@jbrowse/bandage-core 11.1.0 → 11.3.0

package/dist/chunks/chunk-UFUSPK2A.js

@@ -0,0 +1,227 @@
+// src/layout/walkRowLinks.ts
+function barOf(row) {
+  if (!row.complete || !row.visits) {
+    return void 0;
+  }
+  const offsets = /* @__PURE__ */ new Map();
+  const lengths = /* @__PURE__ */ new Map();
+  for (const { node, start, bp } of row.visits) {
+    const at = offsets.get(node);
+    if (at) {
+      at.push(start);
+    } else {
+      offsets.set(node, [start]);
+      lengths.set(node, bp);
+    }
+  }
+  return { visits: row.visits, offsets, lengths };
+}
+function ribbonJoin(rows) {
+  return Math.max(...rows.map((r) => r.bp)) / 2e3;
+}
+function sharedBp(a, b) {
+  let bp = 0;
+  for (const [id, visits] of a.offsets) {
+    const other = b.offsets.get(id);
+    if (other) {
+      bp += a.lengths.get(id) * Math.min(visits.length, other.length);
+    }
+  }
+  return bp;
+}
+function sharedRowOrder(rows) {
+  const bars = rows.map(barOf);
+  const order = [0];
+  const rest = bars.map((_, i) => i).slice(1);
+  while (rest.length > 0) {
+    const last = bars[order.findLast((i) => bars[i]) ?? 0];
+    let best = 0;
+    let bestBp = -1;
+    rest.forEach((i, k) => {
+      const bar = bars[i];
+      const bp = last && bar ? sharedBp(last, bar) : 0;
+      if (bp > bestBp) {
+        best = k;
+        bestBp = bp;
+      }
+    });
+    order.push(...rest.splice(best, 1));
+  }
+  return order;
+}
+function continues(run, b, len, join) {
+  const low = run.dir === 0 ? run.b0 : run.b1;
+  if (run.dir >= 0 && b >= run.b1 && b - run.b1 <= join) {
+    return 1;
+  }
+  if (run.dir <= 0 && b + len <= low && low - b - len <= join) {
+    return -1;
+  }
+  return 0;
+}
+function sharedRuns(upper, lower, join) {
+  const runs = [];
+  let open = [];
+  upper.visits.forEach(({ node, start: a, bp: len }, k) => {
+    const visits = lower.offsets.get(node);
+    if (!visits || len === 0) {
+      return;
+    }
+    open = open.filter((run) => a - run.a1 <= join);
+    for (const b of visits) {
+      let dir = 0;
+      const run = open.find(
+        (r) => r.step !== k && (dir = continues(r, b, len, join)) !== 0
+      );
+      if (!run) {
+        const fresh = {
+          a0: a,
+          a1: a + len,
+          b0: b,
+          b1: b + len,
+          dir: 0,
+          step: k
+        };
+        runs.push(fresh);
+        open.push(fresh);
+      } else if (dir > 0) {
+        Object.assign(run, { a1: a + len, b1: b + len, dir, step: k });
+      } else {
+        const high = run.dir === 0 ? run.b1 : run.b0;
+        Object.assign(run, { a1: a + len, b0: high, b1: b, dir, step: k });
+      }
+    }
+  });
+  return runs;
+}
+function chained(runs, join) {
+  const sorted = runs.filter((r) => r.a1 - r.a0 >= join).sort((x, y) => x.a0 - y.a0);
+  const lo = (r) => Math.min(r.b0, r.b1);
+  const hi = (r) => Math.max(r.b0, r.b1);
+  const best = [];
+  const prev = [];
+  sorted.forEach((run, i2) => {
+    best[i2] = run.a1 - run.a0;
+    prev[i2] = -1;
+    for (let j = 0; j < i2; j++) {
+      const q = sorted[j];
+      const weight = best[j] + run.a1 - run.a0;
+      if (q.a1 <= run.a0 + join && hi(q) <= lo(run) + join && weight > best[i2]) {
+        best[i2] = weight;
+        prev[i2] = j;
+      }
+    }
+  });
+  const out = [];
+  let i = best.indexOf(Math.max(...best));
+  while (i >= 0) {
+    out.unshift(sorted[i]);
+    i = prev[i];
+  }
+  return out;
+}
+function walkRowLinks(rows, join = ribbonJoin(rows)) {
+  const bars = rows.map(barOf);
+  const links = [];
+  for (let i = 0; i + 1 < bars.length; i++) {
+    const [upper, lower] = [bars[i], bars[i + 1]];
+    if (upper && lower) {
+      for (const { a0, a1, b0, b1 } of chained(
+        sharedRuns(upper, lower, join),
+        join
+      )) {
+        links.push({ row: i, a0, a1, b0, b1 });
+      }
+    }
+  }
+  return links;
+}
+function walkRowBlocks(rows, join = ribbonJoin(rows)) {
+  const bars = rows.map(barOf);
+  const carriers = /* @__PURE__ */ new Map();
+  bars.forEach((bar, i) => {
+    for (const { node, onReference } of bar?.visits ?? []) {
+      if (!onReference) {
+        carriers.set(node, (carriers.get(node) ?? /* @__PURE__ */ new Set()).add(rows[i].name));
+      }
+    }
+  });
+  const setKey = /* @__PURE__ */ new Map();
+  for (const [id, carried] of carriers) {
+    if (carried.size > 1) {
+      setKey.set(id, [...carried].sort().join("\n"));
+    }
+  }
+  const parent = new Map([...setKey.keys()].map((id) => [id, id]));
+  const find = (id) => {
+    while (parent.get(id) !== id) {
+      parent.set(id, parent.get(parent.get(id)));
+      id = parent.get(id);
+    }
+    return id;
+  };
+  for (const bar of bars) {
+    const last = /* @__PURE__ */ new Map();
+    for (const { node: id, start, bp } of bar?.visits ?? []) {
+      const key = setKey.get(id);
+      if (key === void 0) {
+        continue;
+      }
+      const prev = last.get(key);
+      if (prev && start - prev.end <= join) {
+        parent.set(find(id), find(prev.id));
+      }
+      last.set(key, { id, end: start + bp });
+    }
+  }
+  const total = /* @__PURE__ */ new Map();
+  const least = /* @__PURE__ */ new Map();
+  let offBp = 0;
+  for (const bar of bars) {
+    for (const { node: id, onReference, bp } of bar?.visits ?? []) {
+      if (onReference) {
+        continue;
+      }
+      offBp += bp;
+      if (setKey.has(id)) {
+        const root = find(id);
+        total.set(root, (total.get(root) ?? 0) + bp);
+        least.set(root, [least.get(root) ?? id, id].sort()[0]);
+      }
+    }
+  }
+  const ranked = [...total.keys()].filter((root) => total.get(root) >= offBp * 3e-3).sort(
+    (a, b) => total.get(b) - total.get(a) || (least.get(a) < least.get(b) ? -1 : 1)
+  );
+  const rank = new Map(ranked.map((root, i) => [root, i]));
+  const spans = [];
+  bars.forEach((bar, i) => {
+    let last;
+    for (const { node: id, start, bp } of bar?.visits ?? []) {
+      const block = setKey.has(id) ? rank.get(find(id)) : void 0;
+      if (block === void 0) {
+        continue;
+      }
+      const end = start + bp;
+      if (last?.block === block && start - last.end <= join) {
+        last.end = end;
+      } else {
+        last = { row: i, start, end, block };
+        spans.push(last);
+      }
+    }
+  });
+  return spans.map(({ row, start, end, block }) => ({
+    row,
+    start,
+    bp: end - start,
+    block
+  }));
+}
+
+export {
+  ribbonJoin,
+  sharedRowOrder,
+  walkRowLinks,
+  walkRowBlocks
+};

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

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.1.0";
+var version = "11.3.0";
 
 export {
   version

package/dist/cli/figure.js

@@ -8,15 +8,15 @@ import {
 import "../chunks/chunk-G6UIYQZR.js";
 import {
   figureSvg
-} from "../chunks/chunk-JFHYG25O.js";
+} from "../chunks/chunk-RNNYRNDU.js";
+import "../chunks/chunk-EJRJAAN7.js";
+import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-V4YML3GR.js";
-import "../chunks/chunk-IZ6Y5D23.js";
+import "../chunks/chunk-PNM6Z3IE.js";
 import {
   genesOnRow,
   placeRowGenes
 } from "../chunks/chunk-XZ6PQBU6.js";
-import "../chunks/chunk-EJRJAAN7.js";
-import "../chunks/chunk-RBCE2OQH.js";
 import "../chunks/chunk-JSUCGZ6K.js";
 import "../chunks/chunk-PSCSZSVK.js";
 import "../chunks/chunk-OMUPUB4J.js";
@@ -25,15 +25,15 @@ import "../chunks/chunk-H2H4Y3TV.js";
 import {
   laidOutGraph,
   walkLayers
-} from "../chunks/chunk-OI4YVAMM.js";
+} from "../chunks/chunk-SLDCKMIP.js";
 import {
   LAYOUT_ENGINE_VALUES,
   isLayoutEngineKind
 } from "../chunks/chunk-JMABOQWL.js";
 import {
   LAYOUT_MODES
-} from "../chunks/chunk-NGUM77EP.js";
-import "../chunks/chunk-LMH5KVJZ.js";
+} from "../chunks/chunk-TEXAKEJX.js";
+import "../chunks/chunk-3LZ334X4.js";
 import "../chunks/chunk-A7H753BA.js";
 import "../chunks/chunk-GJU6BJJA.js";
 import "../chunks/chunk-GJLZ2MKE.js";
@@ -51,9 +51,9 @@ import {
 import "../chunks/chunk-NMWQUFPF.js";
 import "../chunks/chunk-HNWJ4B7S.js";
 import "../chunks/chunk-77EGQQJU.js";
-import "../chunks/chunk-Y3FDMDNT.js";
-import "../chunks/chunk-AI5PTOSV.js";
-import "../chunks/chunk-IVOK5V3H.js";
+import "../chunks/chunk-XEWPWCML.js";
+import "../chunks/chunk-CE6ZIKJX.js";
+import "../chunks/chunk-T35BSLW5.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-DR24UTRS.js";
 import "../chunks/chunk-TABI4JEU.js";
@@ -62,15 +62,16 @@ import "../chunks/chunk-SWCULW6S.js";
 import "../chunks/chunk-G2FD7S3C.js";
 import "../chunks/chunk-GQZVR5DW.js";
 import "../chunks/chunk-WA5WNP6V.js";
-import "../chunks/chunk-YHJ5JLBI.js";
+import "../chunks/chunk-TZLEHZVC.js";
 import {
   filterSamples,
   walkRows
-} from "../chunks/chunk-DEDD7TFJ.js";
+} from "../chunks/chunk-JDZ5GTZT.js";
+import "../chunks/chunk-M75QPZNJ.js";
 import "../chunks/chunk-3GP3KT5L.js";
 import "../chunks/chunk-CRCD3ODN.js";
-import "../chunks/chunk-W6EXQDV5.js";
-import "../chunks/chunk-KDU4EF66.js";
+import "../chunks/chunk-EFD753MS.js";
+import "../chunks/chunk-REOWLPH4.js";
 import "../chunks/chunk-3PZSBNLI.js";
 import "../chunks/chunk-CKUVEHSS.js";
 import "../chunks/chunk-OPPVSPEF.js";
@@ -78,7 +79,7 @@ import "../chunks/chunk-VPE4AYP7.js";
 import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-3XSRT7RQ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-234NFZS4.js";

package/dist/cli/fold.js

@@ -10,7 +10,7 @@ import {
 } from "../chunks/chunk-SOMZGDVS.js";
 import {
   loadGraph
-} from "../chunks/chunk-KDU4EF66.js";
+} from "../chunks/chunk-REOWLPH4.js";
 import "../chunks/chunk-3PZSBNLI.js";
 import "../chunks/chunk-CKUVEHSS.js";
 import "../chunks/chunk-OPPVSPEF.js";
@@ -18,7 +18,7 @@ import "../chunks/chunk-VPE4AYP7.js";
 import "../chunks/chunk-FFHJGWDK.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-5I3K4R2G.js";
-import "../chunks/chunk-3XSRT7RQ.js";
+import "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-DZR37KXT.js";

package/dist/figure.js

@@ -1,20 +1,20 @@
 import {
   figureSvg
-} from "./chunks/chunk-JFHYG25O.js";
-import "./chunks/chunk-V4YML3GR.js";
-import "./chunks/chunk-IZ6Y5D23.js";
-import "./chunks/chunk-XZ6PQBU6.js";
+} from "./chunks/chunk-RNNYRNDU.js";
 import "./chunks/chunk-EJRJAAN7.js";
 import "./chunks/chunk-RBCE2OQH.js";
+import "./chunks/chunk-V4YML3GR.js";
+import "./chunks/chunk-PNM6Z3IE.js";
+import "./chunks/chunk-XZ6PQBU6.js";
 import "./chunks/chunk-JSUCGZ6K.js";
 import "./chunks/chunk-PSCSZSVK.js";
 import "./chunks/chunk-OMUPUB4J.js";
 import "./chunks/chunk-3VCKBSML.js";
 import "./chunks/chunk-H2H4Y3TV.js";
 import "./chunks/chunk-77EGQQJU.js";
-import "./chunks/chunk-Y3FDMDNT.js";
-import "./chunks/chunk-AI5PTOSV.js";
-import "./chunks/chunk-IVOK5V3H.js";
+import "./chunks/chunk-XEWPWCML.js";
+import "./chunks/chunk-CE6ZIKJX.js";
+import "./chunks/chunk-T35BSLW5.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-DR24UTRS.js";
 import "./chunks/chunk-TABI4JEU.js";
@@ -23,12 +23,13 @@ import "./chunks/chunk-SWCULW6S.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";
-import "./chunks/chunk-YHJ5JLBI.js";
-import "./chunks/chunk-DEDD7TFJ.js";
+import "./chunks/chunk-TZLEHZVC.js";
+import "./chunks/chunk-JDZ5GTZT.js";
+import "./chunks/chunk-M75QPZNJ.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-W6EXQDV5.js";
-import "./chunks/chunk-KDU4EF66.js";
+import "./chunks/chunk-EFD753MS.js";
+import "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -36,7 +37,7 @@ import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-3XSRT7RQ.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-234NFZS4.js";

package/dist/figureData.js

@@ -3,10 +3,10 @@ import {
   gfaFigureData,
   laidOutGraph,
   walkLayers
-} from "./chunks/chunk-OI4YVAMM.js";
+} from "./chunks/chunk-SLDCKMIP.js";
 import "./chunks/chunk-JMABOQWL.js";
-import "./chunks/chunk-NGUM77EP.js";
-import "./chunks/chunk-LMH5KVJZ.js";
+import "./chunks/chunk-TEXAKEJX.js";
+import "./chunks/chunk-3LZ334X4.js";
 import "./chunks/chunk-A7H753BA.js";
 import "./chunks/chunk-GJU6BJJA.js";
 import "./chunks/chunk-GJLZ2MKE.js";
@@ -18,9 +18,9 @@ import "./chunks/chunk-TUQKGAK3.js";
 import "./chunks/chunk-NMWQUFPF.js";
 import "./chunks/chunk-HNWJ4B7S.js";
 import "./chunks/chunk-77EGQQJU.js";
-import "./chunks/chunk-Y3FDMDNT.js";
-import "./chunks/chunk-AI5PTOSV.js";
-import "./chunks/chunk-IVOK5V3H.js";
+import "./chunks/chunk-XEWPWCML.js";
+import "./chunks/chunk-CE6ZIKJX.js";
+import "./chunks/chunk-T35BSLW5.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-DR24UTRS.js";
 import "./chunks/chunk-TABI4JEU.js";
@@ -29,12 +29,13 @@ import "./chunks/chunk-SWCULW6S.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";
-import "./chunks/chunk-YHJ5JLBI.js";
-import "./chunks/chunk-DEDD7TFJ.js";
+import "./chunks/chunk-TZLEHZVC.js";
+import "./chunks/chunk-JDZ5GTZT.js";
+import "./chunks/chunk-M75QPZNJ.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-W6EXQDV5.js";
-import "./chunks/chunk-KDU4EF66.js";
+import "./chunks/chunk-EFD753MS.js";
+import "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -42,7 +43,7 @@ import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-3XSRT7RQ.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-234NFZS4.js";

package/dist/figureScene.js

@@ -1,6 +1,6 @@
 import {
   figureScene
-} from "./chunks/chunk-IVOK5V3H.js";
+} from "./chunks/chunk-T35BSLW5.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-DR24UTRS.js";
 import "./chunks/chunk-TABI4JEU.js";
@@ -9,12 +9,13 @@ import "./chunks/chunk-SWCULW6S.js";
 import "./chunks/chunk-G2FD7S3C.js";
 import "./chunks/chunk-GQZVR5DW.js";
 import "./chunks/chunk-WA5WNP6V.js";
-import "./chunks/chunk-YHJ5JLBI.js";
-import "./chunks/chunk-DEDD7TFJ.js";
+import "./chunks/chunk-TZLEHZVC.js";
+import "./chunks/chunk-JDZ5GTZT.js";
+import "./chunks/chunk-M75QPZNJ.js";
 import "./chunks/chunk-3GP3KT5L.js";
 import "./chunks/chunk-CRCD3ODN.js";
-import "./chunks/chunk-W6EXQDV5.js";
-import "./chunks/chunk-KDU4EF66.js";
+import "./chunks/chunk-EFD753MS.js";
+import "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -22,7 +23,7 @@ import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-3XSRT7RQ.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-234NFZS4.js";

package/dist/figureSettings.js

@@ -1,8 +1,8 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-W6EXQDV5.js";
-import "./chunks/chunk-KDU4EF66.js";
+} from "./chunks/chunk-EFD753MS.js";
+import "./chunks/chunk-REOWLPH4.js";
 import "./chunks/chunk-3PZSBNLI.js";
 import "./chunks/chunk-CKUVEHSS.js";
 import "./chunks/chunk-OPPVSPEF.js";
@@ -10,7 +10,7 @@ import "./chunks/chunk-VPE4AYP7.js";
 import "./chunks/chunk-FFHJGWDK.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-5I3K4R2G.js";
-import "./chunks/chunk-3XSRT7RQ.js";
+import "./chunks/chunk-B5ARSBOH.js";
 import "./chunks/chunk-B5X2RLJG.js";
 import "./chunks/chunk-VX656OAZ.js";
 import "./chunks/chunk-DZR37KXT.js";

package/dist/gfa/graphTables.js

@@ -1,11 +1,15 @@
 import {
   graphFromTables,
-  graphTablesGFA
-} from "../chunks/chunk-3XSRT7RQ.js";
+  graphTablesGFA,
+  tableNodeIds,
+  tablePath
+} from "../chunks/chunk-B5ARSBOH.js";
 import "../chunks/chunk-EIY2SKD3.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-4XWZNPQ2.js";
 export {
   graphFromTables,
-  graphTablesGFA
+  graphTablesGFA,
+  tableNodeIds,
+  tablePath
 };