@jbrowse/bandage-core 0.1.3 → 0.1.5

package/dist/index.js

@@ -269,12 +269,12 @@ function parseGFA(file) {
         });
       }
     } else if (line.startsWith("W")) {
-      const [, sample, hap, contig, start, end, body, ...rest] = line.split("	");
-      if (sample && hap && contig && start && end && body) {
+      const [, sample, hap, contig2, start, end, body, ...rest] = line.split("	");
+      if (sample && hap && contig2 && start && end && body) {
         graph.walks.push({
           sample,
           haplotype: +hap,
-          contig,
+          contig: contig2,
           start: start === "*" ? -1 : +start,
           end: end === "*" ? -1 : +end,
           segments: parseWalkBody(body),
@@ -660,6 +660,14 @@ function splitRuns(positions, runs, weightOf) {
   }
   return out;
 }
+function polylineSlice(line, from, to) {
+  if (line.length === 0) {
+    return [];
+  }
+  const arc = arcPrefix(line);
+  const total = arc.at(-1);
+  return slice(line, arc, from * total, to * total);
+}
 function polylineMidpoint(line) {
   const arc = arcPrefix(line);
   return pointAt(line, arc, arc.at(-1) / 2);
@@ -5063,6 +5071,7 @@ var HALO_FACTOR = 3.4;
 var LEGEND_INSET_PX = 6;
 var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
+var GENE_STACK = 2;
 var GLYPH_ROOM_PX = 60;
 var MAX_GLYPH_LABEL_ROWS = 8;
 var TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;
@@ -5151,7 +5160,8 @@ function layoutLabels(m) {
         item: pin,
         x,
         y: y + m.contigThickness + GENE_PIN_DROP_PX,
-        text: pin.covered < 0.98 ? `${pin.gene.name} \u2026` : pin.gene.name
+        text: pin.covered < 0.98 ? `${pin.gene.name} \u2026` : pin.gene.name,
+        stack: GENE_STACK
       };
     }),
     frame,
@@ -5200,6 +5210,86 @@ function layoutLabels(m) {
   };
 }
 
+// src/genes/genePins.ts
+function contig(name) {
+  return name.split("#").at(-1);
+}
+function genePins(graph, genes, positions) {
+  const byContig = /* @__PURE__ */ new Map();
+  const contigOf = /* @__PURE__ */ new Map();
+  for (const node of graph.nodes) {
+    if (isBackbone(node) && positions[node.id]?.length) {
+      const { refName } = node.stable;
+      const name = contigOf.get(refName) ?? contigOf.set(refName, contig(refName)).get(refName);
+      const entry = byContig.get(name) ?? byContig.set(name, { nodes: [], reach: 0 }).get(name);
+      entry.nodes.push(node);
+      entry.reach = Math.max(entry.reach, node.length);
+    }
+  }
+  for (const { nodes } of byContig.values()) {
+    nodes.sort((a, b) => a.stable.start - b.stable.start);
+  }
+  const pins = [];
+  for (const gene of genes) {
+    const backbone = byContig.get(contig(gene.refName));
+    if (!backbone) {
+      continue;
+    }
+    const parts = [];
+    let at;
+    let atDistance = Infinity;
+    let covered = 0;
+    const mid = (gene.start + gene.end) / 2;
+    const { nodes, reach } = backbone;
+    for (let i = firstNodeAtOrAfter(nodes, gene.start - reach); i < nodes.length && nodes[i].stable.start < gene.end; i++) {
+      const node = nodes[i];
+      const nodeStart = node.stable.start;
+      const nodeEnd = nodeStart + node.length;
+      if (nodeEnd <= gene.start) {
+        continue;
+      }
+      const line = positions[node.id];
+      covered += Math.min(nodeEnd, gene.end) - Math.max(nodeStart, gene.start);
+      for (const exon of gene.exons) {
+        const a = Math.max(exon.start, nodeStart);
+        const b = Math.min(exon.end, nodeEnd);
+        if (b <= a) {
+          continue;
+        }
+        const stretch = polylineSlice(
+          line,
+          (a - nodeStart) / node.length,
+          (b - nodeStart) / node.length
+        );
+        if (stretch.length === 1) {
+          stretch.push({ ...stretch[0] });
+        }
+        parts.push(svgPath(stretch));
+      }
+      const pinBp = Math.min(Math.max(mid, nodeStart), nodeEnd);
+      const distance = Math.abs(pinBp - mid);
+      if (distance < atDistance) {
+        atDistance = distance;
+        const [p] = polylineSlice(
+          line,
+          (pinBp - nodeStart) / node.length,
+          (pinBp - nodeStart) / node.length
+        );
+        at = p;
+      }
+    }
+    if (at) {
+      pins.push({
+        gene,
+        exons: parts.join(""),
+        at,
+        covered: covered / (gene.end - gene.start)
+      });
+    }
+  }
+  return pins;
+}
+
 // src/gbzWindow.ts
 var NoReferenceSampleError = class extends Error {
   constructor(anchor, referenceSamples) {
@@ -5372,6 +5462,7 @@ export {
   fitTransform,
   forceLayout,
   formatBp2 as formatBp,
+  genePins,
   getDpr,
   haplotypeWanted,
   layoutExtent,

package/dist/types/index.d.ts

@@ -39,6 +39,8 @@ export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, layoutLabels } from './labelLayout.js';
 export type { BubbleGlyph, LabelLayout, LabelLayoutSource } from './labelLayout.js';
 export { formatBp } from './graphLabels.js';
+export { genePins } from './genes/genePins.js';
+export type { GeneModel, GenePin } from './genes/genePins.js';
 export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
 export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';
 export { cutWindowGFA, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "0.1.3",
+  "version": "0.1.5",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {