@jbrowse/plugin-bed 2.6.1 → 2.6.3

package/dist/BedAdapter/BedAdapter.js

@@ -132,4 +132,3 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedAdapter;
-//# sourceMappingURL=BedAdapter.js.map

package/dist/BedAdapter/configSchema.js

@@ -63,4 +63,3 @@ const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = BedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -71,4 +71,3 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedTabixAdapter;
-//# sourceMappingURL=BedTabixAdapter.js.map

package/dist/BedTabixAdapter/configSchema.js

@@ -60,4 +60,3 @@ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapte
     },
 }, { explicitlyTyped: true });
 exports.default = BedTabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedTabixAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedTabixAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -182,4 +182,3 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = BedpeAdapter;
-//# sourceMappingURL=BedpeAdapter.js.map

package/dist/BedpeAdapter/configSchema.js

@@ -28,4 +28,3 @@ const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
     },
 }, { explicitlyTyped: true });
 exports.default = BedpeAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BedpeAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedpeAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -107,4 +107,3 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     freeResources() { }
 }
 exports.default = BigBedAdapter;
-//# sourceMappingURL=BigBedAdapter.js.map

package/dist/BigBedAdapter/configSchema.js

@@ -15,4 +15,3 @@ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter',
     },
 }, { explicitlyTyped: true });
 exports.default = BigBedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/dist/BigBedAdapter/index.js

@@ -36,4 +36,3 @@ exports.default = (pluginManager) => {
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BigBedAdapter'))).then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -95,4 +95,3 @@ class BedPlugin extends Plugin_1.default {
     }
 }
 exports.default = BedPlugin;
-//# sourceMappingURL=index.js.map

package/dist/util.js

@@ -155,4 +155,3 @@ function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, unique
     return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
 }
 exports.featureData = featureData;
-//# sourceMappingURL=util.js.map

package/esm/BedAdapter/BedAdapter.js

@@ -127,4 +127,3 @@ class BedAdapter extends BaseFeatureDataAdapter {
 }
 BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedAdapter;
-//# sourceMappingURL=BedAdapter.js.map

package/esm/BedAdapter/configSchema.js

@@ -61,4 +61,3 @@ const BedAdapter = ConfigurationSchema('BedAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -66,4 +66,3 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
 }
 BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedTabixAdapter;
-//# sourceMappingURL=BedTabixAdapter.js.map

package/esm/BedTabixAdapter/configSchema.js

@@ -58,4 +58,3 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedTabixAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedTabixAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -175,4 +175,3 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
 }
 BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default BedpeAdapter;
-//# sourceMappingURL=BedpeAdapter.js.map

package/esm/BedpeAdapter/configSchema.js

@@ -26,4 +26,3 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BedpeAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BedpeAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BedpeAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -101,4 +101,3 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     }
     freeResources() { }
 }
-//# sourceMappingURL=BigBedAdapter.js.map

package/esm/BigBedAdapter/configSchema.js

@@ -13,4 +13,3 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
     },
 }, { explicitlyTyped: true });
 export default BigBedAdapter;
-//# sourceMappingURL=configSchema.js.map

package/esm/BigBedAdapter/index.js

@@ -8,4 +8,3 @@ export default (pluginManager) => {
         getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -89,4 +89,3 @@ export default class BedPlugin extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/esm/util.js

@@ -150,4 +150,3 @@ export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser,
     });
     return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
 }
-//# sourceMappingURL=util.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -56,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/BedAdapter/BedAdapter.js.map

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package/dist/BedAdapter/index.js.map

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package/dist/BedpeAdapter/configSchema.js.map

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package/dist/BigBedAdapter/configSchema.js.map

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package/dist/BigBedAdapter/index.js.map

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package/dist/util.js.map

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package/esm/BedAdapter/BedAdapter.js.map

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package/esm/BedAdapter/configSchema.js.map

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package/esm/BedAdapter/index.js.map

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package/esm/BedpeAdapter/configSchema.js.map

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package/esm/BedpeAdapter/index.js.map

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package/esm/BigBedAdapter/BigBedAdapter.js.map

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package/esm/BigBedAdapter/configSchema.js.map

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package/esm/BigBedAdapter/index.js.map

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package/esm/index.js.map

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package/esm/util.js.map

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package/src/BedAdapter/BedAdapter.test.ts

@@ -1,166 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import BedAdapter from './BedAdapter'
-import MyConfigSchema from './configSchema'
-
-test('adapter can fetch features from volvox-bed12.bed', async () => {
-  const adapter = new BedAdapter(
-    MyConfigSchema.create({
-      bedLocation: {
-        localPath: require.resolve('./test_data/volvox-bed12.bed'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch features from volvox.sort.bed simple bed3', async () => {
-  const adapter = new BedAdapter(
-    MyConfigSchema.create({
-      bedLocation: {
-        localPath: require.resolve('./test_data/volvox.sort.bed'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'contigA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('contigA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch features bed with autosql', async () => {
-  const adapter = new BedAdapter(
-    MyConfigSchema.create({
-      bedLocation: {
-        localPath: require.resolve('./test_data/volvox-autosql.bed'),
-        locationType: 'LocalPathLocation',
-      },
-
-      autoSql: `table gdcCancer
-"somatic variants converted from MAF files obtained through the NCI GDC"
-    (
-    string chrom;      "Chromosome (or contig, scaffold, etc.)"
-    uint   chromStart; "Start position in chromosome"
-    uint   chromEnd;   "End position in chromosome"
-    string name;       "Name of item"
-    uint   score;      "Score from 0-1000"
-    char[1] strand;    "+ or -"
-    uint thickStart;   "Start of where display should be thick (start codon)"
-    uint thickEnd;     "End of where display should be thick (stop codon)"
-    uint reserved;     "Used as itemRgb as of 2004-11-22"
-    int blockCount;    "Number of blocks"
-    int[blockCount] blockSizes; "Comma separated list of block sizes"
-    int[blockCount] chromStarts; "Start positions relative to chromStart"
-    string sampleCount;    "Number of samples with this variant"
-    string freq;                    "Variant frequency"
-    lstring Hugo_Symbol;            "Hugo symbol"
-    lstring Entrez_Gene_Id;         "Entrez Gene Id"
-    lstring Variant_Classification; "Class of variant"
-    lstring Variant_Type;           "Type of variant"
-    lstring Reference_Allele;       "Reference allele"
-    lstring Tumor_Seq_Allele1;      "Tumor allele 1"
-    lstring Tumor_Seq_Allele2;      "Tumor allele 2"
-    lstring dbSNP_RS;               "dbSNP RS number"
-    lstring dbSNP_Val_Status;       "dbSNP validation status"
-    lstring days_to_death;          "Number of days till death"
-    lstring cigarettes_per_day;     "Number of cigarettes per day"
-    lstring weight;                 "Weight"
-    lstring alcohol_history;        "Any alcohol consumption?"
-    lstring alcohol_intensity;      "Frequency of alcohol consumption"
-    lstring bmi;                    "Body mass index"
-    lstring years_smoked;           "Number of years smoked"
-    lstring height;                 "Height"
-    lstring gender;                 "Gender"
-    lstring project_id;             "TCGA Project id"
-    lstring ethnicity;              "Ethnicity"
-    lstring Tumor_Sample_Barcode;   "Tumor sample barcode"
-    lstring Matched_Norm_Sample_Barcode;  "Matcheds normal sample barcode"
-    lstring case_id;                "Case ID number"
-)`,
-    }),
-  )
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch bed with header', async () => {
-  const adapter = new BedAdapter(
-    MyConfigSchema.create({
-      bedLocation: {
-        localPath: require.resolve('./test_data/volvox.sort.with.header.bed'),
-        locationType: 'LocalPathLocation',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'contigA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('contigA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can use gwas header', async () => {
-  const adapter = new BedAdapter(
-    MyConfigSchema.create({
-      bedLocation: {
-        localPath: require.resolve('./test_data/gwas.bed'),
-        locationType: 'LocalPathLocation',
-      },
-      colRef: 0,
-      colStart: 1,
-      colEnd: 1,
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: '1',
-    start: 0,
-    end: 100_000,
-    assemblyName: 'hg19',
-  })
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})