@jbrowse/plugin-sequence 2.1.5 → 2.1.7
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/ChromSizesAdapter/ChromSizesAdapter.js +1 -1
- package/dist/ChromSizesAdapter/ChromSizesAdapter.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +1 -1
- package/dist/ReferenceSequenceTrack/configSchema.js +12 -0
- package/dist/ReferenceSequenceTrack/configSchema.js.map +1 -1
- package/dist/TwoBitAdapter/TwoBitAdapter.js +1 -1
- package/dist/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
- package/esm/ChromSizesAdapter/ChromSizesAdapter.js +1 -1
- package/esm/ChromSizesAdapter/ChromSizesAdapter.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/model.d.ts +1 -1
- package/esm/ReferenceSequenceTrack/configSchema.js +12 -0
- package/esm/ReferenceSequenceTrack/configSchema.js.map +1 -1
- package/esm/TwoBitAdapter/TwoBitAdapter.js +1 -1
- package/esm/TwoBitAdapter/TwoBitAdapter.js.map +1 -1
- package/package.json +2 -2
- package/src/ChromSizesAdapter/ChromSizesAdapter.ts +1 -1
- package/src/ReferenceSequenceTrack/configSchema.ts +13 -0
- package/src/TwoBitAdapter/TwoBitAdapter.ts +1 -1
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@@ -8,7 +8,7 @@ class default_1 extends BaseAdapter_1.BaseAdapter {
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const file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
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const data = await file.readFile('utf8');
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return Object.fromEntries(data
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-
.split(
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.split(/\n|\r\n|\r/)
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.map(f => f.trim())
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.filter(f => !!f)
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.map((line) => {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"ChromSizesAdapter.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/ChromSizesAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,8CAAoD;AAEpD,eAAqB,SAAQ,yBAAW;IAItC,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,oBAAoB,CAAC,EAAE,EAAE,CAAC,CAAA;QACjE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;aACD,KAAK,CAAC,
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1
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+
{"version":3,"file":"ChromSizesAdapter.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/ChromSizesAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,8CAAoD;AAEpD,eAAqB,SAAQ,yBAAW;IAItC,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,oBAAoB,CAAC,EAAE,EAAE,CAAC,CAAA;QACjE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;aACD,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;aAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE;YACpB,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;QACxB,CAAC,CAAC,CACL,CAAA;IACH,CAAC;IAED,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAClC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC1C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,OAAO,CAAC,OAAO,CAAC;SACtB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,SAAS;QACd,OAAO,EAAE,CAAA;IACX,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AA5CD,4BA4CC"}
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@@ -104,7 +104,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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readonly adapterConfig: any;
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readonly parentTrack: any;
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renderProps(): any;
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readonly rendererType:
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readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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readonly DisplayMessageComponent: import("react").FC<any> | undefined;
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
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@@ -23,6 +23,18 @@ function createReferenceSeqTrackConfig(pluginManager) {
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description: 'anything to add about this track',
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defaultValue: {},
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},
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formatAbout: (0, configuration_1.ConfigurationSchema)('FormatAbout', {
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config: {
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type: 'frozen',
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description: 'formats configuration in about dialog',
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defaultValue: {},
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contextVariable: ['config'],
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},
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hideUris: {
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type: 'boolean',
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defaultValue: false,
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},
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}),
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}, {
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preProcessSnapshot: s => {
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const snap = JSON.parse(JSON.stringify(s));
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@@ -1 +1 @@
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-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":";;;AAAA,uDAAuD;AACvD,qDAAuC;AACvC,+DAAiE;AAGjE;;;;EAIE;AACF,SAAgB,6BAA6B,CAAC,aAA4B;IACxE,OAAO,IAAA,mCAAmB,EACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":";;;AAAA,uDAAuD;AACvD,qDAAuC;AACvC,+DAAiE;AAGjE;;;;EAIE;AACF,SAAgB,6BAA6B,CAAC,aAA4B;IACxE,OAAO,IAAA,mCAAmB,EACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;QAED,WAAW,EAAE,IAAA,mCAAmB,EAAC,aAAa,EAAE;YAC9C,MAAM,EAAE;gBACN,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,uCAAuC;gBACpD,YAAY,EAAE,EAAE;gBAChB,eAAe,EAAE,CAAC,QAAQ,CAAC;aAC5B;YACD,QAAQ,EAAE;gBACR,IAAI,EAAE,SAAS;gBACf,YAAY,EAAE,KAAK;aACpB;SACF,CAAC;KACH,EACD;QACE,kBAAkB,EAAE,CAAC,CAAC,EAAE;YACtB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,YAAY,GAAG,IAAI,GAAG,EAAE,CAAA;YAC9B,MAAM,EAAE,QAAQ,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;YAC9B,IAAI,IAAI,CAAC,OAAO,KAAK,eAAe,EAAE;gBACpC,oEAAoE;gBACpE,oEAAoE;gBACpE,WAAW;gBACX,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;gBAC3D,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACvD,SAAS,CAAC,YAAY,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE;oBAC3C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE;wBACvC,QAAQ,CAAC,IAAI,CAAC;4BACZ,SAAS,EAAE,GAAG,IAAI,CAAC,OAAO,IAAI,WAAW,CAAC,IAAI,EAAE;4BAChD,IAAI,EAAE,WAAW,CAAC,IAAI;yBACvB,CAAC,CAAA;qBACH;gBACH,CAAC,CAAC,CAAA;aACH;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,QAAQ,EAAE,CAAA;QAC9B,CAAC;QACD,kBAAkB,EAAE,SAAS;QAC7B,eAAe,EAAE,IAAI;QACrB,OAAO,EAAE,CAAC,IAAS,EAAE,EAAE,CAAC,CAAC;YACvB,cAAc,CAAC,WAAgD;gBAC7D,MAAM,EAAE,IAAI,EAAE,GAAG,WAAW,CAAA;gBAC5B,IAAI,CAAC,IAAI,EAAE;oBACT,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;iBAChD;gBACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAChC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,KAAK,WAAW,CAAC,SAAS,CACvD,CAAA;gBACD,IAAI,OAAO,EAAE;oBACX,OAAO,OAAO,CAAA;iBACf;gBACD,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC9C,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;SACF,CAAC;KACH,CACF,CAAA;AACH,CAAC;AAxED,sEAwEC"}
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@@ -25,7 +25,7 @@ class TwoBitAdapter extends BaseAdapter_1.BaseSequenceAdapter {
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if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
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const file = (0, io_1.openLocation)(conf, this.pluginManager);
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const data = await file.readFile('utf8');
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return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split(
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return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split(/\n|\r\n|\r/).filter(line => !!line.trim()).map(line => {
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const [name, length] = line.split('\t');
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return [name, +length];
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}));
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{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,
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{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAA6E;AAE7E,8CAAoD;AACpD,kDAA0D;AAC1D,qFAAyE;AACzE,yCAAyC;AACzC,+DAA4D;AAK5D,MAAqB,aAAc,SAAQ,iCAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,mBAAU,CAAC;YAC3B,UAAU,EAAE,IAAA,iBAAY,EACtB,IAAA,8BAAc,EAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,IAAA,iBAAY,EAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAiBM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAhGD,gCAgGC"}
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.split(
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{"version":3,"file":"ChromSizesAdapter.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/ChromSizesAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,WAAW,GACZ,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AAEpD,MAAM,CAAC,OAAO,MAAO,SAAQ,WAAW;IAItC,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,oBAAoB,CAAC,EAAE,EAAE,CAAC,CAAA;QACjE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;aACD,KAAK,CAAC,
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+
{"version":3,"file":"ChromSizesAdapter.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/ChromSizesAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,WAAW,GACZ,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AAEpD,MAAM,CAAC,OAAO,MAAO,SAAQ,WAAW;IAItC,KAAK,CAAC,QAAQ;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,oBAAoB,CAAC,EAAE,EAAE,CAAC,CAAA;QACjE,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI;aACD,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;aAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,GAAG,CAAC,CAAC,IAAY,EAAE,EAAE;YACpB,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;QACxB,CAAC,CAAC,CACL,CAAA;IACH,CAAC;IAED,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAClC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC1C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,OAAO,CAAC,OAAO,CAAC;SACtB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,SAAS;QACd,OAAO,EAAE,CAAA;IACX,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
|
|
@@ -104,7 +104,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
104
104
|
readonly adapterConfig: any;
|
|
105
105
|
readonly parentTrack: any;
|
|
106
106
|
renderProps(): any;
|
|
107
|
-
readonly rendererType:
|
|
107
|
+
readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
|
|
108
108
|
readonly DisplayMessageComponent: import("react").FC<any> | undefined;
|
|
109
109
|
trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
|
|
110
110
|
readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
|
|
@@ -20,6 +20,18 @@ export function createReferenceSeqTrackConfig(pluginManager) {
|
|
|
20
20
|
description: 'anything to add about this track',
|
|
21
21
|
defaultValue: {},
|
|
22
22
|
},
|
|
23
|
+
formatAbout: ConfigurationSchema('FormatAbout', {
|
|
24
|
+
config: {
|
|
25
|
+
type: 'frozen',
|
|
26
|
+
description: 'formats configuration in about dialog',
|
|
27
|
+
defaultValue: {},
|
|
28
|
+
contextVariable: ['config'],
|
|
29
|
+
},
|
|
30
|
+
hideUris: {
|
|
31
|
+
type: 'boolean',
|
|
32
|
+
defaultValue: false,
|
|
33
|
+
},
|
|
34
|
+
}),
|
|
23
35
|
}, {
|
|
24
36
|
preProcessSnapshot: s => {
|
|
25
37
|
const snap = JSON.parse(JSON.stringify(s));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE;;;;EAIE;AACF,MAAM,UAAU,6BAA6B,CAAC,aAA4B;IACxE,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ReferenceSequenceTrack/configSchema.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE;;;;EAIE;AACF,MAAM,UAAU,6BAA6B,CAAC,aAA4B;IACxE,OAAO,mBAAmB,CACxB,wBAAwB,EACxB;QACE,OAAO,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;QAC3D,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC,CAAC;QACzE,IAAI,EAAE;YACJ,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,EAAE;SACjB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,kCAAkC;YAC/C,YAAY,EAAE,EAAE;SACjB;QAED,WAAW,EAAE,mBAAmB,CAAC,aAAa,EAAE;YAC9C,MAAM,EAAE;gBACN,IAAI,EAAE,QAAQ;gBACd,WAAW,EAAE,uCAAuC;gBACpD,YAAY,EAAE,EAAE;gBAChB,eAAe,EAAE,CAAC,QAAQ,CAAC;aAC5B;YACD,QAAQ,EAAE;gBACR,IAAI,EAAE,SAAS;gBACf,YAAY,EAAE,KAAK;aACpB;SACF,CAAC;KACH,EACD;QACE,kBAAkB,EAAE,CAAC,CAAC,EAAE;YACtB,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1C,MAAM,YAAY,GAAG,IAAI,GAAG,EAAE,CAAA;YAC9B,MAAM,EAAE,QAAQ,GAAG,EAAE,EAAE,GAAG,IAAI,CAAA;YAC9B,IAAI,IAAI,CAAC,OAAO,KAAK,eAAe,EAAE;gBACpC,oEAAoE;gBACpE,oEAAoE;gBACpE,WAAW;gBACX,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;gBAC3D,MAAM,SAAS,GAAG,aAAa,CAAC,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACvD,SAAS,CAAC,YAAY,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE;oBAC3C,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE;wBACvC,QAAQ,CAAC,IAAI,CAAC;4BACZ,SAAS,EAAE,GAAG,IAAI,CAAC,OAAO,IAAI,WAAW,CAAC,IAAI,EAAE;4BAChD,IAAI,EAAE,WAAW,CAAC,IAAI;yBACvB,CAAC,CAAA;qBACH;gBACH,CAAC,CAAC,CAAA;aACH;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,QAAQ,EAAE,CAAA;QAC9B,CAAC;QACD,kBAAkB,EAAE,SAAS;QAC7B,eAAe,EAAE,IAAI;QACrB,OAAO,EAAE,CAAC,IAAS,EAAE,EAAE,CAAC,CAAC;YACvB,cAAc,CAAC,WAAgD;gBAC7D,MAAM,EAAE,IAAI,EAAE,GAAG,WAAW,CAAA;gBAC5B,IAAI,CAAC,IAAI,EAAE;oBACT,MAAM,IAAI,KAAK,CAAC,wBAAwB,IAAI,EAAE,CAAC,CAAA;iBAChD;gBACD,MAAM,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAChC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,KAAK,WAAW,CAAC,SAAS,CACvD,CAAA;gBACD,IAAI,OAAO,EAAE;oBACX,OAAO,OAAO,CAAA;iBACf;gBACD,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;gBAC9C,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;SACF,CAAC;KACH,CACF,CAAA;AACH,CAAC"}
|
|
@@ -20,7 +20,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
|
|
|
20
20
|
if (conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '') {
|
|
21
21
|
const file = openLocation(conf, this.pluginManager);
|
|
22
22
|
const data = await file.readFile('utf8');
|
|
23
|
-
return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split(
|
|
23
|
+
return Object.fromEntries(data === null || data === void 0 ? void 0 : data.split(/\n|\r\n|\r/).filter(line => !!line.trim()).map(line => {
|
|
24
24
|
const [name, length] = line.split('\t');
|
|
25
25
|
return [name, +length];
|
|
26
26
|
}));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAK5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,mBAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,UAAU,CAAC;YAC3B,UAAU,EAAE,YAAY,CACtB,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,
|
|
1
|
+
{"version":3,"file":"TwoBitAdapter.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/TwoBitAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAA;AAE7E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,cAAc,CAAA;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAK5D,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,mBAAmB;IA4B5D,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAC3C,IAAI,CAAC,MAAM,GAAG,IAAI,UAAU,CAAC;YAC3B,UAAU,EAAE,YAAY,CACtB,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,EACxC,IAAI,CAAC,aAAa,CACnB;SACF,CAAC,CAAA;IACJ,CAAC;IAlCO,KAAK,CAAC,cAAc;QAC1B,MAAM,IAAI,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;QAC9D,2EAA2E;QAC3E,yEAAyE;QACzE,SAAS;QACT,IAAI,IAAI,CAAC,GAAG,KAAK,8BAA8B,IAAI,IAAI,CAAC,GAAG,KAAK,EAAE,EAAE;YAClE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,CAAA;YACnD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACxC,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CACA,KAAK,CAAC,YAAY,EACnB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,EAAE,EAC5B,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,CAAC,IAAI,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACvC,OAAO,CAAC,IAAI,EAAE,CAAC,MAAM,CAAC,CAAA;YACxB,CAAC,CAAC,CACL,CAAA;SACF;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAiBM,KAAK,CAAC,WAAW;QACtB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAA;SACnC;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;IACvC,CAAC;IAEM,KAAK,CAAC,UAAU;QACrB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,cAAc,CAAA;QAChD,IAAI,cAAc,EAAE;YAClB,OAAO,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;gBACjD,OAAO;gBACP,KAAK,EAAE,CAAC;gBACR,GAAG,EAAE,cAAc,CAAC,OAAO,CAAC;aAC7B,CAAC,CAAC,CAAA;SACJ;QACD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,gBAAgB,EAAE,CAAA;QACrD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAED;;;;OAIG;IACI,WAAW,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAoB;QAC1D,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,eAAe,CAAC,OAAO,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;YACpE,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-sequence",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.7",
|
|
4
4
|
"description": "JBrowse 2 sequence adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -59,5 +59,5 @@
|
|
|
59
59
|
"distModule": "esm/index.js",
|
|
60
60
|
"srcModule": "src/index.ts",
|
|
61
61
|
"module": "esm/index.js",
|
|
62
|
-
"gitHead": "
|
|
62
|
+
"gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
|
|
63
63
|
}
|
|
@@ -14,7 +14,7 @@ export default class extends BaseAdapter implements RegionsAdapter {
|
|
|
14
14
|
const data = await file.readFile('utf8')
|
|
15
15
|
return Object.fromEntries(
|
|
16
16
|
data
|
|
17
|
-
.split(
|
|
17
|
+
.split(/\n|\r\n|\r/)
|
|
18
18
|
.map(f => f.trim())
|
|
19
19
|
.filter(f => !!f)
|
|
20
20
|
.map((line: string) => {
|
|
@@ -24,6 +24,19 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
|
|
|
24
24
|
description: 'anything to add about this track',
|
|
25
25
|
defaultValue: {},
|
|
26
26
|
},
|
|
27
|
+
|
|
28
|
+
formatAbout: ConfigurationSchema('FormatAbout', {
|
|
29
|
+
config: {
|
|
30
|
+
type: 'frozen',
|
|
31
|
+
description: 'formats configuration in about dialog',
|
|
32
|
+
defaultValue: {},
|
|
33
|
+
contextVariable: ['config'],
|
|
34
|
+
},
|
|
35
|
+
hideUris: {
|
|
36
|
+
type: 'boolean',
|
|
37
|
+
defaultValue: false,
|
|
38
|
+
},
|
|
39
|
+
}),
|
|
27
40
|
},
|
|
28
41
|
{
|
|
29
42
|
preProcessSnapshot: s => {
|
|
@@ -26,7 +26,7 @@ export default class TwoBitAdapter extends BaseSequenceAdapter {
|
|
|
26
26
|
const data = await file.readFile('utf8')
|
|
27
27
|
return Object.fromEntries(
|
|
28
28
|
data
|
|
29
|
-
?.split(
|
|
29
|
+
?.split(/\n|\r\n|\r/)
|
|
30
30
|
.filter(line => !!line.trim())
|
|
31
31
|
.map(line => {
|
|
32
32
|
const [name, length] = line.split('\t')
|