@jbrowse/plugin-bed 2.1.7 → 2.2.1

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

@@ -1,71 +1,71 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
 exports[`adapter can fetch bed with header 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 3009,
     "refName": "contigA",
     "start": 3000,
     "strand": 0,
     "uniqueId": "test-163098",
   },
-  Object {
+  {
     "end": 3114,
     "refName": "contigA",
     "start": 3105,
     "strand": 0,
     "uniqueId": "test-163116",
   },
-  Object {
+  {
     "end": 3161,
     "refName": "contigA",
     "start": 3152,
     "strand": 0,
     "uniqueId": "test-163134",
   },
-  Object {
+  {
     "end": 3180,
     "refName": "contigA",
     "start": 3171,
     "strand": 0,
     "uniqueId": "test-163152",
   },
-  Object {
+  {
     "end": 3183,
     "refName": "contigA",
     "start": 3174,
     "strand": 0,
     "uniqueId": "test-163170",
   },
-  Object {
+  {
     "end": 3222,
     "refName": "contigA",
     "start": 3213,
     "strand": 0,
     "uniqueId": "test-163188",
   },
-  Object {
+  {
     "end": 3474,
     "refName": "contigA",
     "start": 3465,
     "strand": 0,
     "uniqueId": "test-163206",
   },
-  Object {
+  {
     "end": 3804,
     "refName": "contigA",
     "start": 3795,
     "strand": 0,
     "uniqueId": "test-163224",
   },
-  Object {
+  {
     "end": 4044,
     "refName": "contigA",
     "start": 4035,
     "strand": 0,
     "uniqueId": "test-163242",
   },
-  Object {
+  {
     "end": 4082,
     "refName": "contigA",
     "start": 4073,
@@ -76,8 +76,8 @@ Array [
 `;
 
 exports[`adapter can fetch features bed with autosql 1`] = `
-Array [
-  Object {
+[
+  {
     "Entrez_Gene_Id": "2782",
     "Hugo_Symbol": "GNB1",
     "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10",
@@ -108,8 +108,8 @@ Array [
     "score": 1,
     "start": 1,
     "strand": 0,
-    "subfeatures": Array [
-      Object {
+    "subfeatures": [
+      {
         "end": 2,
         "parentId": "test-52985",
         "start": 1,
@@ -127,71 +127,71 @@ Array [
 `;
 
 exports[`adapter can fetch features from volvox.sort.bed.gz simple bed3 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 3009,
     "refName": "contigA",
     "start": 3000,
     "strand": 0,
     "uniqueId": "test-155162",
   },
-  Object {
+  {
     "end": 3114,
     "refName": "contigA",
     "start": 3105,
     "strand": 0,
     "uniqueId": "test-155180",
   },
-  Object {
+  {
     "end": 3161,
     "refName": "contigA",
     "start": 3152,
     "strand": 0,
     "uniqueId": "test-155198",
   },
-  Object {
+  {
     "end": 3180,
     "refName": "contigA",
     "start": 3171,
     "strand": 0,
     "uniqueId": "test-155216",
   },
-  Object {
+  {
     "end": 3183,
     "refName": "contigA",
     "start": 3174,
     "strand": 0,
     "uniqueId": "test-155234",
   },
-  Object {
+  {
     "end": 3222,
     "refName": "contigA",
     "start": 3213,
     "strand": 0,
     "uniqueId": "test-155252",
   },
-  Object {
+  {
     "end": 3474,
     "refName": "contigA",
     "start": 3465,
     "strand": 0,
     "uniqueId": "test-155270",
   },
-  Object {
+  {
     "end": 3804,
     "refName": "contigA",
     "start": 3795,
     "strand": 0,
     "uniqueId": "test-155288",
   },
-  Object {
+  {
     "end": 4044,
     "refName": "contigA",
     "start": 4035,
     "strand": 0,
     "uniqueId": "test-155306",
   },
-  Object {
+  {
     "end": 4082,
     "refName": "contigA",
     "start": 4073,
@@ -202,8 +202,8 @@ Array [
 `;
 
 exports[`adapter can fetch features from volvox-bed12.bed.gz 1`] = `
-Array [
-  Object {
+[
+  {
     "end": 9000,
     "itemRgb": "0,0,0",
     "name": "EDEN.1",
@@ -211,8 +211,8 @@ Array [
     "score": 1000,
     "start": 1049,
     "strand": 1,
-    "subfeatures": Array [
-      Object {
+    "subfeatures": [
+      {
         "end": 1200,
         "parentId": "test-45689",
         "start": 1049,
@@ -220,7 +220,7 @@ Array [
         "type": "five_prime_UTR",
         "uniqueId": "test-45689-0",
       },
-      Object {
+      {
         "end": 1500,
         "parentId": "test-45689",
         "start": 1200,
@@ -228,7 +228,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45689-1",
       },
-      Object {
+      {
         "end": 3902,
         "parentId": "test-45689",
         "start": 2999,
@@ -236,7 +236,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45689-2",
       },
-      Object {
+      {
         "end": 5500,
         "parentId": "test-45689",
         "start": 4999,
@@ -244,7 +244,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45689-3",
       },
-      Object {
+      {
         "end": 7608,
         "parentId": "test-45689",
         "start": 6999,
@@ -252,7 +252,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45689-4",
       },
-      Object {
+      {
         "end": 9000,
         "parentId": "test-45689",
         "start": 7608,
@@ -264,7 +264,7 @@ Array [
     "type": "mRNA",
     "uniqueId": "test-45689",
   },
-  Object {
+  {
     "end": 9000,
     "itemRgb": "0,0,0",
     "name": "EDEN.2",
@@ -272,8 +272,8 @@ Array [
     "score": 1000,
     "start": 1049,
     "strand": 1,
-    "subfeatures": Array [
-      Object {
+    "subfeatures": [
+      {
         "end": 1200,
         "parentId": "test-45786",
         "start": 1049,
@@ -281,7 +281,7 @@ Array [
         "type": "five_prime_UTR",
         "uniqueId": "test-45786-0",
       },
-      Object {
+      {
         "end": 1500,
         "parentId": "test-45786",
         "start": 1200,
@@ -289,7 +289,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45786-1",
       },
-      Object {
+      {
         "end": 5500,
         "parentId": "test-45786",
         "start": 4999,
@@ -297,7 +297,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45786-2",
       },
-      Object {
+      {
         "end": 7608,
         "parentId": "test-45786",
         "start": 6999,
@@ -305,7 +305,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45786-3",
       },
-      Object {
+      {
         "end": 9000,
         "parentId": "test-45786",
         "start": 7608,
@@ -317,7 +317,7 @@ Array [
     "type": "mRNA",
     "uniqueId": "test-45786",
   },
-  Object {
+  {
     "end": 9000,
     "itemRgb": "0,0,0",
     "name": "EDEN.3",
@@ -325,8 +325,8 @@ Array [
     "score": 1000,
     "start": 1299,
     "strand": 1,
-    "subfeatures": Array [
-      Object {
+    "subfeatures": [
+      {
         "end": 1500,
         "parentId": "test-45874",
         "start": 1299,
@@ -334,7 +334,7 @@ Array [
         "type": "five_prime_UTR",
         "uniqueId": "test-45874-0",
       },
-      Object {
+      {
         "end": 3300,
         "parentId": "test-45874",
         "start": 2999,
@@ -342,7 +342,7 @@ Array [
         "type": "five_prime_UTR",
         "uniqueId": "test-45874-1",
       },
-      Object {
+      {
         "end": 3902,
         "parentId": "test-45874",
         "start": 3300,
@@ -350,7 +350,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45874-2",
       },
-      Object {
+      {
         "end": 5500,
         "parentId": "test-45874",
         "start": 4999,
@@ -358,7 +358,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45874-3",
       },
-      Object {
+      {
         "end": 7600,
         "parentId": "test-45874",
         "start": 6999,
@@ -366,7 +366,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45874-4",
       },
-      Object {
+      {
         "end": 9000,
         "parentId": "test-45874",
         "start": 7600,
@@ -378,7 +378,7 @@ Array [
     "type": "mRNA",
     "uniqueId": "test-45874",
   },
-  Object {
+  {
     "end": 23000,
     "itemRgb": "0,0,0",
     "name": "rna-Apple3",
@@ -386,8 +386,8 @@ Array [
     "score": 1000,
     "start": 17399,
     "strand": 1,
-    "subfeatures": Array [
-      Object {
+    "subfeatures": [
+      {
         "end": 17999,
         "parentId": "test-45971",
         "start": 17399,
@@ -395,7 +395,7 @@ Array [
         "type": "five_prime_UTR",
         "uniqueId": "test-45971-0",
       },
-      Object {
+      {
         "end": 18800,
         "parentId": "test-45971",
         "start": 17999,
@@ -403,7 +403,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45971-1",
       },
-      Object {
+      {
         "end": 19500,
         "parentId": "test-45971",
         "start": 18999,
@@ -411,7 +411,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45971-2",
       },
-      Object {
+      {
         "end": 21200,
         "parentId": "test-45971",
         "start": 20999,
@@ -419,7 +419,7 @@ Array [
         "type": "CDS",
         "uniqueId": "test-45971-3",
       },
-      Object {
+      {
         "end": 23000,
         "parentId": "test-45971",
         "start": 21200,
@@ -434,4 +434,4 @@ Array [
 ]
 `;
 
-exports[`adapter can use gwas header 1`] = `Array []`;
+exports[`adapter can use gwas header 1`] = `[]`;

package/src/BedTabixAdapter/configSchema.ts

@@ -1,20 +1,34 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 
-export default ConfigurationSchema(
+/**
+ * #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: {
@@ -24,18 +38,27 @@ export default ConfigurationSchema(
       },
     }),
 
+    /**
+     * #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',
@@ -44,3 +67,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default BedTabixAdapter