@jbrowse/plugin-bed 2.5.0 → 2.6.2

package/src/BedAdapter/__snapshots__/BedAdapter.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-contigA-0",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-contigA-1",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-contigA-2",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-contigA-3",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-contigA-4",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-contigA-5",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-contigA-6",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-contigA-7",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-contigA-8",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-contigA-9",
-  },
-]
-`;
-
-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-ctgA-0",
-        "start": 1,
-        "strand": 0,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-0-0",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-0",
-    "weight": "--",
-    "years_smoked": "--",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox.sort.bed simple bed3 1`] = `
-[
-  {
-    "end": 3009,
-    "refName": "contigA",
-    "start": 3000,
-    "strand": 0,
-    "uniqueId": "test-contigA-0",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-contigA-1",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-contigA-2",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-contigA-3",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-contigA-4",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-contigA-5",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-contigA-6",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-contigA-7",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-contigA-8",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-contigA-9",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
-[
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.1",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-ctgA-0",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-0-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-0",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-ctgA-0",
-        "start": 2999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-0",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-3",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-ctgA-0",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-0",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-0-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-0",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.2",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-ctgA-1",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-1-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-1",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-1",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-1",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-2",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-ctgA-1",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-3",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-1",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-1-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-1",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1299,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-2",
-        "start": 1299,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-2-0",
-      },
-      {
-        "end": 3300,
-        "parentId": "test-ctgA-2",
-        "start": 2999,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-2-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-ctgA-2",
-        "start": 3300,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-2",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-3",
-      },
-      {
-        "end": 7600,
-        "parentId": "test-ctgA-2",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-2",
-        "start": 7600,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-2-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-2",
-  },
-  {
-    "end": 23000,
-    "itemRgb": "0,0,0",
-    "name": "rna-Apple3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 17399,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 17999,
-        "parentId": "test-ctgA-3",
-        "start": 17399,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-3-0",
-      },
-      {
-        "end": 18800,
-        "parentId": "test-ctgA-3",
-        "start": 17999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-1",
-      },
-      {
-        "end": 19500,
-        "parentId": "test-ctgA-3",
-        "start": 18999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-2",
-      },
-      {
-        "end": 21200,
-        "parentId": "test-ctgA-3",
-        "start": 20999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-3",
-      },
-      {
-        "end": 23000,
-        "parentId": "test-ctgA-3",
-        "start": 21200,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-3-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-3",
-  },
-]
-`;
-
-exports[`adapter can use gwas header 1`] = `[]`;

package/src/BedAdapter/configSchema.ts

@@ -1,69 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config BedAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const BedAdapter = ConfigurationSchema(
-  'BedAdapter',
-  {
-    /**
-     * #slot
-     */
-    bedLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bed.gz', 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: '',
-    },
-    /**
-     * #slot
-     */
-    colRef: {
-      type: 'number',
-      description: 'The column to use as a "refName" attribute',
-      defaultValue: 0,
-    },
-    /**
-     * #slot
-     */
-    colStart: {
-      type: 'number',
-      description: 'The column to use as a "start" attribute',
-      defaultValue: 1,
-    },
-    /**
-     * #slot
-     */
-    colEnd: {
-      type: 'number',
-      description: 'The column to use as a "end" attribute',
-      defaultValue: 2,
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default BedAdapter

package/src/BedAdapter/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: 'BedAdapter',
-        displayName: 'BED adapter',
-        configSchema,
-        getAdapterClass: () => import('./BedAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/BedAdapter/test_data/gwas.bed

@@ -1,20 +0,0 @@
-#chrom	pos	rsid	ref	alt	neg_log_pvalue	beta	stderr_beta	alt_allele_freq
-1	721290	rs12565286	G	C	0.275233	.	.	.
-1	752566	rs3094315	G	A	0.0315638	.	.	.
-1	775659	rs2905035	A	G	0.183626	.	.	.
-1	777122	rs2980319	A	T	0.207258	.	.	.
-1	779322	rs4040617	A	G	0.0326393	.	.	.
-1	780785	rs2977612	T	A	0.0225965	.	.	.
-1	785050	rs2905062	G	A	0.0346572	.	.	.
-1	785989	rs2980300	T	C	0.00638744	.	.	.
-1	798959	rs11240777	G	A	0.49853	.	.	.
-1	990380	.	C	A,G,T	0.136915	.	.	.
-1	998501	rs3813193	G	C	0.450384	.	.	.
-1	1003629	rs4075116	C	T	0.881074	.	.	.
-1	1005806	rs3934834	C	T	0.756218	.	.	.
-1	1017170	rs3766193	C	G	0.336111	.	.	.
-1	1017197	rs3766192	C	T	0.381743	.	.	.
-1	1017587	rs3766191	C	T	0.775467	.	.	.
-1	1018562	rs9442371	C	T	0.233364	.	.	.
-1	1018704	rs9442372	A	G	0.248721	.	.	.
-1	1021346	rs10907177	A	G	0.842846	.	.	.

package/src/BedAdapter/test_data/volvox-autosql.bed

@@ -1 +0,0 @@
-ctgA	1	10	T>G	1	.	1815756	1815757	0,0,0	1	1	0	1	0.0108695652174	GNB1	2782	Splice_Region	SNP	T	T	G	novel		--	--	--	--	--	--	--	--	female	TCGA-ACC	not hispanic or latino	TCGA-OR-A5KB-01A-11D-A30A-10	TCGA-OR-A5KB-11A-11D-A30A-10	09454ed6-64bc-4a35-af44-7c4344623d45

package/src/BedAdapter/test_data/volvox-bed12.bed

@@ -1,4 +0,0 @@
-ctgA	1049	9000	EDEN.1	1000	+	1200	7608	0,0,0	4	451,903,501,2001	0,1950,3950,5950	EDEN	EDEN	-	-	-
-ctgA	1049	9000	EDEN.2	1000	+	1200	7608	0,0,0	3	451,501,2001	0,3950,5950	EDEN	EDEN	-	-	-
-ctgA	1299	9000	EDEN.3	1000	+	3300	7600	0,0,0	4	201,903,501,2001	0,1700,3700,5700	EDEN	EDEN	-	-	-
-ctgA	17399	23000	rna-Apple3	1000	+	17999	21200	0,0,0	3	1401,501,2001	0,1600,3600	rna-Apple3	rna-Apple3	-	-	-

package/src/BedAdapter/test_data/volvox.sort.bed

@@ -1,109 +0,0 @@
-contigA	3000	3009
-contigA	3105	3114
-contigA	3152	3161
-contigA	3171	3180
-contigA	3174	3183
-contigA	3213	3222
-contigA	3465	3474
-contigA	3795	3804
-contigA	4035	4044
-contigA	4073	4082
-contigA	4074	4083
-contigA	4166	4175
-contigA	4179	4188
-contigA	4204	4213
-contigA	4248	4257
-contigA	4260	4269
-contigA	4577	4586
-contigA	4828	4837
-contigA	4901	4910
-contigA	5006	5015
-contigA	5051	5060
-contigA	5201	5210
-contigA	5260	5269
-contigA	5281	5290
-contigA	5349	5358
-contigA	5353	5362
-contigA	5423	5432
-contigA	5457	5466
-contigA	5548	5557
-contigA	5626	5635
-contigA	5835	5844
-contigA	5909	5918
-contigA	5927	5936
-contigA	5969	5978
-contigA	6070	6079
-contigA	6185	6194
-contigA	6285	6294
-contigA	6363	6372
-contigA	6559	6568
-contigA	6834	6843
-contigA	6908	6917
-contigA	6918	6927
-contigA	7141	7150
-contigA	7173	7182
-contigA	7569	7578
-contigA	7619	7628
-contigA	7654	7663
-contigA	7671	7680
-contigA	7707	7716
-contigA	7739	7748
-contigA	8077	8086
-contigA	8128	8137
-contigA	8132	8141
-contigA	8210	8219
-contigA	8267	8276
-contigA	8328	8337
-contigA	8524	8533
-contigA	8659	8668
-contigA	8660	8669
-contigA	8742	8751
-contigA	8811	8820
-contigA	8816	8825
-contigA	8964	8973
-contigA	9048	9057
-contigA	9054	9063
-contigA	9136	9145
-contigA	9243	9252
-contigA	9320	9329
-contigA	9366	9375
-contigA	9525	9534
-contigA	9580	9589
-contigA	9610	9619
-contigA	9744	9753
-contigA	9753	9762
-contigA	9759	9768
-contigA	9807	9816
-contigA	9853	9862
-contigA	9884	9893
-contigA	9920	9929
-contigA	10043	10052
-contigA	10216	10225
-contigA	10217	10226
-contigA	10252	10261
-contigA	10384	10393
-contigA	10498	10507
-contigA	10585	10594
-contigA	10684	10693
-contigA	10781	10790
-contigA	10875	10884
-contigA	11004	11013
-contigA	11095	11104
-contigA	11182	11191
-contigA	11207	11216
-contigA	11241	11250
-contigA	11335	11344
-contigA	11340	11349
-contigA	11535	11544
-contigA	11543	11552
-contigA	11549	11558
-contigA	11653	11662
-contigA	11675	11684
-contigA	11689	11698
-contigA	11774	11783
-contigA	11832	11841
-contigA	12386	12395
-contigA	12408	12417
-contigA	12441	12450
-contigA	12530	12539
-contigA	12738	12747