@jbrowse/plugin-gff3 2.1.6 → 2.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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": "2.1.6",
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": "df810d2a4f057adcd8f5345d54972508fba007a7"
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