@jbrowse/plugin-trix 2.5.0 → 2.6.2

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Files changed (26) hide show
  1. package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js +1 -2
  2. package/dist/TrixTextSearchAdapter/configSchema.js +0 -1
  3. package/dist/TrixTextSearchAdapter/index.js +0 -1
  4. package/dist/index.js +0 -1
  5. package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js +1 -2
  6. package/esm/TrixTextSearchAdapter/configSchema.js +0 -1
  7. package/esm/TrixTextSearchAdapter/index.js +0 -1
  8. package/esm/index.js +0 -1
  9. package/package.json +3 -4
  10. package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map +0 -1
  11. package/dist/TrixTextSearchAdapter/configSchema.js.map +0 -1
  12. package/dist/TrixTextSearchAdapter/index.js.map +0 -1
  13. package/dist/index.js.map +0 -1
  14. package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map +0 -1
  15. package/esm/TrixTextSearchAdapter/configSchema.js.map +0 -1
  16. package/esm/TrixTextSearchAdapter/index.js.map +0 -1
  17. package/esm/index.js.map +0 -1
  18. package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts +0 -43
  19. package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.ts +0 -120
  20. package/src/TrixTextSearchAdapter/configSchema.ts +0 -61
  21. package/src/TrixTextSearchAdapter/index.ts +0 -2
  22. package/src/TrixTextSearchAdapter/test_data/volvox.ix +0 -194
  23. package/src/TrixTextSearchAdapter/test_data/volvox.ixx +0 -1
  24. package/src/TrixTextSearchAdapter/test_data/volvox2_meta.json +0 -1
  25. package/src/TrixTextSearchAdapter/test_data/volvox_meta.json +0 -163
  26. package/src/index.ts +0 -24
package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js CHANGED
@@ -51,7 +51,7 @@ class TrixTextSearchAdapter extends BaseAdapter_1.BaseAdapter {
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  // if multi-word search try to filter out relevant items
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  .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
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  .map(([term, data]) => {
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- const result = JSON.parse(data.replace(/\|/g, ','));
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+ const result = JSON.parse(data.replaceAll('|', ','));
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  const [loc, trackId, ...rest] = result.map(record => decodeURIComponentNoThrow(record));
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  const labelFieldIdx = rest.findIndex(elt => !!elt);
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  const contextIdx = rest
@@ -79,4 +79,3 @@ class TrixTextSearchAdapter extends BaseAdapter_1.BaseAdapter {
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  freeResources() { }
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  }
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  exports.default = TrixTextSearchAdapter;
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- //# sourceMappingURL=TrixTextSearchAdapter.js.map
package/dist/TrixTextSearchAdapter/configSchema.js CHANGED
@@ -54,4 +54,3 @@ const TrixTextSearchAdapter = (0, configuration_1.ConfigurationSchema)('TrixText
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  explicitIdentifier: 'textSearchAdapterId',
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  });
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  exports.default = TrixTextSearchAdapter;
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- //# sourceMappingURL=configSchema.js.map
package/dist/TrixTextSearchAdapter/index.js CHANGED
@@ -8,4 +8,3 @@ var TrixTextSearchAdapter_1 = require("./TrixTextSearchAdapter");
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  Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(TrixTextSearchAdapter_1).default; } });
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  var configSchema_1 = require("./configSchema");
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  Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
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- //# sourceMappingURL=index.js.map
package/dist/index.js CHANGED
@@ -22,4 +22,3 @@ class default_1 extends Plugin_1.default {
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  }
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  }
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  exports.default = default_1;
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- //# sourceMappingURL=index.js.map
package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js CHANGED
@@ -46,7 +46,7 @@ export default class TrixTextSearchAdapter extends BaseAdapter {
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  // if multi-word search try to filter out relevant items
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  .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
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  .map(([term, data]) => {
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- const result = JSON.parse(data.replace(/\|/g, ','));
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+ const result = JSON.parse(data.replaceAll('|', ','));
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  const [loc, trackId, ...rest] = result.map(record => decodeURIComponentNoThrow(record));
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  const labelFieldIdx = rest.findIndex(elt => !!elt);
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  const contextIdx = rest
@@ -73,4 +73,3 @@ export default class TrixTextSearchAdapter extends BaseAdapter {
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  }
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  freeResources() { }
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  }
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- //# sourceMappingURL=TrixTextSearchAdapter.js.map
package/esm/TrixTextSearchAdapter/configSchema.js CHANGED
@@ -52,4 +52,3 @@ const TrixTextSearchAdapter = ConfigurationSchema('TrixTextSearchAdapter', {
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  explicitIdentifier: 'textSearchAdapterId',
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  });
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  export default TrixTextSearchAdapter;
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- //# sourceMappingURL=configSchema.js.map
package/esm/TrixTextSearchAdapter/index.js CHANGED
@@ -1,3 +1,2 @@
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  export { default as AdapterClass } from './TrixTextSearchAdapter';
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  export { default as configSchema } from './configSchema';
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- //# sourceMappingURL=index.js.map
package/esm/index.js CHANGED
@@ -16,4 +16,3 @@ export default class extends Plugin {
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  }));
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  }
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  }
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- //# sourceMappingURL=index.js.map
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-trix",
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- "version": "2.5.0",
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+ "version": "2.6.2",
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  "description": "JBrowse 2 trix text search adapter",
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  "keywords": [
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  "jbrowse",
@@ -20,7 +20,6 @@
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  "main": "dist/index.js",
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  "files": [
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  "dist",
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- "src",
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  "esm"
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  ],
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  "scripts": {
@@ -33,7 +32,7 @@
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  "useSrc": "node ../../scripts/useSrc.js",
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  "prebuild": "npm run clean",
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  "build:esm": "tsc --build tsconfig.build.esm.json",
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- "build:es5": "tsc --build tsconfig.build.es5.json",
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+ "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
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  "clean": "rimraf dist esm *.tsbuildinfo"
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  },
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  "peerDependencies": {
@@ -53,5 +52,5 @@
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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": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
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+ "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
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  }
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package/esm/index.js.map DELETED
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package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.test.ts DELETED
@@ -1,43 +0,0 @@
1
- import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
2
- import Adapter from './TrixTextSearchAdapter'
3
- import path from 'path'
4
- import configSchema from './configSchema'
5
-
6
- test('adapter can fetch output files', async () => {
7
- const args = {
8
- type: 'TrixTextSearchAdapter',
9
- textSearchAdapterId: 'TrixTextSearchAdapterTest',
10
- ixFilePath: {
11
- localPath: path.resolve(__dirname, `test_data/volvox.ix`),
12
- locationType: 'LocalPathLocation',
13
- },
14
- ixxFilePath: {
15
- localPath: path.resolve(__dirname, `test_data/volvox.ixx`),
16
- locationType: 'LocalPathLocation',
17
- },
18
- metaFilePath: {
19
- localPath: path.resolve(__dirname, `test_data/volvox_meta.json`),
20
- locationType: 'LocalPathLocation',
21
- },
22
- }
23
- // create adapter
24
- const adapter = new Adapter(configSchema.create(args))
25
- // prefix search
26
- const results = await adapter.searchIndex({
27
- queryString: 'apple',
28
- })
29
- // check results are of type BaseResult for prefix search
30
- expect(results[0] instanceof BaseResult).toBeTruthy()
31
- expect(results[0].getLabel()).toEqual('Apple2')
32
- expect(results[1].getLabel()).toEqual('Apple3')
33
- // exact search
34
- const results2 = await adapter.searchIndex({
35
- queryString: 'apple3',
36
- })
37
- // check results are of type location for exact search
38
- expect(results2.length).toEqual(1)
39
- const test2 = results2[0]
40
- expect(test2 instanceof BaseResult).toBeTruthy()
41
- expect(test2.getLabel()).toEqual('Apple3')
42
- expect(test2.getLocation()).toEqual('ctgA:17400..23000')
43
- })
package/src/TrixTextSearchAdapter/TrixTextSearchAdapter.ts DELETED
@@ -1,120 +0,0 @@
1
- import Trix from '@gmod/trix'
2
- import {
3
- BaseTextSearchAdapter,
4
- BaseAdapter,
5
- BaseTextSearchArgs,
6
- } from '@jbrowse/core/data_adapters/BaseAdapter'
7
- import { openLocation } from '@jbrowse/core/util/io'
8
- import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
9
- import {
10
- AnyConfigurationModel,
11
- readConfObject,
12
- } from '@jbrowse/core/configuration'
13
- import PluginManager from '@jbrowse/core/PluginManager'
14
- import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
15
-
16
- function decodeURIComponentNoThrow(uri: string) {
17
- try {
18
- return decodeURIComponent(uri)
19
- } catch (e) {
20
- // avoid throwing exception on a failure to decode URI component
21
- return uri
22
- }
23
- }
24
-
25
- function shorten(str: string, term: string, w = 15) {
26
- const tidx = str.toLowerCase().indexOf(term)
27
-
28
- return str.length < 40
29
- ? str
30
- : (Math.max(0, tidx - w) > 0 ? '...' : '') +
31
- str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +
32
- (tidx + term.length < str.length ? '...' : '')
33
- }
34
-
35
- export default class TrixTextSearchAdapter
36
- extends BaseAdapter
37
- implements BaseTextSearchAdapter
38
- {
39
- indexingAttributes?: string[]
40
- trixJs: Trix
41
- tracksNames?: string[]
42
-
43
- constructor(
44
- config: AnyConfigurationModel,
45
- getSubAdapter?: getSubAdapterType,
46
- pluginManager?: PluginManager,
47
- ) {
48
- super(config, getSubAdapter, pluginManager)
49
- const ixFilePath = readConfObject(config, 'ixFilePath')
50
- const ixxFilePath = readConfObject(config, 'ixxFilePath')
51
-
52
- if (!ixFilePath) {
53
- throw new Error('must provide out.ix')
54
- }
55
- if (!ixxFilePath) {
56
- throw new Error('must provide out.ixx')
57
- }
58
- this.trixJs = new Trix(
59
- openLocation(ixxFilePath, pluginManager),
60
- openLocation(ixFilePath, pluginManager),
61
- 1500,
62
- )
63
- }
64
-
65
- /**
66
- * Returns list of results
67
- * @param args - search options/arguments include: search query
68
- * limit of results to return, searchType...prefix | full | exact", etc.
69
- */
70
- async searchIndex(args: BaseTextSearchArgs) {
71
- const query = args.queryString.toLowerCase()
72
- const strs = query.split(' ')
73
- const results = await this.trixJs.search(query)
74
- const formatted = results
75
- // if multi-word search try to filter out relevant items
76
- .filter(([, data]) =>
77
- strs.every(r =>
78
- decodeURIComponentNoThrow(data).toLowerCase().includes(r),
79
- ),
80
- )
81
- .map(([term, data]) => {
82
- const result = JSON.parse(data.replace(/\|/g, ',')) as string[]
83
- const [loc, trackId, ...rest] = result.map(record =>
84
- decodeURIComponentNoThrow(record),
85
- )
86
-
87
- const labelFieldIdx = rest.findIndex(elt => !!elt)
88
- const contextIdx = rest
89
- .map(elt => elt.toLowerCase())
90
- .findIndex(f => f.includes(term.toLowerCase()))
91
-
92
- const labelField = rest[labelFieldIdx]
93
- const contextField = rest[contextIdx]
94
- const context =
95
- contextIdx !== -1 ? shorten(contextField, term) : undefined
96
- const label = shorten(labelField, term)
97
-
98
- const displayString =
99
- !context || label.toLowerCase() === context.toLowerCase()
100
- ? label
101
- : `${label} (${context})`
102
-
103
- return new BaseResult({
104
- locString: loc,
105
- label: labelField,
106
- displayString,
107
- matchedObject: result.map(record => decodeURIComponent(record)),
108
- trackId,
109
- })
110
- })
111
-
112
- return args.searchType === 'exact'
113
- ? formatted.filter(
114
- r => r.getLabel().toLowerCase() === args.queryString.toLowerCase(),
115
- )
116
- : formatted
117
- }
118
-
119
- freeResources() {}
120
- }
package/src/TrixTextSearchAdapter/configSchema.ts DELETED
@@ -1,61 +0,0 @@
1
- import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
-
3
- /**
4
- * #config TrixTextSearchAdapter
5
- */
6
- function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
-
8
- const TrixTextSearchAdapter = ConfigurationSchema(
9
- 'TrixTextSearchAdapter',
10
- {
11
- /**
12
- * #slot
13
- */
14
- ixFilePath: {
15
- type: 'fileLocation',
16
- defaultValue: { uri: 'out.ix', locationType: 'UriLocation' },
17
- description: 'the location of the trix ix file',
18
- },
19
- /**
20
- * #slot
21
- */
22
- ixxFilePath: {
23
- type: 'fileLocation',
24
- defaultValue: { uri: 'out.ixx', locationType: 'UriLocation' },
25
- description: 'the location of the trix ixx file',
26
- },
27
- /**
28
- * #slot
29
- */
30
- metaFilePath: {
31
- type: 'fileLocation',
32
- defaultValue: { uri: 'meta.json', locationType: 'UriLocation' },
33
- description: 'the location of the metadata json file for the trix index',
34
- },
35
- /**
36
- * #slot
37
- */
38
- tracks: {
39
- type: 'stringArray',
40
- defaultValue: [],
41
- description: 'List of tracks covered by text search adapter',
42
- },
43
- /**
44
- * #slot
45
- */
46
- assemblyNames: {
47
- type: 'stringArray',
48
- defaultValue: [],
49
- description: 'List of assemblies covered by text search adapter',
50
- },
51
- },
52
- {
53
- explicitlyTyped: true,
54
- /**
55
- * #identifier
56
- */
57
- explicitIdentifier: 'textSearchAdapterId',
58
- },
59
- )
60
-
61
- export default TrixTextSearchAdapter
package/src/TrixTextSearchAdapter/index.ts DELETED
@@ -1,2 +0,0 @@
1
- export { default as AdapterClass } from './TrixTextSearchAdapter'
2
- export { default as configSchema } from './configSchema'
package/src/TrixTextSearchAdapter/test_data/volvox.ix DELETED
@@ -1,194 +0,0 @@
1
- 1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2
2
- 1000 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
3
- 2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
4
- 3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
5
- 7-transmembrane ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],2 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],3
6
- a ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
7
- agt221.3 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
8
- agt221.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt221.5"],1 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt221.5"],3 ["ctgA%3A7000..7300"|"gff3tabix_genes"|"agt221.5"],4
9
- agt767.3 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
10
- agt767.5 ["ctgA%3A1150..1500"|"gff3tabix_genes"|"agt767.5"],1 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],2 ["ctgA%3A5000..5500"|"gff3tabix_genes"|"agt767.5"],3 ["ctgA%3A7000..7200"|"gff3tabix_genes"|"agt767.5"],4
11
- agt830.3 ["ctgA%3A5410..5500"|"gff3tabix_genes"|"agt830.3"],1 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],2 ["ctgA%3A7000..7503"|"gff3tabix_genes"|"agt830.3"],3
12
- agt830.5 ["ctgA%3A1050..1500"|"gff3tabix_genes"|"agt830.5"],1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],2 ["ctgA%3A3000..3202"|"gff3tabix_genes"|"agt830.5"],3
13
- an ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
14
- and ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
15
- another ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
16
- appear ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
17
- apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
18
- apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
19
- at ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
20
- b101.2 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
21
- bac ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
22
- bnd_a ["A%3A2700..2701"|"volvox_sv_test_renamed"|"bnd_A"],1 ["ctgA%3A2700..2701"|"volvox_sv_test"|"bnd_A"],2
23
- bnd_b ["A%3A34200..34201"|"volvox_sv_test_renamed"|"bnd_B"],1 ["ctgA%3A34200..34201"|"volvox_sv_test"|"bnd_B"],2
24
- bnd_u ["A%3A23456..23457"|"volvox_sv_test_renamed"|"bnd_U"],1 ["ctgA%3A23456..23457"|"volvox_sv_test"|"bnd_U"],2
25
- bnd_v ["A%3A21682..21683"|"volvox_sv_test_renamed"|"bnd_V"],1 ["ctgA%3A21682..21683"|"volvox_sv_test"|"bnd_V"],2
26
- bnd_w ["A%3A21681..21682"|"volvox_sv_test_renamed"|"bnd_W"],1 ["ctgA%3A21681..21682"|"volvox_sv_test"|"bnd_W"],2
27
- bnd_x ["A%3A23457..23458"|"volvox_sv_test_renamed"|"bnd_X"],1 ["ctgA%3A23457..23458"|"volvox_sv_test"|"bnd_X"],2
28
- bnd_y ["B%3A1982..1983"|"volvox_sv_test_renamed"|"bnd_Y"],1 ["ctgB%3A1982..1983"|"volvox_sv_test"|"bnd_Y"],2
29
- bnd_z ["B%3A1983..1984"|"volvox_sv_test_renamed"|"bnd_Z"],1 ["ctgB%3A1983..1984"|"volvox_sv_test"|"bnd_Z"],2
30
- both ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
31
- box ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
32
- but ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
33
- cds-apple2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
34
- cdss ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
35
- ctga ["ctgA%3A1..50001"|"gff3tabix_genes"|"ctgA"],1
36
- ctgb ["ctgB%3A1..6079"|"gff3tabix_genes"|"ctgB"],1
37
- dead ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],2
38
- eden ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],4
39
- eden.1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1
40
- eden.2 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],1
41
- eden.3 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],1
42
- end ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
43
- example ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],3 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],4
44
- f01 ["ctgA%3A44705..47713"|"gff3tabix_genes"|"f01"],1
45
- f02 ["ctgA%3A24562..28338"|"gff3tabix_genes"|"f02"],1
46
- f03 ["ctgA%3A36649..40440"|"gff3tabix_genes"|"f03"],1
47
- f04 ["ctgA%3A37242..38653"|"gff3tabix_genes"|"f04"],1
48
- f05 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],2
49
- f06 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],1 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],2
50
- f07 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],1 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2
51
- f08 ["ctgA%3A13280..16394"|"gff3tabix_genes"|"f08"],1
52
- f09 ["ctgA%3A36034..38167"|"gff3tabix_genes"|"f09"],1
53
- f10 ["ctgA%3A15329..15533"|"gff3tabix_genes"|"f10"],1
54
- f11 ["ctgA%3A46990..48410"|"gff3tabix_genes"|"f11"],1
55
- f12 ["ctgA%3A49758..50000"|"gff3tabix_genes"|"f12"],1
56
- f13 ["ctgA%3A19157..22915"|"gff3tabix_genes"|"f13"],1
57
- f14 ["ctgA%3A23072..23185"|"gff3tabix_genes"|"f14"],1
58
- f15 ["ctgA%3A22132..24633"|"gff3tabix_genes"|"f15"],1
59
- fake ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
60
- fakesnp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
61
- fakesnp1 ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
62
- finger ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
63
- fingerprinted ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
64
- form ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
65
- gene1 ["ctgA%3A1201..1500"|"single_exon_gene"|"gene1"],1
66
- gene2 ["ctgA%3A1201..3902"|"single_exon_gene"|"gene2"],1
67
- gene:hga ["ctgA%3A1100..2000"|"gff3tabix_genes"|"Gene%3Ahga"],1
68
- gene:hgb ["ctgA%3A1600..3000"|"gff3tabix_genes"|"Gene%3Ahgb"],1
69
- get ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
70
- helix ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],2
71
- hox ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
72
- i ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
73
- ig-like ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
74
- inv134 ["ctgA%3A2700..10000"|"volvox.inv.vcf"|"inv134"],1
75
- inv135 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],1 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv135"],2
76
- inv9000 ["ctgA%3A6000..9000"|"volvox.inv.vcf"|"inv9000"],1
77
- is ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
78
- kinase ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],2 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],3 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],4 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],5
79
- length ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
80
- loop ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
81
- m01 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
82
- m02 ["ctgA%3A28332..30033"|"gff3tabix_genes"|"m02"|"HOX"],1
83
- m03 ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
84
- m04 ["ctgA%3A33325..35791"|"gff3tabix_genes"|"m04"|"Ig-like"],1
85
- m05 ["ctgA%3A13801..14007"|"gff3tabix_genes"|"m05"|"helix%20loop%20helix"],1
86
- m06 ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
87
- m07 ["ctgA%3A18048..18552"|"gff3tabix_genes"|"m07"|"7-transmembrane"],1
88
- m08 ["ctgA%3A17023..17675"|"gff3tabix_genes"|"m08"|"7-transmembrane"],1
89
- m09 ["ctgA%3A46012..48851"|"gff3tabix_genes"|"m09"|"kinase"],1
90
- m10 ["ctgA%3A28342..28447"|"gff3tabix_genes"|"m10"|"DEAD%20box"],1
91
- m11 ["ctgA%3A11911..15561"|"gff3tabix_genes"|"m11"|"kinase"],1
92
- m12 ["ctgA%3A21748..25612"|"gff3tabix_genes"|"m12"|"kinase"],1
93
- m13 ["ctgA%3A17667..17690"|"gff3tabix_genes"|"m13"|"DEAD%20box"],1
94
- m14 ["ctgA%3A14731..17239"|"gff3tabix_genes"|"m14"|"kinase"],1
95
- m15 ["ctgA%3A37497..40559"|"gff3tabix_genes"|"m15"|"7-transmembrane"],1
96
- match1 ["ctgA%3A1050..3202"|"gff3tabix_genes"|"agt830.5"|"Match1"],1
97
- match2 ["ctgA%3A5410..7503"|"gff3tabix_genes"|"agt830.3"|"Match2"],1
98
- match3 ["ctgA%3A1050..7300"|"gff3tabix_genes"|"agt221.5"|"Match3"],1
99
- match4 ["ctgA%3A7500..8000"|"gff3tabix_genes"|"agt221.3"|"Match4"],1
100
- match5 ["ctgA%3A1150..7200"|"gff3tabix_genes"|"agt767.5"|"Match5"],1
101
- match6 ["ctgA%3A8000..9000"|"gff3tabix_genes"|"agt767.3"|"Match6"],1
102
- message. ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
103
- mrna ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
104
- mrna1 ["ctgA%3A1201..1500"|"single_exon_gene"|"mRNA1"],1
105
- mrna2 ["ctgA%3A1201..3902"|"single_exon_gene"|"mRNA2"],1
106
- no ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1
107
- ok! ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1 ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],2
108
- protein ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN"|"EDEN"|"protein%20kinase"],1
109
- protein:hga ["ctgA%3A1200..1900"|"gff3tabix_genes"|"Protein%3AHGA"],1
110
- protein:hgb ["ctgA%3A1800..2900"|"gff3tabix_genes"|"Protein%3AHGB"],1
111
- reads ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],1
112
- remark:hga ["ctgA%3A1000..2000"|"gff3tabix_genes"|"Remark%3Ahga"],1
113
- repeat ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
114
- rna-apple3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],1
115
- rs1041740 ["contigA%3A11340..11341"|"volvox_test_vcf"|"rs1041740"],1
116
- rs10432782 ["contigA%3A7569..7570"|"volvox_test_vcf"|"rs10432782"],1
117
- rs112989936 ["contigA%3A10684..10685"|"volvox_test_vcf"|"rs112989936"],1
118
- rs114905802 ["contigA%3A4035..4036"|"volvox_test_vcf"|"rs114905802"],1
119
- rs11567845 ["contigA%3A8742..8743"|"volvox_test_vcf"|"rs11567845"],1
120
- rs116260263 ["contigA%3A6834..6835"|"volvox_test_vcf"|"rs116260263"],1
121
- rs117304270 ["contigA%3A11832..11833"|"volvox_test_vcf"|"rs117304270"],1
122
- rs117466144 ["contigA%3A11241..11242"|"volvox_test_vcf"|"rs117466144"],1
123
- rs118132937 ["contigA%3A9136..9137"|"volvox_test_vcf"|"rs118132937"],1
124
- rs16988404 ["contigA%3A7173..7174"|"volvox_test_vcf"|"rs16988404"],1
125
- rs17878802 ["contigA%3A5281..5282"|"volvox_test_vcf"|"rs17878802"],1
126
- rs17878855 ["contigA%3A3105..3106"|"volvox_test_vcf"|"rs17878855"],1
127
- rs17880044 ["contigA%3A11774..11775"|"volvox_test_vcf"|"rs17880044"],1
128
- rs17880487 ["contigA%3A12408..12409"|"volvox_test_vcf"|"rs17880487"],1
129
- rs17880490 ["contigA%3A8077..8078"|"volvox_test_vcf"|"rs17880490"],1
130
- rs17880795 ["contigA%3A4260..4261"|"volvox_test_vcf"|"rs17880795"],1
131
- rs17881180 ["contigA%3A3465..3466"|"volvox_test_vcf"|"rs17881180"],1
132
- rs17881581 ["contigA%3A3171..3172"|"volvox_test_vcf"|"rs17881581"],1
133
- rs17881732 ["contigA%3A11335..11336"|"volvox_test_vcf"|"rs17881732"],1
134
- rs17881807 ["contigA%3A5349..5350"|"volvox_test_vcf"|"rs17881807"],1
135
- rs17882967 ["contigA%3A5006..5007"|"volvox_test_vcf"|"rs17882967"],1
136
- rs17883234 ["contigA%3A11182..11183"|"volvox_test_vcf"|"rs17883234"],1
137
- rs17883270 ["contigA%3A5260..5261"|"volvox_test_vcf"|"rs17883270"],1
138
- rs17883296 ["contigA%3A3000..3001"|"volvox_test_vcf"|"rs17883296"],1
139
- rs17883461 ["contigA%3A8210..8211"|"volvox_test_vcf"|"rs17883461"],1
140
- rs17883998 ["contigA%3A9853..9854"|"volvox_test_vcf"|"rs17883998"],1
141
- rs17884040 ["contigA%3A4248..4249"|"volvox_test_vcf"|"rs17884040"],1
142
- rs17884233 ["contigA%3A7141..7142"|"volvox_test_vcf"|"rs17884233"],1
143
- rs17884260 ["contigA%3A4074..4075"|"volvox_test_vcf"|"rs17884260"],1
144
- rs17884462 ["contigA%3A11689..11690"|"volvox_test_vcf"|"rs17884462"],1
145
- rs17885219 ["contigA%3A4901..4902"|"volvox_test_vcf"|"rs17885219"],1
146
- rs17885303 ["contigA%3A9048..9049"|"volvox_test_vcf"|"rs17885303"],1
147
- rs17885634 ["contigA%3A10252..10253"|"volvox_test_vcf"|"rs17885634"],1
148
- rs17885833 ["contigA%3A9920..9921"|"volvox_test_vcf"|"rs17885833"],1
149
- rs17886025 ["contigA%3A8132..8133"|"volvox_test_vcf"|"rs17886025"],1
150
- rs17886606 ["contigA%3A8328..8329"|"volvox_test_vcf"|"rs17886606"],1
151
- rs17886692 ["contigA%3A10875..10876"|"volvox_test_vcf"|"rs17886692"],1
152
- rs2070424 ["contigA%3A10498..10499"|"volvox_test_vcf"|"rs2070424"],1
153
- rs2234694 ["contigA%3A10043..10044"|"volvox_test_vcf"|"rs2234694"],1
154
- rs4816405 ["contigA%3A4179..4180"|"volvox_test_vcf"|"rs4816405"],1
155
- rs4816407 ["contigA%3A11207..11208"|"volvox_test_vcf"|"rs4816407"],1
156
- rs4817420 ["contigA%3A11549..11550"|"volvox_test_vcf"|"rs4817420"],1
157
- rs4998557 ["contigA%3A6070..6071"|"volvox_test_vcf"|"rs4998557"],1
158
- rs6650814 ["contigA%3A4166..4167"|"volvox_test_vcf"|"rs6650814"],1
159
- rs7277748 ["contigA%3A3152..3153"|"volvox_test_vcf"|"rs7277748"],1
160
- rs76067554 ["contigA%3A8524..8525"|"volvox_test_vcf"|"rs76067554"],1
161
- rs76734991 ["contigA%3A11095..11096"|"volvox_test_vcf"|"rs76734991"],1
162
- rs77112488 ["contigA%3A9884..9885"|"volvox_test_vcf"|"rs77112488"],1
163
- rs77319474 ["contigA%3A10217..10218"|"volvox_test_vcf"|"rs77319474"],1
164
- rs78694163 ["contigA%3A8816..8817"|"volvox_test_vcf"|"rs78694163"],1
165
- rs80265967 ["contigA%3A10781..10782"|"volvox_test_vcf"|"rs80265967"],1
166
- rs8133032 ["contigA%3A9525..9526"|"volvox_test_vcf"|"rs8133032"],1
167
- rs9967983 ["contigA%3A8660..8661"|"volvox_test_vcf"|"rs9967983"],1
168
- seg01 ["ctgA%3A32329..32359"|"gff3tabix_genes"|"seg01"],1
169
- seg02 ["ctgA%3A26122..26126"|"gff3tabix_genes"|"seg02"],1 ["ctgA%3A26497..26869"|"gff3tabix_genes"|"seg02"],2 ["ctgA%3A27201..27325"|"gff3tabix_genes"|"seg02"],3 ["ctgA%3A27372..27433"|"gff3tabix_genes"|"seg02"],4 ["ctgA%3A27565..27565"|"gff3tabix_genes"|"seg02"],5 ["ctgA%3A27813..28091"|"gff3tabix_genes"|"seg02"],6 ["ctgA%3A28093..28201"|"gff3tabix_genes"|"seg02"],7 ["ctgA%3A28329..28377"|"gff3tabix_genes"|"seg02"],8 ["ctgA%3A28829..29194"|"gff3tabix_genes"|"seg02"],9 ["ctgA%3A29517..29702"|"gff3tabix_genes"|"seg02"],10 ["ctgA%3A29713..30061"|"gff3tabix_genes"|"seg02"],11 ["ctgA%3A30329..30774"|"gff3tabix_genes"|"seg02"],12 ["ctgA%3A30808..31306"|"gff3tabix_genes"|"seg02"],13 ["ctgA%3A31516..31729"|"gff3tabix_genes"|"seg02"],14 ["ctgA%3A31753..32154"|"gff3tabix_genes"|"seg02"],15 ["ctgA%3A32595..32696"|"gff3tabix_genes"|"seg02"],16 ["ctgA%3A32892..32901"|"gff3tabix_genes"|"seg02"],17 ["ctgA%3A33127..33388"|"gff3tabix_genes"|"seg02"],18 ["ctgA%3A33439..33443"|"gff3tabix_genes"|"seg02"],19 ["ctgA%3A33759..34209"|"gff3tabix_genes"|"seg02"],20 ["ctgA%3A34401..34466"|"gff3tabix_genes"|"seg02"],21
170
- seg03 ["ctgA%3A6885..7241"|"gff3tabix_genes"|"seg03"],1 ["ctgA%3A7410..7737"|"gff3tabix_genes"|"seg03"],2 ["ctgA%3A8055..8080"|"gff3tabix_genes"|"seg03"],3 ["ctgA%3A8306..8999"|"gff3tabix_genes"|"seg03"],4
171
- seg04 ["ctgA%3A5233..5302"|"gff3tabix_genes"|"seg04"],1 ["ctgA%3A5800..6101"|"gff3tabix_genes"|"seg04"],2 ["ctgA%3A6442..6854"|"gff3tabix_genes"|"seg04"],3 ["ctgA%3A7106..7211"|"gff3tabix_genes"|"seg04"],4 ["ctgA%3A7695..8177"|"gff3tabix_genes"|"seg04"],5 ["ctgA%3A8545..8783"|"gff3tabix_genes"|"seg04"],6 ["ctgA%3A8869..8935"|"gff3tabix_genes"|"seg04"],7 ["ctgA%3A9404..9825"|"gff3tabix_genes"|"seg04"],8
172
- seg05 ["ctgA%3A26503..26799"|"gff3tabix_genes"|"seg05"],1 ["ctgA%3A27172..27185"|"gff3tabix_genes"|"seg05"],2 ["ctgA%3A27448..27860"|"gff3tabix_genes"|"seg05"],3 ["ctgA%3A27887..28076"|"gff3tabix_genes"|"seg05"],4 ["ctgA%3A28225..28316"|"gff3tabix_genes"|"seg05"],5 ["ctgA%3A28777..29058"|"gff3tabix_genes"|"seg05"],6 ["ctgA%3A29513..29647"|"gff3tabix_genes"|"seg05"],7 ["ctgA%3A30108..30216"|"gff3tabix_genes"|"seg05"],8 ["ctgA%3A30465..30798"|"gff3tabix_genes"|"seg05"],9 ["ctgA%3A31232..31236"|"gff3tabix_genes"|"seg05"],10 ["ctgA%3A31421..31817"|"gff3tabix_genes"|"seg05"],11 ["ctgA%3A32010..32057"|"gff3tabix_genes"|"seg05"],12 ["ctgA%3A32208..32680"|"gff3tabix_genes"|"seg05"],13 ["ctgA%3A33053..33325"|"gff3tabix_genes"|"seg05"],14 ["ctgA%3A33438..33868"|"gff3tabix_genes"|"seg05"],15 ["ctgA%3A34244..34313"|"gff3tabix_genes"|"seg05"],16 ["ctgA%3A34605..34983"|"gff3tabix_genes"|"seg05"],17 ["ctgA%3A35333..35507"|"gff3tabix_genes"|"seg05"],18 ["ctgA%3A35642..35904"|"gff3tabix_genes"|"seg05"],19
173
- seg06 ["ctgA%3A19249..19559"|"gff3tabix_genes"|"seg06"],1 ["ctgA%3A19975..20260"|"gff3tabix_genes"|"seg06"],2 ["ctgA%3A20379..20491"|"gff3tabix_genes"|"seg06"],3 ["ctgA%3A20533..21005"|"gff3tabix_genes"|"seg06"],4 ["ctgA%3A21122..21331"|"gff3tabix_genes"|"seg06"],5 ["ctgA%3A21682..22176"|"gff3tabix_genes"|"seg06"],6 ["ctgA%3A22374..22570"|"gff3tabix_genes"|"seg06"],7 ["ctgA%3A23025..23427"|"gff3tabix_genes"|"seg06"],8
174
- seg07 ["ctgA%3A44191..44514"|"gff3tabix_genes"|"seg07"],1 ["ctgA%3A44552..45043"|"gff3tabix_genes"|"seg07"],2 ["ctgA%3A45373..45600"|"gff3tabix_genes"|"seg07"],3 ["ctgA%3A45897..46315"|"gff3tabix_genes"|"seg07"],4 ["ctgA%3A46491..46890"|"gff3tabix_genes"|"seg07"],5 ["ctgA%3A47126..47297"|"gff3tabix_genes"|"seg07"],6 ["ctgA%3A47735..47983"|"gff3tabix_genes"|"seg07"],7 ["ctgA%3A48447..48709"|"gff3tabix_genes"|"seg07"],8 ["ctgA%3A48931..49186"|"gff3tabix_genes"|"seg07"],9 ["ctgA%3A49472..49699"|"gff3tabix_genes"|"seg07"],10 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],11 ["ctgA%3A49957..50000"|"gff3tabix_genes"|"seg07"],12
175
- seg08 ["ctgA%3A18509..18985"|"gff3tabix_genes"|"seg08"],1 ["ctgA%3A18989..19388"|"gff3tabix_genes"|"seg08"],2 ["ctgA%3A19496..19962"|"gff3tabix_genes"|"seg08"],3 ["ctgA%3A20093..20580"|"gff3tabix_genes"|"seg08"],4 ["ctgA%3A20970..21052"|"gff3tabix_genes"|"seg08"],5 ["ctgA%3A21270..21277"|"gff3tabix_genes"|"seg08"],6 ["ctgA%3A21685..22168"|"gff3tabix_genes"|"seg08"],7 ["ctgA%3A22564..22869"|"gff3tabix_genes"|"seg08"],8 ["ctgA%3A22958..23298"|"gff3tabix_genes"|"seg08"],9 ["ctgA%3A23412..23469"|"gff3tabix_genes"|"seg08"],10 ["ctgA%3A23932..23932"|"gff3tabix_genes"|"seg08"],11 ["ctgA%3A24328..24787"|"gff3tabix_genes"|"seg08"],12 ["ctgA%3A25228..25367"|"gff3tabix_genes"|"seg08"],13
176
- seg09 ["ctgA%3A36616..37057"|"gff3tabix_genes"|"seg09"],1 ["ctgA%3A37208..37227"|"gff3tabix_genes"|"seg09"],2
177
- seg10 ["ctgA%3A29771..29942"|"gff3tabix_genes"|"seg10"],1 ["ctgA%3A30042..30340"|"gff3tabix_genes"|"seg10"],2 ["ctgA%3A30810..31307"|"gff3tabix_genes"|"seg10"],3 ["ctgA%3A31761..31984"|"gff3tabix_genes"|"seg10"],4 ["ctgA%3A32374..32937"|"gff3tabix_genes"|"seg10"],5
178
- seg11 ["ctgA%3A24228..24510"|"gff3tabix_genes"|"seg11"],1 ["ctgA%3A24868..25012"|"gff3tabix_genes"|"seg11"],2 ["ctgA%3A25212..25426"|"gff3tabix_genes"|"seg11"],3 ["ctgA%3A25794..25874"|"gff3tabix_genes"|"seg11"],4 ["ctgA%3A26075..26519"|"gff3tabix_genes"|"seg11"],5 ["ctgA%3A26930..26940"|"gff3tabix_genes"|"seg11"],6 ["ctgA%3A26975..27063"|"gff3tabix_genes"|"seg11"],7 ["ctgA%3A27415..27799"|"gff3tabix_genes"|"seg11"],8 ["ctgA%3A27880..27943"|"gff3tabix_genes"|"seg11"],9 ["ctgA%3A28225..28346"|"gff3tabix_genes"|"seg11"],10 ["ctgA%3A28375..28570"|"gff3tabix_genes"|"seg11"],11 ["ctgA%3A28758..29041"|"gff3tabix_genes"|"seg11"],12 ["ctgA%3A29101..29302"|"gff3tabix_genes"|"seg11"],13 ["ctgA%3A29604..29702"|"gff3tabix_genes"|"seg11"],14 ["ctgA%3A29867..29885"|"gff3tabix_genes"|"seg11"],15 ["ctgA%3A30241..30246"|"gff3tabix_genes"|"seg11"],16 ["ctgA%3A30575..30738"|"gff3tabix_genes"|"seg11"],17
179
- seg12 ["ctgA%3A12531..12895"|"gff3tabix_genes"|"seg12"],1 ["ctgA%3A13122..13449"|"gff3tabix_genes"|"seg12"],2 ["ctgA%3A13452..13745"|"gff3tabix_genes"|"seg12"],3 ["ctgA%3A13908..13965"|"gff3tabix_genes"|"seg12"],4 ["ctgA%3A13998..14488"|"gff3tabix_genes"|"seg12"],5 ["ctgA%3A14564..14899"|"gff3tabix_genes"|"seg12"],6 ["ctgA%3A15185..15276"|"gff3tabix_genes"|"seg12"],7 ["ctgA%3A15639..15736"|"gff3tabix_genes"|"seg12"],8 ["ctgA%3A15745..15870"|"gff3tabix_genes"|"seg12"],9
180
- seg13 ["ctgA%3A49406..49476"|"gff3tabix_genes"|"seg13"],1 ["ctgA%3A49762..50000"|"gff3tabix_genes"|"seg13"],2
181
- seg14 ["ctgA%3A41137..41318"|"gff3tabix_genes"|"seg14"],1 ["ctgA%3A41754..41948"|"gff3tabix_genes"|"seg14"],2 ["ctgA%3A42057..42474"|"gff3tabix_genes"|"seg14"],3 ["ctgA%3A42890..43270"|"gff3tabix_genes"|"seg14"],4 ["ctgA%3A43395..43811"|"gff3tabix_genes"|"seg14"],5 ["ctgA%3A44065..44556"|"gff3tabix_genes"|"seg14"],6 ["ctgA%3A44763..45030"|"gff3tabix_genes"|"seg14"],7 ["ctgA%3A45231..45488"|"gff3tabix_genes"|"seg14"],8 ["ctgA%3A45790..46022"|"gff3tabix_genes"|"seg14"],9 ["ctgA%3A46092..46318"|"gff3tabix_genes"|"seg14"],10 ["ctgA%3A46816..46992"|"gff3tabix_genes"|"seg14"],11 ["ctgA%3A47449..47829"|"gff3tabix_genes"|"seg14"],12
182
- seg15 ["ctgA%3A39265..39361"|"gff3tabix_genes"|"seg15"],1 ["ctgA%3A39753..40034"|"gff3tabix_genes"|"seg15"],2 ["ctgA%3A40515..40954"|"gff3tabix_genes"|"seg15"],3 ["ctgA%3A41252..41365"|"gff3tabix_genes"|"seg15"],4 ["ctgA%3A41492..41504"|"gff3tabix_genes"|"seg15"],5 ["ctgA%3A41941..42377"|"gff3tabix_genes"|"seg15"],6 ["ctgA%3A42748..42954"|"gff3tabix_genes"|"seg15"],7 ["ctgA%3A43401..43897"|"gff3tabix_genes"|"seg15"],8 ["ctgA%3A44043..44113"|"gff3tabix_genes"|"seg15"],9 ["ctgA%3A44399..44888"|"gff3tabix_genes"|"seg15"],10 ["ctgA%3A45281..45375"|"gff3tabix_genes"|"seg15"],11 ["ctgA%3A45711..46041"|"gff3tabix_genes"|"seg15"],12 ["ctgA%3A46425..46564"|"gff3tabix_genes"|"seg15"],13 ["ctgA%3A46738..47087"|"gff3tabix_genes"|"seg15"],14 ["ctgA%3A47329..47595"|"gff3tabix_genes"|"seg15"],15 ["ctgA%3A47858..47979"|"gff3tabix_genes"|"seg15"],16 ["ctgA%3A48169..48453"|"gff3tabix_genes"|"seg15"],17
183
- should ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
184
- snp ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
185
- splice ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.1"|"EDEN.1"|"Eden%20splice%20form%201"],1 ["ctgA%3A1050..9000"|"gff3tabix_genes"|"EDEN.2"|"EDEN.2"|"Eden%20splice%20form%202"],2 ["ctgA%3A1300..9000"|"gff3tabix_genes"|"EDEN.3"|"EDEN.3"|"Eden%20splice%20form%203"],3
186
- sushi ["ctgA%3A30578..31748"|"gff3tabix_genes"|"m06"|"SUSHI%20repeat"],1
187
- that ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1
188
- the ["ctgA%3A4715..5968"|"gff3tabix_genes"|"f05"|"Ok!%20Ok!%20I%20get%20the%20message."],1
189
- this ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],2 ["ctgA%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],3 ["ctgB%3A1659..1984"|"gff3tabix_genes"|"f07"|"This%20is%20an%20example"],4 ["ctgB%3A3014..6130"|"gff3tabix_genes"|"f06"|"This%20is%20another%20example"],5
190
- utrs ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],1 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],2
191
- wd40 ["ctgA%3A48253..48366"|"gff3tabix_genes"|"m01"|"WD40"],1
192
- with ["ctgA%3A1000..1000"|"gff3tabix_genes"|"FakeSNP"|"FakeSNP1"|"This%20is%20a%20fake%20SNP%20that%20should%20appear%20at%201000%20with%20length%201"],1 ["ctgA%3A1000..20000"|"gff3tabix_genes"|"b101.2"|"b101.2"|"Fingerprinted%20BAC%20with%20end%20reads"],2 ["ctgA%3A13000..17200"|"gff3tabix_genes"|"Apple2"|"cds-Apple2"|"mRNA%20with%20CDSs%20but%20no%20UTRs"],3 ["ctgA%3A17400..23000"|"gff3tabix_genes"|"Apple3"|"rna-Apple3"|"mRNA%20with%20both%20CDSs%20and%20UTRs"],4
193
- zinc ["ctgA%3A15396..16159"|"gff3tabix_genes"|"m03"|"zinc%20finger"],1
194
- ああ、この機能は、世界中を旅しています！ ["ctgB%3A4715..5968"|"gff3tabix_genes"|"f05"|"%E3%81%82%E3%81%82%E3%80%81%E3%81%93%E3%81%AE%E6%A9%9F%E8%83%BD%E3%81%AF%E3%80%81%E4%B8%96%E7%95%8C%E4%B8%AD%E3%82%92%E6%97%85%E3%81%97%E3%81%A6%E3%81%84%E3%81%BE%E3%81%99%EF%BC%81"],1
package/src/TrixTextSearchAdapter/test_data/volvox.ixx DELETED
@@ -1 +0,0 @@
1
- 1 0000000000
package/src/TrixTextSearchAdapter/test_data/volvox_meta.json DELETED
@@ -1,163 +0,0 @@
1
- {
2
- "dateCreated": "2022-06-17T10:57:18.370Z",
3
- "tracks": [
4
- {
5
- "trackId": "volvox_sv_test",
6
- "attributesIndexed": ["Name", "ID", "Note"],
7
- "excludedTypes": ["CDS", "exon"],
8
- "adapterConf": {
9
- "type": "VcfTabixAdapter",
10
- "vcfGzLocation": {
11
- "uri": "volvox.dup.vcf.gz",
12
- "locationType": "UriLocation"
13
- },
14
- "index": {
15
- "location": {
16
- "uri": "volvox.dup.vcf.gz.tbi",
17
- "locationType": "UriLocation"
18
- }
19
- }
20
- }
21
- },
22
- {
23
- "trackId": "volvox_sv_test_renamed",
24
- "attributesIndexed": ["Name", "ID", "Note"],
25
- "excludedTypes": ["CDS", "exon"],
26
- "adapterConf": {
27
- "type": "VcfTabixAdapter",
28
- "vcfGzLocation": {
29
- "uri": "volvox.dup.renamed.vcf.gz",
30
- "locationType": "UriLocation"
31
- },
32
- "index": {
33
- "location": {
34
- "uri": "volvox.dup.renamed.vcf.gz.tbi",
35
- "locationType": "UriLocation"
36
- }
37
- }
38
- }
39
- },
40
- {
41
- "trackId": "volvox_test_vcf",
42
- "attributesIndexed": ["Name", "ID", "Note"],
43
- "excludedTypes": ["CDS", "exon"],
44
- "adapterConf": {
45
- "type": "VcfTabixAdapter",
46
- "vcfGzLocation": {
47
- "uri": "volvox.test.vcf.gz",
48
- "locationType": "UriLocation"
49
- },
50
- "index": {
51
- "location": {
52
- "uri": "volvox.test.vcf.gz.tbi",
53
- "locationType": "UriLocation"
54
- }
55
- }
56
- }
57
- },
58
- {
59
- "trackId": "gff3tabix_genes",
60
- "attributesIndexed": ["Name", "ID", "Note"],
61
- "excludedTypes": ["CDS", "exon"],
62
- "adapterConf": {
63
- "type": "Gff3TabixAdapter",
64
- "gffGzLocation": {
65
- "uri": "volvox.sort.gff3.gz",
66
- "locationType": "UriLocation"
67
- },
68
- "index": {
69
- "location": {
70
- "uri": "volvox.sort.gff3.gz.tbi",
71
- "locationType": "UriLocation"
72
- }
73
- }
74
- }
75
- },
76
- {
77
- "trackId": "volvox_filtered_vcf",
78
- "attributesIndexed": ["Name", "ID", "Note"],
79
- "excludedTypes": ["CDS", "exon"],
80
- "adapterConf": {
81
- "type": "VcfTabixAdapter",
82
- "vcfGzLocation": {
83
- "uri": "volvox.filtered.vcf.gz",
84
- "locationType": "UriLocation"
85
- },
86
- "index": {
87
- "location": {
88
- "uri": "volvox.filtered.vcf.gz.tbi",
89
- "locationType": "UriLocation"
90
- }
91
- }
92
- }
93
- },
94
- {
95
- "trackId": "variant_colors",
96
- "attributesIndexed": ["Name", "ID", "Note"],
97
- "excludedTypes": ["CDS", "exon"],
98
- "adapterConf": {
99
- "type": "VcfTabixAdapter",
100
- "vcfGzLocation": {
101
- "uri": "volvox.filtered.vcf.gz",
102
- "locationType": "UriLocation"
103
- },
104
- "index": {
105
- "location": {
106
- "uri": "volvox.filtered.vcf.gz.tbi",
107
- "locationType": "UriLocation"
108
- }
109
- }
110
- }
111
- },
112
- {
113
- "trackId": "single_exon_gene",
114
- "attributesIndexed": ["Name", "ID", "Note"],
115
- "excludedTypes": ["CDS", "exon"],
116
- "adapterConf": {
117
- "type": "Gff3TabixAdapter",
118
- "gffGzLocation": {
119
- "uri": "single_exon_gene.sorted.gff.gz",
120
- "locationType": "UriLocation"
121
- },
122
- "index": {
123
- "location": {
124
- "uri": "single_exon_gene.sorted.gff.gz.tbi",
125
- "locationType": "UriLocation"
126
- }
127
- }
128
- }
129
- },
130
- {
131
- "trackId": "volvox.inv.vcf",
132
- "attributesIndexed": ["Name", "ID", "Note"],
133
- "excludedTypes": ["CDS", "exon"],
134
- "adapterConf": {
135
- "type": "VcfTabixAdapter",
136
- "vcfGzLocation": {
137
- "uri": "volvox.inv.vcf.gz",
138
- "locationType": "UriLocation"
139
- },
140
- "index": {
141
- "location": {
142
- "uri": "volvox.inv.vcf.gz.tbi",
143
- "locationType": "UriLocation"
144
- },
145
- "indexType": "TBI"
146
- }
147
- }
148
- },
149
- {
150
- "trackId": "volvox.filtered.lowercase",
151
- "attributesIndexed": ["Name", "ID", "Note"],
152
- "excludedTypes": ["CDS", "exon"],
153
- "adapterConf": {
154
- "type": "VcfAdapter",
155
- "vcfLocation": {
156
- "uri": "volvox.filtered.lowercase.vcf",
157
- "locationType": "UriLocation"
158
- }
159
- }
160
- }
161
- ],
162
- "assemblyNames": ["volvox"]
163
- }
package/src/index.ts DELETED
@@ -1,24 +0,0 @@
1
- import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType'
2
- import Plugin from '@jbrowse/core/Plugin'
3
- import PluginManager from '@jbrowse/core/PluginManager'
4
- import {
5
- AdapterClass as TrixTextSearchAdapterClass,
6
- configSchema as trixAdapterConfigSchema,
7
- } from './TrixTextSearchAdapter'
8
-
9
- export default class extends Plugin {
10
- name = 'TrixPlugin'
11
-
12
- install(pluginManager: PluginManager) {
13
- pluginManager.addTextSearchAdapterType(
14
- () =>
15
- new TextSearchAdapterType({
16
- name: 'TrixTextSearchAdapter',
17
- displayName: 'Trix text search adapter',
18
- configSchema: trixAdapterConfigSchema,
19
- AdapterClass: TrixTextSearchAdapterClass,
20
- description: 'Trix adapter',
21
- }),
22
- )
23
- }
24
- }