@jbrowse/plugin-config 2.2.0 → 2.2.1

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Files changed (30) hide show
  1. package/dist/FromConfigAdapter/fromConfig.js +0 -7
  2. package/dist/FromConfigAdapter/fromConfig.js.map +1 -1
  3. package/dist/FromConfigAdapter/fromConfigRegions.js +0 -7
  4. package/dist/FromConfigAdapter/fromConfigRegions.js.map +1 -1
  5. package/dist/FromConfigAdapter/fromConfigSequence.js +0 -7
  6. package/dist/FromConfigAdapter/fromConfigSequence.js.map +1 -1
  7. package/dist/RefNameAliasAdapter/configSchema.js +4 -0
  8. package/dist/RefNameAliasAdapter/configSchema.js.map +1 -1
  9. package/esm/FromConfigAdapter/fromConfig.js +0 -7
  10. package/esm/FromConfigAdapter/fromConfig.js.map +1 -1
  11. package/esm/FromConfigAdapter/fromConfigRegions.js +0 -7
  12. package/esm/FromConfigAdapter/fromConfigRegions.js.map +1 -1
  13. package/esm/FromConfigAdapter/fromConfigSequence.js +0 -7
  14. package/esm/FromConfigAdapter/fromConfigSequence.js.map +1 -1
  15. package/esm/RefNameAliasAdapter/configSchema.js +4 -0
  16. package/esm/RefNameAliasAdapter/configSchema.js.map +1 -1
  17. package/package.json +2 -2
  18. package/src/FromConfigAdapter/FromConfigAdapter.test.ts +1 -1
  19. package/src/FromConfigAdapter/fromConfig.ts +0 -7
  20. package/src/FromConfigAdapter/fromConfigRegions.ts +0 -7
  21. package/src/FromConfigAdapter/fromConfigSequence.ts +0 -7
  22. package/src/RefNameAliasAdapter/configSchema.ts +4 -0
  23. package/src/__snapshots__/index.test.js.snap +2 -2
  24. package/dist/FromConfigAdapter/configSchema.d.ts +0 -1
  25. package/dist/FromConfigAdapter/configSchema.js +0 -25
  26. package/dist/FromConfigAdapter/configSchema.js.map +0 -1
  27. package/esm/FromConfigAdapter/configSchema.d.ts +0 -1
  28. package/esm/FromConfigAdapter/configSchema.js +0 -22
  29. package/esm/FromConfigAdapter/configSchema.js.map +0 -1
  30. package/src/FromConfigAdapter/configSchema.ts +0 -27
@@ -13,13 +13,6 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter
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  type: 'frozen',
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  defaultValue: [],
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  },
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- /**
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- * #slot
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- */
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- featureClass: {
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- type: 'string',
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- defaultValue: 'SimpleFeature',
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- },
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  }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
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  exports.default = configSchema;
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  //# sourceMappingURL=fromConfig.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,YAAY,CAAA"}
1
+ {"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,YAAY,CAAA"}
@@ -14,13 +14,6 @@ const regionsConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfig
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  type: 'frozen',
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  defaultValue: [],
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  },
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- /**
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- * #slot
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- */
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- featureClass: {
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- type: 'string',
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- defaultValue: 'SimpleFeature',
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- },
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  }, {
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  explicitlyTyped: true,
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  implicitIdentifier: 'adapterId',
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,kBAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,kBAAe,mBAAmB,CAAA"}
@@ -13,13 +13,6 @@ const sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfi
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  type: 'frozen',
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  defaultValue: [],
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  },
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- /**
17
- * #slot
18
- */
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- featureClass: {
20
- type: 'string',
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- defaultValue: 'SimpleFeature',
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- },
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  }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
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  exports.default = sequenceConfigSchema;
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  //# sourceMappingURL=fromConfigSequence.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,IAAA,mCAAmB,EAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
1
+ {"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,IAAA,mCAAmB,EAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,kBAAe,oBAAoB,CAAA"}
@@ -3,6 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  const configuration_1 = require("@jbrowse/core/configuration");
4
4
  /**
5
5
  * #config RefNameAliasAdapter
6
+ * can read "chromAliases" type files from UCSC or any tab separated file of
7
+ * refName aliases
6
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  */
7
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  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
8
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  const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAliasAdapter', {
@@ -18,6 +20,8 @@ const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAli
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  },
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  /**
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  * #slot
23
+ * by default, the "ref names that match the fasta" are assumed to be in the
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+ * first column (0), change this variable if needed
21
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  */
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  refNameColumn: {
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  type: 'number',
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;;;OAIG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,mBAAmB,CAAA"}
@@ -11,13 +11,6 @@ const configSchema = ConfigurationSchema('FromConfigAdapter', {
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  type: 'frozen',
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  defaultValue: [],
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  },
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- /**
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- * #slot
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- */
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- featureClass: {
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- type: 'string',
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- defaultValue: 'SimpleFeature',
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- },
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  }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
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  export default configSchema;
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  //# sourceMappingURL=fromConfig.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,YAAY,CAAA"}
1
+ {"version":3,"file":"fromConfig.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,YAAY,CAAA"}
@@ -12,13 +12,6 @@ const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
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  type: 'frozen',
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  defaultValue: [],
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  },
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- /**
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- * #slot
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- */
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- featureClass: {
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- type: 'string',
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- defaultValue: 'SimpleFeature',
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- },
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  }, {
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  explicitlyTyped: true,
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  implicitIdentifier: 'adapterId',
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,eAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"fromConfigRegions.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigRegions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,0BAA0B,EAC1B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD;IACE,eAAe,EAAE,IAAI;IACrB,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AACD,eAAe,mBAAmB,CAAA"}
@@ -11,13 +11,6 @@ const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
11
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  type: 'frozen',
12
12
  defaultValue: [],
13
13
  },
14
- /**
15
- * #slot
16
- */
17
- featureClass: {
18
- type: 'string',
19
- defaultValue: 'SimpleFeature',
20
- },
21
14
  }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
22
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  export default sequenceConfigSchema;
23
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  //# sourceMappingURL=fromConfigSequence.js.map
@@ -1 +1 @@
1
- {"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,mBAAmB,CAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,oBAAoB,CAAA"}
1
+ {"version":3,"file":"fromConfigSequence.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/fromConfigSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,oBAAoB,GAAG,mBAAmB,CAC9C,2BAA2B,EAC3B;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAED,eAAe,oBAAoB,CAAA"}
@@ -1,6 +1,8 @@
1
1
  import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
2
  /**
3
3
  * #config RefNameAliasAdapter
4
+ * can read "chromAliases" type files from UCSC or any tab separated file of
5
+ * refName aliases
4
6
  */
5
7
  function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
8
  const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
@@ -16,6 +18,8 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
16
18
  },
17
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  /**
18
20
  * #slot
21
+ * by default, the "ref names that match the fasta" are assumed to be in the
22
+ * first column (0), change this variable if needed
19
23
  */
20
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  refNameColumn: {
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  type: 'number',
@@ -1 +1 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,mBAAmB,GAAG,mBAAmB,CAC7C,qBAAqB,EACrB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;;;OAIG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,mBAAmB,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-config",
3
- "version": "2.2.0",
3
+ "version": "2.2.1",
4
4
  "description": "JBrowse 2 config utilities",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "distModule": "esm/index.js",
59
59
  "srcModule": "src/index.ts",
60
60
  "module": "esm/index.js",
61
- "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
61
+ "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
62
62
  }
@@ -1,6 +1,6 @@
1
1
  import { toArray } from 'rxjs/operators'
2
2
  import Adapter from './FromConfigAdapter'
3
- import { configSchema } from './configSchema'
3
+ import configSchema from './fromConfig'
4
4
 
5
5
  test('adapter can fetch features', async () => {
6
6
  const features = [
@@ -15,13 +15,6 @@ const configSchema = ConfigurationSchema(
15
15
  type: 'frozen',
16
16
  defaultValue: [],
17
17
  },
18
- /**
19
- * #slot
20
- */
21
- featureClass: {
22
- type: 'string',
23
- defaultValue: 'SimpleFeature',
24
- },
25
18
  },
26
19
  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
27
20
  )
@@ -15,13 +15,6 @@ const regionsConfigSchema = ConfigurationSchema(
15
15
  type: 'frozen',
16
16
  defaultValue: [],
17
17
  },
18
- /**
19
- * #slot
20
- */
21
- featureClass: {
22
- type: 'string',
23
- defaultValue: 'SimpleFeature',
24
- },
25
18
  },
26
19
  {
27
20
  explicitlyTyped: true,
@@ -14,13 +14,6 @@ const sequenceConfigSchema = ConfigurationSchema(
14
14
  type: 'frozen',
15
15
  defaultValue: [],
16
16
  },
17
- /**
18
- * #slot
19
- */
20
- featureClass: {
21
- type: 'string',
22
- defaultValue: 'SimpleFeature',
23
- },
24
17
  },
25
18
  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
26
19
  )
@@ -2,6 +2,8 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
2
 
3
3
  /**
4
4
  * #config RefNameAliasAdapter
5
+ * can read "chromAliases" type files from UCSC or any tab separated file of
6
+ * refName aliases
5
7
  */
6
8
  function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
9
 
@@ -20,6 +22,8 @@ const RefNameAliasAdapter = ConfigurationSchema(
20
22
  },
21
23
  /**
22
24
  * #slot
25
+ * by default, the "ref names that match the fasta" are assumed to be in the
26
+ * first column (0), change this variable if needed
23
27
  */
24
28
  refNameColumn: {
25
29
  type: 'number',
@@ -1,9 +1,9 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
- exports[`Config editing adds config editor widget 1`] = `Object {}`;
3
+ exports[`Config editing adds config editor widget 1`] = `{}`;
4
4
 
5
5
  exports[`Config editing creates proper FromConfigAdapter 1`] = `
6
- Object {
6
+ {
7
7
  "adapterId": "testFromConfigAdapterId",
8
8
  "type": "FromConfigAdapter",
9
9
  }
@@ -1 +0,0 @@
1
- export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
@@ -1,25 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.configSchema = void 0;
4
- const configuration_1 = require("@jbrowse/core/configuration");
5
- /**
6
- * #config FromConfigAdapter
7
- */
8
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
9
- exports.configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter', {
10
- /**
11
- * #slot
12
- */
13
- features: {
14
- type: 'frozen',
15
- defaultValue: [],
16
- },
17
- /**
18
- * #slot
19
- */
20
- featureClass: {
21
- type: 'string',
22
- defaultValue: 'SimpleFeature',
23
- },
24
- }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
25
- //# sourceMappingURL=configSchema.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":";;;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAE3D,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}
@@ -1 +0,0 @@
1
- export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
@@ -1,22 +0,0 @@
1
- import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
- /**
3
- * #config FromConfigAdapter
4
- */
5
- function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
6
- export const configSchema = ConfigurationSchema('FromConfigAdapter', {
7
- /**
8
- * #slot
9
- */
10
- features: {
11
- type: 'frozen',
12
- defaultValue: [],
13
- },
14
- /**
15
- * #slot
16
- */
17
- featureClass: {
18
- type: 'string',
19
- defaultValue: 'SimpleFeature',
20
- },
21
- }, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
22
- //# sourceMappingURL=configSchema.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,mBAAmB,CAC7C,mBAAmB,EACnB;IACE;;OAEG;IACH,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}
@@ -1,27 +0,0 @@
1
- import { ConfigurationSchema } from '@jbrowse/core/configuration'
2
-
3
- /**
4
- * #config FromConfigAdapter
5
- */
6
- function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
7
-
8
- export const configSchema = ConfigurationSchema(
9
- 'FromConfigAdapter',
10
- {
11
- /**
12
- * #slot
13
- */
14
- features: {
15
- type: 'frozen',
16
- defaultValue: [],
17
- },
18
- /**
19
- * #slot
20
- */
21
- featureClass: {
22
- type: 'string',
23
- defaultValue: 'SimpleFeature',
24
- },
25
- },
26
- { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
27
- )