@jbrowse/plugin-config 3.4.0 → 3.5.0

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Files changed (3) hide show
  1. package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +14 -9
  2. package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js +14 -9
  3. package/package.json +3 -3
package/dist/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -8,26 +8,31 @@ 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);
package/esm/NcbiSequenceReportAliasAdapter/NcbiSequenceReportAliasAdapter.js CHANGED
@@ -6,26 +6,31 @@ 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);
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": "3.4.0",
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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": {
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- "@jbrowse/core": "^3.4.0",
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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": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
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+ "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
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  }