@jbrowse/plugin-config 3.0.3 → 3.0.5

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Files changed (7) hide show
  1. package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +15 -5
  2. package/dist/NcbiSequenceReportAliasAdapter/configSchema.d.ts +1 -1
  3. package/dist/NcbiSequenceReportAliasAdapter/configSchema.js +1 -1
  4. package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +15 -5
  5. package/esm/NcbiSequenceReportAliasAdapter/configSchema.d.ts +1 -1
  6. package/esm/NcbiSequenceReportAliasAdapter/configSchema.js +1 -1
  7. package/package.json +3 -3
package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -10,14 +10,24 @@ class NcbiSequenceReportAliasAdapter extends BaseAdapter_1.BaseAdapter {
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  }
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  const override = this.getConf('useUcscNameOverride');
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  const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
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- return results
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+ const lines = results
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  .split(/\n|\r\n|\r/)
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- .slice(1)
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  .filter(f => !!f.trim())
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- .map(row => row.split('\t'))
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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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+ 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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  .map(cols => ({
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- refName: cols[12],
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- aliases: [cols[9], cols[6]].filter((f) => !!f),
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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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  override,
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  }))
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  .filter(f => !!f.refName);
package/dist/NcbiSequenceReportAliasAdapter/configSchema.d.ts CHANGED
@@ -6,7 +6,7 @@ declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/
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  locationType: string;
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  };
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  };
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- useUcscNameOverride: {
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+ useNameOverride: {
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  type: string;
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  defaultValue: boolean;
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  description: string;
package/dist/NcbiSequenceReportAliasAdapter/configSchema.js CHANGED
@@ -10,7 +10,7 @@ const NcbiSequenceReportAliasAdapterConfigSchema = (0, configuration_1.Configura
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  locationType: 'UriLocation',
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  },
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  },
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- useUcscNameOverride: {
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+ useNameOverride: {
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  type: 'boolean',
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  defaultValue: true,
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  description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -8,14 +8,24 @@ export default class NcbiSequenceReportAliasAdapter extends BaseAdapter {
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  }
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  const override = this.getConf('useUcscNameOverride');
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  const results = await openLocation(loc, this.pluginManager).readFile('utf8');
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- return results
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+ const lines = results
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  .split(/\n|\r\n|\r/)
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- .slice(1)
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  .filter(f => !!f.trim())
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- .map(row => row.split('\t'))
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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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+ 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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  .map(cols => ({
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- refName: cols[12],
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- aliases: [cols[9], cols[6]].filter((f) => !!f),
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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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  override,
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  }))
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  .filter(f => !!f.refName);
package/esm/NcbiSequenceReportAliasAdapter/configSchema.d.ts CHANGED
@@ -6,7 +6,7 @@ declare const NcbiSequenceReportAliasAdapterConfigSchema: import("@jbrowse/core/
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  locationType: string;
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  };
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  };
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- useUcscNameOverride: {
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+ useNameOverride: {
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  type: string;
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  defaultValue: boolean;
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  description: string;
package/esm/NcbiSequenceReportAliasAdapter/configSchema.js CHANGED
@@ -8,7 +8,7 @@ const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequ
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  locationType: 'UriLocation',
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  },
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  },
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- useUcscNameOverride: {
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+ useNameOverride: {
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  type: 'boolean',
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  defaultValue: true,
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  description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-config",
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- "version": "3.0.3",
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+ "version": "3.0.5",
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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": {
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- "@jbrowse/core": "^3.0.3",
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+ "@jbrowse/core": "^3.0.5",
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  "@mui/icons-material": "^6.0.0",
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  "@mui/material": "^6.0.0",
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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": "f516540428282351d26e46743e69a724651bfb2c"
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+ "gitHead": "a03749efe19e51609922272b845a331897346789"
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  }