7CHJKABZ.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  FORCE_LAYOUT_LABEL,
+  LAYOUT_MODES,
+  LAYOUT_MODE_VALUES,
+  layoutModeByValue,
+  modeUsesLayoutEngine
+};

package/dist/loadBandage.js

@@ -0,0 +1,6 @@
+import {
+  loadBandage
+} from "./chunks/chunk-7XHHVYG7.js";
+export {
+  loadBandage as default
+};

package/dist/nodeWidths.js

@@ -0,0 +1,18 @@
+import {
+  NODE_WIDTHS,
+  NODE_WIDTH_VALUES,
+  depthWidthFactor,
+  maxNodeWidthPx,
+  meanDepth,
+  nodeInk,
+  nodeWidthPx
+} from "./chunks/chunk-PBENCR5L.js";
+export {
+  NODE_WIDTHS,
+  NODE_WIDTH_VALUES,
+  depthWidthFactor,
+  maxNodeWidthPx,
+  meanDepth,
+  nodeInk,
+  nodeWidthPx
+};

package/dist/overlayLabels.js

@@ -0,0 +1,18 @@
+import {
+  LABEL_CHAR_PX,
+  LABEL_PAD,
+  LABEL_PX,
+  labelWidth,
+  occupancy,
+  overlaps,
+  placeLabels
+} from "./chunks/chunk-AB35TJST.js";
+export {
+  LABEL_CHAR_PX,
+  LABEL_PAD,
+  LABEL_PX,
+  labelWidth,
+  occupancy,
+  overlaps,
+  placeLabels
+};

package/dist/pansn.js

@@ -0,0 +1,18 @@
+import {
+  assemblyByPanSNPrefix,
+  isGenericSample,
+  panSNContig,
+  panSNHaplotype,
+  panSNMatchesPrefix,
+  panSNSample,
+  resolvePanSNPrefix
+} from "./chunks/chunk-BPLIXMH7.js";
+export {
+  assemblyByPanSNPrefix,
+  isGenericSample,
+  panSNContig,
+  panSNHaplotype,
+  panSNMatchesPrefix,
+  panSNSample,
+  resolvePanSNPrefix
+};

package/dist/pathAnchoring.js

@@ -0,0 +1,18 @@
+import {
+  anchorFromPaths,
+  anchorGraph,
+  chooseReferencePath,
+  pathOrigin,
+  surveyPaths,
+  trimOrigins
+} from "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  anchorFromPaths,
+  anchorGraph,
+  chooseReferencePath,
+  pathOrigin,
+  surveyPaths,
+  trimOrigins
+};

package/dist/pathColors.js

@@ -0,0 +1,31 @@
+import {
+  MAX_PATH_COLORS,
+  PATH_LIGHTNESS,
+  PATH_SATURATION,
+  nameHue,
+  pathColorsLegible,
+  pathCssColor,
+  pathGreyCssColor,
+  pathHueAt,
+  pathLegend
+} from "./chunks/chunk-7CHJKABZ.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  MAX_PATH_COLORS,
+  PATH_LIGHTNESS,
+  PATH_SATURATION,
+  nameHue,
+  pathColorsLegible,
+  pathCssColor,
+  pathGreyCssColor,
+  pathHueAt,
+  pathLegend
+};

package/dist/pipeline.js

@@ -0,0 +1,40 @@
+import {
+  FIT_PADDING,
+  clampZoom,
+  drawingBounds,
+  engineKey,
+  engineRequest,
+  fitTransform,
+  fittedTranslateY,
+  forceLayout,
+  layoutExtent,
+  loadGraph
+} from "./chunks/chunk-VKB57ZYE.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-ST2IBUAN.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-UVBGRJQX.js";
+import "./chunks/chunk-6JEWNXCQ.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  FIT_PADDING,
+  clampZoom,
+  drawingBounds,
+  engineKey,
+  engineRequest,
+  fitTransform,
+  fittedTranslateY,
+  forceLayout,
+  layoutExtent,
+  loadGraph
+};

package/dist/reference.js

@@ -0,0 +1,24 @@
+import {
+  WELL_KNOWN_SAMPLES,
+  assemblyWalk,
+  backboneAssembly,
+  contigNames,
+  featuresOnBackbone,
+  graphBackbone,
+  refNameBinding,
+  referenceLabel,
+  wellKnownSample
+} from "./chunks/chunk-RAKOB6IV.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  WELL_KNOWN_SAMPLES,
+  assemblyWalk,
+  backboneAssembly,
+  contigNames,
+  featuresOnBackbone,
+  graphBackbone,
+  refNameBinding,
+  referenceLabel,
+  wellKnownSample
+};

package/dist/referenceRampCss.js

@@ -0,0 +1,29 @@
+import {
+  RAMP_GRADIENT_CSS,
+  RAMP_GRADIENT_STOPS,
+  rampHue,
+  rampHueCss,
+  rampStops
+} from "./chunks/chunk-5QT6NPSO.js";
+import "./chunks/chunk-3WHKR5TY.js";
+import "./chunks/chunk-MNUSQCLG.js";
+import "./chunks/chunk-6YRRNX2P.js";
+import "./chunks/chunk-7CHJKABZ.js";
+import "./chunks/chunk-ST2IBUAN.js";
+import "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-HCANBJDD.js";
+import "./chunks/chunk-AB35TJST.js";
+import "./chunks/chunk-SDGM243E.js";
+import "./chunks/chunk-PBENCR5L.js";
+import "./chunks/chunk-X32PABB7.js";
+import "./chunks/chunk-3PLYZLYV.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-BPLIXMH7.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  RAMP_GRADIENT_CSS,
+  RAMP_GRADIENT_STOPS,
+  rampHue,
+  rampHueCss,
+  rampStops
+};

package/dist/referenceSpan.js

@@ -0,0 +1,11 @@
+import {
+  buildNeighbors,
+  nodeReferenceSpan,
+  referenceMidpoints
+} from "./chunks/chunk-ES2N6V56.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  buildNeighbors,
+  nodeReferenceSpan,
+  referenceMidpoints
+};