@jbrowse/plugin-gff3 2.1.7 → 2.2.0

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Files changed (15) hide show
  1. package/dist/Gff3Adapter/configSchema.d.ts +2 -2
  2. package/dist/Gff3Adapter/configSchema.js +9 -1
  3. package/dist/Gff3Adapter/configSchema.js.map +1 -1
  4. package/dist/Gff3TabixAdapter/configSchema.d.ts +2 -2
  5. package/dist/Gff3TabixAdapter/configSchema.js +22 -1
  6. package/dist/Gff3TabixAdapter/configSchema.js.map +1 -1
  7. package/esm/Gff3Adapter/configSchema.d.ts +2 -2
  8. package/esm/Gff3Adapter/configSchema.js +9 -1
  9. package/esm/Gff3Adapter/configSchema.js.map +1 -1
  10. package/esm/Gff3TabixAdapter/configSchema.d.ts +2 -2
  11. package/esm/Gff3TabixAdapter/configSchema.js +22 -1
  12. package/esm/Gff3TabixAdapter/configSchema.js.map +1 -1
  13. package/package.json +2 -2
  14. package/src/Gff3Adapter/configSchema.ts +11 -1
  15. package/src/Gff3TabixAdapter/configSchema.ts +25 -1
package/dist/Gff3Adapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const Gff3Adapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default Gff3Adapter;
package/dist/Gff3Adapter/configSchema.js CHANGED
@@ -1,10 +1,18 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  const configuration_1 = require("@jbrowse/core/configuration");
4
- exports.default = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
4
+ /**
5
+ * #config Gff3Adapter
6
+ */
7
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
+ const Gff3Adapter = (0, configuration_1.ConfigurationSchema)('Gff3Adapter', {
9
+ /**
10
+ * #slot
11
+ */
5
12
  gffLocation: {
6
13
  type: 'fileLocation',
7
14
  defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
8
15
  },
9
16
  }, { explicitlyTyped: true });
17
+ exports.default = Gff3Adapter;
10
18
  //# sourceMappingURL=configSchema.js.map
package/dist/Gff3Adapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,aAAa,EACb;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,WAAW,GAAG,IAAA,mCAAmB,EACrC,aAAa,EACb;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,WAAW,CAAA"}
package/dist/Gff3TabixAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default Gff3TabixAdapter;
package/dist/Gff3TabixAdapter/configSchema.js CHANGED
@@ -2,17 +2,30 @@
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  const mobx_state_tree_1 = require("mobx-state-tree");
4
4
  const configuration_1 = require("@jbrowse/core/configuration");
5
- exports.default = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
5
+ /**
6
+ * #config Gff3TabixAdapter
7
+ */
8
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
9
+ const Gff3TabixAdapter = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
10
+ /**
11
+ * #slot
12
+ */
6
13
  gffGzLocation: {
7
14
  type: 'fileLocation',
8
15
  defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
9
16
  },
10
17
  index: (0, configuration_1.ConfigurationSchema)('Gff3TabixIndex', {
18
+ /**
19
+ * #slot index.indexType
20
+ */
11
21
  indexType: {
12
22
  model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
13
23
  type: 'stringEnum',
14
24
  defaultValue: 'TBI',
15
25
  },
26
+ /**
27
+ * #slot index.indexType
28
+ */
16
29
  location: {
17
30
  type: 'fileLocation',
18
31
  defaultValue: {
@@ -21,9 +34,17 @@ exports.default = (0, configuration_1.ConfigurationSchema)('Gff3TabixAdapter', {
21
34
  },
22
35
  },
23
36
  }),
37
+ /**
38
+ * #slot
39
+ * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
40
+ * features it finds inside that region extend outside the region we requested.
41
+ * you can disable this for certain feature types to avoid fetching e.g. the
42
+ * entire chromosome
43
+ */
24
44
  dontRedispatch: {
25
45
  type: 'stringArray',
26
46
  defaultValue: ['chromosome', 'region'],
27
47
  },
28
48
  }, { explicitlyTyped: true });
49
+ exports.default = Gff3TabixAdapter;
29
50
  //# sourceMappingURL=configSchema.js.map
package/dist/Gff3TabixAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,kBAAkB,EAClB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,IAAA,mCAAmB,EAAC,gBAAgB,EAAE;QAC3C,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF,cAAc,EAAE;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,CAAC,YAAY,EAAE,QAAQ,CAAC;KACvC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,gBAAgB,GAAG,IAAA,mCAAmB,EAC1C,kBAAkB,EAClB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,KAAK,EAAE,IAAA,mCAAmB,EAAC,gBAAgB,EAAE;QAC3C;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;;;;;OAMG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,CAAC,YAAY,EAAE,QAAQ,CAAC;KACvC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,gBAAgB,CAAA"}
package/esm/Gff3Adapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const Gff3Adapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default Gff3Adapter;
package/esm/Gff3Adapter/configSchema.js CHANGED
@@ -1,8 +1,16 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- export default ConfigurationSchema('Gff3Adapter', {
2
+ /**
3
+ * #config Gff3Adapter
4
+ */
5
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
+ const Gff3Adapter = ConfigurationSchema('Gff3Adapter', {
7
+ /**
8
+ * #slot
9
+ */
3
10
  gffLocation: {
4
11
  type: 'fileLocation',
5
12
  defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
6
13
  },
7
14
  }, { explicitlyTyped: true });
15
+ export default Gff3Adapter;
8
16
  //# sourceMappingURL=configSchema.js.map
package/esm/Gff3Adapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,aAAa,EACb;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3Adapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,WAAW,GAAG,mBAAmB,CACrC,aAAa,EACb;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,WAAW,CAAA"}
package/esm/Gff3TabixAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const Gff3TabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default Gff3TabixAdapter;
package/esm/Gff3TabixAdapter/configSchema.js CHANGED
@@ -1,16 +1,29 @@
1
1
  import { types } from 'mobx-state-tree';
2
2
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
3
- export default ConfigurationSchema('Gff3TabixAdapter', {
3
+ /**
4
+ * #config Gff3TabixAdapter
5
+ */
6
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
7
+ const Gff3TabixAdapter = ConfigurationSchema('Gff3TabixAdapter', {
8
+ /**
9
+ * #slot
10
+ */
4
11
  gffGzLocation: {
5
12
  type: 'fileLocation',
6
13
  defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
7
14
  },
8
15
  index: ConfigurationSchema('Gff3TabixIndex', {
16
+ /**
17
+ * #slot index.indexType
18
+ */
9
19
  indexType: {
10
20
  model: types.enumeration('IndexType', ['TBI', 'CSI']),
11
21
  type: 'stringEnum',
12
22
  defaultValue: 'TBI',
13
23
  },
24
+ /**
25
+ * #slot index.indexType
26
+ */
14
27
  location: {
15
28
  type: 'fileLocation',
16
29
  defaultValue: {
@@ -19,9 +32,17 @@ export default ConfigurationSchema('Gff3TabixAdapter', {
19
32
  },
20
33
  },
21
34
  }),
35
+ /**
36
+ * #slot
37
+ * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
38
+ * features it finds inside that region extend outside the region we requested.
39
+ * you can disable this for certain feature types to avoid fetching e.g. the
40
+ * entire chromosome
41
+ */
22
42
  dontRedispatch: {
23
43
  type: 'stringArray',
24
44
  defaultValue: ['chromosome', 'region'],
25
45
  },
26
46
  }, { explicitlyTyped: true });
47
+ export default Gff3TabixAdapter;
27
48
  //# sourceMappingURL=configSchema.js.map
package/esm/Gff3TabixAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,kBAAkB,EAClB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,KAAK,EAAE,mBAAmB,CAAC,gBAAgB,EAAE;QAC3C,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF,cAAc,EAAE;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,CAAC,YAAY,EAAE,QAAQ,CAAC;KACvC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,gBAAgB,GAAG,mBAAmB,CAC1C,kBAAkB,EAClB;IACE;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,KAAK,EAAE,mBAAmB,CAAC,gBAAgB,EAAE;QAC3C;;WAEG;QACH,SAAS,EAAE;YACT,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;YACrD,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,KAAK;SACpB;QACD;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;gBAC7B,YAAY,EAAE,aAAa;aAC5B;SACF;KACF,CAAC;IACF;;;;;;OAMG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,CAAC,YAAY,EAAE,QAAQ,CAAC;KACvC;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,gBAAgB,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-gff3",
3
- "version": "2.1.7",
3
+ "version": "2.2.0",
4
4
  "description": "JBrowse 2 gff3.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -59,5 +59,5 @@
59
59
  "distModule": "esm/index.js",
60
60
  "srcModule": "src/index.ts",
61
61
  "module": "esm/index.js",
62
- "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
62
+ "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
63
63
  }
package/src/Gff3Adapter/configSchema.ts CHANGED
@@ -1,8 +1,16 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
2
 
3
- export default ConfigurationSchema(
3
+ /**
4
+ * #config Gff3Adapter
5
+ */
6
+ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
+
8
+ const Gff3Adapter = ConfigurationSchema(
4
9
  'Gff3Adapter',
5
10
  {
11
+ /**
12
+ * #slot
13
+ */
6
14
  gffLocation: {
7
15
  type: 'fileLocation',
8
16
  defaultValue: { uri: '/path/to/my.gff', locationType: 'UriLocation' },
@@ -10,3 +18,5 @@ export default ConfigurationSchema(
10
18
  },
11
19
  { explicitlyTyped: true },
12
20
  )
21
+
22
+ export default Gff3Adapter
package/src/Gff3TabixAdapter/configSchema.ts CHANGED
@@ -1,19 +1,34 @@
1
1
  import { types } from 'mobx-state-tree'
2
2
  import { ConfigurationSchema } from '@jbrowse/core/configuration'
3
3
 
4
- export default ConfigurationSchema(
4
+ /**
5
+ * #config Gff3TabixAdapter
6
+ */
7
+ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
8
+
9
+ const Gff3TabixAdapter = ConfigurationSchema(
5
10
  'Gff3TabixAdapter',
6
11
  {
12
+ /**
13
+ * #slot
14
+ */
7
15
  gffGzLocation: {
8
16
  type: 'fileLocation',
9
17
  defaultValue: { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' },
10
18
  },
19
+
11
20
  index: ConfigurationSchema('Gff3TabixIndex', {
21
+ /**
22
+ * #slot index.indexType
23
+ */
12
24
  indexType: {
13
25
  model: types.enumeration('IndexType', ['TBI', 'CSI']),
14
26
  type: 'stringEnum',
15
27
  defaultValue: 'TBI',
16
28
  },
29
+ /**
30
+ * #slot index.indexType
31
+ */
17
32
  location: {
18
33
  type: 'fileLocation',
19
34
  defaultValue: {
@@ -22,6 +37,13 @@ export default ConfigurationSchema(
22
37
  },
23
38
  },
24
39
  }),
40
+ /**
41
+ * #slot
42
+ * the Gff3TabixAdapter has to "redispatch" if it fetches a region and
43
+ * features it finds inside that region extend outside the region we requested.
44
+ * you can disable this for certain feature types to avoid fetching e.g. the
45
+ * entire chromosome
46
+ */
25
47
  dontRedispatch: {
26
48
  type: 'stringArray',
27
49
  defaultValue: ['chromosome', 'region'],
@@ -29,3 +51,5 @@ export default ConfigurationSchema(
29
51
  },
30
52
  { explicitlyTyped: true },
31
53
  )
54
+
55
+ export default Gff3TabixAdapter