@jbrowse/plugin-gff3 3.2.0 → 3.4.0

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Files changed (11) hide show
  1. package/dist/Gff3Adapter/Gff3Adapter.d.ts +0 -1
  2. package/dist/Gff3Adapter/Gff3Adapter.js +1 -2
  3. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +0 -1
  4. package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +1 -6
  5. package/dist/Gff3TabixAdapter/configSchema.js +1 -1
  6. package/esm/Gff3Adapter/Gff3Adapter.d.ts +0 -1
  7. package/esm/Gff3Adapter/Gff3Adapter.js +1 -2
  8. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts +0 -1
  9. package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +1 -6
  10. package/esm/Gff3TabixAdapter/configSchema.js +1 -1
  11. package/package.json +7 -7
package/dist/Gff3Adapter/Gff3Adapter.d.ts CHANGED
@@ -15,6 +15,5 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getHeader(opts?: BaseOptions): Promise<string>;
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  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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- freeResources(): void;
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  }
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  export {};
package/dist/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -18,7 +18,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  async loadDataP(opts) {
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  const { statusCallback = () => { } } = opts || {};
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- const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('gffLocation'), this.pluginManager));
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+ const buffer = await (0, util_1.fetchAndMaybeUnzip)((0, io_1.openLocation)(this.getConf('gffLocation'), this.pluginManager), opts);
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  const headerLines = [];
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  const featureMap = {};
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  const decoder = new TextDecoder('utf8');
@@ -109,6 +109,5 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }
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  }, opts.stopToken);
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  }
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- freeResources() { }
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  }
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  exports.default = Gff3Adapter;
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -19,5 +19,4 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  private getFeaturesHelper;
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  private parseLine;
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- freeResources(): void;
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  }
package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -17,11 +17,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  const gffGzLocation = this.getConf('gffGzLocation');
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  const indexType = this.getConf(['index', 'indexType']);
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  const loc = this.getConf(['index', 'location']);
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- const dontRedispatch = this.getConf('dontRedispatch') || [
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- 'chromosome',
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- 'contig',
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- 'region',
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- ];
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+ const dontRedispatch = this.getConf('dontRedispatch');
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  const gff = new tabix_1.TabixIndexedFile({
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  filehandle: (0, io_1.openLocation)(gffGzLocation, this.pluginManager),
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  csiFilehandle: indexType === 'CSI' ? (0, io_1.openLocation)(loc, this.pluginManager) : undefined,
@@ -131,6 +127,5 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  fields,
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  };
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  }
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- freeResources() { }
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  }
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  exports.default = Gff3TabixAdapter;
package/dist/Gff3TabixAdapter/configSchema.js CHANGED
@@ -41,7 +41,7 @@ const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdap
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  },
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  index: {
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  location: {
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- uri: snap.uri,
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+ uri: `${snap.uri}.tbi`,
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  baseUri: snap.baseUri,
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  },
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  },
package/esm/Gff3Adapter/Gff3Adapter.d.ts CHANGED
@@ -15,6 +15,5 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getHeader(opts?: BaseOptions): Promise<string>;
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  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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- freeResources(): void;
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  }
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  export {};
package/esm/Gff3Adapter/Gff3Adapter.js CHANGED
@@ -13,7 +13,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  }
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  async loadDataP(opts) {
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  const { statusCallback = () => { } } = opts || {};
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- const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('gffLocation'), this.pluginManager));
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+ const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('gffLocation'), this.pluginManager), opts);
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  const headerLines = [];
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  const featureMap = {};
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  const decoder = new TextDecoder('utf8');
@@ -104,5 +104,4 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
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  }
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  }, opts.stopToken);
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  }
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- freeResources() { }
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  }
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts CHANGED
@@ -19,5 +19,4 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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  getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  private getFeaturesHelper;
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  private parseLine;
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- freeResources(): void;
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  }
package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js CHANGED
@@ -12,11 +12,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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  const gffGzLocation = this.getConf('gffGzLocation');
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  const indexType = this.getConf(['index', 'indexType']);
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  const loc = this.getConf(['index', 'location']);
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- const dontRedispatch = this.getConf('dontRedispatch') || [
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- 'chromosome',
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- 'contig',
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- 'region',
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- ];
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+ const dontRedispatch = this.getConf('dontRedispatch');
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  const gff = new TabixIndexedFile({
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  filehandle: openLocation(gffGzLocation, this.pluginManager),
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  csiFilehandle: indexType === 'CSI' ? openLocation(loc, this.pluginManager) : undefined,
@@ -126,5 +122,4 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
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  fields,
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  };
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  }
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- freeResources() { }
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  }
package/esm/Gff3TabixAdapter/configSchema.js CHANGED
@@ -39,7 +39,7 @@ const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
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  },
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  index: {
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  location: {
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- uri: snap.uri,
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+ uri: `${snap.uri}.tbi`,
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  baseUri: snap.baseUri,
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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-gff3",
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- "version": "3.2.0",
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+ "version": "3.4.0",
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  "description": "JBrowse 2 gff3.",
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  "keywords": [
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  "jbrowse",
@@ -37,11 +37,11 @@
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  },
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  "dependencies": {
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  "@flatten-js/interval-tree": "^1.0.15",
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- "@gmod/bgzf-filehandle": "^2.0.1",
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- "@gmod/tabix": "^2.0.0",
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- "@jbrowse/core": "^3.2.0",
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- "@jbrowse/plugin-linear-genome-view": "^3.2.0",
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- "@mui/material": "^6.0.0",
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+ "@gmod/bgzf-filehandle": "^3.0.2",
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+ "@gmod/tabix": "^3.0.1",
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+ "@jbrowse/core": "^3.4.0",
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+ "@jbrowse/plugin-linear-genome-view": "^3.4.0",
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+ "@mui/material": "^7.0.0",
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  "gff-nostream": "^1.3.3",
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  "mobx": "^6.0.0",
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  "mobx-state-tree": "^5.0.0",
@@ -53,5 +53,5 @@
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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": "c750e3f56706a490c19ba75abd807fec5e38aebf"
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+ "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
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  }