@jbrowse/plugin-bed 2.7.2 → 2.8.0

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Files changed (5) hide show
  1. package/dist/BedpeAdapter/BedpeAdapter.js +13 -22
  2. package/dist/index.js +4 -9
  3. package/esm/BedpeAdapter/BedpeAdapter.js +13 -22
  4. package/esm/index.js +4 -9
  5. package/package.json +2 -2
package/dist/BedpeAdapter/BedpeAdapter.js CHANGED
@@ -18,21 +18,26 @@ function featureData(line, uniqueId, flip, names) {
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  const ref1 = l[flip ? 3 : 0];
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  const start1 = +l[flip ? 4 : 1];
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  const end1 = +l[flip ? 5 : 2];
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- const ref2 = +l[!flip ? 3 : 0];
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+ const ref2 = l[!flip ? 3 : 0];
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  const start2 = +l[!flip ? 4 : 1];
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  const end2 = +l[!flip ? 5 : 2];
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  const name = l[6];
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  const score = +l[7];
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  const strand1 = parseStrand(l[8]);
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  const strand2 = parseStrand(l[9]);
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- const extra = l.slice(9);
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+ const extra = l.slice(10);
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  const rest = names
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- ? Object.fromEntries(names.slice(9).map((n, idx) => [n, extra[idx]]))
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+ ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
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  : extra;
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+ let ALT;
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+ if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])) {
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+ ALT = `<${extra[0]}>`;
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+ }
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  return new util_1.SimpleFeature({
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  start: start1,
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  end: end1,
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  refName: ref1,
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+ ...(ALT ? { ALT: [ALT] } : {}),
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  strand: strand1,
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  name,
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  ...rest,
@@ -134,28 +139,14 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  : undefined;
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  }
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  async loadFeatureTreeP(refName) {
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+ var _a, _b, _c, _d;
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  const { feats1, feats2 } = await this.loadData();
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- const lines1 = feats1[refName];
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- const lines2 = feats2[refName];
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  const names = await this.getNames();
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  const intervalTree = new interval_tree_1.default();
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- const ret1 = lines1 === null || lines1 === void 0 ? void 0 : lines1.map((f, i) => {
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- const uniqueId = `${this.id}-${refName}-${i}`;
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- return featureData(f, uniqueId, false, names);
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- });
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- const ret2 = lines2 === null || lines2 === void 0 ? void 0 : lines2.map((f, i) => {
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- const uniqueId = `${this.id}-${refName}-${i}`;
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- return featureData(f, uniqueId, true, names);
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- });
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- if (ret1) {
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- for (const obj of ret1) {
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- intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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- }
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- }
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- if (ret2) {
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- for (const obj of ret2) {
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- intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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- }
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+ const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
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+ const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
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+ for (const obj of [...ret1, ...ret2]) {
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+ intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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  }
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  return intervalTree;
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  }
package/dist/index.js CHANGED
@@ -39,7 +39,7 @@ class BedPlugin extends Plugin_1.default {
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  });
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  pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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  return (file, index, adapterHint) => {
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- const regexGuess = /\.bedpe\.gz$/i;
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+ const regexGuess = /\.bedpe(\.gz)?$/i;
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  const adapterName = 'BedpeAdapter';
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  const fileName = (0, tracks_1.getFileName)(file);
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  if (regexGuess.test(fileName) || adapterHint === adapterName) {
@@ -84,14 +84,9 @@ class BedPlugin extends Plugin_1.default {
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  return adapterGuesser(file, index, adapterHint);
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  };
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  });
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- pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
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- return (adapterName) => {
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- if (adapterName === 'BedpeAdapter') {
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- return 'VariantTrack';
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- }
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- return trackTypeGuesser(adapterName);
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- };
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- });
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+ pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => adapterName === 'BedpeAdapter'
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+ ? 'VariantTrack'
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+ : trackTypeGuesser(adapterName));
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  }
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  }
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  exports.default = BedPlugin;
package/esm/BedpeAdapter/BedpeAdapter.js CHANGED
@@ -12,21 +12,26 @@ export function featureData(line, uniqueId, flip, names) {
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  const ref1 = l[flip ? 3 : 0];
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  const start1 = +l[flip ? 4 : 1];
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  const end1 = +l[flip ? 5 : 2];
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- const ref2 = +l[!flip ? 3 : 0];
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+ const ref2 = l[!flip ? 3 : 0];
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  const start2 = +l[!flip ? 4 : 1];
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  const end2 = +l[!flip ? 5 : 2];
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  const name = l[6];
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  const score = +l[7];
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  const strand1 = parseStrand(l[8]);
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  const strand2 = parseStrand(l[9]);
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- const extra = l.slice(9);
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+ const extra = l.slice(10);
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  const rest = names
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- ? Object.fromEntries(names.slice(9).map((n, idx) => [n, extra[idx]]))
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+ ? Object.fromEntries(names.slice(10).map((n, idx) => [n, extra[idx]]))
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  : extra;
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+ let ALT;
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+ if (['DUP', 'TRA', 'INV', 'CNV', 'DEL'].includes(extra[0])) {
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+ ALT = `<${extra[0]}>`;
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+ }
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  return new SimpleFeature({
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  start: start1,
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  end: end1,
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  refName: ref1,
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+ ...(ALT ? { ALT: [ALT] } : {}),
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  strand: strand1,
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  name,
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  ...rest,
@@ -127,28 +132,14 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
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  : undefined;
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  }
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  async loadFeatureTreeP(refName) {
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+ var _a, _b, _c, _d;
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  const { feats1, feats2 } = await this.loadData();
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- const lines1 = feats1[refName];
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- const lines2 = feats2[refName];
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  const names = await this.getNames();
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  const intervalTree = new IntervalTree();
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- const ret1 = lines1 === null || lines1 === void 0 ? void 0 : lines1.map((f, i) => {
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- const uniqueId = `${this.id}-${refName}-${i}`;
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- return featureData(f, uniqueId, false, names);
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- });
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- const ret2 = lines2 === null || lines2 === void 0 ? void 0 : lines2.map((f, i) => {
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- const uniqueId = `${this.id}-${refName}-${i}`;
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- return featureData(f, uniqueId, true, names);
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- });
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- if (ret1) {
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- for (const obj of ret1) {
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- intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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- }
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- }
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- if (ret2) {
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- for (const obj of ret2) {
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- intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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- }
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+ const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
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+ const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
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+ for (const obj of [...ret1, ...ret2]) {
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+ intervalTree.insert([obj.get('start'), obj.get('end')], obj);
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  }
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  return intervalTree;
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  }
package/esm/index.js CHANGED
@@ -34,7 +34,7 @@ export default class BedPlugin extends Plugin {
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  });
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  pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
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  return (file, index, adapterHint) => {
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- const regexGuess = /\.bedpe\.gz$/i;
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+ const regexGuess = /\.bedpe(\.gz)?$/i;
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  const adapterName = 'BedpeAdapter';
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  const fileName = getFileName(file);
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  if (regexGuess.test(fileName) || adapterHint === adapterName) {
@@ -79,13 +79,8 @@ export default class BedPlugin extends Plugin {
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  return adapterGuesser(file, index, adapterHint);
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  };
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  });
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- pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
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- return (adapterName) => {
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- if (adapterName === 'BedpeAdapter') {
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- return 'VariantTrack';
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- }
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- return trackTypeGuesser(adapterName);
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- };
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- });
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+ pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => adapterName === 'BedpeAdapter'
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+ ? 'VariantTrack'
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+ : trackTypeGuesser(adapterName));
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  }
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  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-bed",
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- "version": "2.7.2",
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+ "version": "2.8.0",
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  "description": "JBrowse 2 bed adapters, tracks, etc.",
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  "keywords": [
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  "jbrowse",
@@ -55,5 +55,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "9052b295f2d322e729254457ed9fe2231fb22cce"
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+ "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
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  }