@jbrowse/bandage-core 10.2.2 → 10.2.3

package/README.md

@@ -10,8 +10,10 @@ npm install @jbrowse/bandage-core
 
 - GFA and rGFA text in (`loadGraph`), or the same graph as typed arrays a worker
   can transfer (`GraphTables`)
-- Layouts: Bandage's FMMM engine as WASM (`loadBandage`, `forceLayout`),
-  ordered, anchored, sample rows, walk rows, tube map
+- 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,
+  tube map
 - A Canvas2D renderer (`buildGeometry`, `Canvas2DRenderer`), hit testing and
   label placement
 - Bubbles, deletion edges, path colors, gbz-base windows cut to GFA
@@ -42,13 +44,10 @@ the worked example.
 pnpm install
 pnpm test          # unit tests
 pnpm build         # dist/ with declarations
-pnpm test:wasm     # the committed layout engine still loads
 ```
 
-The Bandage layout engine is OGDF's FMMM compiled to WASM and committed at
-`src/bandage/bandage-layout.js`; [src/bandage/README.md](src/bandage/README.md)
-says how to rebuild it from `src/bandage/native` and the vendored `vendor/ogdf`.
-A weekly workflow proves the committed artifact still reproduces.
+The FMMM engine and its wasm build live in
+[graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout).
 
 CI also packs the core and runs
 [BandageJS](https://github.com/cmdcolin/BandageJS) and

package/dist/bubbles/bubbleHalos.js

@@ -3,10 +3,14 @@ import {
   WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-EHUBJDDB.js";
-import "../chunks/chunk-XKWD2RY3.js";
+} from "../chunks/chunk-JFY5PWQC.js";
+import "../chunks/chunk-URZ3CH2R.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/bubbles/bubblesFromGraph.js

@@ -1,14 +1,16 @@
 import {
   bubblesFromGraph,
+  relax,
   walkIndexOf,
   walkRoutes
-} from "../chunks/chunk-CLOP7UVD.js";
+} from "../chunks/chunk-CQHUZHET.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-CM6LO6OC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
   bubblesFromGraph,
+  relax,
   walkIndexOf,
   walkRoutes
 };

package/dist/bubbles/classifyBubble.js

@@ -2,14 +2,19 @@ import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
-  classifyBubble,
-  formatBp
-} from "../chunks/chunk-XKWD2RY3.js";
+  classifyBubble
+} from "../chunks/chunk-URZ3CH2R.js";
 import "../chunks/chunk-FX4RDMDN.js";
+import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
-  classifyBubble,
-  formatBp
+  classifyBubble
 };

package/dist/bubbles/superbubbles.js

@@ -1,17 +1,21 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-FNGIQF43.js";
-import "../chunks/chunk-CLOP7UVD.js";
+} from "../chunks/chunk-XA5A27CS.js";
+import "../chunks/chunk-CQHUZHET.js";
 import "../chunks/chunk-T6V4KI2L.js";
-import "../chunks/chunk-EHUBJDDB.js";
-import "../chunks/chunk-XKWD2RY3.js";
+import "../chunks/chunk-JFY5PWQC.js";
+import "../chunks/chunk-URZ3CH2R.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-CM6LO6OC.js";
 import "../chunks/chunk-M6LK4GII.js";
 import "../chunks/chunk-RAEABQNW.js";
 import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-N73TI3VG.js";
+import "../chunks/chunk-24WITXQY.js";
+import "../chunks/chunk-7SRWJLSC.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {

package/dist/chunks/{chunk-N6FECAXP.js → chunk-24WITXQY.js}

@@ -3,7 +3,7 @@ import {
   edgeJoinOf,
   routedEdgeCurves,
   strandSides
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 import {
   firstNodeAtOrAfter,
   isBackbone
@@ -15,8 +15,18 @@ function bypassedPoints(nodePositions, bypassed) {
   return bypassed.flatMap((id) => nodePositions[id] ?? []);
 }
 function deletionArcCurves(nodePositions, deletion, axis, route, stranded = false) {
-  const from = nodePositions[deletion.from];
-  const to = nodePositions[deletion.to];
+  return edgeCurvesOf(
+    nodePositions,
+    deletion,
+    axis,
+    deletion.bypassed,
+    route,
+    stranded
+  );
+}
+function edgeCurvesOf(nodePositions, edge, axis, bypassed, route, stranded) {
+  const from = nodePositions[edge.from];
+  const to = nodePositions[edge.to];
   if (!from?.length || !to?.length) {
     return void 0;
   }
@@ -24,15 +34,13 @@ function deletionArcCurves(nodePositions, deletion, axis, route, stranded = fals
     from,
     to,
     route,
-    stranded ? strandSides(deletion) : void 0
+    stranded ? strandSides(edge) : void 0
   ) : computeEdgeCurves(
     from,
     to,
-    edgeJoinOf(deletion, stranded),
-    0,
-    0,
+    edgeJoinOf(edge, stranded),
     axis,
-    bypassedPoints(nodePositions, deletion.bypassed)
+    bypassed ? bypassedPoints(nodePositions, bypassed) : []
   );
 }
 function backboneBySequence(graph) {
@@ -161,6 +169,7 @@ function deletionDrawing(graph, deletions, show = true) {
 export {
   bypassedPoints,
   deletionArcCurves,
+  edgeCurvesOf,
   deletionEdges,
   closableDeletions,
   deletionDrawing

package/dist/chunks/{chunk-XTCNEKO5.js → chunk-2QLLQJ72.js}

@@ -1,3 +1,6 @@
+import {
+  orientToReference
+} from "./chunk-PUG7LXDF.js";
 import {
   seededNodes
 } from "./chunk-IGVV37VI.js";
@@ -9,18 +12,15 @@ import {
   takeRoutes,
   withDeletionRoutes
 } from "./chunk-VPE4AYP7.js";
-import {
-  orientToReference
-} from "./chunk-PUG7LXDF.js";
 import {
   convertGFAToGraph
-} from "./chunk-IW6CYVX2.js";
+} from "./chunk-AR4BUBMU.js";
+import {
+  parseGFA
+} from "./chunk-5I3K4R2G.js";
 import {
   graphFromTables
 } from "./chunk-PSMKPSO4.js";
-import {
-  parseGFA
-} from "./chunk-CDLPYR5O.js";
 import {
   anchorGraph
 } from "./chunk-M6LK4GII.js";
@@ -30,7 +30,7 @@ import {
 import {
   mergeRuns,
   splitRuns
-} from "./chunk-TAMCZHLW.js";
+} from "./chunk-N73TI3VG.js";
 import {
   spreadFor
 } from "./chunk-UVBGRJQX.js";
@@ -40,9 +40,9 @@ import {
   layoutScaling
 } from "./chunk-6JEWNXCQ.js";
 import {
-  closableDeletions,
+  deletionDrawing,
   deletionEdges
-} from "./chunk-N6FECAXP.js";
+} from "./chunk-24WITXQY.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
@@ -118,9 +118,11 @@ function engineKey(graph, settings) {
 }
 async function forceLayout(graph, settings, engine) {
   const spread = spreadFor(settings.bubbleSpread);
-  const found = deletionEdges(graph);
-  const dropped = settings.showDeletionEdges === false ? closableDeletions(graph, found) : /* @__PURE__ */ new Set();
-  const deletions = found.filter((d) => !dropped.has(d.edgeIndex));
+  const { shown: deletions, hidden: dropped } = deletionDrawing(
+    graph,
+    deletionEdges(graph),
+    settings.showDeletionEdges !== false
+  );
   const routed = withDeletionRoutes(graph, deletions, dropped);
   const merged = mergeRuns(routed.graph, routed.ids);
   const runs = {

package/dist/chunks/{chunk-ASSNZXCF.js → chunk-3AOGOCCQ.js}

@@ -1,79 +1,63 @@
 import {
   svgCanvas
-} from "./chunk-47DYCZOK.js";
+} from "./chunk-RUCH6ZFL.js";
 import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-JUIJI7RC.js";
-import {
-  Canvas2DRenderer
-} from "./chunk-WBCOREDZ.js";
+} from "./chunk-BAETMD3J.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-NRV7R36Q.js";
+} from "./chunk-EFQLEGWM.js";
+import {
+  Canvas2DRenderer
+} from "./chunk-QLWI2PZ3.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
-} from "./chunk-3S3YVOJ7.js";
+} from "./chunk-JSUCGZ6K.js";
 import {
   genePins
-} from "./chunk-BUBZ32IC.js";
+} from "./chunk-RPRHR56C.js";
 import {
   geneLabelCandidates
-} from "./chunk-DRG4236Y.js";
+} from "./chunk-YN6FDIBT.js";
 import {
   nodesUnderBox
-} from "./chunk-FP4H7SFT.js";
+} from "./chunk-4HWM3FNK.js";
 import {
+  escapeAttr,
   serializeEl
-} from "./chunk-NNODIW4U.js";
-import {
-  layoutGeometryInputs
-} from "./chunk-LOCJN3BZ.js";
+} from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-EYK7DJZV.js";
+} from "./chunk-J5FWKGOY.js";
 import {
   axisScaleOf
-} from "./chunk-L5WF4ZPS.js";
-import {
-  facetLifts,
-  walkLift
-} from "./chunk-R456ME6J.js";
-import {
-  encodingStops
-} from "./chunk-ALDGONEI.js";
+} from "./chunk-BS4UZ44I.js";
 import {
   rangeText,
   walkKey
-} from "./chunk-2LQ5BWT7.js";
+} from "./chunk-4ETPXDO6.js";
 import {
-  buildGeometry,
-  computeReferenceRamp
-} from "./chunk-SBMJNRTV.js";
+  figureScene
+} from "./chunk-D5D36ZF6.js";
 import {
-  walkRowLabels,
-  walkRowsExtent
-} from "./chunk-C7MZJSPT.js";
+  encodingStops
+} from "./chunk-VQC7KELB.js";
 import {
-  pathLegend,
-  walkLabelsOf
-} from "./chunk-TWRLC3KK.js";
+  walkRowLabels
+} from "./chunk-54POIBVC.js";
 import {
   nodeInk
-} from "./chunk-PBENCR5L.js";
+} from "./chunk-JBCZIBFC.js";
 import {
   FIT_PADDING,
-  drawingBounds,
   fitTransform
-} from "./chunk-XTCNEKO5.js";
-import {
-  referenceLabel
-} from "./chunk-RAKOB6IV.js";
+} from "./chunk-2QLLQJ72.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -81,20 +65,12 @@ import {
   occupancy,
   placeLabels
 } from "./chunk-AB35TJST.js";
-import {
-  resolveColorScheme
-} from "./chunk-JKJWSY4V.js";
-import {
-  deletionDrawing,
-  deletionEdges
-} from "./chunk-N6FECAXP.js";
 import {
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
   facetCells,
-  facetGrid,
-  facetSettingOf
+  facetGrid
 } from "./chunk-XV4P5KEQ.js";
 
 // src/figure.ts
@@ -105,9 +81,6 @@ var KEY_GAP_PX = 16;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
 var GENE_INK = "#1c1c22";
-function esc(s) {
-  return s.replaceAll("&", "&amp;").replaceAll("<", "&lt;").replaceAll(">", "&gt;").replaceAll('"', "&quot;");
-}
 function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   const bar = stops.length > 1 ? BAR_PX : SWATCH_PX;
   const fill = stops.length > 1 ? `fill="url(#${id})"` : `fill="${stops[0].color}"${opacity < 1 ? ` fill-opacity="${opacity}"` : ""}`;
@@ -118,7 +91,7 @@ function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   );
   return {
     width,
-    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">${esc(label)}</tspan>${esc(after)}</text>${under ? `<text y="28">${esc(under)}</text>` : ""}</g>`
+    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) {
@@ -146,47 +119,32 @@ function screenPath(d, t) {
   );
 }
 function chip(x, y, w, name, note) {
-  return `<rect x="${x - w / 2}" y="${y - LABEL_PX - LABEL_PAD + 2}" width="${w}" height="${LABEL_PX + LABEL_PAD * 2 - 2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${EXON_COLOR}"/><text x="${x}" y="${y}" font-family="Helvetica, Arial, sans-serif" font-size="${LABEL_PX}" fill="${GENE_INK}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${esc(name)}</tspan>${note ? esc(note) : ""}</text>`;
+  return `<rect x="${x - w / 2}" y="${y - LABEL_PX - LABEL_PAD + 2}" width="${w}" height="${LABEL_PX + LABEL_PAD * 2 - 2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${EXON_COLOR}"/><text x="${x}" y="${y}" font-family="Helvetica, Arial, sans-serif" font-size="${LABEL_PX}" fill="${GENE_INK}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${escapeAttr(name)}</tspan>${note ? escapeAttr(note) : ""}</text>`;
 }
 function figureSvg(graph, layout, o = {}) {
   const width = o.width ?? 1200;
   const room = o.height ?? 800;
-  const region = o.region;
-  const rampDomain = o.colorDomain ?? region;
   const rows = o.walkRows;
-  const bounds = drawingBounds(layout, {
-    region: o.fitToDrawing ? void 0 : region,
-    extent: rows && layout.extent ? walkRowsExtent(rows, o.walkRowPitch) : void 0
-  });
+  const {
+    bounds,
+    nodeById,
+    referenceRamp,
+    layers,
+    lift,
+    facet,
+    panels,
+    labelOf,
+    referenceName,
+    reference,
+    contigThickness,
+    nodeWidth,
+    geometry
+  } = figureScene(graph, layout, o);
   const pixelRows = layout.pixelRows ?? false;
-  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
-  const colorScheme = resolveColorScheme(o.colorScheme ?? "auto", graph);
-  const referenceRamp = colorScheme === "reference-position" && !layout.tubeMap ? computeReferenceRamp(graph, rampDomain) : void 0;
   const rampInterval = referenceRamp && {
     start: referenceRamp.start,
     end: referenceRamp.start + referenceRamp.span
   };
-  const drawnDeletions = deletionDrawing(
-    graph,
-    layout.tubeMap ? [] : deletionEdges(graph),
-    o.showDeletionEdges
-  );
-  const layers = o.walks ?? [];
-  const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, rampDomain) : void 0;
-  const lift = layers.length > 0 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
-  const facet = facetSettingOf(o.facet);
-  const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
-  const labels = walkLabelsOf(
-    graph.paths?.length ? pathLegend(graph.paths) : []
-  );
-  const labelOf = (name) => labels.get(name) ?? name;
-  const referenceName = o.referenceName ?? referenceLabel(graph, region);
-  const reference = lift?.referenceDomain && {
-    ...lift.referenceDomain,
-    name: referenceName
-  };
-  const contigThickness = o.contigThickness ?? 6;
-  const nodeWidth = o.nodeWidth ?? "depth";
   const pins = o.genes?.length && !layout.tubeMap && !rows ? genePins(graph, o.genes, layout.nodePositions) : [];
   const ink = nodeInk(graph, nodeById, contigThickness, nodeWidth);
   let masks = 0;
@@ -239,7 +197,7 @@ function figureSvg(graph, layout, o = {}) {
       const sy = y * t.scaleY + t.translateY;
       if (sy >= 0 && sy <= h) {
         out.push(
-          `<text x="6" y="${sy + 4}" ${FONT} stroke="#fff" stroke-width="3" paint-order="stroke">${esc(label)}</text>`
+          `<text x="6" y="${sy + 4}" ${FONT} stroke="#fff" stroke-width="3" paint-order="stroke">${escapeAttr(label)}</text>`
         );
       }
     }
@@ -264,24 +222,7 @@ function figureSvg(graph, layout, o = {}) {
     const axis = axisScaleOf(fit.scale, pixelRows);
     const { canvas, markup } = svgCanvas(w, h);
     const renderer = new Canvas2DRenderer(canvas);
-    renderer.uploadGeometry(
-      buildGeometry({
-        ...layoutGeometryInputs(layout, drawnDeletions, {
-          drawsRows: !!rows
-        }),
-        graph,
-        nodeById,
-        colorScheme,
-        contigThickness,
-        connectorThickness: o.connectorThickness ?? 2,
-        drawPaths: false,
-        nodeWidth,
-        linearLayout: o.linearLayout,
-        highlight,
-        axis,
-        referenceRamp
-      })
-    );
+    renderer.uploadGeometry(geometry(highlight, axis));
     const t = {
       scaleX: axis.scaleX,
       scaleY: axis.scaleY,
@@ -420,7 +361,7 @@ function figureSvg(graph, layout, o = {}) {
     generator: `@jbrowse/bandage-core@${version}`,
     ...o.spec === void 0 ? {} : { spec: o.spec }
   });
-  return `<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height}" viewBox="0 0 ${width} ${height}"><metadata>${esc(metadata)}</metadata><rect width="${width}" height="${height}" fill="#fff"/>${parts.join("")}</svg>
+  return `<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height}" viewBox="0 0 ${width} ${height}"><metadata>${escapeAttr(metadata)}</metadata><rect width="${width}" height="${height}" fill="#fff"/>${parts.join("")}</svg>
 `;
 }
 

package/dist/chunks/{chunk-TWRLC3KK.js → chunk-3XSM4OZU.js}

@@ -6,7 +6,7 @@ import {
 } from "./chunk-BPLIXMH7.js";
 import {
   groupDigits
-} from "./chunk-3ZZSX5HN.js";
+} from "./chunk-PTABFYQ7.js";
 
 // src/pathColors.ts
 function nameHue(name) {

package/dist/chunks/{chunk-WEDZ76AK.js → chunk-4DRQTBBE.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-BPRXQ2SS.js";
+} from "./chunk-XMW266WS.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-2LQ5BWT7.js → chunk-4ETPXDO6.js}

@@ -1,7 +1,7 @@
 import {
   formatBp,
   groupDigits
-} from "./chunk-3ZZSX5HN.js";
+} from "./chunk-PTABFYQ7.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-FP4H7SFT.js → chunk-4HWM3FNK.js}

@@ -1,12 +1,12 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-MLSWIMZO.js";
+} from "./chunk-KBEP7VYK.js";
 import {
   pathRibbonOffsets,
   translateCurves,
   yToXOf
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 
 // src/util/hitDetection.ts
 function distanceToSegment(px, py, x1, y1, x2, y2) {

package/dist/chunks/{chunk-C7MZJSPT.js → chunk-54POIBVC.js}

@@ -47,16 +47,9 @@ function walkRowLayout(graph, region) {
   const nodePositions = backbonePositions(
     overWindow.length > 0 ? overWindow : backbone
   );
-  const rowLabels = [
-    { label: walks.reference.label, y: 0 },
-    ...walks.rows.map((row, i) => ({
-      label: row.label,
-      y: (i + 1) * ROW_HEIGHT_PX
-    }))
-  ];
   return {
     nodePositions,
-    rowLabels,
+    rowLabels: walkRowLabels(walks),
     referenceAxis: true,
     pixelRows: true,
     extent: walkRowsExtent(walks)
@@ -64,6 +57,7 @@ function walkRowLayout(graph, region) {
 }
 
 export {
+  READOUT_ROOM,
   walkRowsExtent,
   walkRowLabels,
   walkRowLayout

package/dist/chunks/{chunk-PKFMP65V.js → chunk-5GMFEPWR.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-DK5P2YOL.js";
+} from "./chunk-XI3ZUTWF.js";
 import {
   pathOrigin
 } from "./chunk-M6LK4GII.js";

package/dist/chunks/{chunk-CDLPYR5O.js → chunk-5I3K4R2G.js}

@@ -57,10 +57,11 @@ function parseGFA(file) {
   };
   for (const rawLine of file.split("\n")) {
     const line = rawLine.endsWith("\r") ? rawLine.slice(0, -1) : rawLine;
-    if (line.startsWith("H")) {
+    const type = line.split("	", 1)[0];
+    if (type === "H") {
       const [, ...rest] = line.split("	");
       graph.header.push(parseTags(rest));
-    } else if (line.startsWith("S")) {
+    } else if (type === "S") {
       const [, name, ...rest] = line.split("	");
       let len;
       let seq;
@@ -82,7 +83,7 @@ function parseGFA(file) {
         len = +tags.LN;
       }
       graph.nodes.push({ id: name, length: len, sequence: seq, tags });
-    } else if (line.startsWith("E")) {
+    } else if (type === "E") {
       const [, , source, target, , , , , cigar, ...rest] = line.split("	");
       if (source && target) {
         graph.links.push({
@@ -94,7 +95,7 @@ function parseGFA(file) {
           tags: parseTags(rest)
         });
       }
-    } else if (line.startsWith("L")) {
+    } else if (type === "L") {
       const [, source, strand1, target, strand2, cigar, ...rest] = line.split("	");
       if (source && target && strand2) {
         graph.links.push({
@@ -106,7 +107,7 @@ function parseGFA(file) {
           tags: parseTags(rest)
         });
       }
-    } else if (line.startsWith("W")) {
+    } else if (type === "W") {
       const [, sample, hap, contig, start, end, body, ...rest] = line.split("	");
       if (sample && hap && contig && start && end && body) {
         graph.walks.push({
@@ -119,7 +120,7 @@ function parseGFA(file) {
           tags: parseTags(rest)
         });
       }
-    } else if (line.startsWith("P")) {
+    } else if (type === "P") {
       const [, name, path, ...rest] = line.split("	");
       if (name && path) {
         graph.paths.push({ name, path, rest });