@jbrowse/plugin-gff3 2.3.4 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (12) hide show
  1. package/dist/Gff3Adapter/Gff3Adapter.js +14 -19
  2. package/dist/Gff3Adapter/Gff3Adapter.js.map +1 -1
  3. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +7 -9
  4. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
  5. package/esm/Gff3Adapter/Gff3Adapter.js +14 -19
  6. package/esm/Gff3Adapter/Gff3Adapter.js.map +1 -1
  7. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +7 -9
  8. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
  9. package/package.json +3 -3
  10. package/src/Gff3Adapter/Gff3Adapter.ts +23 -26
  11. package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts +9 -9
  12. package/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap +4 -4
package/dist/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -36,20 +36,17 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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  parseSequences: false,
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  disableDerivesFromReferences: true,
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  });
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- const intervalTree = feats
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- .flat()
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- .map((f, i) => new simpleFeature_1.default({
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+ const intervalTree = {};
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+ for (const obj of feats.flat().map((f, i) => new simpleFeature_1.default({
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  data: this.featureData(f),
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  id: `${this.id}-offset-${i}`,
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- }))
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- .reduce((acc, obj) => {
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+ }))) {
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  const key = obj.get('refName');
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- if (!acc[key]) {
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- acc[key] = new interval_tree_1.default();
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+ if (!intervalTree[key]) {
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+ intervalTree[key] = new interval_tree_1.default();
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  }
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- acc[key].insert([obj.get('start'), obj.get('end')], obj);
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- return acc;
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- }, {});
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+ intervalTree[key].insert([obj.get('start'), obj.get('end')], obj);
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+ }
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  return { header, intervalTree };
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  }
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  async loadData() {
@@ -106,7 +103,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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  if (data.phase === null) {
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  delete f.score;
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  }
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- const defaultFields = [
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+ const defaultFields = new Set([
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  'start',
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  'end',
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  'seq_id',
@@ -115,11 +112,11 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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  'source',
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  'phase',
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  'strand',
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- ];
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+ ]);
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  const dataAttributes = data.attributes || {};
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- Object.keys(dataAttributes).forEach(a => {
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+ for (const a of Object.keys(dataAttributes)) {
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  let b = a.toLowerCase();
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- if (defaultFields.includes(b)) {
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+ if (defaultFields.has(b)) {
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  // add "suffix" to tag name if it already exists
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  // reproduces behavior of NCList
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  b += '2';
@@ -132,13 +129,11 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  f[b] = attr;
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  }
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- });
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+ }
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  f.refName = f.seq_id;
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  // the SimpleFeature constructor takes care of recursively inflating subfeatures
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- if (data.child_features && data.child_features.length) {
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- f.subfeatures = data.child_features
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- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
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- .flat();
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+ if (data.child_features && data.child_features.length > 0) {
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+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
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  }
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  delete f.child_features;
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  delete f.data;
package/dist/Gff3Adapter/Gff3Adapter.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"Gff3Adapter.js","sourceRoot":"","sources":["../../src/Gff3Adapter/Gff3Adapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,qFAAyE;AACzE,2DAA6C;AAE7C,oDAAwD;AAExD,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,eAAqB,SAAQ,oCAAsB;IAMzC,KAAK,CAAC,SAAS;QACrB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAC1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QACtC,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACjE,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAErC,MAAM,KAAK,GAAG,aAAG,CAAC,eAAe,CAAC,IAAI,EAAE;YACtC,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,KAAK;YACpB,eAAe,EAAE,KAAK;YACtB,cAAc,EAAE,KAAK;YACrB,4BAA4B,EAAE,IAAI;SACnC,CAAC,CAAA;QAEF,MAAM,YAAY,GAAG,EAAkC,CAAA;QACvD,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,GAAG,CAChC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,IAAI,uBAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC;YACzB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,EAAE;SAC7B,CAAC,CACL,EAAE;YACD,MAAM,GAAG,GAAG,GAAG,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YAC9B,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAClE;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,QAAQ;QACpB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC5C,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACxC,OAAO,MAAM,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;gBACrC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;gBAC9C,MAAA,YAAY,CAAC,OAAO,CAAC,0CACjB,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EACpB,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjC,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC;YAC5B,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAC,CAAA;QACF,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE;YAC3C,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;gBACxB,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;SACF;QACD,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,EAAE;YACzD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,CACtD,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CACtD,CAAA;SACF;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,4BAA4B;QAC5B,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QACf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C;AApJD,4BAoJC"}
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -145,7 +145,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
145
145
  if (data.phase === null) {
146
146
  delete f.score;
147
147
  }
148
- const defaultFields = [
148
+ const defaultFields = new Set([
149
149
  'start',
150
150
  'end',
151
151
  'seq_id',
@@ -154,11 +154,11 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
154
154
  'source',
155
155
  'phase',
156
156
  'strand',
157
- ];
157
+ ]);
158
158
  const dataAttributes = data.attributes || {};
159
- Object.keys(dataAttributes).forEach(a => {
159
+ for (const a of Object.keys(dataAttributes)) {
160
160
  let b = a.toLowerCase();
161
- if (defaultFields.includes(b)) {
161
+ if (defaultFields.has(b)) {
162
162
  // add "suffix" to tag name if it already exists
163
163
  // reproduces behavior of NCList
164
164
  b += '2';
@@ -171,13 +171,11 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
171
171
  }
172
172
  f[b] = attr;
173
173
  }
174
- });
174
+ }
175
175
  f.refName = f.seq_id;
176
176
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
177
- if (data.child_features && data.child_features.length) {
178
- f.subfeatures = data.child_features
179
- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
180
- .flat();
177
+ if (data.child_features && data.child_features.length > 0) {
178
+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
181
179
  }
182
180
  delete f.child_features;
183
181
  delete f.data;
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -31,20 +31,17 @@ export default class extends BaseFeatureDataAdapter {
31
31
  parseSequences: false,
32
32
  disableDerivesFromReferences: true,
33
33
  });
34
- const intervalTree = feats
35
- .flat()
36
- .map((f, i) => new SimpleFeature({
34
+ const intervalTree = {};
35
+ for (const obj of feats.flat().map((f, i) => new SimpleFeature({
37
36
  data: this.featureData(f),
38
37
  id: `${this.id}-offset-${i}`,
39
- }))
40
- .reduce((acc, obj) => {
38
+ }))) {
41
39
  const key = obj.get('refName');
42
- if (!acc[key]) {
43
- acc[key] = new IntervalTree();
40
+ if (!intervalTree[key]) {
41
+ intervalTree[key] = new IntervalTree();
44
42
  }
45
- acc[key].insert([obj.get('start'), obj.get('end')], obj);
46
- return acc;
47
- }, {});
43
+ intervalTree[key].insert([obj.get('start'), obj.get('end')], obj);
44
+ }
48
45
  return { header, intervalTree };
49
46
  }
50
47
  async loadData() {
@@ -101,7 +98,7 @@ export default class extends BaseFeatureDataAdapter {
101
98
  if (data.phase === null) {
102
99
  delete f.score;
103
100
  }
104
- const defaultFields = [
101
+ const defaultFields = new Set([
105
102
  'start',
106
103
  'end',
107
104
  'seq_id',
@@ -110,11 +107,11 @@ export default class extends BaseFeatureDataAdapter {
110
107
  'source',
111
108
  'phase',
112
109
  'strand',
113
- ];
110
+ ]);
114
111
  const dataAttributes = data.attributes || {};
115
- Object.keys(dataAttributes).forEach(a => {
112
+ for (const a of Object.keys(dataAttributes)) {
116
113
  let b = a.toLowerCase();
117
- if (defaultFields.includes(b)) {
114
+ if (defaultFields.has(b)) {
118
115
  // add "suffix" to tag name if it already exists
119
116
  // reproduces behavior of NCList
120
117
  b += '2';
@@ -127,13 +124,11 @@ export default class extends BaseFeatureDataAdapter {
127
124
  }
128
125
  f[b] = attr;
129
126
  }
130
- });
127
+ }
131
128
  f.refName = f.seq_id;
132
129
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
133
- if (data.child_features && data.child_features.length) {
134
- f.subfeatures = data.child_features
135
- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
136
- .flat();
130
+ if (data.child_features && data.child_features.length > 0) {
131
+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
137
132
  }
138
133
  delete f.child_features;
139
134
  delete f.data;
package/esm/Gff3Adapter/Gff3Adapter.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -140,7 +140,7 @@ export default class extends BaseFeatureDataAdapter {
140
140
  if (data.phase === null) {
141
141
  delete f.score;
142
142
  }
143
- const defaultFields = [
143
+ const defaultFields = new Set([
144
144
  'start',
145
145
  'end',
146
146
  'seq_id',
@@ -149,11 +149,11 @@ export default class extends BaseFeatureDataAdapter {
149
149
  'source',
150
150
  'phase',
151
151
  'strand',
152
- ];
152
+ ]);
153
153
  const dataAttributes = data.attributes || {};
154
- Object.keys(dataAttributes).forEach(a => {
154
+ for (const a of Object.keys(dataAttributes)) {
155
155
  let b = a.toLowerCase();
156
- if (defaultFields.includes(b)) {
156
+ if (defaultFields.has(b)) {
157
157
  // add "suffix" to tag name if it already exists
158
158
  // reproduces behavior of NCList
159
159
  b += '2';
@@ -166,13 +166,11 @@ export default class extends BaseFeatureDataAdapter {
166
166
  }
167
167
  f[b] = attr;
168
168
  }
169
- });
169
+ }
170
170
  f.refName = f.seq_id;
171
171
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
172
- if (data.child_features && data.child_features.length) {
173
- f.subfeatures = data.child_features
174
- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
175
- .flat();
172
+ if (data.child_features && data.child_features.length > 0) {
173
+ f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => this.featureData(childLoc)));
176
174
  }
177
175
  delete f.child_features;
178
176
  delete f.data;
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gff3",
3
- "version": "2.3.4",
3
+ "version": "2.4.1",
4
4
  "description": "JBrowse 2 gff3.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -40,7 +40,7 @@
40
40
  "@flatten-js/interval-tree": "^1.0.15",
41
41
  "@gmod/bgzf-filehandle": "^1.4.3",
42
42
  "@gmod/gff": "^1.3.0",
43
- "@gmod/tabix": "^1.5.2"
43
+ "@gmod/tabix": "^1.5.6"
44
44
  },
45
45
  "peerDependencies": {
46
46
  "@jbrowse/core": "^2.0.0",
@@ -56,5 +56,5 @@
56
56
  "distModule": "esm/index.js",
57
57
  "srcModule": "src/index.ts",
58
58
  "module": "esm/index.js",
59
- "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
59
+ "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
60
60
  }
package/src/Gff3Adapter/Gff3Adapter.ts CHANGED
@@ -45,23 +45,20 @@ export default class extends BaseFeatureDataAdapter {
45
45
  disableDerivesFromReferences: true,
46
46
  })
47
47
 
48
- const intervalTree = feats
49
- .flat()
50
- .map(
51
- (f, i) =>
52
- new SimpleFeature({
53
- data: this.featureData(f),
54
- id: `${this.id}-offset-${i}`,
55
- }),
56
- )
57
- .reduce((acc, obj) => {
58
- const key = obj.get('refName')
59
- if (!acc[key]) {
60
- acc[key] = new IntervalTree()
61
- }
62
- acc[key].insert([obj.get('start'), obj.get('end')], obj)
63
- return acc
64
- }, {} as Record<string, IntervalTree>)
48
+ const intervalTree = {} as Record<string, IntervalTree>
49
+ for (const obj of feats.flat().map(
50
+ (f, i) =>
51
+ new SimpleFeature({
52
+ data: this.featureData(f),
53
+ id: `${this.id}-offset-${i}`,
54
+ }),
55
+ )) {
56
+ const key = obj.get('refName')
57
+ if (!intervalTree[key]) {
58
+ intervalTree[key] = new IntervalTree()
59
+ }
60
+ intervalTree[key].insert([obj.get('start'), obj.get('end')], obj)
61
+ }
65
62
 
66
63
  return { header, intervalTree }
67
64
  }
@@ -122,7 +119,7 @@ export default class extends BaseFeatureDataAdapter {
122
119
  if (data.phase === null) {
123
120
  delete f.score
124
121
  }
125
- const defaultFields = [
122
+ const defaultFields = new Set([
126
123
  'start',
127
124
  'end',
128
125
  'seq_id',
@@ -131,11 +128,11 @@ export default class extends BaseFeatureDataAdapter {
131
128
  'source',
132
129
  'phase',
133
130
  'strand',
134
- ]
131
+ ])
135
132
  const dataAttributes = data.attributes || {}
136
- Object.keys(dataAttributes).forEach(a => {
133
+ for (const a of Object.keys(dataAttributes)) {
137
134
  let b = a.toLowerCase()
138
- if (defaultFields.includes(b)) {
135
+ if (defaultFields.has(b)) {
139
136
  // add "suffix" to tag name if it already exists
140
137
  // reproduces behavior of NCList
141
138
  b += '2'
@@ -147,14 +144,14 @@ export default class extends BaseFeatureDataAdapter {
147
144
  }
148
145
  f[b] = attr
149
146
  }
150
- })
147
+ }
151
148
  f.refName = f.seq_id
152
149
 
153
150
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
154
- if (data.child_features && data.child_features.length) {
155
- f.subfeatures = data.child_features
156
- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
157
- .flat()
151
+ if (data.child_features && data.child_features.length > 0) {
152
+ f.subfeatures = data.child_features.flatMap(childLocs =>
153
+ childLocs.map(childLoc => this.featureData(childLoc)),
154
+ )
158
155
  }
159
156
 
160
157
  delete f.child_features
package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts CHANGED
@@ -211,7 +211,7 @@ export default class extends BaseFeatureDataAdapter {
211
211
  if (data.phase === null) {
212
212
  delete f.score
213
213
  }
214
- const defaultFields = [
214
+ const defaultFields = new Set([
215
215
  'start',
216
216
  'end',
217
217
  'seq_id',
@@ -220,11 +220,11 @@ export default class extends BaseFeatureDataAdapter {
220
220
  'source',
221
221
  'phase',
222
222
  'strand',
223
- ]
223
+ ])
224
224
  const dataAttributes = data.attributes || {}
225
- Object.keys(dataAttributes).forEach(a => {
225
+ for (const a of Object.keys(dataAttributes)) {
226
226
  let b = a.toLowerCase()
227
- if (defaultFields.includes(b)) {
227
+ if (defaultFields.has(b)) {
228
228
  // add "suffix" to tag name if it already exists
229
229
  // reproduces behavior of NCList
230
230
  b += '2'
@@ -236,14 +236,14 @@ export default class extends BaseFeatureDataAdapter {
236
236
  }
237
237
  f[b] = attr
238
238
  }
239
- })
239
+ }
240
240
  f.refName = f.seq_id
241
241
 
242
242
  // the SimpleFeature constructor takes care of recursively inflating subfeatures
243
- if (data.child_features && data.child_features.length) {
244
- f.subfeatures = data.child_features
245
- .map(childLocs => childLocs.map(childLoc => this.featureData(childLoc)))
246
- .flat()
243
+ if (data.child_features && data.child_features.length > 0) {
244
+ f.subfeatures = data.child_features.flatMap(childLocs =>
245
+ childLocs.map(childLoc => this.featureData(childLoc)),
246
+ )
247
247
  }
248
248
 
249
249
  delete f.child_features
package/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap CHANGED
@@ -12,7 +12,7 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla
12
12
  "start": 0,
13
13
  "strand": undefined,
14
14
  "type": "contig",
15
- "uniqueId": "test-offset-794327",
15
+ "uniqueId": "test-offset-794328",
16
16
  },
17
17
  {
18
18
  "derived_features": [],
@@ -25,7 +25,7 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla
25
25
  "start": 1658,
26
26
  "strand": 1,
27
27
  "type": "remark",
28
- "uniqueId": "test-offset-794370",
28
+ "uniqueId": "test-offset-794371",
29
29
  },
30
30
  {
31
31
  "derived_features": [],
@@ -38,7 +38,7 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla
38
38
  "start": 3013,
39
39
  "strand": 1,
40
40
  "type": "remark",
41
- "uniqueId": "test-offset-794439",
41
+ "uniqueId": "test-offset-794440",
42
42
  },
43
43
  {
44
44
  "derived_features": [],
@@ -51,7 +51,7 @@ exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff pla
51
51
  "start": 4714,
52
52
  "strand": -1,
53
53
  "type": "remark",
54
- "uniqueId": "test-offset-794513",
54
+ "uniqueId": "test-offset-794514",
55
55
  },
56
56
  ]
57
57
  `;