@jbrowse/plugin-bed 2.4.1 → 2.5.0
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.
- package/dist/BedAdapter/BedAdapter.js +1 -1
- package/dist/BedAdapter/BedAdapter.js.map +1 -1
- package/dist/BedAdapter/configSchema.d.ts +60 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.d.ts +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js +1 -1
- package/dist/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/dist/BedTabixAdapter/configSchema.d.ts +56 -1
- package/dist/BedpeAdapter/BedpeAdapter.js +1 -1
- package/dist/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/dist/BedpeAdapter/configSchema.d.ts +21 -1
- package/dist/BigBedAdapter/configSchema.d.ts +12 -1
- package/esm/BedAdapter/BedAdapter.js +2 -1
- package/esm/BedAdapter/BedAdapter.js.map +1 -1
- package/esm/BedAdapter/configSchema.d.ts +60 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.d.ts +1 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.js +2 -1
- package/esm/BedTabixAdapter/BedTabixAdapter.js.map +1 -1
- package/esm/BedTabixAdapter/configSchema.d.ts +56 -1
- package/esm/BedpeAdapter/BedpeAdapter.js +2 -1
- package/esm/BedpeAdapter/BedpeAdapter.js.map +1 -1
- package/esm/BedpeAdapter/configSchema.d.ts +21 -1
- package/esm/BigBedAdapter/configSchema.d.ts +12 -1
- package/package.json +2 -2
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@@ -130,6 +130,6 @@ class BedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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}
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freeResources() { }
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}
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133
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-
exports.default = BedAdapter;
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BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
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134
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+
exports.default = BedAdapter;
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//# sourceMappingURL=BedAdapter.js.map
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@@ -1 +1 @@
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1
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-
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CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;
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1
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{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,kCAAqC;AACrC,8EAAoD;AACpD,2DAA6C;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAA9D;;QAYY,kBAAa,GAEnB,EAAE,CAAA;IA4IR,CAAC;IAxIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,EAA8B,CAAA;QAC/C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;gBACtB,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;aACvB;YACD,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAC7B;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAW,CAAA;QACjD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAErC,OAAO;YACL,MAAM;YACN,QAAQ;YACR,MAAM;YACN,WAAW;YACX,WAAW;YACX,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC/B,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,6BAA6B,CAAC,OAAe;QACzD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,GAC/D,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACvB,MAAM,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC/B,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,MAAM,YAAY,GAAG,IAAI,uBAAY,EAAE,CAAA;QACvC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7B,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,IAAA,kBAAW,EAChB,CAAC,EACD,MAAM,EACN,QAAQ,EACR,MAAM,EACN,WAAW,EACX,MAAM,EACN,QAAQ,EACR,KAAK,CACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,KAAK,MAAM,GAAG,IAAI,GAAG,EAAE;YACrB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;IAEO,KAAK,CAAC,uBAAuB,CAAC,OAAe;QACnD,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,6BAA6B,CAC9D,OAAO,CACR,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACV,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBACvC,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,OAAO,CAAC,CAAA;YAChE,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;YACjE,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzIjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,AAAjC,CAAiC;kBAhBxC,UAAU"}
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declare const BedAdapter: import("@jbrowse/core/configuration").
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declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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/**
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* #slot
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*/
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bedLocation: {
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type: string;
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defaultValue: {
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uri: string;
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locationType: string;
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};
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};
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/**
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* #slot
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*/
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columnNames: {
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+
type: string;
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description: string;
|
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defaultValue: never[];
|
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};
|
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/**
|
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* #slot
|
|
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|
+
*/
|
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+
scoreColumn: {
|
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type: string;
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description: string;
|
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defaultValue: string;
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};
|
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|
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/**
|
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* #slot
|
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+
*/
|
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autoSql: {
|
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type: string;
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description: string;
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defaultValue: string;
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};
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|
+
/**
|
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* #slot
|
|
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|
+
*/
|
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|
+
colRef: {
|
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|
+
type: string;
|
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description: string;
|
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|
+
defaultValue: number;
|
|
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|
+
};
|
|
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|
+
/**
|
|
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|
+
* #slot
|
|
46
|
+
*/
|
|
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|
+
colStart: {
|
|
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|
+
type: string;
|
|
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|
+
description: string;
|
|
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|
+
defaultValue: number;
|
|
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|
+
};
|
|
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|
+
/**
|
|
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|
+
* #slot
|
|
54
|
+
*/
|
|
55
|
+
colEnd: {
|
|
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|
+
type: string;
|
|
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|
+
description: string;
|
|
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|
+
defaultValue: number;
|
|
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|
+
};
|
|
60
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
61
|
export default BedAdapter;
|
|
@@ -11,7 +11,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
11
11
|
protected scoreColumn: string;
|
|
12
12
|
static capabilities: string[];
|
|
13
13
|
constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
|
|
14
|
-
getRefNames(opts?: BaseOptions): Promise<
|
|
14
|
+
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
15
15
|
getHeader(): Promise<string>;
|
|
16
16
|
getNames(): Promise<string[] | undefined>;
|
|
17
17
|
getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
|
|
@@ -69,6 +69,6 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
69
69
|
}
|
|
70
70
|
freeResources() { }
|
|
71
71
|
}
|
|
72
|
-
exports.default = BedTabixAdapter;
|
|
73
72
|
BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
|
|
73
|
+
exports.default = BedTabixAdapter;
|
|
74
74
|
//# sourceMappingURL=BedTabixAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,kCAAqC;AAKrC,MAAqB,eAAgB,SAAQ,oCAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAA,kBAAW,EACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;
|
|
1
|
+
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,oDAA2B;AAC3B,yEAGgD;AAChD,8CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,kCAAqC;AAKrC,MAAqB,eAAgB,SAAQ,oCAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC9B,UAAU,EAAE,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAA,kBAAW,EACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAhFjB,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;kBATxC,eAAe"}
|
|
@@ -1,2 +1,57 @@
|
|
|
1
|
-
declare const BedTabixAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
*/
|
|
5
|
+
bedGzLocation: {
|
|
6
|
+
type: string;
|
|
7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
|
|
9
|
+
locationType: string;
|
|
10
|
+
};
|
|
11
|
+
};
|
|
12
|
+
index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
13
|
+
/**
|
|
14
|
+
* #slot index.indexType
|
|
15
|
+
*/
|
|
16
|
+
indexType: {
|
|
17
|
+
model: import("mobx-state-tree").ISimpleType<string>;
|
|
18
|
+
type: string;
|
|
19
|
+
defaultValue: string;
|
|
20
|
+
};
|
|
21
|
+
/**
|
|
22
|
+
* #slot index.location
|
|
23
|
+
*/
|
|
24
|
+
location: {
|
|
25
|
+
type: string;
|
|
26
|
+
defaultValue: {
|
|
27
|
+
uri: string;
|
|
28
|
+
locationType: string;
|
|
29
|
+
};
|
|
30
|
+
};
|
|
31
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
32
|
+
/**
|
|
33
|
+
* #slot
|
|
34
|
+
*/
|
|
35
|
+
columnNames: {
|
|
36
|
+
type: string;
|
|
37
|
+
description: string;
|
|
38
|
+
defaultValue: never[];
|
|
39
|
+
};
|
|
40
|
+
/**
|
|
41
|
+
* #slot
|
|
42
|
+
*/
|
|
43
|
+
scoreColumn: {
|
|
44
|
+
type: string;
|
|
45
|
+
description: string;
|
|
46
|
+
defaultValue: string;
|
|
47
|
+
};
|
|
48
|
+
/**
|
|
49
|
+
* #slot
|
|
50
|
+
*/
|
|
51
|
+
autoSql: {
|
|
52
|
+
type: string;
|
|
53
|
+
description: string;
|
|
54
|
+
defaultValue: string;
|
|
55
|
+
};
|
|
56
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
57
|
export default BedTabixAdapter;
|
|
@@ -174,6 +174,6 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
174
174
|
}
|
|
175
175
|
freeResources() { }
|
|
176
176
|
}
|
|
177
|
-
exports.default = BedpeAdapter;
|
|
178
177
|
BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
|
|
178
|
+
exports.default = BedpeAdapter;
|
|
179
179
|
//# sourceMappingURL=BedpeAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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|
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@@ -1,2 +1,22 @@
|
|
|
1
|
-
declare const BedpeAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
* can be plaintext or gzipped, not indexed so loaded into memory on startup
|
|
5
|
+
*/
|
|
6
|
+
bedpeLocation: {
|
|
7
|
+
type: string;
|
|
8
|
+
defaultValue: {
|
|
9
|
+
uri: string;
|
|
10
|
+
locationType: string;
|
|
11
|
+
};
|
|
12
|
+
};
|
|
13
|
+
/**
|
|
14
|
+
* #slot
|
|
15
|
+
*/
|
|
16
|
+
columnNames: {
|
|
17
|
+
type: string;
|
|
18
|
+
description: string;
|
|
19
|
+
defaultValue: never[];
|
|
20
|
+
};
|
|
21
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
22
|
export default BedpeAdapter;
|
|
@@ -1,2 +1,13 @@
|
|
|
1
|
-
declare const BigBedAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
*/
|
|
5
|
+
bigBedLocation: {
|
|
6
|
+
type: string;
|
|
7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
|
|
9
|
+
locationType: string;
|
|
10
|
+
};
|
|
11
|
+
};
|
|
12
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
13
|
export default BigBedAdapter;
|
|
@@ -8,7 +8,7 @@ import { unzip } from '@gmod/bgzf-filehandle';
|
|
|
8
8
|
function isGzip(buf) {
|
|
9
9
|
return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
|
|
10
10
|
}
|
|
11
|
-
|
|
11
|
+
class BedAdapter extends BaseFeatureDataAdapter {
|
|
12
12
|
constructor() {
|
|
13
13
|
super(...arguments);
|
|
14
14
|
this.intervalTrees = {};
|
|
@@ -126,4 +126,5 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
|
|
|
126
126
|
freeResources() { }
|
|
127
127
|
}
|
|
128
128
|
BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
|
|
129
|
+
export default BedAdapter;
|
|
129
130
|
//# sourceMappingURL=BedAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AACrC,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,
|
|
1
|
+
{"version":3,"file":"BedAdapter.js","sourceRoot":"","sources":["../../src/BedAdapter/BedAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AACrC,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAsB;IAA9D;;QAYY,kBAAa,GAEnB,EAAE,CAAA;IA4IR,CAAC;IAxIS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC1C,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,EAA8B,CAAA;QAC/C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YAC9B,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;YAClC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE;gBACtB,QAAQ,CAAC,OAAO,CAAC,GAAG,EAAE,CAAA;aACvB;YACD,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAC7B;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAW,CAAA;QACjD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QACnC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,CAAA;QACzC,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAErC,OAAO;YACL,MAAM;YACN,QAAQ;YACR,MAAM;YACN,WAAW;YACX,WAAW;YACX,MAAM;YACN,QAAQ;YACR,MAAM;SACP,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC/B,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,6BAA6B,CAAC,OAAe;QACzD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,GAC/D,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACvB,MAAM,KAAK,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC/B,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,MAAM,YAAY,GAAG,IAAI,YAAY,EAAE,CAAA;QACvC,MAAM,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAC7B,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,WAAW,CAChB,CAAC,EACD,MAAM,EACN,QAAQ,EACR,MAAM,EACN,WAAW,EACX,MAAM,EACN,QAAQ,EACR,KAAK,CACN,CAAA;QACH,CAAC,CAAC,CAAA;QAEF,KAAK,MAAM,GAAG,IAAI,GAAG,EAAE;YACrB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;IAEO,KAAK,CAAC,uBAAuB,CAAC,OAAe;QACnD,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,6BAA6B,CAC9D,OAAO,CACR,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACV,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBACvC,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,uBAAuB,CAAC,OAAO,CAAC,CAAA;YAChE,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;YACjE,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzIjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,AAAjC,CAAiC;eAhBxC,UAAU"}
|
|
@@ -1,2 +1,61 @@
|
|
|
1
|
-
declare const BedAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
*/
|
|
5
|
+
bedLocation: {
|
|
6
|
+
type: string;
|
|
7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
|
|
9
|
+
locationType: string;
|
|
10
|
+
};
|
|
11
|
+
};
|
|
12
|
+
/**
|
|
13
|
+
* #slot
|
|
14
|
+
*/
|
|
15
|
+
columnNames: {
|
|
16
|
+
type: string;
|
|
17
|
+
description: string;
|
|
18
|
+
defaultValue: never[];
|
|
19
|
+
};
|
|
20
|
+
/**
|
|
21
|
+
* #slot
|
|
22
|
+
*/
|
|
23
|
+
scoreColumn: {
|
|
24
|
+
type: string;
|
|
25
|
+
description: string;
|
|
26
|
+
defaultValue: string;
|
|
27
|
+
};
|
|
28
|
+
/**
|
|
29
|
+
* #slot
|
|
30
|
+
*/
|
|
31
|
+
autoSql: {
|
|
32
|
+
type: string;
|
|
33
|
+
description: string;
|
|
34
|
+
defaultValue: string;
|
|
35
|
+
};
|
|
36
|
+
/**
|
|
37
|
+
* #slot
|
|
38
|
+
*/
|
|
39
|
+
colRef: {
|
|
40
|
+
type: string;
|
|
41
|
+
description: string;
|
|
42
|
+
defaultValue: number;
|
|
43
|
+
};
|
|
44
|
+
/**
|
|
45
|
+
* #slot
|
|
46
|
+
*/
|
|
47
|
+
colStart: {
|
|
48
|
+
type: string;
|
|
49
|
+
description: string;
|
|
50
|
+
defaultValue: number;
|
|
51
|
+
};
|
|
52
|
+
/**
|
|
53
|
+
* #slot
|
|
54
|
+
*/
|
|
55
|
+
colEnd: {
|
|
56
|
+
type: string;
|
|
57
|
+
description: string;
|
|
58
|
+
defaultValue: number;
|
|
59
|
+
};
|
|
60
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
61
|
export default BedAdapter;
|
|
@@ -11,7 +11,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
11
11
|
protected scoreColumn: string;
|
|
12
12
|
static capabilities: string[];
|
|
13
13
|
constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
|
|
14
|
-
getRefNames(opts?: BaseOptions): Promise<
|
|
14
|
+
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
15
15
|
getHeader(): Promise<string>;
|
|
16
16
|
getNames(): Promise<string[] | undefined>;
|
|
17
17
|
getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
|
|
@@ -4,7 +4,7 @@ import { openLocation } from '@jbrowse/core/util/io';
|
|
|
4
4
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
5
5
|
import { TabixIndexedFile } from '@gmod/tabix';
|
|
6
6
|
import { featureData } from '../util';
|
|
7
|
-
|
|
7
|
+
class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
8
8
|
constructor(config, getSubAdapter, pluginManager) {
|
|
9
9
|
super(config, getSubAdapter, pluginManager);
|
|
10
10
|
const bedGzLoc = this.getConf('bedGzLocation');
|
|
@@ -65,4 +65,5 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
|
|
|
65
65
|
freeResources() { }
|
|
66
66
|
}
|
|
67
67
|
BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
|
|
68
|
+
export default BedTabixAdapter;
|
|
68
69
|
//# sourceMappingURL=BedTabixAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAKrC,
|
|
1
|
+
{"version":3,"file":"BedTabixAdapter.js","sourceRoot":"","sources":["../../src/BedTabixAdapter/BedTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,WAAW,CAAA;AAC3B,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAKrC,MAAqB,eAAgB,SAAQ,sBAAsB;IAWjE,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QAC9D,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACjD,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC/C,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAA;QACvC,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC;YACtC,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,aAAa,EAAE,IAAI,KAAK,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YACjE,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;SAC7B,CAAC,CAAA;QACF,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC9C,IAAI,CAAC,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;IACpC,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,SAAS;QACb,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YAC3B,OAAO,IAAI,CAAC,WAAW,CAAA;SACxB;QACD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;QACzC,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;YACvB,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YACzC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;YAC9B,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,MAAM,QAAQ,GAAG,aAAa,CAAC,KAAK,GAAG,CAAC,CAAA;YACxC,MAAM,MAAM,GAAG,aAAa,CAAC,GAAG,GAAG,CAAC,CAAA;YACpC,uEAAuE;YACvE,qEAAqE;YACrE,8DAA8D;YAC9D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YACnC,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,GAAG,EAAE;gBAC7D,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,WAAW,CACT,IAAI,EACJ,MAAM,EACN,QAAQ,EACR,MAAM,EACN,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,MAAM,EACX,GAAG,IAAI,CAAC,EAAE,IAAI,UAAU,EAAE,EAC1B,KAAK,CACN,CACF,CAAA;gBACH,CAAC;gBACD,MAAM,EAAE,IAAI,CAAC,MAAM;aACpB,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAhFjB,4BAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;eATxC,eAAe"}
|
|
@@ -1,2 +1,57 @@
|
|
|
1
|
-
declare const BedTabixAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
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4
|
+
*/
|
|
5
|
+
bedGzLocation: {
|
|
6
|
+
type: string;
|
|
7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
|
|
9
|
+
locationType: string;
|
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10
|
+
};
|
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+
};
|
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|
+
index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
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+
/**
|
|
14
|
+
* #slot index.indexType
|
|
15
|
+
*/
|
|
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|
+
indexType: {
|
|
17
|
+
model: import("mobx-state-tree").ISimpleType<string>;
|
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+
type: string;
|
|
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|
+
defaultValue: string;
|
|
20
|
+
};
|
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21
|
+
/**
|
|
22
|
+
* #slot index.location
|
|
23
|
+
*/
|
|
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|
+
location: {
|
|
25
|
+
type: string;
|
|
26
|
+
defaultValue: {
|
|
27
|
+
uri: string;
|
|
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|
+
locationType: string;
|
|
29
|
+
};
|
|
30
|
+
};
|
|
31
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
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|
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/**
|
|
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|
+
* #slot
|
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34
|
+
*/
|
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+
columnNames: {
|
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|
+
type: string;
|
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|
+
description: string;
|
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|
+
defaultValue: never[];
|
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|
+
};
|
|
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|
+
/**
|
|
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|
+
* #slot
|
|
42
|
+
*/
|
|
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|
+
scoreColumn: {
|
|
44
|
+
type: string;
|
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|
+
description: string;
|
|
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|
+
defaultValue: string;
|
|
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|
+
};
|
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|
+
/**
|
|
49
|
+
* #slot
|
|
50
|
+
*/
|
|
51
|
+
autoSql: {
|
|
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|
+
type: string;
|
|
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|
+
description: string;
|
|
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|
+
defaultValue: string;
|
|
55
|
+
};
|
|
56
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
57
|
export default BedTabixAdapter;
|
|
@@ -49,7 +49,7 @@ function parseStrand(strand) {
|
|
|
49
49
|
return undefined;
|
|
50
50
|
}
|
|
51
51
|
}
|
|
52
|
-
|
|
52
|
+
class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
53
53
|
constructor() {
|
|
54
54
|
super(...arguments);
|
|
55
55
|
this.intervalTrees = {};
|
|
@@ -168,4 +168,5 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
|
|
|
168
168
|
freeResources() { }
|
|
169
169
|
}
|
|
170
170
|
BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
|
|
171
|
+
export default BedpeAdapter;
|
|
171
172
|
//# sourceMappingURL=BedpeAdapter.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,
|
|
1
|
+
{"version":3,"file":"BedpeAdapter.js","sourceRoot":"","sources":["../../src/BedpeAdapter/BedpeAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,WAAW,CACzB,IAAY,EACZ,QAAgB,EAChB,IAAa,EACb,KAAgB;IAEhB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAChC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACjB,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACnB,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACjC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;QACrE,CAAC,CAAC,KAAK,CAAA;IAET,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK,EAAE,MAAM;QACb,GAAG,EAAE,IAAI;QACT,OAAO,EAAE,IAAI;QACb,MAAM,EAAE,OAAO;QACf,IAAI;QACJ,GAAG,IAAI;QACP,KAAK;QACL,QAAQ;QACR,IAAI,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE;KACnE,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,WAAW,CAAC,MAAc;IACjC,IAAI,MAAM,KAAK,GAAG,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAC,CAAA;KACV;SAAM,IAAI,MAAM,KAAK,GAAG,EAAE;QACzB,OAAO,CAAC,CAAA;KACT;SAAM;QACL,OAAO,SAAS,CAAA;KACjB;AACH,CAAC;AAED,MAAqB,YAAa,SAAQ,sBAAsB;IAAhE;;QAQY,kBAAa,GAEnB,EAAE,CAAA;IAkIR,CAAC;IA9HS,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QAC5C,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACzD,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QACnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QACD,MAAM,IAAI,GAAG,IAAI,WAAW,CAAC,MAAM,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACxD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SAC3B;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACrC,MAAM,MAAM,GAAG,EAA8B,CAAA;QAC7C,MAAM,MAAM,GAAG,EAA8B,CAAA;QAC7C,OAAO,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5B,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YAClB,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE;gBACf,MAAM,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;aAChB;YACD,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SACtB;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAE/C,OAAO;YACL,MAAM;YACN,MAAM;YACN,MAAM;YACN,WAAW;SACZ,CAAA;IACH,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAoB,EAAE;QAC3C,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAClD,IAAI,CAAC,aAAa,GAAG,SAAS,CAAA;gBAC9B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QAED,OAAO,IAAI,CAAC,aAAa,CAAA;IAC3B,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpD,OAAO,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAoB,EAAE;QACpC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACrD,IAAI,WAAW,CAAC,MAAM,EAAE;YACtB,OAAO,WAAW,CAAA;SACnB;QACD,MAAM,IAAI,GAAG,MAAM,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,OAAO,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,IAAI,CAAC;YAC5B,CAAC,CAAC,OAAO;iBACJ,KAAK,CAAC,CAAC,CAAC;iBACR,KAAK,CAAC,IAAI,CAAC;iBACX,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;YAC/B,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAEO,KAAK,CAAC,gBAAgB,CAAC,OAAe;QAC5C,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAChD,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;QAC9B,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;QAC9B,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,MAAM,YAAY,GAAG,IAAI,YAAY,EAAE,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,aAAN,MAAM,uBAAN,MAAM,CAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAChC,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,WAAW,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,EAAE,KAAK,CAAC,CAAA;QAC/C,CAAC,CAAC,CAAA;QACF,MAAM,IAAI,GAAG,MAAM,aAAN,MAAM,uBAAN,MAAM,CAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YAChC,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,EAAE,IAAI,OAAO,IAAI,CAAC,EAAE,CAAA;YAC7C,OAAO,WAAW,CAAC,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,CAAA;QAC9C,CAAC,CAAC,CAAA;QAEF,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE;YACtB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QAED,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE;YACtB,YAAY,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;SAC7D;QAED,OAAO,YAAY,CAAA;IACrB,CAAC;IAEO,KAAK,CAAC,eAAe,CAAC,OAAe;QAC3C,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAI,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACrE,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBACvC,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,YAAY,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACxD,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;YACjE,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AA/HjB,yBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,AAAjC,CAAiC;eAZxC,YAAY"}
|
|
@@ -1,2 +1,22 @@
|
|
|
1
|
-
declare const BedpeAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
* can be plaintext or gzipped, not indexed so loaded into memory on startup
|
|
5
|
+
*/
|
|
6
|
+
bedpeLocation: {
|
|
7
|
+
type: string;
|
|
8
|
+
defaultValue: {
|
|
9
|
+
uri: string;
|
|
10
|
+
locationType: string;
|
|
11
|
+
};
|
|
12
|
+
};
|
|
13
|
+
/**
|
|
14
|
+
* #slot
|
|
15
|
+
*/
|
|
16
|
+
columnNames: {
|
|
17
|
+
type: string;
|
|
18
|
+
description: string;
|
|
19
|
+
defaultValue: never[];
|
|
20
|
+
};
|
|
21
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
22
|
export default BedpeAdapter;
|
|
@@ -1,2 +1,13 @@
|
|
|
1
|
-
declare const BigBedAdapter: import("@jbrowse/core/configuration").
|
|
1
|
+
declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
*/
|
|
5
|
+
bigBedLocation: {
|
|
6
|
+
type: string;
|
|
7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
|
|
9
|
+
locationType: string;
|
|
10
|
+
};
|
|
11
|
+
};
|
|
12
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
13
|
export default BigBedAdapter;
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-bed",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.5.0",
|
|
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": "
|
|
59
|
+
"gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
|
|
60
60
|
}
|