@jbrowse/plugin-config 3.3.0 → 3.5.0

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Files changed (23) hide show
  1. package/dist/ConfigurationEditorWidget/components/useSlotEditorStyles.d.ts +2 -2
  2. package/dist/FromConfigAdapter/FromConfigAdapter.d.ts +0 -1
  3. package/dist/FromConfigAdapter/FromConfigAdapter.js +0 -1
  4. package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts +0 -1
  5. package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js +0 -1
  6. package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts +0 -1
  7. package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js +0 -1
  8. package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts +0 -1
  9. package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +14 -10
  10. package/dist/RefNameAliasAdapter/RefNameAliasAdapter.d.ts +0 -1
  11. package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js +6 -2
  12. package/esm/ConfigurationEditorWidget/components/useSlotEditorStyles.d.ts +2 -2
  13. package/esm/FromConfigAdapter/FromConfigAdapter.d.ts +0 -1
  14. package/esm/FromConfigAdapter/FromConfigAdapter.js +0 -1
  15. package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts +0 -1
  16. package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js +0 -1
  17. package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts +0 -1
  18. package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js +0 -1
  19. package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts +0 -1
  20. package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +14 -10
  21. package/esm/RefNameAliasAdapter/RefNameAliasAdapter.d.ts +0 -1
  22. package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js +6 -2
  23. package/package.json +3 -3
package/dist/ConfigurationEditorWidget/components/useSlotEditorStyles.d.ts CHANGED
@@ -4,6 +4,6 @@ export declare const useSlotEditorStyles: (params: void, muiStyleOverridesParams
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  } | undefined) => {
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  classes: Record<"paper" | "paperContent" | "slotModeSwitch", string>;
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  theme: import("@mui/material").Theme;
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- css: import("tss-react").Css;
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- cx: import("tss-react").Cx;
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+ css: import("tss-react/types").Css;
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+ cx: import("tss-react/types").Cx;
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  };
package/dist/FromConfigAdapter/FromConfigAdapter.d.ts CHANGED
@@ -14,5 +14,4 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
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  aliases: any;
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  }[]>;
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  getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
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- freeResources(): void;
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  }
package/dist/FromConfigAdapter/FromConfigAdapter.js CHANGED
@@ -52,6 +52,5 @@ class FromConfigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  observer.complete();
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  });
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  }
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- freeResources() { }
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  }
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  exports.default = FromConfigAdapter;
package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts CHANGED
@@ -11,5 +11,4 @@ export default class FromConfigRegionsAdapter extends BaseAdapter implements Reg
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  start: number;
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  end: number;
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  }[]>;
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- freeResources(): void;
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  }
package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js CHANGED
@@ -37,6 +37,5 @@ class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
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  regions.sort((a, b) => a.refName.localeCompare(b.refName));
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  return regions;
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  }
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- freeResources() { }
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  }
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  exports.default = FromConfigRegionsAdapter;
package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts CHANGED
@@ -9,5 +9,4 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
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  end: number;
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  refName: string;
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  }[]>;
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- freeResources(): void;
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  }
package/dist/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js CHANGED
@@ -52,6 +52,5 @@ class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
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  }
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  return regions;
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  }
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- freeResources() { }
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  }
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  exports.default = FromConfigSequenceAdapter;
package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts CHANGED
@@ -6,5 +6,4 @@ export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implemen
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  aliases: string[];
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  override: any;
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  }[]>;
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- freeResources(): Promise<void>;
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  }
package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -8,30 +8,34 @@ class NcbiSequenceReportAliasAdapter extends BaseAdapter_1.BaseAdapter {
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  if (loc.uri === '' || loc.uri === '/path/to/my/sequence_report.tsv') {
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  return [];
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  }
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- const override = this.getConf('useUcscNameOverride');
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+ const override = this.getConf('useNameOverride');
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  const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
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  const lines = results
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  .split(/\n|\r\n|\r/)
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  .filter(f => !!f.trim())
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  .map(row => row.split('\t'));
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  const r = lines[0] || [];
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- const idx0 = r.indexOf('GenBank seq accession');
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- const idx1 = r.indexOf('RefSeq seq accession');
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- const idx2 = r.indexOf('UCSC style name');
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- const idx3 = r.indexOf('Sequence name');
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- if (idx0 === -1 || idx1 === -1 || idx2 === -1) {
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+ const genBankIdx = r.indexOf('GenBank seq accession');
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+ const refSeqIdx = r.indexOf('RefSeq seq accession');
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+ const ucscIdx = r.indexOf('UCSC style name');
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+ const seqNameIdx = r.indexOf('Sequence name');
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+ if (genBankIdx === -1 || refSeqIdx === -1 || ucscIdx === -1) {
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  throw new Error('Header line must include "GenBank seq accession", "RefSeq seq accession", "UCSC style name", and "Sequence name"');
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  }
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  return lines
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  .slice(1)
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- .filter(cols => !!cols[idx2] || !!cols[idx3])
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+ .filter(cols => !!cols[ucscIdx] || !!cols[seqNameIdx])
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  .map(cols => ({
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- refName: (cols[idx2] || cols[idx3]),
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- aliases: [cols[idx0], cols[idx1], cols[idx2], cols[idx3]].filter((f) => !!f),
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+ refName: (cols[ucscIdx] || cols[seqNameIdx]),
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+ aliases: [
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+ cols[genBankIdx],
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+ cols[refSeqIdx],
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+ cols[ucscIdx],
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+ cols[seqNameIdx],
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+ ].filter((f) => !!f),
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  override,
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  }))
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  .filter(f => !!f.refName);
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  }
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- async freeResources() { }
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  }
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  exports.default = NcbiSequenceReportAliasAdapter;
package/dist/RefNameAliasAdapter/RefNameAliasAdapter.d.ts CHANGED
@@ -5,5 +5,4 @@ export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefN
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  refName: string;
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  aliases: string[];
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  }[]>;
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- freeResources(): Promise<void>;
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  }
package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js CHANGED
@@ -17,7 +17,12 @@ class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
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  .filter(f => !!f);
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  const header = lines.filter(f => f.startsWith('#'));
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  const headerCol = refColumnHeaderName && header.length
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- ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
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+ ? header
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+ .at(-1)
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+ .slice(1)
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+ .split('\t')
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+ .map(t => t.trim())
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+ .indexOf(refColumnHeaderName)
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  : refColumn;
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  return lines
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  .filter(f => !f.startsWith('#'))
@@ -30,6 +35,5 @@ class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
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  };
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  });
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  }
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- async freeResources() { }
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  }
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  exports.default = RefNameAliasAdapter;
package/esm/ConfigurationEditorWidget/components/useSlotEditorStyles.d.ts CHANGED
@@ -4,6 +4,6 @@ export declare const useSlotEditorStyles: (params: void, muiStyleOverridesParams
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  } | undefined) => {
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  classes: Record<"paper" | "paperContent" | "slotModeSwitch", string>;
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  theme: import("@mui/material").Theme;
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- css: import("tss-react").Css;
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- cx: import("tss-react").Cx;
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+ css: import("tss-react/types").Css;
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+ cx: import("tss-react/types").Cx;
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  };
package/esm/FromConfigAdapter/FromConfigAdapter.d.ts CHANGED
@@ -14,5 +14,4 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
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  aliases: any;
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  }[]>;
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  getFeatures(region: NoAssemblyRegion): import("rxjs").Observable<Feature>;
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- freeResources(): void;
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  }
package/esm/FromConfigAdapter/FromConfigAdapter.js CHANGED
@@ -46,5 +46,4 @@ export default class FromConfigAdapter extends BaseFeatureDataAdapter {
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  observer.complete();
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  });
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  }
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- freeResources() { }
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  }
package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.d.ts CHANGED
@@ -11,5 +11,4 @@ export default class FromConfigRegionsAdapter extends BaseAdapter implements Reg
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  start: number;
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  end: number;
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  }[]>;
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- freeResources(): void;
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  }
package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js CHANGED
@@ -35,5 +35,4 @@ export default class FromConfigRegionsAdapter extends BaseAdapter {
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  regions.sort((a, b) => a.refName.localeCompare(b.refName));
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  return regions;
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  }
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- freeResources() { }
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  }
package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.d.ts CHANGED
@@ -9,5 +9,4 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter impleme
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  end: number;
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  refName: string;
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  }[]>;
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- freeResources(): void;
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  }
package/esm/FromConfigSequenceAdapter/FromConfigSequenceAdapter.js CHANGED
@@ -47,5 +47,4 @@ export default class FromConfigSequenceAdapter extends FromConfigAdapter {
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  }
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  return regions;
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  }
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- freeResources() { }
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  }
package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.d.ts CHANGED
@@ -6,5 +6,4 @@ export default class NcbiSequenceReportAliasAdapter extends BaseAdapter implemen
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  aliases: string[];
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  override: any;
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  }[]>;
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- freeResources(): Promise<void>;
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  }
package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -6,29 +6,33 @@ export default class NcbiSequenceReportAliasAdapter extends BaseAdapter {
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  if (loc.uri === '' || loc.uri === '/path/to/my/sequence_report.tsv') {
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  return [];
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  }
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- const override = this.getConf('useUcscNameOverride');
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+ const override = this.getConf('useNameOverride');
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  const results = await openLocation(loc, this.pluginManager).readFile('utf8');
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  const lines = results
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  .split(/\n|\r\n|\r/)
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  .filter(f => !!f.trim())
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  .map(row => row.split('\t'));
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  const r = lines[0] || [];
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- const idx0 = r.indexOf('GenBank seq accession');
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- const idx1 = r.indexOf('RefSeq seq accession');
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- const idx2 = r.indexOf('UCSC style name');
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- const idx3 = r.indexOf('Sequence name');
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- if (idx0 === -1 || idx1 === -1 || idx2 === -1) {
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+ const genBankIdx = r.indexOf('GenBank seq accession');
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+ const refSeqIdx = r.indexOf('RefSeq seq accession');
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+ const ucscIdx = r.indexOf('UCSC style name');
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+ const seqNameIdx = r.indexOf('Sequence name');
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+ if (genBankIdx === -1 || refSeqIdx === -1 || ucscIdx === -1) {
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  throw new Error('Header line must include "GenBank seq accession", "RefSeq seq accession", "UCSC style name", and "Sequence name"');
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  }
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  return lines
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  .slice(1)
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- .filter(cols => !!cols[idx2] || !!cols[idx3])
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+ .filter(cols => !!cols[ucscIdx] || !!cols[seqNameIdx])
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  .map(cols => ({
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- refName: (cols[idx2] || cols[idx3]),
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- aliases: [cols[idx0], cols[idx1], cols[idx2], cols[idx3]].filter((f) => !!f),
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+ refName: (cols[ucscIdx] || cols[seqNameIdx]),
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+ aliases: [
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+ cols[genBankIdx],
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+ cols[refSeqIdx],
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+ cols[ucscIdx],
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+ cols[seqNameIdx],
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+ ].filter((f) => !!f),
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  override,
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  }))
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  .filter(f => !!f.refName);
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  }
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- async freeResources() { }
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  }
package/esm/RefNameAliasAdapter/RefNameAliasAdapter.d.ts CHANGED
@@ -5,5 +5,4 @@ export default class RefNameAliasAdapter extends BaseAdapter implements BaseRefN
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  refName: string;
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  aliases: string[];
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  }[]>;
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- freeResources(): Promise<void>;
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  }
package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js CHANGED
@@ -15,7 +15,12 @@ export default class RefNameAliasAdapter extends BaseAdapter {
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  .filter(f => !!f);
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  const header = lines.filter(f => f.startsWith('#'));
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  const headerCol = refColumnHeaderName && header.length
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- ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
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+ ? header
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+ .at(-1)
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+ .slice(1)
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+ .split('\t')
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+ .map(t => t.trim())
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+ .indexOf(refColumnHeaderName)
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  : refColumn;
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  return lines
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  .filter(f => !f.startsWith('#'))
@@ -28,5 +33,4 @@ export default class RefNameAliasAdapter extends BaseAdapter {
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  };
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  });
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  }
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- async freeResources() { }
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  }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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  "name": "@jbrowse/plugin-config",
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- "version": "3.3.0",
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+ "version": "3.5.0",
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  "description": "JBrowse 2 config utilities",
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  "keywords": [
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  "jbrowse",
@@ -36,7 +36,7 @@
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  "clean": "rimraf dist esm *.tsbuildinfo"
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  },
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  "dependencies": {
39
- "@jbrowse/core": "^3.3.0",
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+ "@jbrowse/core": "^3.5.0",
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  "@mui/icons-material": "^7.0.0",
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  "@mui/material": "^7.0.0",
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  "mobx": "^6.0.0",
@@ -56,5 +56,5 @@
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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": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
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+ "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
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  }