@jbrowse/plugin-bed 2.1.7 → 2.2.0

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Files changed (22) hide show
  1. package/dist/BedAdapter/configSchema.d.ts +2 -2
  2. package/dist/BedAdapter/configSchema.js +27 -1
  3. package/dist/BedAdapter/configSchema.js.map +1 -1
  4. package/dist/BedTabixAdapter/configSchema.d.ts +2 -2
  5. package/dist/BedTabixAdapter/configSchema.js +24 -1
  6. package/dist/BedTabixAdapter/configSchema.js.map +1 -1
  7. package/dist/BigBedAdapter/configSchema.d.ts +2 -2
  8. package/dist/BigBedAdapter/configSchema.js +9 -1
  9. package/dist/BigBedAdapter/configSchema.js.map +1 -1
  10. package/esm/BedAdapter/configSchema.d.ts +2 -2
  11. package/esm/BedAdapter/configSchema.js +27 -1
  12. package/esm/BedAdapter/configSchema.js.map +1 -1
  13. package/esm/BedTabixAdapter/configSchema.d.ts +2 -2
  14. package/esm/BedTabixAdapter/configSchema.js +24 -1
  15. package/esm/BedTabixAdapter/configSchema.js.map +1 -1
  16. package/esm/BigBedAdapter/configSchema.d.ts +2 -2
  17. package/esm/BigBedAdapter/configSchema.js +9 -1
  18. package/esm/BigBedAdapter/configSchema.js.map +1 -1
  19. package/package.json +2 -2
  20. package/src/BedAdapter/configSchema.ts +28 -4
  21. package/src/BedTabixAdapter/configSchema.ts +26 -1
  22. package/src/BigBedAdapter/configSchema.ts +11 -1
package/dist/BedAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BedAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BedAdapter;
package/dist/BedAdapter/configSchema.js CHANGED
@@ -1,40 +1,66 @@
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)('BedAdapter', {
4
+ /**
5
+ * #config BedAdapter
6
+ */
7
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
+ const BedAdapter = (0, configuration_1.ConfigurationSchema)('BedAdapter', {
9
+ /**
10
+ * #slot
11
+ */
5
12
  bedLocation: {
6
13
  type: 'fileLocation',
7
14
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
8
15
  },
16
+ /**
17
+ * #slot
18
+ */
9
19
  columnNames: {
10
20
  type: 'stringArray',
11
21
  description: 'List of column names',
12
22
  defaultValue: [],
13
23
  },
24
+ /**
25
+ * #slot
26
+ */
14
27
  scoreColumn: {
15
28
  type: 'string',
16
29
  description: 'The column to use as a "score" attribute',
17
30
  defaultValue: '',
18
31
  },
32
+ /**
33
+ * #slot
34
+ */
19
35
  autoSql: {
20
36
  type: 'string',
21
37
  description: 'The autoSql definition for the data fields in the file',
22
38
  defaultValue: '',
23
39
  },
40
+ /**
41
+ * #slot
42
+ */
24
43
  colRef: {
25
44
  type: 'number',
26
45
  description: 'The column to use as a "refName" attribute',
27
46
  defaultValue: 0,
28
47
  },
48
+ /**
49
+ * #slot
50
+ */
29
51
  colStart: {
30
52
  type: 'number',
31
53
  description: 'The column to use as a "start" attribute',
32
54
  defaultValue: 1,
33
55
  },
56
+ /**
57
+ * #slot
58
+ */
34
59
  colEnd: {
35
60
  type: 'number',
36
61
  description: 'The column to use as a "end" attribute',
37
62
  defaultValue: 2,
38
63
  },
39
64
  }, { explicitlyTyped: true });
65
+ exports.default = BedAdapter;
40
66
  //# sourceMappingURL=configSchema.js.map
package/dist/BedAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,GAAG,IAAA,mCAAmB,EACpC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,UAAU,CAAA"}
package/dist/BedTabixAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BedTabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BedTabixAdapter;
package/dist/BedTabixAdapter/configSchema.js CHANGED
@@ -2,17 +2,30 @@
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  const configuration_1 = require("@jbrowse/core/configuration");
4
4
  const mobx_state_tree_1 = require("mobx-state-tree");
5
- exports.default = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
5
+ /**
6
+ * #config BedTabixAdapter
7
+ */
8
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
9
+ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
10
+ /**
11
+ * #slot
12
+ */
6
13
  bedGzLocation: {
7
14
  type: 'fileLocation',
8
15
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
9
16
  },
10
17
  index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
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.location
28
+ */
16
29
  location: {
17
30
  type: 'fileLocation',
18
31
  defaultValue: {
@@ -21,20 +34,30 @@ exports.default = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
21
34
  },
22
35
  },
23
36
  }),
37
+ /**
38
+ * #slot
39
+ */
24
40
  columnNames: {
25
41
  type: 'stringArray',
26
42
  description: 'List of column names',
27
43
  defaultValue: [],
28
44
  },
45
+ /**
46
+ * #slot
47
+ */
29
48
  scoreColumn: {
30
49
  type: 'string',
31
50
  description: 'The column to use as a "score" attribute',
32
51
  defaultValue: '',
33
52
  },
53
+ /**
54
+ * #slot
55
+ */
34
56
  autoSql: {
35
57
  type: 'string',
36
58
  description: 'The autoSql definition for the data fields in the file',
37
59
  defaultValue: '',
38
60
  },
39
61
  }, { explicitlyTyped: true });
62
+ exports.default = BedTabixAdapter;
40
63
  //# sourceMappingURL=configSchema.js.map
package/dist/BedTabixAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,IAAA,mCAAmB,EAChC,iBAAiB,EACjB;IACE,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,YAAY,EAAE;QACvC,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;IAEF,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,eAAe,GAAG,IAAA,mCAAmB,EACzC,iBAAiB,EACjB;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,YAAY,EAAE;QACvC;;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;IAEF;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,eAAe,CAAA"}
package/dist/BigBedAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BigBedAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BigBedAdapter;
package/dist/BigBedAdapter/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)('BigBedAdapter', {
4
+ /**
5
+ * #config BigBedAdapter
6
+ */
7
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
+ const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
9
+ /**
10
+ * #slot
11
+ */
5
12
  bigBedLocation: {
6
13
  type: 'fileLocation',
7
14
  defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
8
15
  },
9
16
  }, { explicitlyTyped: true });
17
+ exports.default = BigBedAdapter;
10
18
  //# sourceMappingURL=configSchema.js.map
package/dist/BigBedAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,aAAa,GAAG,IAAA,mCAAmB,EACvC,eAAe,EACf;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,aAAa,CAAA"}
package/esm/BedAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BedAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BedAdapter;
package/esm/BedAdapter/configSchema.js CHANGED
@@ -1,38 +1,64 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- export default ConfigurationSchema('BedAdapter', {
2
+ /**
3
+ * #config BedAdapter
4
+ */
5
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
+ const BedAdapter = ConfigurationSchema('BedAdapter', {
7
+ /**
8
+ * #slot
9
+ */
3
10
  bedLocation: {
4
11
  type: 'fileLocation',
5
12
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
6
13
  },
14
+ /**
15
+ * #slot
16
+ */
7
17
  columnNames: {
8
18
  type: 'stringArray',
9
19
  description: 'List of column names',
10
20
  defaultValue: [],
11
21
  },
22
+ /**
23
+ * #slot
24
+ */
12
25
  scoreColumn: {
13
26
  type: 'string',
14
27
  description: 'The column to use as a "score" attribute',
15
28
  defaultValue: '',
16
29
  },
30
+ /**
31
+ * #slot
32
+ */
17
33
  autoSql: {
18
34
  type: 'string',
19
35
  description: 'The autoSql definition for the data fields in the file',
20
36
  defaultValue: '',
21
37
  },
38
+ /**
39
+ * #slot
40
+ */
22
41
  colRef: {
23
42
  type: 'number',
24
43
  description: 'The column to use as a "refName" attribute',
25
44
  defaultValue: 0,
26
45
  },
46
+ /**
47
+ * #slot
48
+ */
27
49
  colStart: {
28
50
  type: 'number',
29
51
  description: 'The column to use as a "start" attribute',
30
52
  defaultValue: 1,
31
53
  },
54
+ /**
55
+ * #slot
56
+ */
32
57
  colEnd: {
33
58
  type: 'number',
34
59
  description: 'The column to use as a "end" attribute',
35
60
  defaultValue: 2,
36
61
  },
37
62
  }, { explicitlyTyped: true });
63
+ export default BedAdapter;
38
64
  //# sourceMappingURL=configSchema.js.map
package/esm/BedAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,YAAY,EACZ;IACE,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,GAAG,mBAAmB,CACpC,YAAY,EACZ;IACE;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4CAA4C;QACzD,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,CAAC;KAChB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wCAAwC;QACrD,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,UAAU,CAAA"}
package/esm/BedTabixAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BedTabixAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BedTabixAdapter;
package/esm/BedTabixAdapter/configSchema.js CHANGED
@@ -1,16 +1,29 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  import { types } from 'mobx-state-tree';
3
- export default ConfigurationSchema('BedTabixAdapter', {
3
+ /**
4
+ * #config BedTabixAdapter
5
+ */
6
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
7
+ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
8
+ /**
9
+ * #slot
10
+ */
4
11
  bedGzLocation: {
5
12
  type: 'fileLocation',
6
13
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
7
14
  },
8
15
  index: ConfigurationSchema('TabixIndex', {
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.location
26
+ */
14
27
  location: {
15
28
  type: 'fileLocation',
16
29
  defaultValue: {
@@ -19,20 +32,30 @@ export default ConfigurationSchema('BedTabixAdapter', {
19
32
  },
20
33
  },
21
34
  }),
35
+ /**
36
+ * #slot
37
+ */
22
38
  columnNames: {
23
39
  type: 'stringArray',
24
40
  description: 'List of column names',
25
41
  defaultValue: [],
26
42
  },
43
+ /**
44
+ * #slot
45
+ */
27
46
  scoreColumn: {
28
47
  type: 'string',
29
48
  description: 'The column to use as a "score" attribute',
30
49
  defaultValue: '',
31
50
  },
51
+ /**
52
+ * #slot
53
+ */
32
54
  autoSql: {
33
55
  type: 'string',
34
56
  description: 'The autoSql definition for the data fields in the file',
35
57
  defaultValue: '',
36
58
  },
37
59
  }, { explicitlyTyped: true });
60
+ export default BedTabixAdapter;
38
61
  //# sourceMappingURL=configSchema.js.map
package/esm/BedTabixAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,mBAAmB,CAChC,iBAAiB,EACjB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IAED,KAAK,EAAE,mBAAmB,CAAC,YAAY,EAAE;QACvC,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;IAEF,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,eAAe,GAAG,mBAAmB,CACzC,iBAAiB,EACjB;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,YAAY,EAAE;QACvC;;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;IAEF;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,sBAAsB;QACnC,YAAY,EAAE,EAAE;KACjB;IAED;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,0CAA0C;QACvD,YAAY,EAAE,EAAE;KACjB;IAED;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,wDAAwD;QACrE,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,eAAe,CAAA"}
package/esm/BigBedAdapter/configSchema.d.ts CHANGED
@@ -1,2 +1,2 @@
1
- declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
- export default _default;
1
+ declare const BigBedAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default BigBedAdapter;
package/esm/BigBedAdapter/configSchema.js CHANGED
@@ -1,8 +1,16 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- export default ConfigurationSchema('BigBedAdapter', {
2
+ /**
3
+ * #config BigBedAdapter
4
+ */
5
+ function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
+ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
7
+ /**
8
+ * #slot
9
+ */
3
10
  bigBedLocation: {
4
11
  type: 'fileLocation',
5
12
  defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
6
13
  },
7
14
  }, { explicitlyTyped: true });
15
+ export default BigBedAdapter;
8
16
  //# sourceMappingURL=configSchema.js.map
package/esm/BigBedAdapter/configSchema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigBedAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,aAAa,GAAG,mBAAmB,CACvC,eAAe,EACf;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,gBAAgB,EAAE,YAAY,EAAE,aAAa,EAAE;KACrE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,aAAa,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-bed",
3
- "version": "2.1.7",
3
+ "version": "2.2.0",
4
4
  "description": "JBrowse 2 bed adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -56,5 +56,5 @@
56
56
  "distModule": "esm/index.js",
57
57
  "srcModule": "src/index.ts",
58
58
  "module": "esm/index.js",
59
- "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
59
+ "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
60
60
  }
package/src/BedAdapter/configSchema.ts CHANGED
@@ -1,40 +1,63 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
2
 
3
- export default ConfigurationSchema(
3
+ /**
4
+ * #config BedAdapter
5
+ */
6
+ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
+
8
+ const BedAdapter = ConfigurationSchema(
4
9
  'BedAdapter',
5
10
  {
11
+ /**
12
+ * #slot
13
+ */
6
14
  bedLocation: {
7
15
  type: 'fileLocation',
8
16
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
9
17
  },
10
-
18
+ /**
19
+ * #slot
20
+ */
11
21
  columnNames: {
12
22
  type: 'stringArray',
13
23
  description: 'List of column names',
14
24
  defaultValue: [],
15
25
  },
16
-
26
+ /**
27
+ * #slot
28
+ */
17
29
  scoreColumn: {
18
30
  type: 'string',
19
31
  description: 'The column to use as a "score" attribute',
20
32
  defaultValue: '',
21
33
  },
22
-
34
+ /**
35
+ * #slot
36
+ */
23
37
  autoSql: {
24
38
  type: 'string',
25
39
  description: 'The autoSql definition for the data fields in the file',
26
40
  defaultValue: '',
27
41
  },
42
+ /**
43
+ * #slot
44
+ */
28
45
  colRef: {
29
46
  type: 'number',
30
47
  description: 'The column to use as a "refName" attribute',
31
48
  defaultValue: 0,
32
49
  },
50
+ /**
51
+ * #slot
52
+ */
33
53
  colStart: {
34
54
  type: 'number',
35
55
  description: 'The column to use as a "start" attribute',
36
56
  defaultValue: 1,
37
57
  },
58
+ /**
59
+ * #slot
60
+ */
38
61
  colEnd: {
39
62
  type: 'number',
40
63
  description: 'The column to use as a "end" attribute',
@@ -43,3 +66,4 @@ export default ConfigurationSchema(
43
66
  },
44
67
  { explicitlyTyped: true },
45
68
  )
69
+ export default BedAdapter
package/src/BedTabixAdapter/configSchema.ts CHANGED
@@ -1,20 +1,34 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
2
  import { types } from 'mobx-state-tree'
3
3
 
4
- export default ConfigurationSchema(
4
+ /**
5
+ * #config BedTabixAdapter
6
+ */
7
+ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
8
+
9
+ const BedTabixAdapter = ConfigurationSchema(
5
10
  'BedTabixAdapter',
6
11
  {
12
+ /**
13
+ * #slot
14
+ */
7
15
  bedGzLocation: {
8
16
  type: 'fileLocation',
9
17
  defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
10
18
  },
11
19
 
12
20
  index: ConfigurationSchema('TabixIndex', {
21
+ /**
22
+ * #slot index.indexType
23
+ */
13
24
  indexType: {
14
25
  model: types.enumeration('IndexType', ['TBI', 'CSI']),
15
26
  type: 'stringEnum',
16
27
  defaultValue: 'TBI',
17
28
  },
29
+ /**
30
+ * #slot index.location
31
+ */
18
32
  location: {
19
33
  type: 'fileLocation',
20
34
  defaultValue: {
@@ -24,18 +38,27 @@ export default ConfigurationSchema(
24
38
  },
25
39
  }),
26
40
 
41
+ /**
42
+ * #slot
43
+ */
27
44
  columnNames: {
28
45
  type: 'stringArray',
29
46
  description: 'List of column names',
30
47
  defaultValue: [],
31
48
  },
32
49
 
50
+ /**
51
+ * #slot
52
+ */
33
53
  scoreColumn: {
34
54
  type: 'string',
35
55
  description: 'The column to use as a "score" attribute',
36
56
  defaultValue: '',
37
57
  },
38
58
 
59
+ /**
60
+ * #slot
61
+ */
39
62
  autoSql: {
40
63
  type: 'string',
41
64
  description: 'The autoSql definition for the data fields in the file',
@@ -44,3 +67,5 @@ export default ConfigurationSchema(
44
67
  },
45
68
  { explicitlyTyped: true },
46
69
  )
70
+
71
+ export default BedTabixAdapter
package/src/BigBedAdapter/configSchema.ts CHANGED
@@ -1,8 +1,16 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
2
 
3
- export default ConfigurationSchema(
3
+ /**
4
+ * #config BigBedAdapter
5
+ */
6
+ function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
+
8
+ const BigBedAdapter = ConfigurationSchema(
4
9
  'BigBedAdapter',
5
10
  {
11
+ /**
12
+ * #slot
13
+ */
6
14
  bigBedLocation: {
7
15
  type: 'fileLocation',
8
16
  defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
@@ -10,3 +18,5 @@ export default ConfigurationSchema(
10
18
  },
11
19
  { explicitlyTyped: true },
12
20
  )
21
+
22
+ export default BigBedAdapter