@jbrowse/bandage-core 11.2.0 → 11.4.0

package/README.md

@@ -61,8 +61,10 @@ against it. An API change lands with the consumer's side on a `core-next` branch
 in that repo, which CI tests in place of `main` until the release.
 
 Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
-writes the changelog with git-cliff and pushes the `v*` tag, and `publish.yml`
-publishes to npm with trusted publishing.
+writes the changelog with git-cliff and pushes the `v*` tag. `publish.yml` then
+runs CI, consumers included, and publishes to npm with trusted publishing only
+if it passes. When a consumer fails, land its side on `core-next` and rerun the
+failed jobs.
 
 ## See also
 

package/dist/chunks/{chunk-5GRF7PJX.js → chunk-3HGYGISG.js}

@@ -1,15 +1,15 @@
-import {
-  MAX_GAP_PX
-} from "./chunk-MYDHU2UV.js";
 import {
   tubeMapMismatches
 } from "./chunk-BX4AUMZE.js";
+import {
+  MAX_GAP_PX
+} from "./chunk-MYDHU2UV.js";
 import {
   readColor
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-5DHOFF4C.js";
+} from "./chunk-M75QPZNJ.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-A7VSP7MQ.js → chunk-3LZ334X4.js}

@@ -5,7 +5,7 @@ import {
 } from "./chunk-A7H753BA.js";
 import {
   referenceWalkName
-} from "./chunk-5DHOFF4C.js";
+} from "./chunk-M75QPZNJ.js";
 import {
   pathCssColor,
   pathGreyCssColor

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-VWT3WZRQ.js → chunk-6YJESZND.js}

@@ -1,3 +1,6 @@
+import {
+  Canvas2DRenderer
+} from "./chunk-EJRJAAN7.js";
 import {
   svgCanvas
 } from "./chunk-V4YML3GR.js";
@@ -5,15 +8,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-ZU54STUX.js";
+} from "./chunk-I4BYUNJN.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-XZ6PQBU6.js";
-import {
-  Canvas2DRenderer
-} from "./chunk-EJRJAAN7.js";
+} from "./chunk-VIQL7GZ4.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -34,32 +34,32 @@ import {
 } from "./chunk-77EGQQJU.js";
 import {
   version
-} from "./chunk-WAST7UVB.js";
+} from "./chunk-QM7KEWWT.js";
 import {
   axisScaleOf
-} from "./chunk-AI5PTOSV.js";
+} from "./chunk-CE6ZIKJX.js";
 import {
   figureScene
-} from "./chunk-S2PUF4SX.js";
+} from "./chunk-JQ52XYD2.js";
 import {
   encodingStops
-} from "./chunk-TABI4JEU.js";
+} from "./chunk-GM7M25NW.js";
 import {
   rangeText
 } from "./chunk-D4ZFRBB4.js";
 import {
   walkRowLabels
-} from "./chunk-QR5XR5XL.js";
+} from "./chunk-TZLEHZVC.js";
 import {
   nodeInk
 } from "./chunk-CRCD3ODN.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-W6EXQDV5.js";
+} from "./chunk-EFD753MS.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-KDU4EF66.js";
+} from "./chunk-REOWLPH4.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-QTDBOJJO.js → chunk-7O7EGTYG.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-A7VSP7MQ.js";
+} from "./chunk-3LZ334X4.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/{chunk-3XSRT7RQ.js → chunk-B5ARSBOH.js}

@@ -15,6 +15,20 @@ import {
 function pLineName(name, start, end) {
   return start === 0 ? name : `${name}:${start}-${end}`;
 }
+function tablePath(w, p) {
+  const walkName = w.names[p];
+  const fields = panSNFields(walkName);
+  const start = w.starts[p];
+  return fields ? {
+    name: `${fields.sample}#${fields.haplotype}#${fields.contig}`,
+    start,
+    ...fields,
+    ...stopFields(
+      w.before && stopAt(w.before, p),
+      w.after && stopAt(w.after, p)
+    )
+  } : { name: pLineName(walkName, start, w.ends[p]), start };
+}
 function namesByList(lists, names, listCount, pathNames) {
   const starts = new Int32Array(listCount + 1);
   for (const list of lists) {
@@ -41,10 +55,8 @@ function namesByList(lists, names, listCount, pathNames) {
     return out;
   });
 }
-function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA") {
-  const count = n.names.length;
-  const declared = n.lengths.length;
-  const canonical = new Uint8Array(count);
+function tableNodeIds({ nodes: n, links: l, walks: w }) {
+  const canonical = new Uint8Array(n.names.length);
   const claim = (node, reversed) => {
     if (canonical[node] === 0) {
       canonical[node] = reversed ? 2 : 1;
@@ -54,6 +66,17 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
     claim(l.from[i], l.strands[i] & 1);
     claim(l.to[i], l.strands[i] & 2);
   }
+  const stepCount = w.offsets[w.names.length] ?? 0;
+  for (let s = 0; s < stepCount; s++) {
+    claim(w.steps[s], w.reversed[s]);
+  }
+  return n.names.map(
+    (segment, i) => `${segment}${canonical[i] === 2 ? "-" : "+"}`
+  );
+}
+function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA") {
+  const count = n.names.length;
+  const declared = n.lengths.length;
   const drawnWalks = [];
   for (let p = 0; p < w.names.length; p++) {
     if (w.offsets[p + 1] > w.offsets[p]) {
@@ -61,18 +84,10 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
     }
   }
   const traversals = new Int32Array(count);
-  for (const p of drawnWalks) {
-    for (let s = w.offsets[p]; s < w.offsets[p + 1]; s++) {
-      const node = w.steps[s];
-      if (traversals[node] === 0) {
-        claim(node, w.reversed[s]);
-      }
-      traversals[node]++;
-    }
+  for (const node of w.steps.subarray(0, w.offsets[w.names.length])) {
+    traversals[node]++;
   }
-  const ids = n.names.map(
-    (segment, i) => `${segment}${canonical[i] === 2 ? "-" : "+"}`
-  );
+  const ids = tableNodeIds({ nodes: n, links: l, walks: w });
   const nodes = [];
   for (let i = 0; i < declared; i++) {
     const ref = n.refs[i];
@@ -168,11 +183,9 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
   const edgeNameIndex = /* @__PURE__ */ new Map();
   const edgeNames = [];
   for (const p of drawnWalks) {
-    const walkName = w.names[p];
-    const fields = panSNFields(walkName);
-    const start = w.starts[p];
-    const visitName = fields ? `${fields.sample}#${fields.haplotype}#${fields.contig}` : walkName;
-    const pathName = fields ? visitName : pLineName(walkName, start, w.ends[p]);
+    const head = tablePath(w, p);
+    const { start, name: pathName } = head;
+    const visitName = head.sample === void 0 ? w.names[p] : pathName;
     let named = nameIndex.get(visitName);
     if (named === void 0) {
       named = pathNames.length;
@@ -214,16 +227,7 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
       }
       prev = node;
     }
-    paths.push({
-      name: pathName,
-      nodeIds,
-      start,
-      ...fields,
-      ...fields ? stopFields(
-        w.before && stopAt(w.before, p),
-        w.after && stopAt(w.after, p)
-      ) : {}
-    });
+    paths.push({ ...head, nodeIds });
     anchorPaths.push({
       name: visitName,
       sample: visitSample,
@@ -293,6 +297,8 @@ function graphTablesGFA({ nodes, links, walks }) {
 }
 
 export {
+  tablePath,
+  tableNodeIds,
   graphFromTables,
   graphTablesGFA
 };

package/dist/chunks/{chunk-RNYPCQZ3.js → chunk-BXLLMWC3.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-KDU4EF66.js";
+} from "./chunk-REOWLPH4.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-AI5PTOSV.js → chunk-CE6ZIKJX.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-KDU4EF66.js";
+} from "./chunk-REOWLPH4.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-W6EXQDV5.js → chunk-EFD753MS.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-KDU4EF66.js";
+} from "./chunk-REOWLPH4.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

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-ZU54STUX.js → chunk-I4BYUNJN.js}

@@ -3,14 +3,14 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-XZ6PQBU6.js";
+} from "./chunk-VIQL7GZ4.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";
 import {
   READOUT_ROOM,
   longestBar
-} from "./chunk-QR5XR5XL.js";
+} from "./chunk-TZLEHZVC.js";
 import {
   pathOrigin
 } from "./chunk-B5X2RLJG.js";

package/dist/chunks/chunk-JDZ5GTZT.js

@@ -0,0 +1,20 @@
+import {
+  walkRowRuns,
+  walkRowsOf
+} from "./chunk-M75QPZNJ.js";
+
+// src/layout/walkRows.ts
+function filterSamples(rows, samples) {
+  return samples ? rows.filter((r) => samples.includes(r.sample)).sort(
+    (a, b) => samples.indexOf(a.sample) - samples.indexOf(b.sample) || a.label.localeCompare(b.label)
+  ) : rows;
+}
+function walkRows(graph, region, unit, o = {}) {
+  const runs = walkRowRuns(graph, region, o);
+  return runs && walkRowsOf(runs, unit);
+}
+
+export {
+  filterSamples,
+  walkRows
+};

package/dist/chunks/{chunk-S2PUF4SX.js → chunk-JQ52XYD2.js}

@@ -4,27 +4,27 @@ 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-QR5XR5XL.js";
+} from "./chunk-TZLEHZVC.js";
 import {
   pathLegend,
   walkLabelsOf
 } from "./chunk-3GP3KT5L.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-W6EXQDV5.js";
+} from "./chunk-EFD753MS.js";
 import {
   drawingBounds
-} from "./chunk-KDU4EF66.js";
+} from "./chunk-REOWLPH4.js";
 import {
   referenceLabel
 } from "./chunk-234NFZS4.js";