@jbrowse/bandage-core 11.7.3 → 11.8.0

package/dist/chunks/{chunk-AJQRKN3X.js → chunk-L2RQV23D.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.7.3";
+var version = "11.8.0";
 
 export {
   version

package/dist/chunks/{chunk-EPOPGV5G.js → chunk-LA6JHEVV.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-VXKL2ZLR.js";
+} from "./chunk-2H3ALI6L.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-G7SG4XMK.js → chunk-LODKC7PJ.js}

@@ -13,6 +13,7 @@ import {
 } from "./chunk-BSOZW3FC.js";
 import {
   panSNContig,
+  panSNHaplotype,
   panSNSample
 } from "./chunk-2JL2JVZ2.js";
 
@@ -466,6 +467,12 @@ function walkRowRuns(source, region, o = {}) {
     meta: rowOf(pieces),
     row: i + 1
   }));
+  const metas = [referenceRow, ...rows.map((r) => r.meta)];
+  if (new Set(metas.map((m) => m.label)).size < metas.length) {
+    for (const meta of metas) {
+      meta.label = panSNHaplotype(meta.name) ?? meta.label;
+    }
+  }
   rows.sort(
     (a, b) => Number(b.meta.complete) - Number(a.meta.complete) || b.meta.bp - a.meta.bp || a.meta.label.localeCompare(b.meta.label)
   );

package/dist/chunks/{chunk-QXBQDHKL.js → chunk-MO4DIRHD.js}

@@ -2,7 +2,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-PKGPSTRW.js";
+} from "./chunk-4OVIUCSB.js";
 import {
   Canvas2DRenderer
 } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-EPOPGV5G.js";
+} from "./chunk-LA6JHEVV.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,45 +21,50 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-QJC63NFR.js";
+} from "./chunk-G3GLGDKV.js";
 import {
   nodesUnderBox
-} from "./chunk-LH436HS2.js";
+} from "./chunk-NHOXLUIL.js";
 import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
 import {
   genePins
-} from "./chunk-BFUS3ENH.js";
+} from "./chunk-X5ULFAMM.js";
 import {
   version
-} from "./chunk-AJQRKN3X.js";
+} from "./chunk-L2RQV23D.js";
 import {
   axisScaleOf
-} from "./chunk-F4CDC72I.js";
+} from "./chunk-2RCKHCF7.js";
 import {
   figureScene
-} from "./chunk-UTDMFVC7.js";
+} from "./chunk-R3NPBUKT.js";
 import {
   encodingStops
-} from "./chunk-6RB5ZQ34.js";
+} from "./chunk-N4AJV4GH.js";
+import {
+  THREAD_PX,
+  passesKey,
+  threadsPasses
+} from "./chunk-7GDNDQD7.js";
 import {
   rangeText
-} from "./chunk-SG7VQB4F.js";
+} from "./chunk-SDDMV2MM.js";
 import {
   walkRowLabels
-} from "./chunk-SENPGW4O.js";
+} from "./chunk-VCUOYVLC.js";
 import {
   nodeInk
 } from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-4SN7R4UF.js";
+} from "./chunk-6MD4VS2F.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-S3ICPPXC.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -79,6 +84,8 @@ var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
 var BAR_PX = 48;
 var SWATCH_PX = 18;
 var KEY_GAP_PX = 16;
+var KEY_LINE_PX = 16;
+var KEY_TALL_PX = 32;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
 var GENE_INK = "#1c1c22";
@@ -92,15 +99,45 @@ function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   );
   return {
     width,
+    height: under ? KEY_TALL_PX : KEY_LINE_PX,
     markup: `${defs}<g transform="translate(${x} ${y})" ${FONT}><rect y="5" width="${bar}" height="8" rx="2" ${fill}/><text x="${bar + 5}" y="13"><tspan font-weight="bold">${escapeAttr(label)}</tspan>${escapeAttr(after)}</text>${under ? `<text y="28">${escapeAttr(under)}</text>` : ""}</g>`
   };
 }
 function exonKeySvg(x, y) {
   return {
     width: SWATCH_PX + 5 + 4 * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
     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 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}"/>`
+  ).join("");
+  return {
+    width: SWATCH_PX + 5 + note.length * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
+    markup: `<g transform="translate(${x} ${y})" ${FONT}>${lines}<text x="${SWATCH_PX + 5}" y="13">${note}</text></g>`
+  };
+}
+function keyLines(keys, width) {
+  const markup = [];
+  let x = 6;
+  let y = 2;
+  let line = 0;
+  for (const key of keys) {
+    const size = key(0, 0);
+    if (x > 6 && x + size.width > width - 6) {
+      x = 6;
+      y += line + 4;
+      line = 0;
+    }
+    markup.push(key(x, y).markup);
+    x += size.width + KEY_GAP_PX;
+    line = Math.max(line, size.height);
+  }
+  return { markup, height: y + line };
+}
 function walkKeySvg(id, x, y, walk, label, key) {
   return keySvg(
     id,
@@ -264,22 +301,18 @@ function figureSvg(graph, layout, o = {}) {
     });
     height = grid.total;
   } else {
-    let x = 6;
-    const push = (key) => {
-      parts.push(key.markup);
-      x += key.width + KEY_GAP_PX;
-    };
+    const keys = [];
     if (lift) {
       lift.walks.forEach((walk, i) => {
-        push(
-          walkKeySvg(`key${i}`, x, 2, walk, labelOf(walk.name), keyText(walk))
+        keys.push(
+          (x, y) => walkKeySvg(`key${i}`, x, y, walk, labelOf(walk.name), keyText(walk))
         );
       });
-      push(
-        keySvg(
+      keys.push(
+        (x, y) => keySvg(
           "faded",
           x,
-          2,
+          y,
           [{ offset: 0, color: FADED }],
           "",
           `not on ${lift.walks.length === 1 ? labelOf(lift.walks[0].name) : "these walks"}`,
@@ -287,24 +320,31 @@ function figureSvg(graph, layout, o = {}) {
           0.3
         )
       );
+      if (threadsPasses(lift.walks)) {
+        keys.push((x, y) => passesKeySvg(x, y, passesKey(lift.walks)));
+      }
     }
     if (rows) {
-      const key = walkRowsKeyTree(
-        walkRowsKey(rows, {
-          ramp: rampInterval,
-          genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
-        }),
-        x,
-        2,
-        "rows-key"
-      );
-      push({ width: key.width, markup: serializeEl(key.tree) });
+      const entries = walkRowsKey(rows, {
+        ramp: rampInterval,
+        genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
+      });
+      entries.forEach((entry, i) => {
+        keys.push((x, y) => {
+          const key = walkRowsKeyTree([entry], x, y, `rows-key-${i}`);
+          return {
+            width: key.width - KEY_GAP_PX,
+            height: KEY_LINE_PX,
+            markup: serializeEl(key.tree)
+          };
+        });
+      });
     } else if (!lift && referenceRamp) {
-      push(
-        keySvg(
+      keys.push(
+        (x, y) => keySvg(
           "ramp",
           x,
-          2,
+          y,
           encodingStops({ field: "reference", scheme: "rainbow" }),
           referenceName ? `${referenceName} position` : "Reference position",
           "",
@@ -317,9 +357,11 @@ function figureSvg(graph, layout, o = {}) {
       );
     }
     if (pins.some((pin) => pin.exonsByNode.length > 0)) {
-      push(exonKeySvg(x, 2));
+      keys.push((x, y) => exonKeySvg(x, y));
     }
-    const header = parts.length > 0 ? FACET_TITLE_PX : 0;
+    const keyed = keyLines(keys, width);
+    parts.push(...keyed.markup);
+    const header = keys.length > 0 ? Math.max(FACET_TITLE_PX, keyed.height) : 0;
     const usable = width - 2 * FIT_PADDING;
     const drawn = pixelRows || !(bounds.w > 0) ? bounds.h : bounds.h * usable / bounds.w;
     const h = Math.max(

package/dist/chunks/{chunk-IHM43Y7B.js → chunk-N2GAA7RB.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-W5YRBEWQ.js";
+} from "./chunk-XOIYBEU7.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-6RB5ZQ34.js → chunk-N4AJV4GH.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-VXKL2ZLR.js";
+} from "./chunk-2H3ALI6L.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";
@@ -33,9 +33,12 @@ function resolveEncoding(layer, reference, picked, alone = true) {
   const field = isField(askedField) ? askedField : alone ? "progress" : "walk";
   const family = reference ? "grey" : FAMILIES[picked % FAMILIES.length];
   const scheme = isScheme(askedScheme) ? askedScheme === "rainbow" && field !== "reference" ? family : askedScheme : family;
-  return { field, scheme };
+  const round = Math.floor(picked / FAMILIES.length) % SHADES.length;
+  return field === "walk" && scheme === family && round > 0 ? { field, scheme, shade: SHADES[round] } : alone || field === "walk" ? { field, scheme } : { field, scheme, darkest: TOGETHER_DARKEST };
 }
+var TOGETHER_DARKEST = 0.55;
 var BASE_T = 0.5;
+var SHADES = [BASE_T, 0.85, 0.2];
 var toLinear = (c) => c <= 0.04045 ? c / 12.92 : ((c + 0.055) / 1.055) ** 2.4;
 var toGamma = (c) => c <= 31308e-7 ? c * 12.92 : 1.055 * c ** (1 / 2.4) - 0.055;
 function oklab(hex) {
@@ -72,7 +75,7 @@ function oklabEnds(scheme) {
   }
   return endsCache.get(scheme);
 }
-function schemeRgb(scheme, t) {
+function schemeRgb(scheme, t, darkest = 0) {
   const x = Math.max(0, Math.min(1, t));
   const ends = oklabEnds(scheme);
   if (!ends) {
@@ -83,27 +86,35 @@ function schemeRgb(scheme, t) {
     ).map((c) => c * 255);
   }
   const [from, to] = ends;
-  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x));
+  const light = from[0];
+  const dark = to[0];
+  const reach = dark < darkest && light > darkest ? (light - darkest) / (light - dark) : 1;
+  return oklabToRgb(from.map((v, i) => v + (to[i] - v) * x * reach));
 }
-function schemeCss(scheme, t) {
-  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);
+function schemeCss(scheme, t, darkest) {
+  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);
   return `rgb(${r}, ${g}, ${b})`;
 }
-function schemeColor(scheme, t) {
-  const [r, g, b] = schemeRgb(scheme, t).map(Math.round);
+function schemeColor(scheme, t, darkest) {
+  const [r, g, b] = schemeRgb(scheme, t, darkest).map(Math.round);
   return packAbgr(r, g, b, 255);
 }
-function encodedColor({ field, scheme }, t) {
-  return field === "walk" ? schemeColor(scheme, BASE_T) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t);
+function encodedColor({ field, scheme, darkest, shade = BASE_T }, t) {
+  return field === "walk" ? schemeColor(scheme, shade) : t === void 0 ? NO_VALUE_COLOR : schemeColor(scheme, t, darkest);
 }
 var NO_VALUE_COLOR = REFERENCE_RAMP_ALT_COLOR;
-function encodingStops({ field, scheme }) {
+function encodingStops({
+  field,
+  scheme,
+  darkest,
+  shade = BASE_T
+}) {
   const stop = (offset, t) => ({
     offset,
-    color: schemeCss(scheme, t),
-    abgr: schemeColor(scheme, t)
+    color: schemeCss(scheme, t, darkest),
+    abgr: schemeColor(scheme, t, darkest)
   });
-  return field === "walk" ? [stop(0, BASE_T)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, i / 6));
+  return field === "walk" ? [stop(0, shade)] : Array.from({ length: 7 }, (_, i) => stop(i / 6, i / 6));
 }
 function encodingSwatchCss(encoding) {
   const stops = encodingStops(encoding);

package/dist/chunks/{chunk-LH436HS2.js → chunk-NHOXLUIL.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-2US43KNG.js";
+} from "./chunk-7PEYA3NA.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";
@@ -9,7 +9,7 @@ import {
   pathRibbonOffsets,
   translateCurves,
   yToXOf
-} from "./chunk-VACK24HF.js";
+} from "./chunk-735MPLUL.js";
 
 // src/util/hitDetection.ts
 function distanceToSegment(px, py, x1, y1, x2, y2) {

package/dist/chunks/{chunk-QLLKALSH.js → chunk-NQWEYJDD.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-VXKL2ZLR.js";
+} from "./chunk-2H3ALI6L.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-AWJJSA7D.js → chunk-OIOAK7BS.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-N73RA4DR.js";
+} from "./chunk-6CXLLJ2C.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-UTDMFVC7.js → chunk-R3NPBUKT.js}

@@ -4,27 +4,27 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-Z4HXW6ZH.js";
+} from "./chunk-YF6T33PU.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-VXKL2ZLR.js";
+} from "./chunk-2H3ALI6L.js";
 import {
   walkKey
-} from "./chunk-SG7VQB4F.js";
+} from "./chunk-SDDMV2MM.js";
 import {
   walkRowsExtent
-} from "./chunk-SENPGW4O.js";
+} from "./chunk-VCUOYVLC.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-GD6RUZU5.js";
+} from "./chunk-JKIAHYAW.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-4SN7R4UF.js";
+} from "./chunk-6MD4VS2F.js";
 import {
   drawingBounds
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-S3ICPPXC.js";
 import {
   referenceLabel
 } from "./chunk-5ORP7EFJ.js";
@@ -34,7 +34,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-P276TWPM.js";
+} from "./chunk-3CXZUC2Y.js";
 import {
   facetCells,
   facetSettingOf

package/dist/chunks/{chunk-4KOYS5WR.js → chunk-R4XCTRIU.js}

@@ -1,6 +1,6 @@
 import {
   ownStrand
-} from "./chunk-VACK24HF.js";
+} from "./chunk-735MPLUL.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-XKPXOIWD.js → chunk-S3ICPPXC.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-OPPVSPEF.js";
 import {
   orientToReference
-} from "./chunk-ZZZ6NVLW.js";
+} from "./chunk-22ZMVREZ.js";
 import {
   seededNodes
 } from "./chunk-CKUVEHSS.js";
@@ -27,7 +27,7 @@ import {
 import {
   mergeRuns,
   splitRuns
-} from "./chunk-2VMKQKVO.js";
+} from "./chunk-YIWN32ZX.js";
 import {
   spreadFor
 } from "./chunk-HKYXWZQS.js";
@@ -39,7 +39,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-P276TWPM.js";
+} from "./chunk-3CXZUC2Y.js";
 import {
   anchorGraph
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-K4KVAMEF.js → chunk-S4CH434Z.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-S3ICPPXC.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-HMEAGAGC.js → chunk-S7BCZVRK.js}

@@ -6,10 +6,10 @@ import {
 } from "./chunk-MYDHU2UV.js";
 import {
   readColor
-} from "./chunk-SDI6BVG7.js";
+} from "./chunk-J4PDHWP2.js";
 import {
   referenceWalkName
-} from "./chunk-G7SG4XMK.js";
+} from "./chunk-LODKC7PJ.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-SG7VQB4F.js → chunk-SDDMV2MM.js}

@@ -5,7 +5,7 @@ import {
 import {
   formatBp,
   groupDigits
-} from "./chunk-N73RA4DR.js";
+} from "./chunk-6CXLLJ2C.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-KMLATBNT.js → chunk-SIXFXXRI.js}

@@ -1,6 +1,6 @@
 import {
   coversGraph
-} from "./chunk-BLDUBB7X.js";
+} from "./chunk-4YPCUVMC.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -10,13 +10,13 @@ import {
 } from "./chunk-RFG42VIO.js";
 import {
   bubbleSegmentIds
-} from "./chunk-AWJJSA7D.js";
+} from "./chunk-OIOAK7BS.js";
 import {
   bubbleSubgraph
 } from "./chunk-MHZTTLBU.js";
 import {
   strandSides
-} from "./chunk-VACK24HF.js";
+} from "./chunk-735MPLUL.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";