@jbrowse/bandage-core 10.3.0 → 11.0.0

package/README.md

@@ -10,6 +10,11 @@ npm install @jbrowse/bandage-core
 
 - GFA and rGFA text in (`loadGraph`), or the same graph as typed arrays a worker
   can transfer (`GraphTables`)
+- A walk-file cut's W lines tag what lies past each fragment's start and end as
+  `ws:Z:`/`we:Z:`, such as `break,bp=19021` or
+  `elsewhere,trimmed=400,chunk=GRCh38#0#chr22:20316160`
+  (`src/gfa/walkStops.ts`). Walk rows split each gap by those stops into parts
+  that name their cause
 - Layouts: Bandage's FMMM engine as WASM from
   [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout)
   (`loadBandage`, `forceLayout`), ordered, anchored, sample rows, walk rows,

package/dist/bubbles/popBubble.js

@@ -1,7 +1,7 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-PPDE4IVT.js";
-import "../chunks/chunk-LGJBB5BP.js";
+} from "../chunks/chunk-PNMJFFNB.js";
+import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-BSOZW3FC.js";
 import "../chunks/chunk-RJWPJCIB.js";

package/dist/bubbles/superbubbles.js

@@ -1,14 +1,14 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-EHXBZ5JZ.js";
+} from "../chunks/chunk-2Q22S52W.js";
 import "../chunks/chunk-RFG42VIO.js";
-import "../chunks/chunk-PPDE4IVT.js";
+import "../chunks/chunk-PNMJFFNB.js";
 import "../chunks/chunk-E4ZM4OOJ.js";
 import "../chunks/chunk-A4JDEUAI.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-UAFATXYA.js";
-import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-B5X2RLJG.js";
 import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-ZPZ7GNBT.js";
 import "../chunks/chunk-PFRQBCGC.js";

package/dist/chunks/{chunk-EHXBZ5JZ.js → chunk-2Q22S52W.js}

@@ -7,7 +7,7 @@ import {
 } from "./chunk-RFG42VIO.js";
 import {
   bubbleSubgraph
-} from "./chunk-PPDE4IVT.js";
+} from "./chunk-PNMJFFNB.js";
 import {
   coversGraph
 } from "./chunk-E4ZM4OOJ.js";

package/dist/chunks/{chunk-IYALCKNB.js → chunk-3GP3KT5L.js}

@@ -1,6 +1,6 @@
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   groupDigits
 } from "./chunk-PFRQBCGC.js";

package/dist/chunks/{chunk-A54O52XZ.js → chunk-3UST3ZQE.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-2XEQR54X.js";
+} from "./chunk-SWCULW6S.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-DBLV7PGG.js → chunk-3XSRT7RQ.js}

@@ -1,3 +1,8 @@
+import {
+  stopAt,
+  stopFields,
+  walkStopTags
+} from "./chunk-EIY2SKD3.js";
 import {
   PathVisits
 } from "./chunk-ZPZ7GNBT.js";
@@ -209,7 +214,16 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
       }
       prev = node;
     }
-    paths.push({ name: pathName, nodeIds, start, ...fields });
+    paths.push({
+      name: pathName,
+      nodeIds,
+      start,
+      ...fields,
+      ...fields ? stopFields(
+        w.before && stopAt(w.before, p),
+        w.after && stopAt(w.after, p)
+      ) : {}
+    });
     anchorPaths.push({
       name: visitName,
       sample: visitSample,
@@ -272,7 +286,7 @@ function graphTablesGFA({ nodes, links, walks }) {
       steps.push([names[walks.steps[s]], walks.reversed[s]]);
     }
     lines.push(
-      fields ? `W	${fields.sample}	${fields.haplotype}	${fields.contig}	${start}	${end}	${steps.map(([id, rev]) => (rev ? "<" : ">") + id).join("")}` : `P	${pLineName(name, start, end)}	${steps.map(([id, rev]) => id + (rev ? "-" : "+")).join(",")}	*`
+      fields ? `W	${fields.sample}	${fields.haplotype}	${fields.contig}	${start}	${end}	${steps.map(([id, rev]) => (rev ? "<" : ">") + id).join("")}${walkStopTags(walks, p)}` : `P	${pLineName(name, start, end)}	${steps.map(([id, rev]) => id + (rev ? "-" : "+")).join(",")}	*`
     );
   }
   return lines.join("\n");

package/dist/chunks/{chunk-7JGLJK44.js → chunk-5LTZVKZQ.js}

@@ -5,12 +5,12 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-SHKGYGM4.js";
+} from "./chunk-TEF3NBG3.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-SZHQK6GL.js";
+} from "./chunk-XZ6PQBU6.js";
 import {
   Canvas2DRenderer
 } from "./chunk-EJRJAAN7.js";
@@ -34,32 +34,32 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-PTQPTDZH.js";
+} from "./chunk-6OP4HPXG.js";
 import {
   axisScaleOf
-} from "./chunk-WONB6LMC.js";
+} from "./chunk-AI5PTOSV.js";
 import {
   figureScene
-} from "./chunk-XUT4HXVE.js";
+} from "./chunk-CZT33FZG.js";
 import {
   encodingStops
-} from "./chunk-V7J6U4XC.js";
+} from "./chunk-DO62DG26.js";
 import {
   rangeText
-} from "./chunk-CGFPFBT2.js";
+} from "./chunk-D4ZFRBB4.js";
 import {
   walkRowLabels
-} from "./chunk-QQCOVMMT.js";
+} from "./chunk-OLKXMZ6J.js";
 import {
   nodeInk
 } from "./chunk-CRCD3ODN.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-ZPBEUOBM.js";
+} from "./chunk-W6EXQDV5.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-KWHWNOTY.js";
+} from "./chunk-KDU4EF66.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-PTQPTDZH.js → chunk-6OP4HPXG.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.3.0";
+var version = "11.0.0";
 
 export {
   version

package/dist/chunks/{chunk-WONB6LMC.js → chunk-AI5PTOSV.js}

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

package/dist/chunks/{chunk-LGJBB5BP.js → chunk-B5X2RLJG.js}

@@ -121,7 +121,15 @@ function anchorFromPaths(graph, preferred) {
   };
 }
 function anchorGraph(graph, preferred) {
-  return graph.anchoredBy === "tags" ? graph : anchorFromPaths(graph, preferred);
+  if (graph.anchoredBy !== "tags") {
+    return anchorFromPaths(graph, preferred);
+  }
+  const referencePath = taggedReferencePath(graph);
+  return referencePath ? { ...graph, referencePath } : graph;
+}
+function taggedReferencePath(graph) {
+  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;
+  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;
 }
 function trimOrigins(graph, kept) {
   if (!graph.anchorPaths) {

package/dist/chunks/{chunk-TCOLHD7N.js → chunk-BIOKXS3M.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-ZNJ4JAPT.js";
+} from "./chunk-PK5QQOMN.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-BVYR7IFN.js → chunk-C3NT37C3.js}

@@ -1,10 +1,13 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-V7J6U4XC.js";
+} from "./chunk-DO62DG26.js";
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
+import {
+  gapParts
+} from "./chunk-EIY2SKD3.js";
 import {
   panSNContig
 } from "./chunk-4XWZNPQ2.js";
@@ -68,6 +71,22 @@ function highlightOf(graph, name, { byId, edgeAt }) {
       before += length;
     });
   }
+  let missingBp = 0;
+  let unknownBp = 0;
+  let end;
+  pieces.forEach((piece, p) => {
+    if (end !== void 0 && piece.start !== void 0 && piece.start > end) {
+      for (const part of gapParts(
+        piece.start - end,
+        pieces[p - 1].after,
+        piece.before
+      )) {
+        missingBp += part.cause === "missing" ? part.bp : 0;
+        unknownBp += part.cause === "unknown" ? part.bp : 0;
+      }
+    }
+    end = piece.start === void 0 ? void 0 : piece.start + bpOf(piece);
+  });
   const reference = isReference(graph, name);
   const referenceSpan = () => {
     const referencePieces = reference ? [] : (graph.paths ?? []).filter((p) => isReference(graph, p.name));
@@ -86,7 +105,9 @@ function highlightOf(graph, name, { byId, edgeAt }) {
     progress,
     steps: pieces.reduce((sum, piece) => sum + piece.nodeIds.length, 0),
     bp,
-    referenceBp: referenceSpan()
+    referenceBp: referenceSpan(),
+    missingBp,
+    unknownBp
   };
 }
 function laneColors(byId, walk, encoding, ramp) {

package/dist/chunks/{chunk-5YILQTHE.js → chunk-CIDSF47D.js}

@@ -1,6 +1,9 @@
 import {
   pathOrigin
-} from "./chunk-LGJBB5BP.js";
+} from "./chunk-B5X2RLJG.js";
+import {
+  gapParts
+} from "./chunk-EIY2SKD3.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";
@@ -50,10 +53,13 @@ var NodeTable = class {
 };
 function stepsOf(pieces, table) {
   const out = [];
+  const gaps = [];
   let end;
+  let previous;
   for (const piece of pieces) {
     if (end !== void 0 && piece.start !== void 0 && piece.start > end) {
-      out.push(end - piece.start);
+      gaps.push(gapParts(piece.start - end, previous?.after, piece.before));
+      out.push(-gaps.length);
     }
     let bp = 0;
     for (const node of piece.nodes) {
@@ -61,8 +67,9 @@ function stepsOf(pieces, table) {
       bp += table.lengths[node];
     }
     end = piece.start === void 0 ? void 0 : piece.start + bp;
+    previous = piece;
   }
-  return Float64Array.from(out);
+  return { steps: Float64Array.from(out), gaps };
 }
 function stepSpan(pieces, table, k) {
   let end;
@@ -203,10 +210,13 @@ function walkRows(graph, region, unit) {
     const path = paths2[0];
     const pieces = paths2.map((piece, p) => ({
       start: piece.start,
-      nodes: nodes?.[p] ?? table.nodesOf(piece)
+      nodes: nodes?.[p] ?? table.nodesOf(piece),
+      before: piece.before,
+      after: piece.after
     })).sort((a, b) => (a.start ?? 0) - (b.start ?? 0));
+    const { steps, gaps } = stepsOf(pieces, table);
     const { ids, complete, from, to, stop } = sliceBetween(
-      stepsOf(pieces, table),
+      steps,
       table,
       cut,
       flanked
@@ -221,12 +231,22 @@ function walkRows(graph, region, unit) {
     let offReferenceBp = 0;
     let gapBp = 0;
     let step = 0;
+    const backwards = from >= 0 && from > to;
     for (const node of ids) {
       if (node < 0) {
-        last = { start: bp, bp: -node, onReference: false, gap: true };
-        runs.push(last);
-        bp -= node;
-        gapBp -= node;
+        const parts = gaps[-node - 1];
+        for (const { bp: partBp, ...why } of backwards ? [...parts].reverse() : parts) {
+          last = {
+            start: bp,
+            bp: partBp,
+            onReference: false,
+            gap: true,
+            ...why
+          };
+          runs.push(last);
+          bp += partBp;
+          gapBp += partBp;
+        }
         step = 0;
         continue;
       }

package/dist/chunks/{chunk-AMX4OQAW.js → chunk-CTZRIDMY.js}

@@ -3,19 +3,19 @@ import {
 } from "./chunk-JMABOQWL.js";
 import {
   layoutModeByValue
-} from "./chunk-MD5VPXXT.js";
+} from "./chunk-EDWU7OM4.js";
 import {
   parseRegion
-} from "./chunk-M5NPD55W.js";
+} from "./chunk-TUQKGAK3.js";
 import {
   version
-} from "./chunk-PTQPTDZH.js";
+} from "./chunk-6OP4HPXG.js";
 import {
   axisScaleOf
-} from "./chunk-WONB6LMC.js";
+} from "./chunk-AI5PTOSV.js";
 import {
   figureScene
-} from "./chunk-XUT4HXVE.js";
+} from "./chunk-CZT33FZG.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -24,13 +24,13 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-ZPBEUOBM.js";
+} from "./chunk-W6EXQDV5.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-KWHWNOTY.js";
+} from "./chunk-KDU4EF66.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";

package/dist/chunks/{chunk-XUT4HXVE.js → chunk-CZT33FZG.js}

@@ -4,27 +4,27 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-BVYR7IFN.js";
+} from "./chunk-C3NT37C3.js";
 import {
   walkKey
-} from "./chunk-CGFPFBT2.js";
+} from "./chunk-D4ZFRBB4.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-2XEQR54X.js";
+} from "./chunk-SWCULW6S.js";
 import {
   walkRowsExtent
-} from "./chunk-QQCOVMMT.js";
+} from "./chunk-OLKXMZ6J.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-IYALCKNB.js";
+} from "./chunk-3GP3KT5L.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-ZPBEUOBM.js";
+} from "./chunk-W6EXQDV5.js";
 import {
   drawingBounds
-} from "./chunk-KWHWNOTY.js";
+} from "./chunk-KDU4EF66.js";
 import {
   referenceLabel
 } from "./chunk-234NFZS4.js";
@@ -97,7 +97,7 @@ function figureScene(graph, layout, o) {
     referenceName,
     keyText: (walk) => {
       const key = walkKey(walk, reference);
-      return { note: key.delta + key.outside + key.reversed, scale: key.scale };
+      return { note: key.delta + key.gaps + key.reversed, scale: key.scale };
     },
     contigThickness,
     nodeWidth,

package/dist/chunks/{chunk-CGFPFBT2.js → chunk-D4ZFRBB4.js}

@@ -1,3 +1,7 @@
+import {
+  GAP_CAUSE_TEXT,
+  OUTSIDE_TEXT
+} from "./chunk-EIY2SKD3.js";
 import {
   formatBp,
   groupDigits
@@ -14,10 +18,15 @@ function walkKey(walk, reference) {
   const own = walk.range ? rangeText(walk.range.contig, walk.range.start, walk.range.end) : void 0;
   const scale = field === "progress" ? own : field === "reference" && reference ? rangeText(reference.name, reference.start, reference.end) : void 0;
   const spanned = walk.range ? walk.range.end - walk.range.start : walk.bp;
-  const outside = spanned - walk.bp;
+  const outside = spanned - walk.bp - walk.missingBp - walk.unknownBp;
+  const gaps = [
+    [walk.missingBp, GAP_CAUSE_TEXT.missing],
+    [walk.unknownBp, GAP_CAUSE_TEXT.unknown],
+    [outside, OUTSIDE_TEXT]
+  ];
   return {
     delta: walk.referenceBp === void 0 || spanned === walk.referenceBp ? "" : ` ${spanned > walk.referenceBp ? "+" : "\u2212"}${formatBp(Math.abs(spanned - walk.referenceBp))}`,
-    outside: outside > 0 ? `, ${formatBp(outside)} outside the cut` : "",
+    gaps: gaps.filter(([bp]) => bp > 0).map(([bp, text]) => `, ${formatBp(bp)} ${text}`).join(""),
     reversed: walk.reversedBp > 0 ? `, ${formatBp(walk.reversedBp)} reversed` : "",
     shades: field !== "walk",
     scale,

package/dist/chunks/{chunk-V7J6U4XC.js → chunk-DO62DG26.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-2XEQR54X.js";
+} from "./chunk-SWCULW6S.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-Z6XZWPXK.js → chunk-DZR37KXT.js}

@@ -1,3 +1,9 @@
+import {
+  END_STOP_TAG,
+  START_STOP_TAG,
+  StopColumns,
+  parseStopTag
+} from "./chunk-EIY2SKD3.js";
 import {
   Column
 } from "./chunk-ZPZ7GNBT.js";
@@ -103,6 +109,7 @@ function readWalkBody(line, from, segments, steps) {
     }
   }
   finish(i);
+  return i;
 }
 function walkFields(line) {
   const fields = [];
@@ -159,6 +166,8 @@ function gfaTables(text) {
   const walkEnds = [];
   const offsets = [0];
   const steps = stepColumns();
+  const before = new StopColumns();
+  const after = new StopColumns();
   for (const raw of lines) {
     if (raw.startsWith("L	")) {
       const [, source, strand1, target, strand2] = trimCR(raw).split("	");
@@ -174,7 +183,17 @@ function gfaTables(text) {
         names.push(`${w.sample}#${w.haplotype}#${w.contig}`);
         walkStarts.push(w.start === "*" ? 0 : +w.start);
         walkEnds.push(w.end === "*" ? -1 : +w.end);
-        readWalkBody(line, w.body, segments, steps);
+        const end = readWalkBody(line, w.body, segments, steps);
+        const tags = walkTags(line, end);
+        if (tags === void 0) {
+          return void 0;
+        }
+        if (tags.before) {
+          before.push(tags.before);
+        }
+        if (tags.after) {
+          after.push(tags.after);
+        }
         if (steps.nodes.length === offsets.at(-1)) {
           return void 0;
         }
@@ -182,6 +201,11 @@ function gfaTables(text) {
       }
     }
   }
+  if ([before.kinds.length, after.kinds.length].some(
+    (n) => n > 0 && n < names.length
+  )) {
+    return void 0;
+  }
   return {
     nodes: {
       names: segments.names,
@@ -202,8 +226,33 @@ function gfaTables(text) {
       ends: Float64Array.from(walkEnds),
       offsets: Int32Array.from(offsets),
       steps: steps.nodes.data.slice(0, steps.nodes.length),
-      reversed: steps.reversed.data.slice(0, steps.reversed.length)
+      reversed: steps.reversed.data.slice(0, steps.reversed.length),
+      ...stopColumns(names.length, before, after)
+    }
+  };
+}
+function walkTags(line, from) {
+  const out = {};
+  for (const tag of from < line.length ? line.slice(from + 1).split("	") : []) {
+    const value = tag.slice(5);
+    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {
+      out.before = parseStopTag(value);
+      if (!out.before) {
+        return void 0;
+      }
+    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {
+      out.after = parseStopTag(value);
+      if (!out.after) {
+        return void 0;
+      }
     }
+  }
+  return out;
+}
+function stopColumns(walks, before, after) {
+  return {
+    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},
+    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}
   };
 }
 

package/dist/chunks/{chunk-MD5VPXXT.js → chunk-EDWU7OM4.js}

@@ -1,12 +1,12 @@
-import {
-  sampleRowLayout
-} from "./chunk-GJU6BJJA.js";
 import {
   hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-ZNJ4JAPT.js";
+} from "./chunk-PK5QQOMN.js";
+import {
+  sampleRowLayout
+} from "./chunk-GJU6BJJA.js";
 import {
   anchoredLayout
 } from "./chunk-GJLZ2MKE.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-QQCOVMMT.js";
+} from "./chunk-OLKXMZ6J.js";
 import {
   isBackbone,
   isOffReference