@jbrowse/bandage-core 9.1.0 → 9.3.0

package/dist/chunks/{chunk-3TGUKQWQ.js → chunk-TL3TYSCP.js}

@@ -1,37 +1,40 @@
+import {
+  stripGeneGaps,
+  walkStripFrame,
+  walkStripLabelsTree
+} from "./chunk-UD5FOCI2.js";
+import {
+  Canvas2DRenderer
+} from "./chunk-WBCOREDZ.js";
 import {
   layoutGeometryInputs
 } from "./chunk-LOCJN3BZ.js";
 import {
   svgCanvas
 } from "./chunk-47DYCZOK.js";
-import {
-  stripGeneGaps,
-  walkStripFrame,
-  walkStripLabelsTree
-} from "./chunk-WDTXW7T2.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-MIW3HYPE.js";
+} from "./chunk-GFRPX6M2.js";
 import {
-  Canvas2DRenderer
-} from "./chunk-WBCOREDZ.js";
+  genePins
+} from "./chunk-BUBZ32IC.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
 } from "./chunk-3S3YVOJ7.js";
 import {
-  genePins
-} from "./chunk-BUBZ32IC.js";
+  axisScaleOf
+} from "./chunk-XKM5OHQQ.js";
 import {
   facetLifts,
   walkLift
-} from "./chunk-MBB7ATM6.js";
+} from "./chunk-LFKMASER.js";
 import {
   encodingStops
-} from "./chunk-DPV2CUIE.js";
+} from "./chunk-XPT66H6H.js";
 import {
   rangeText,
   walkKey
@@ -39,30 +42,27 @@ import {
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-HBEKUQO4.js";
+} from "./chunk-BR25DGIJ.js";
 import {
   version
-} from "./chunk-UID3QBWH.js";
-import {
-  axisScaleOf
-} from "./chunk-MXDQGA7A.js";
+} from "./chunk-BTMPPLDF.js";
 import {
   walkRowLabels,
   walkRowsExtent
 } from "./chunk-3C5UXR2U.js";
-import {
-  nodeInk
-} from "./chunk-PBENCR5L.js";
 import {
   pathLegend,
   walkLabelsOf
 } from "./chunk-7GBL7SJY.js";
+import {
+  nodeInk
+} from "./chunk-PBENCR5L.js";
 import {
   referenceLabel
 } from "./chunk-RAKOB6IV.js";
 import {
   geneLabelCandidates
-} from "./chunk-GJMC3PGM.js";
+} from "./chunk-3FOOZ5VL.js";
 import {
   nodesUnderBox
 } from "./chunk-FP4H7SFT.js";
@@ -91,7 +91,7 @@ import {
   FIT_PADDING,
   drawingBounds,
   fitTransform
-} from "./chunk-OOXIMURX.js";
+} from "./chunk-ZGRYFUXE.js";
 import {
   deletionDrawing,
   deletionEdges

package/dist/chunks/{chunk-WDTXW7T2.js → chunk-UD5FOCI2.js}

@@ -2,7 +2,7 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-MIW3HYPE.js";
+} from "./chunk-GFRPX6M2.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-MXDQGA7A.js → chunk-XKM5OHQQ.js}

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

package/dist/chunks/{chunk-DPV2CUIE.js → chunk-XPT66H6H.js}

@@ -2,7 +2,7 @@ import {
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_MAX_HUE,
   hslToRgb
-} from "./chunk-HBEKUQO4.js";
+} from "./chunk-BR25DGIJ.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/cli/figure.js

@@ -4,18 +4,26 @@ import {
   genesFromGff3Lines,
   genesFromText
 } from "../chunks/chunk-BXEPA4KS.js";
+import {
+  LAYOUT_ENGINE_VALUES,
+  isLayoutEngineKind,
+  layoutEngine
+} from "../chunks/chunk-6EJIU6IA.js";
+import "../chunks/chunk-UNOE2NDN.js";
+import "../chunks/chunk-LYJ4US66.js";
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} from "../chunks/chunk-WNUZP3WQ.js";
+} from "../chunks/chunk-M7SRZJ32.js";
+import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-INJ2UVOT.js";
 import "../chunks/chunk-CWFNEKST.js";
-import "../chunks/chunk-LOEA5IHZ.js";
 import "../chunks/chunk-L3O7AWLI.js";
 import "../chunks/chunk-TZFWUT2C.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-RVS2QCOX.js";
 import "../chunks/chunk-HNQPEMYE.js";
+import "../chunks/chunk-7XHHVYG7.js";
 import {
   HPRC_GBZ,
   cutGbzRegion,
@@ -25,49 +33,41 @@ import {
 } from "../chunks/chunk-73RSLGZT.js";
 import "../chunks/chunk-LTUWJKHD.js";
 import "../chunks/chunk-WSIFAZU7.js";
-import {
-  LAYOUT_ENGINE_VALUES,
-  isLayoutEngineKind,
-  layoutEngine
-} from "../chunks/chunk-6EJIU6IA.js";
-import "../chunks/chunk-UNOE2NDN.js";
-import "../chunks/chunk-LYJ4US66.js";
-import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-3TGUKQWQ.js";
+} from "../chunks/chunk-TL3TYSCP.js";
+import "../chunks/chunk-UD5FOCI2.js";
+import "../chunks/chunk-WBCOREDZ.js";
+import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
-import "../chunks/chunk-WDTXW7T2.js";
 import {
   genesOnRow,
   placeRowGenes
-} from "../chunks/chunk-MIW3HYPE.js";
-import "../chunks/chunk-WBCOREDZ.js";
-import "../chunks/chunk-4BYTEJGW.js";
-import "../chunks/chunk-3S3YVOJ7.js";
+} from "../chunks/chunk-GFRPX6M2.js";
 import "../chunks/chunk-BUBZ32IC.js";
-import "../chunks/chunk-MBB7ATM6.js";
-import "../chunks/chunk-DPV2CUIE.js";
+import "../chunks/chunk-3S3YVOJ7.js";
+import "../chunks/chunk-XKM5OHQQ.js";
+import "../chunks/chunk-LFKMASER.js";
+import "../chunks/chunk-XPT66H6H.js";
 import "../chunks/chunk-2LQ5BWT7.js";
-import "../chunks/chunk-6ZNQJ5ZD.js";
-import "../chunks/chunk-HBEKUQO4.js";
+import "../chunks/chunk-OXTR3BVF.js";
+import "../chunks/chunk-BR25DGIJ.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-UID3QBWH.js";
-import "../chunks/chunk-MXDQGA7A.js";
+import "../chunks/chunk-BTMPPLDF.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {
   filterSamples,
   walkRows
 } from "../chunks/chunk-MAUEPAMG.js";
-import "../chunks/chunk-PBENCR5L.js";
 import "../chunks/chunk-7GBL7SJY.js";
+import "../chunks/chunk-PBENCR5L.js";
 import {
   featuresOnBackbone,
   graphBackbone,
   refNameBinding
 } from "../chunks/chunk-RAKOB6IV.js";
-import "../chunks/chunk-GJMC3PGM.js";
+import "../chunks/chunk-3FOOZ5VL.js";
 import "../chunks/chunk-FP4H7SFT.js";
 import "../chunks/chunk-MLSWIMZO.js";
 import "../chunks/chunk-WFB5TXRA.js";
@@ -80,18 +80,18 @@ import {
   engineSettingsOf,
   forceLayout,
   loadGraph
-} from "../chunks/chunk-OOXIMURX.js";
+} from "../chunks/chunk-ZGRYFUXE.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
-import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-OCMBULGN.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";
 import "../chunks/chunk-TAMCZHLW.js";
-import "../chunks/chunk-JVLURPFW.js";
 import "../chunks/chunk-UVBGRJQX.js";
 import "../chunks/chunk-6JEWNXCQ.js";
 import "../chunks/chunk-N6FECAXP.js";

package/dist/cli/fold.js

@@ -0,0 +1,72 @@
+#!/usr/bin/env node
+import {
+  writeRgfa
+} from "../chunks/chunk-B4YH42OP.js";
+import {
+  foldVariants
+} from "../chunks/chunk-B4645SM2.js";
+import {
+  loadGraph
+} from "../chunks/chunk-ZGRYFUXE.js";
+import "../chunks/chunk-PUG7LXDF.js";
+import "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-OCMBULGN.js";
+import "../chunks/chunk-OA7RIMZ2.js";
+import "../chunks/chunk-QYBZZI5H.js";
+import "../chunks/chunk-CDLPYR5O.js";
+import "../chunks/chunk-JVLURPFW.js";
+import "../chunks/chunk-ES2N6V56.js";
+import "../chunks/chunk-ST2IBUAN.js";
+import "../chunks/chunk-BPLIXMH7.js";
+import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-UVBGRJQX.js";
+import "../chunks/chunk-6JEWNXCQ.js";
+import "../chunks/chunk-N6FECAXP.js";
+import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
+
+// src/cli/fold.ts
+import { readFile, writeFile } from "node:fs/promises";
+import { parseArgs } from "node:util";
+import { gunzipSync } from "node:zlib";
+var USAGE = "usage: bandage-fold <graph.gfa[.gz] | -> --below <bp> [-o out.gfa]";
+async function readInput(location) {
+  const bytes = await readFile(location === "-" ? "/dev/stdin" : location);
+  const gzipped = bytes[0] === 31 && bytes[1] === 139;
+  return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
+}
+async function main() {
+  const { values, positionals } = parseArgs({
+    allowPositionals: true,
+    options: {
+      below: { type: "string" },
+      out: { type: "string", short: "o" },
+      reference: { type: "string" }
+    }
+  });
+  const below = Number(values.below);
+  const input = positionals[0];
+  if (!input || !(below > 0)) {
+    throw new Error(USAGE);
+  }
+  const graph = loadGraph(await readInput(input), input, {
+    referencePath: values.reference
+  });
+  const folded = foldVariants({ ...graph, paths: void 0 }, below);
+  const text = writeRgfa(folded);
+  if (values.out) {
+    await writeFile(values.out, text);
+  } else {
+    process.stdout.write(text);
+  }
+  process.stderr.write(
+    `${graph.nodes.length} segments, ${graph.edges.length} links -> ${folded.nodes.length} segments, ${folded.edges.length} links
+`
+  );
+}
+main().catch((e) => {
+  process.stderr.write(`${e instanceof Error ? e.message : String(e)}
+`);
+  process.exit(1);
+});

package/dist/figure.js

@@ -1,28 +1,28 @@
 import {
   figureSvg
-} from "./chunks/chunk-3TGUKQWQ.js";
-import "./chunks/chunk-LOCJN3BZ.js";
-import "./chunks/chunk-47DYCZOK.js";
-import "./chunks/chunk-WDTXW7T2.js";
-import "./chunks/chunk-MIW3HYPE.js";
+} from "./chunks/chunk-TL3TYSCP.js";
+import "./chunks/chunk-UD5FOCI2.js";
 import "./chunks/chunk-WBCOREDZ.js";
 import "./chunks/chunk-4BYTEJGW.js";
-import "./chunks/chunk-3S3YVOJ7.js";
+import "./chunks/chunk-LOCJN3BZ.js";
+import "./chunks/chunk-47DYCZOK.js";
+import "./chunks/chunk-GFRPX6M2.js";
 import "./chunks/chunk-BUBZ32IC.js";
-import "./chunks/chunk-MBB7ATM6.js";
-import "./chunks/chunk-DPV2CUIE.js";
+import "./chunks/chunk-3S3YVOJ7.js";
+import "./chunks/chunk-XKM5OHQQ.js";
+import "./chunks/chunk-LFKMASER.js";
+import "./chunks/chunk-XPT66H6H.js";
 import "./chunks/chunk-2LQ5BWT7.js";
-import "./chunks/chunk-6ZNQJ5ZD.js";
-import "./chunks/chunk-HBEKUQO4.js";
+import "./chunks/chunk-OXTR3BVF.js";
+import "./chunks/chunk-BR25DGIJ.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-UID3QBWH.js";
-import "./chunks/chunk-MXDQGA7A.js";
+import "./chunks/chunk-BTMPPLDF.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";
-import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-7GBL7SJY.js";
+import "./chunks/chunk-PBENCR5L.js";
 import "./chunks/chunk-RAKOB6IV.js";
-import "./chunks/chunk-GJMC3PGM.js";
+import "./chunks/chunk-3FOOZ5VL.js";
 import "./chunks/chunk-FP4H7SFT.js";
 import "./chunks/chunk-MLSWIMZO.js";
 import "./chunks/chunk-WFB5TXRA.js";
@@ -31,18 +31,18 @@ import "./chunks/chunk-AB35TJST.js";
 import "./chunks/chunk-JKJWSY4V.js";
 import "./chunks/chunk-NNODIW4U.js";
 import "./chunks/chunk-XV4P5KEQ.js";
-import "./chunks/chunk-OOXIMURX.js";
+import "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
-import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/figureSettings.js

@@ -1,19 +1,19 @@
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-XLCTQHBE.js";
-import "./chunks/chunk-OOXIMURX.js";
+} from "./chunks/chunk-BLRJ6IGK.js";
+import "./chunks/chunk-ZGRYFUXE.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
-import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
+import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";
 import "./chunks/chunk-TAMCZHLW.js";
-import "./chunks/chunk-JVLURPFW.js";
 import "./chunks/chunk-UVBGRJQX.js";
 import "./chunks/chunk-6JEWNXCQ.js";
 import "./chunks/chunk-N6FECAXP.js";

package/dist/foldVariants.js

@@ -0,0 +1,9 @@
+import {
+  foldVariants
+} from "./chunks/chunk-B4645SM2.js";
+import "./chunks/chunk-2CVHXFK7.js";
+import "./chunks/chunk-CPMHA4W5.js";
+import "./chunks/chunk-FYQWPEEY.js";
+export {
+  foldVariants
+};

package/dist/gfa/writeRgfa.js

@@ -0,0 +1,6 @@
+import {
+  writeRgfa
+} from "../chunks/chunk-B4YH42OP.js";
+export {
+  writeRgfa
+};