@jbrowse/plugin-bed 2.5.0 → 2.6.2

package/src/BedTabixAdapter/__snapshots__/BedTabixAdapter.test.ts.snap

@@ -1,437 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch bed with header 1`] = `
-[
-  {
-    "end": 3009,
-    "refName": "contigA",
-    "start": 3000,
-    "strand": 0,
-    "uniqueId": "test-163099",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-163117",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-163135",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-163153",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-163171",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-163189",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-163207",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-163225",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-163243",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-163261",
-  },
-]
-`;
-
-exports[`adapter can fetch features bed with autosql 1`] = `
-[
-  {
-    "Entrez_Gene_Id": "2782",
-    "Hugo_Symbol": "GNB1",
-    "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10",
-    "Reference_Allele": "T",
-    "Tumor_Sample_Barcode": "TCGA-OR-A5KB-01A-11D-A30A-10",
-    "Tumor_Seq_Allele1": "T",
-    "Tumor_Seq_Allele2": "G",
-    "Variant_Classification": "Splice_Region",
-    "Variant_Type": "SNP",
-    "alcohol_history": "--",
-    "alcohol_intensity": "--",
-    "bmi": "--",
-    "case_id": "09454ed6-64bc-4a35-af44-7c4344623d45",
-    "cigarettes_per_day": "--",
-    "days_to_death": "--",
-    "dbSNP_RS": "novel",
-    "dbSNP_Val_Status": "",
-    "end": 10,
-    "ethnicity": "not hispanic or latino",
-    "freq": "0.0108695652174",
-    "gender": "female",
-    "height": "--",
-    "name": "T>G",
-    "project_id": "TCGA-ACC",
-    "refName": "ctgA",
-    "reserved": "0,0,0",
-    "sampleCount": "1",
-    "score": 1,
-    "start": 1,
-    "strand": 0,
-    "subfeatures": [
-      {
-        "end": 2,
-        "parentId": "test-52986",
-        "start": 1,
-        "strand": 0,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-52986-0",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-52986",
-    "weight": "--",
-    "years_smoked": "--",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox.sort.bed.gz simple bed3 1`] = `
-[
-  {
-    "end": 3009,
-    "refName": "contigA",
-    "start": 3000,
-    "strand": 0,
-    "uniqueId": "test-155163",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-155181",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-155199",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-155217",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-155235",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-155253",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-155271",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-155289",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-155307",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-155325",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
-[
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.1",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-45690",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-45690-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-45690",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45690-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-45690",
-        "start": 2999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45690-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-45690",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45690-3",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-45690",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45690-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-45690",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-45690-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-45690",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.2",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-45787",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-45787-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-45787",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45787-1",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-45787",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45787-2",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-45787",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45787-3",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-45787",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-45787-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-45787",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1299,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1500,
-        "parentId": "test-45875",
-        "start": 1299,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-45875-0",
-      },
-      {
-        "end": 3300,
-        "parentId": "test-45875",
-        "start": 2999,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-45875-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-45875",
-        "start": 3300,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45875-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-45875",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45875-3",
-      },
-      {
-        "end": 7600,
-        "parentId": "test-45875",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45875-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-45875",
-        "start": 7600,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-45875-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-45875",
-  },
-  {
-    "end": 23000,
-    "itemRgb": "0,0,0",
-    "name": "rna-Apple3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 17399,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 17999,
-        "parentId": "test-45972",
-        "start": 17399,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-45972-0",
-      },
-      {
-        "end": 18800,
-        "parentId": "test-45972",
-        "start": 17999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45972-1",
-      },
-      {
-        "end": 19500,
-        "parentId": "test-45972",
-        "start": 18999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45972-2",
-      },
-      {
-        "end": 21200,
-        "parentId": "test-45972",
-        "start": 20999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-45972-3",
-      },
-      {
-        "end": 23000,
-        "parentId": "test-45972",
-        "start": 21200,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-45972-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-45972",
-  },
-]
-`;
-
-exports[`adapter can use gwas header 1`] = `[]`;

package/src/BedTabixAdapter/configSchema.ts

@@ -1,71 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config BedTabixAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const BedTabixAdapter = ConfigurationSchema(
-  'BedTabixAdapter',
-  {
-    /**
-     * #slot
-     */
-    bedGzLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
-    },
-
-    index: ConfigurationSchema('TabixIndex', {
-      /**
-       * #slot index.indexType
-       */
-      indexType: {
-        model: types.enumeration('IndexType', ['TBI', 'CSI']),
-        type: 'stringEnum',
-        defaultValue: 'TBI',
-      },
-      /**
-       * #slot index.location
-       */
-      location: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.bed.gz.tbi',
-          locationType: 'UriLocation',
-        },
-      },
-    }),
-
-    /**
-     * #slot
-     */
-    columnNames: {
-      type: 'stringArray',
-      description: 'List of column names',
-      defaultValue: [],
-    },
-
-    /**
-     * #slot
-     */
-    scoreColumn: {
-      type: 'string',
-      description: 'The column to use as a "score" attribute',
-      defaultValue: '',
-    },
-
-    /**
-     * #slot
-     */
-    autoSql: {
-      type: 'string',
-      description: 'The autoSql definition for the data fields in the file',
-      defaultValue: '',
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default BedTabixAdapter

package/src/BedTabixAdapter/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'BedTabixAdapter',
-        displayName: 'BED tabix adapter',
-        configSchema,
-        getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default),
-      }),
-  )
-}