@jbrowse/plugin-alignments 2.3.2 → 2.3.4
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/BamAdapter/BamAdapter.js +2 -1
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +3 -3
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/dist/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/dist/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/dist/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/dist/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/util.js +3 -3
- package/dist/util.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -1
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/CramAdapter/CramAdapter.js +3 -3
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/esm/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/esm/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/esm/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/esm/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/util.js +3 -3
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/AlignmentsFeatureDetail/__snapshots__/{index.test.js.snap → index.test.tsx.snap} +6 -6
- package/src/AlignmentsFeatureDetail/{index.test.js → index.test.tsx} +4 -2
- package/src/BamAdapter/BamAdapter.test.ts +5 -4
- package/src/BamAdapter/BamAdapter.ts +2 -1
- package/src/CombinationTest.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.ts +11 -9
- package/src/LinearAlignmentsDisplay/models/{configSchema.test.js → configSchema.test.ts} +5 -1
- package/src/LinearSNPCoverageDisplay/models/{configSchema.test.js → configSchema.test.ts} +3 -1
- package/src/PileupRPC/methods/GetGlobalValueForTag.ts +4 -1
- package/src/PileupRPC/methods/GetReducedFeatures.ts +4 -5
- package/src/PileupRPC/methods/GetVisibleModifications.ts +4 -4
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +6 -4
- package/src/index.test.ts +0 -1
- package/src/util.ts +10 -8
- package/src/PileupRenderer/components/PileupRendering.test.js +0 -21
- package/src/PileupRenderer/components/__snapshots__/PileupRendering.test.js.snap +0 -23
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@@ -11,6 +11,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
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const operators_1 = require("rxjs/operators");
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// locals
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const BamSlightlyLazyFeature_1 = __importDefault(require("./BamSlightlyLazyFeature"));
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const rxjs_2 = require("rxjs");
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class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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// derived classes may not use the same configuration so a custom
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// configure method allows derived classes to override this behavior
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@@ -109,7 +110,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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end,
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assemblyName: '',
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});
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-
const seqChunks = await features.pipe((0, operators_1.toArray)())
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const seqChunks = await (0, rxjs_2.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
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let sequence = '';
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seqChunks
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.sort((a, b) => a.get('start') - b.get('start'))
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAAmC;AACnC,yEAGgD;AAEhD,6CAA2E;AAC3E,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AAExC,SAAS;AACT,sFAA6D;
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1
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+
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAAmC;AACnC,yEAGgD;AAEhD,6CAA2E;AAC3E,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AAExC,SAAS;AACT,sFAA6D;AAC7D,+BAAqC;AAOrC,MAAqB,UAAW,SAAQ,oCAAsB;IAS5D,iEAAiE;IACjE,oEAAoE;IAC1D,KAAK,CAAC,YAAY;QAC1B,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACtD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,SAAS,KAAK,KAAK,CAAA;QAC/B,MAAM,GAAG,GAAG,IAAI,aAAO,CAAC;YACtB,aAAa,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,EAAE,CAAC;YAC5C,aAAa,EAAE,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC3D,aAAa,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAE5D,8DAA8D;YAC9D,gEAAgE;YAChE,mEAAmE;YACnE,cAAc,EAAE,QAAQ;YACxB,cAAc,EAAE,QAAQ;YACxB,eAAe,EAAE,QAAQ;SAC1B,CAAC,CAAA;QAEF,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YAC/D,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,WAAqC;aACvD,CAAA;SACF;aAAM;YACL,OAAO,EAAE,GAAG,EAAE,CAAA;SACf;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,IAAI,CAAC,SAAS,GAAG,MAAM,IAAA,mBAAY,EACjC,mBAAmB,EACnB,cAAc,EACd,KAAK,IAAI,EAAE;YACT,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAE3C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS;iBACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAA;QAC/B,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3C,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAa,EAAE,GAAW;QAChE,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,WAAW,GAAG,eAAe,CAAA;QACnC,IAAI,CAAC,WAAW,EAAE;YAChB,OAAO,SAAS,CAAA;SACjB;QACD,IAAI,CAAC,OAAO,EAAE;YACZ,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,QAAQ,GAAG,WAAW,CAAC,WAAW,CAAC;YACvC,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC,CAAA;QAEF,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EAAC,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;QAEhE,IAAI,QAAQ,GAAG,EAAE,CAAA;QACjB,SAAS;aACN,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,OAAO,CAAC,KAAK,CAAC,EAAE;YACf,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,QAAQ,IAAI,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QACpD,CAAC,CAAC,CAAA;QAEJ,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAOC;QAED,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QACvD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACtC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACtB,cAAc,CAAC,wBAAwB,CAAC,CAAA;YACxC,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,kBAAkB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;YAEvE,MAAM,EACJ,WAAW,GAAG,CAAC,EACf,WAAW,GAAG,CAAC,EACf,SAAS,EACT,QAAQ,GACT,GAAG,QAAQ,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@@ -9,6 +9,7 @@ const util_1 = require("@jbrowse/core/util");
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{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAAsE;AACtE,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;
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+
{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qCAAmE;AACnE,yEAIgD;AAChD,6CAAsE;AACtE,8CAAoD;AACpD,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AACrC,wFAA+D;AAe/D,MAAqB,WAAY,SAAQ,oCAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAwQ/C,CAAC;IAtQQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,sBAAe,CAAC;YAC/B,cAAc,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,gBAAS,CAAC,EAAE,UAAU,EAAE,IAAA,iBAAY,EAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,IAAA,qBAAc,EACpC,eAAe;aACZ,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;QAED,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QAC/C,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACnC,cAAc,CAAC,mBAAmB,CAAC,CAAA;QACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;QACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;QAEhD,oDAAoD;QACpD,2CAA2C;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;QAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,SAAS;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;YACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,uBAAuB;oBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iBAC1B;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEJ,MAAM,UAAU,GAAG,SAAS;aACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;QAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;QAC/C,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;IACrC,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,OAAO,SAAS,CAAC,QAAQ,CAAA;IAC3B,CAAC;IAED,mEAAmE;IACnE,gEAAgE;IAChE,WAAW,CAAC,OAAe;QACzB,IAAI,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE;YAC3B,OAAO,IAAI,CAAC,SAAS,CAAC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@@ -45,7 +45,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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}) => any;
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|
renderProps: any;
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} & {
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-
doReload(): void;
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doReload(): void; /**
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* #action
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+
*/
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afterAttach(): void;
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setStatus(message: string): void;
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|
setLoading(abortController: AbortController): void;
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@@ -56,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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layout: any;
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maxHeightReached: boolean;
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renderProps: any;
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} | undefined): void;
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* #getter
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-
*/
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} | undefined): void;
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|
setError(error: unknown): void;
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reload(): void;
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beforeDestroy(): void;
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@@ -152,13 +152,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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|
rendererTypeName: string;
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error: unknown;
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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* #getter
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*/
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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|
type: import("mobx-state-tree").ISimpleType<string>;
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|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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rendererTypeName: string;
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+
rendererTypeName: string; /**
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* #method
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*/
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error: unknown;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}> | null;
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@@ -5,6 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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|
Object.defineProperty(exports, "__esModule", { value: true });
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6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
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7
7
|
const operators_1 = require("rxjs/operators");
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8
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+
const rxjs_1 = require("rxjs");
|
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9
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+
// locals
|
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8
10
|
const base_1 = __importDefault(require("../base"));
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9
11
|
const util_1 = require("../../util");
|
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10
12
|
class PileupGetGlobalValueForTag extends base_1.default {
|
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@@ -16,7 +18,7 @@ class PileupGetGlobalValueForTag extends base_1.default {
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18
|
const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
|
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|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
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|
const features = dataAdapter.getFeaturesInMultipleRegions(regions);
|
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19
|
-
const featuresArray = await features.pipe((0, operators_1.toArray)())
|
|
21
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
|
|
20
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|
return [
|
|
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23
|
...new Set(featuresArray
|
|
22
24
|
.map(feature => (0, util_1.getTag)(feature, tag))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,mDAAmC;AACnC,qCAAmC;AAEnC,MAAqB,0BAA2B,SAAQ,cAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,mDAAmC;AACnC,qCAAmC;AAEnC,MAAqB,0BAA2B,SAAQ,cAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EAAC,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;QACpE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,IAAA,aAAM,EAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF;AAhCD,6CAgCC"}
|
|
@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
6
6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
|
|
7
7
|
const util_1 = require("@jbrowse/core/util");
|
|
8
8
|
const operators_1 = require("rxjs/operators");
|
|
9
|
+
const rxjs_1 = require("rxjs");
|
|
9
10
|
// locals
|
|
10
11
|
const util_2 = require("../util");
|
|
11
12
|
const base_1 = __importDefault(require("../base"));
|
|
@@ -20,10 +21,7 @@ class PileupGetReducedFeatures extends base_1.default {
|
|
|
20
21
|
const des = await this.deserializeArguments(args, rpcDriver);
|
|
21
22
|
const { adapterConfig, sessionId, regions } = des;
|
|
22
23
|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
23
|
-
const featuresArray = await dataAdapter
|
|
24
|
-
.getFeaturesInMultipleRegions(regions, des)
|
|
25
|
-
.pipe((0, operators_1.toArray)())
|
|
26
|
-
.toPromise();
|
|
24
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe((0, operators_1.toArray)()));
|
|
27
25
|
const reduced = (0, util_1.dedupe)(featuresArray.map(f => ({
|
|
28
26
|
id: f.id(),
|
|
29
27
|
refName: f.get('refName'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AACzE,6CAAmD;AAGnD,8CAAwC;
|
|
1
|
+
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AACzE,6CAAmD;AAGnD,8CAAwC;AACxC,+BAAqC;AACrC,SAAS;AACT,kCAA4D;AAE5D,mDAAmC;AACnC,qCAAmC;AAEnC,mEAAmE;AACnE,MAAqB,wBAAyB,SAAQ,cAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA4DnC,CAAC;IA1DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACvE,CAAA;QAED,MAAM,OAAO,GAAG,IAAA,aAAM,EACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,IAAA,aAAM,EAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,IAAA,qBAAc,EAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,IAAA,yBAAkB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF;AA7DD,2CA6DC"}
|
|
@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
|
|
7
7
|
const operators_1 = require("rxjs/operators");
|
|
8
|
+
const rxjs_1 = require("rxjs");
|
|
8
9
|
// locals
|
|
9
10
|
const MismatchParser_1 = require("../../MismatchParser");
|
|
10
11
|
const base_1 = __importDefault(require("../base"));
|
|
@@ -17,10 +18,7 @@ class PileupGetVisibleModifications extends base_1.default {
|
|
|
17
18
|
async execute(args, rpcDriver) {
|
|
18
19
|
const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
|
|
19
20
|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
20
|
-
const featuresArray = await dataAdapter
|
|
21
|
-
.getFeaturesInMultipleRegions(regions)
|
|
22
|
-
.pipe((0, operators_1.toArray)())
|
|
23
|
-
.toPromise();
|
|
21
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions).pipe((0, operators_1.toArray)()));
|
|
24
22
|
const uniqueValues = new Set();
|
|
25
23
|
featuresArray.forEach(f => {
|
|
26
24
|
(0, MismatchParser_1.getModificationTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;
|
|
1
|
+
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,yDAA2D;AAC3D,mDAAmC;AACnC,qCAAsC;AAEtC,MAAqB,6BAA8B,SAAQ,cAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IA+BxC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAClE,CAAA;QAED,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,IAAA,qCAAoB,EAAC,IAAA,gBAAS,EAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF;AAhCD,gDAgCC"}
|
|
@@ -8,6 +8,8 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
|
|
|
8
8
|
const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
|
|
9
9
|
const rxjs_1 = require("@jbrowse/core/util/rxjs");
|
|
10
10
|
const operators_1 = require("rxjs/operators");
|
|
11
|
+
const rxjs_2 = require("rxjs");
|
|
12
|
+
// locals
|
|
11
13
|
const generateCoverageBins_1 = __importDefault(require("./generateCoverageBins"));
|
|
12
14
|
const util_1 = require("../util");
|
|
13
15
|
class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
@@ -37,10 +39,7 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
37
39
|
getFeatures(region, opts = {}) {
|
|
38
40
|
return (0, rxjs_1.ObservableCreate)(async (observer) => {
|
|
39
41
|
const { subadapter } = await this.configure();
|
|
40
|
-
const feats = await subadapter
|
|
41
|
-
.getFeatures(region, opts)
|
|
42
|
-
.pipe((0, operators_1.toArray)())
|
|
43
|
-
.toPromise();
|
|
42
|
+
const feats = await (0, rxjs_2.firstValueFrom)(subadapter.getFeatures(region, opts).pipe((0, operators_1.toArray)()));
|
|
44
43
|
const { bins, skipmap } = await (0, generateCoverageBins_1.default)(feats, region, opts, arg => this.fetchSequence(arg));
|
|
45
44
|
bins.forEach((bin, index) => {
|
|
46
45
|
const start = region.start + index;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,kFAAyD;AACzD,kCAAuC;AAEvC,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,kFAAyD;AACzD,kCAAuC;AAEvC,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,UAAU,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACrD,CAAA;YAED,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAA,8BAAoB,EAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AA7FD,qCA6FC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAClC,oCAAY"}
|
package/dist/util.js
CHANGED
|
@@ -2,6 +2,7 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
|
|
4
4
|
const operators_1 = require("rxjs/operators");
|
|
5
|
+
const rxjs_1 = require("rxjs");
|
|
5
6
|
// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
|
|
6
7
|
// BAM does not
|
|
7
8
|
function getTag(feature, tag) {
|
|
@@ -72,14 +73,13 @@ exports.getColorWGBS = getColorWGBS;
|
|
|
72
73
|
async function fetchSequence(region, adapter) {
|
|
73
74
|
var _a;
|
|
74
75
|
const { end, originalRefName, refName } = region;
|
|
75
|
-
const feats = await adapter
|
|
76
|
+
const feats = await (0, rxjs_1.firstValueFrom)(adapter
|
|
76
77
|
.getFeatures({
|
|
77
78
|
...region,
|
|
78
79
|
refName: originalRefName || refName,
|
|
79
80
|
end: end + 1,
|
|
80
81
|
})
|
|
81
|
-
.pipe((0, operators_1.toArray)())
|
|
82
|
-
.toPromise();
|
|
82
|
+
.pipe((0, operators_1.toArray)()));
|
|
83
83
|
return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
|
|
84
84
|
}
|
|
85
85
|
exports.fetchSequence = fetchSequence;
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AACA,8CAAwC;AAGxC,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAEM,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,OAAO;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AACA,8CAAwC;AAGxC,+BAAqC;AACrC,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAEM,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;KACb,CAAC;SACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAhBD,sCAgBC;AAED,kEAAkE;AAClE,SAAgB,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC;AAFD,oEAEC"}
|
|
@@ -6,6 +6,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
|
6
6
|
import { toArray } from 'rxjs/operators';
|
|
7
7
|
// locals
|
|
8
8
|
import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
|
|
9
|
+
import { firstValueFrom } from 'rxjs';
|
|
9
10
|
export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
10
11
|
// derived classes may not use the same configuration so a custom
|
|
11
12
|
// configure method allows derived classes to override this behavior
|
|
@@ -104,7 +105,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
|
104
105
|
end,
|
|
105
106
|
assemblyName: '',
|
|
106
107
|
});
|
|
107
|
-
const seqChunks = await features.pipe(toArray())
|
|
108
|
+
const seqChunks = await firstValueFrom(features.pipe(toArray()));
|
|
108
109
|
let sequence = '';
|
|
109
110
|
seqChunks
|
|
110
111
|
.sort((a, b) => a.get('start') - b.get('start'))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,eAAe,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC3E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;
|
|
1
|
+
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,eAAe,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC3E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAOrC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAS5D,iEAAiE;IACjE,oEAAoE;IAC1D,KAAK,CAAC,YAAY;QAC1B,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,CAAA;QAC/C,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QACtD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,SAAS,KAAK,KAAK,CAAA;QAC/B,MAAM,GAAG,GAAG,IAAI,OAAO,CAAC;YACtB,aAAa,EAAE,YAAY,CAAC,WAAW,EAAE,EAAE,CAAC;YAC5C,aAAa,EAAE,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC3D,aAAa,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAE5D,8DAA8D;YAC9D,gEAAgE;YAChE,mEAAmE;YACnE,cAAc,EAAE,QAAQ;YACxB,cAAc,EAAE,QAAQ;YACxB,eAAe,EAAE,QAAQ;SAC1B,CAAC,CAAA;QAEF,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YAC/D,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,WAAqC;aACvD,CAAA;SACF;aAAM;YACL,OAAO,EAAE,GAAG,EAAE,CAAA;SACf;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,IAAI,CAAC,SAAS,GAAG,MAAM,YAAY,CACjC,mBAAmB,EACnB,cAAc,EACd,KAAK,IAAI,EAAE;YACT,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAE3C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,SAAS;iBACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;iBAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;gBACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEJ,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,CAAA;QAC/B,CAAC,CACF,CAAA;QACD,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,IAAkB;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC3C,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAa,EAAE,GAAW;QAChE,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,WAAW,GAAG,eAAe,CAAA;QACnC,IAAI,CAAC,WAAW,EAAE;YAChB,OAAO,SAAS,CAAA;SACjB;QACD,IAAI,CAAC,OAAO,EAAE;YACZ,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,QAAQ,GAAG,WAAW,CAAC,WAAW,CAAC;YACvC,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC,CAAA;QAEF,MAAM,SAAS,GAAG,MAAM,cAAc,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;QAEhE,IAAI,QAAQ,GAAG,EAAE,CAAA;QACjB,SAAS;aACN,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,OAAO,CAAC,KAAK,CAAC,EAAE;YACf,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,QAAQ,IAAI,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QACpD,CAAC,CAAC,CAAA;QAEJ,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAED,WAAW,CACT,MAA6C,EAC7C,IAOC;QAED,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,eAAe,EAAE,GAAG,MAAM,CAAA;QACvD,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAClE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YACtC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;Y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@@ -4,6 +4,7 @@ import { checkAbortSignal } from '@jbrowse/core/util';
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4
4
|
import { openLocation } from '@jbrowse/core/util/io';
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|
5
5
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
6
6
|
import { toArray } from 'rxjs/operators';
|
|
7
|
+
import { firstValueFrom } from 'rxjs';
|
|
7
8
|
import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
|
|
8
9
|
export default class CramAdapter extends BaseFeatureDataAdapter {
|
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9
10
|
constructor() {
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@@ -59,15 +60,14 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
|
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59
60
|
if (!refName) {
|
|
60
61
|
throw new Error('unknown');
|
|
61
62
|
}
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|
62
|
-
const seqChunks = await sequenceAdapter
|
|
63
|
+
const seqChunks = await firstValueFrom(sequenceAdapter
|
|
63
64
|
.getFeatures({
|
|
64
65
|
refName,
|
|
65
66
|
start,
|
|
66
67
|
end,
|
|
67
68
|
assemblyName: '',
|
|
68
69
|
})
|
|
69
|
-
.pipe(toArray())
|
|
70
|
-
.toPromise();
|
|
70
|
+
.pipe(toArray()));
|
|
71
71
|
const sequence = seqChunks
|
|
72
72
|
.sort((a, b) => a.get('start') - b.get('start'))
|
|
73
73
|
.map(chunk => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,eAAe,EAAc,MAAM,YAAY,CAAA;AACnE,OAAO,EACL,sBAAsB,GAGvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAmB,MAAM,oBAAoB,CAAA;AACtE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAe/D,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,sBAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;
|
|
1
|
+
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|
@@ -45,7 +45,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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45
45
|
}) => any;
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|
renderProps: any;
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|
} & {
|
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|
-
doReload(): void;
|
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48
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+
doReload(): void; /**
|
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+
* #action
|
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50
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+
*/
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49
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|
afterAttach(): void;
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setStatus(message: string): void;
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|
setLoading(abortController: AbortController): void;
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@@ -56,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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layout: any;
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maxHeightReached: boolean;
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|
renderProps: any;
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-
} | undefined): void;
|
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|
-
* #getter
|
|
61
|
-
*/
|
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61
|
+
} | undefined): void;
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|
setError(error: unknown): void;
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reload(): void;
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|
beforeDestroy(): void;
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@@ -152,13 +152,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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152
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|
rendererTypeName: string;
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error: unknown;
|
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} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
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-
* #getter
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-
*/
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+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
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|
type: import("mobx-state-tree").ISimpleType<string>;
|
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|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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-
rendererTypeName: string;
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159
|
+
rendererTypeName: string; /**
|
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+
* #method
|
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+
*/
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error: unknown;
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|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
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164
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|
}> | null;
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@@ -1,5 +1,7 @@
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1
1
|
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
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2
2
|
import { toArray } from 'rxjs/operators';
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3
|
+
import { firstValueFrom } from 'rxjs';
|
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4
|
+
// locals
|
|
3
5
|
import PileupBaseRPC from '../base';
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4
6
|
import { getTag } from '../../util';
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|
5
7
|
export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
|
|
@@ -11,7 +13,7 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
|
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|
11
13
|
const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
|
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12
14
|
const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
13
15
|
const features = dataAdapter.getFeaturesInMultipleRegions(regions);
|
|
14
|
-
const featuresArray = await features.pipe(toArray())
|
|
16
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()));
|
|
15
17
|
return [
|
|
16
18
|
...new Set(featuresArray
|
|
17
19
|
.map(feature => getTag(feature, tag))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,0BAA2B,SAAQ,aAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,0BAA2B,SAAQ,aAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,cAAc,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;QACpE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF"}
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
|
|
2
2
|
import { dedupe } from '@jbrowse/core/util';
|
|
3
3
|
import { toArray } from 'rxjs/operators';
|
|
4
|
+
import { firstValueFrom } from 'rxjs';
|
|
4
5
|
// locals
|
|
5
6
|
import { filterForPairs, getInsertSizeStats } from '../util';
|
|
6
7
|
import PileupBaseRPC from '../base';
|
|
@@ -15,10 +16,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
|
|
|
15
16
|
const des = await this.deserializeArguments(args, rpcDriver);
|
|
16
17
|
const { adapterConfig, sessionId, regions } = des;
|
|
17
18
|
const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
18
|
-
const featuresArray = await dataAdapter
|
|
19
|
-
.getFeaturesInMultipleRegions(regions, des)
|
|
20
|
-
.pipe(toArray())
|
|
21
|
-
.toPromise();
|
|
19
|
+
const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe(toArray()));
|
|
22
20
|
const reduced = dedupe(featuresArray.map(f => ({
|
|
23
21
|
id: f.id(),
|
|
24
22
|
refName: f.get('refName'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,EAAU,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAGnD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;
|
|
1
|
+
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,EAAU,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAGnD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,SAAS;AACT,OAAO,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAE5D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,mEAAmE;AACnE,MAAM,CAAC,OAAO,OAAO,wBAAyB,SAAQ,aAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA4DnC,CAAC;IA1DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,cAAc,CACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QAED,MAAM,OAAO,GAAG,MAAM,CACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,kBAAkB,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}
|
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
|
|
2
2
|
import { toArray } from 'rxjs/operators';
|
|
3
|
+
import { firstValueFrom } from 'rxjs';
|
|
3
4
|
// locals
|
|
4
5
|
import { getModificationTypes } from '../../MismatchParser';
|
|
5
6
|
import PileupBaseRPC from '../base';
|
|
@@ -12,10 +13,7 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
|
|
|
12
13
|
async execute(args, rpcDriver) {
|
|
13
14
|
const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
|
|
14
15
|
const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
15
|
-
const featuresArray = await dataAdapter
|
|
16
|
-
.getFeaturesInMultipleRegions(regions)
|
|
17
|
-
.pipe(toArray())
|
|
18
|
-
.toPromise();
|
|
16
|
+
const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions).pipe(toArray()));
|
|
19
17
|
const uniqueValues = new Set();
|
|
20
18
|
featuresArray.forEach(f => {
|
|
21
19
|
getModificationTypes(getTagAlt(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;
|
|
1
|
+
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAA;AAC3D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AAEtC,MAAM,CAAC,OAAO,OAAO,6BAA8B,SAAQ,aAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IA+BxC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,cAAc,CACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAClE,CAAA;QAED,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,oBAAoB,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF"}
|
|
@@ -2,6 +2,8 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
|
|
|
2
2
|
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
|
|
3
3
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
4
4
|
import { toArray } from 'rxjs/operators';
|
|
5
|
+
import { firstValueFrom } from 'rxjs';
|
|
6
|
+
// locals
|
|
5
7
|
import generateCoverageBins from './generateCoverageBins';
|
|
6
8
|
import { fetchSequence } from '../util';
|
|
7
9
|
export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
@@ -31,10 +33,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
31
33
|
getFeatures(region, opts = {}) {
|
|
32
34
|
return ObservableCreate(async (observer) => {
|
|
33
35
|
const { subadapter } = await this.configure();
|
|
34
|
-
const feats = await subadapter
|
|
35
|
-
.getFeatures(region, opts)
|
|
36
|
-
.pipe(toArray())
|
|
37
|
-
.toPromise();
|
|
36
|
+
const feats = await firstValueFrom(subadapter.getFeatures(region, opts).pipe(toArray()));
|
|
38
37
|
const { bins, skipmap } = await generateCoverageBins(feats, region, opts, arg => this.fetchSequence(arg));
|
|
39
38
|
bins.forEach((bin, index) => {
|
|
40
39
|
const start = region.start + index;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,UAAU,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACrD,CAAA;YAED,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}
|
package/esm/util.js
CHANGED
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
import { toArray } from 'rxjs/operators';
|
|
2
|
+
import { firstValueFrom } from 'rxjs';
|
|
2
3
|
// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
|
|
3
4
|
// BAM does not
|
|
4
5
|
export function getTag(feature, tag) {
|
|
@@ -66,14 +67,13 @@ export function getColorWGBS(strand, base) {
|
|
|
66
67
|
export async function fetchSequence(region, adapter) {
|
|
67
68
|
var _a;
|
|
68
69
|
const { end, originalRefName, refName } = region;
|
|
69
|
-
const feats = await adapter
|
|
70
|
+
const feats = await firstValueFrom(adapter
|
|
70
71
|
.getFeatures({
|
|
71
72
|
...region,
|
|
72
73
|
refName: originalRefName || refName,
|
|
73
74
|
end: end + 1,
|
|
74
75
|
})
|
|
75
|
-
.pipe(toArray())
|
|
76
|
-
.toPromise();
|
|
76
|
+
.pipe(toArray()));
|
|
77
77
|
return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
|
|
78
78
|
}
|
|
79
79
|
// has to check underlying C-G (aka CpG) on the reference sequence
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAGxC,4EAA4E;AAC5E,eAAe;AACf,MAAM,UAAU,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,MAAM,UAAU,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAED,gDAAgD;AAChD,kFAAkF;AAClF,MAAM,CAAC,MAAM,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,OAAO;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAGxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,4EAA4E;AAC5E,eAAe;AACf,MAAM,UAAU,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,MAAM,UAAU,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAED,gDAAgD;AAChD,kFAAkF;AAClF,MAAM,CAAC,MAAM,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;KACb,CAAC;SACD,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED,kEAAkE;AAClE,MAAM,UAAU,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-alignments",
|
|
3
|
-
"version": "2.3.
|
|
3
|
+
"version": "2.3.4",
|
|
4
4
|
"description": "JBrowse 2 alignments adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -56,7 +56,7 @@
|
|
|
56
56
|
"mobx-react": "^7.0.0",
|
|
57
57
|
"mobx-state-tree": "^5.0.0",
|
|
58
58
|
"react": ">=16.8.0",
|
|
59
|
-
"rxjs": "^
|
|
59
|
+
"rxjs": "^7.0.0",
|
|
60
60
|
"tss-react": "^4.0.0"
|
|
61
61
|
},
|
|
62
62
|
"publishConfig": {
|
|
@@ -65,5 +65,5 @@
|
|
|
65
65
|
"distModule": "esm/index.js",
|
|
66
66
|
"srcModule": "src/index.ts",
|
|
67
67
|
"module": "esm/index.js",
|
|
68
|
-
"gitHead": "
|
|
68
|
+
"gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
|
|
69
69
|
}
|
package/src/AlignmentsFeatureDetail/__snapshots__/{index.test.js.snap → index.test.tsx.snap}
RENAMED
|
@@ -87,9 +87,9 @@ exports[`open up a widget 1`] = `
|
|
|
87
87
|
<div
|
|
88
88
|
class="css-1omt041-fieldValue"
|
|
89
89
|
>
|
|
90
|
-
<
|
|
90
|
+
<span>
|
|
91
91
|
ctgA_3_555_0:0:0_2:0:0_102d
|
|
92
|
-
</
|
|
92
|
+
</span>
|
|
93
93
|
</div>
|
|
94
94
|
</div>
|
|
95
95
|
<div
|
|
@@ -103,9 +103,9 @@ exports[`open up a widget 1`] = `
|
|
|
103
103
|
<div
|
|
104
104
|
class="css-1omt041-fieldValue"
|
|
105
105
|
>
|
|
106
|
-
<
|
|
106
|
+
<span>
|
|
107
107
|
100
|
|
108
|
-
</
|
|
108
|
+
</span>
|
|
109
109
|
</div>
|
|
110
110
|
</div>
|
|
111
111
|
<div
|
|
@@ -119,9 +119,9 @@ exports[`open up a widget 1`] = `
|
|
|
119
119
|
<div
|
|
120
120
|
class="css-1omt041-fieldValue"
|
|
121
121
|
>
|
|
122
|
-
<
|
|
122
|
+
<span>
|
|
123
123
|
match
|
|
124
|
-
</
|
|
124
|
+
</span>
|
|
125
125
|
</div>
|
|
126
126
|
</div>
|
|
127
127
|
<hr
|
|
@@ -1,13 +1,14 @@
|
|
|
1
|
+
import React from 'react'
|
|
1
2
|
import { render } from '@testing-library/react'
|
|
2
3
|
import { types } from 'mobx-state-tree'
|
|
3
|
-
import React from 'react'
|
|
4
4
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
5
5
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
6
|
+
|
|
7
|
+
// locals
|
|
6
8
|
import { stateModelFactory } from '.'
|
|
7
9
|
import ReactComponent from './AlignmentsFeatureDetail'
|
|
8
10
|
|
|
9
11
|
test('open up a widget', () => {
|
|
10
|
-
console.warn = jest.fn()
|
|
11
12
|
const pluginManager = new PluginManager([])
|
|
12
13
|
|
|
13
14
|
const Session = types.model({
|
|
@@ -17,6 +18,7 @@ test('open up a widget', () => {
|
|
|
17
18
|
})
|
|
18
19
|
const session = Session.create(
|
|
19
20
|
{
|
|
21
|
+
// @ts-ignore
|
|
20
22
|
widget: { type: 'AlignmentsFeatureWidget' },
|
|
21
23
|
},
|
|
22
24
|
{ pluginManager },
|
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
import { toArray } from 'rxjs/operators'
|
|
2
|
+
import { firstValueFrom } from 'rxjs'
|
|
2
3
|
import Adapter from './BamAdapter'
|
|
3
4
|
import configSchema from './configSchema'
|
|
4
5
|
|
|
@@ -25,7 +26,7 @@ test('adapter can fetch features from volvox.bam', async () => {
|
|
|
25
26
|
end: 20000,
|
|
26
27
|
})
|
|
27
28
|
|
|
28
|
-
const featuresArray = await features.pipe(toArray())
|
|
29
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
29
30
|
expect(featuresArray[0].get('refName')).toBe('ctgA')
|
|
30
31
|
const featuresJsonArray = featuresArray.map(f => f.toJSON())
|
|
31
32
|
expect(featuresJsonArray.length).toEqual(3809)
|
|
@@ -58,7 +59,7 @@ test('adapter can fetch features from volvox.bam', async () => {
|
|
|
58
59
|
start: 0,
|
|
59
60
|
end: 20000,
|
|
60
61
|
})
|
|
61
|
-
const featuresArrayCSI = await featuresCSI.pipe(toArray())
|
|
62
|
+
const featuresArrayCSI = await firstValueFrom(featuresCSI.pipe(toArray()))
|
|
62
63
|
const featuresJsonArrayCSI = featuresArrayCSI.map(f => f.toJSON())
|
|
63
64
|
expect(featuresJsonArrayCSI).toEqual(featuresJsonArray)
|
|
64
65
|
})
|
|
@@ -86,7 +87,7 @@ test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', async (
|
|
|
86
87
|
start: 0,
|
|
87
88
|
end: 100,
|
|
88
89
|
})
|
|
89
|
-
const featuresArray = await features.pipe(toArray())
|
|
90
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
90
91
|
const f = featuresArray[0].toJSON()
|
|
91
92
|
expect(f.refName).toBe('ctgA')
|
|
92
93
|
expect(f.start).toBe(2)
|
|
@@ -117,7 +118,7 @@ test('test usage of BamSlightlyLazyFeature for extended CIGAR', async () => {
|
|
|
117
118
|
start: 13260,
|
|
118
119
|
end: 13340,
|
|
119
120
|
})
|
|
120
|
-
const featuresArray = await features.pipe(toArray())
|
|
121
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
121
122
|
const f = featuresArray[0]
|
|
122
123
|
expect(f.get('mismatches')).toMatchSnapshot()
|
|
123
124
|
})
|
|
@@ -11,6 +11,7 @@ import { toArray } from 'rxjs/operators'
|
|
|
11
11
|
|
|
12
12
|
// locals
|
|
13
13
|
import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
|
|
14
|
+
import { firstValueFrom } from 'rxjs'
|
|
14
15
|
|
|
15
16
|
interface Header {
|
|
16
17
|
idToName: string[]
|
|
@@ -138,7 +139,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
|
138
139
|
assemblyName: '',
|
|
139
140
|
})
|
|
140
141
|
|
|
141
|
-
const seqChunks = await features.pipe(toArray())
|
|
142
|
+
const seqChunks = await firstValueFrom(features.pipe(toArray()))
|
|
142
143
|
|
|
143
144
|
let sequence = ''
|
|
144
145
|
seqChunks
|
|
@@ -9,6 +9,7 @@ import { SequenceAdapter } from './CramAdapter/CramTestAdapters'
|
|
|
9
9
|
|
|
10
10
|
import cramConfigSchema from './CramAdapter/configSchema'
|
|
11
11
|
import bamConfigSchema from './BamAdapter/configSchema'
|
|
12
|
+
import { firstValueFrom } from 'rxjs'
|
|
12
13
|
|
|
13
14
|
const pluginManager = new PluginManager()
|
|
14
15
|
|
|
@@ -55,8 +56,8 @@ async function getFeats(f1: string, f2: string) {
|
|
|
55
56
|
}
|
|
56
57
|
const bamFeatures = bamAdapter.getFeatures(query)
|
|
57
58
|
const cramFeatures = cramAdapter.getFeatures(query)
|
|
58
|
-
const bamFeaturesArray = await bamFeatures.pipe(toArray())
|
|
59
|
-
const cramFeaturesArray = await cramFeatures.pipe(toArray())
|
|
59
|
+
const bamFeaturesArray = await firstValueFrom(bamFeatures.pipe(toArray()))
|
|
60
|
+
const cramFeaturesArray = await firstValueFrom(cramFeatures.pipe(toArray()))
|
|
60
61
|
return { bamFeaturesArray, cramFeaturesArray }
|
|
61
62
|
}
|
|
62
63
|
|
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
import { toArray } from 'rxjs/operators'
|
|
2
|
+
import { firstValueFrom } from 'rxjs'
|
|
2
3
|
import { LocalFile } from 'generic-filehandle'
|
|
3
4
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
4
5
|
import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
|
|
@@ -40,7 +41,7 @@ test('adapter can fetch features from volvox-sorted.cram', async () => {
|
|
|
40
41
|
end: 20000,
|
|
41
42
|
})
|
|
42
43
|
|
|
43
|
-
const featuresArray = await features.pipe(toArray())
|
|
44
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
44
45
|
expect(featuresArray[0].get('refName')).toBe('ctgA')
|
|
45
46
|
const featuresJsonArray = featuresArray.map(f => f.toJSON())
|
|
46
47
|
expect(featuresJsonArray.length).toEqual(3809)
|
|
@@ -74,7 +75,7 @@ test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', async
|
|
|
74
75
|
start: 0,
|
|
75
76
|
end: 100,
|
|
76
77
|
})
|
|
77
|
-
const featuresArray = await features.pipe(toArray())
|
|
78
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
78
79
|
const f = featuresArray[0].toJSON()
|
|
79
80
|
expect(f.refName).toBe('ctgA')
|
|
80
81
|
expect(f.start).toBe(2)
|
|
@@ -8,6 +8,7 @@ import { checkAbortSignal, Region, Feature } from '@jbrowse/core/util'
|
|
|
8
8
|
import { openLocation } from '@jbrowse/core/util/io'
|
|
9
9
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
|
|
10
10
|
import { toArray } from 'rxjs/operators'
|
|
11
|
+
import { firstValueFrom } from 'rxjs'
|
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12
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import CramSlightlyLazyFeature from './CramSlightlyLazyFeature'
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12
13
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|
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|
interface Header {
|
|
@@ -103,15 +104,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
|
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104
|
throw new Error('unknown')
|
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}
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106
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-
const seqChunks = await
|
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-
|
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-
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-
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110
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-
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-
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-
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-
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-
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+
const seqChunks = await firstValueFrom(
|
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sequenceAdapter
|
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.getFeatures({
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+
refName,
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+
start,
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end,
|
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assemblyName: '',
|
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})
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.pipe(toArray()),
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+
)
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117
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const sequence = seqChunks
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.sort((a, b) => a.get('start') - b.get('start'))
|
|
@@ -5,6 +5,8 @@ import {
|
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5
5
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svgFeatureRendererConfigSchema,
|
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6
6
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SvgFeatureRendererReactComponent,
|
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7
7
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} from '@jbrowse/plugin-svg'
|
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8
|
+
|
|
9
|
+
// locals
|
|
8
10
|
import PileupRenderer from '../../PileupRenderer'
|
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9
11
|
import SNPCoverageRenderer from '../../SNPCoverageRenderer'
|
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10
12
|
import LinearPileupDisplay from '../../LinearPileupDisplay'
|
|
@@ -17,11 +19,13 @@ beforeEach(() => {
|
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|
})
|
|
18
20
|
|
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19
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|
afterEach(() => {
|
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+
// @ts-ignore
|
|
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23
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console.warn.mockRestore()
|
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24
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})
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22
25
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class AlignmentsPlugin extends Plugin {
|
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|
-
|
|
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|
+
name = 'AlignmentsPlugin'
|
|
28
|
+
install(pluginManager: PluginManager) {
|
|
25
29
|
PileupRenderer(pluginManager)
|
|
26
30
|
|
|
27
31
|
pluginManager.addRendererType(
|
|
@@ -9,11 +9,13 @@ beforeEach(() => {
|
|
|
9
9
|
})
|
|
10
10
|
|
|
11
11
|
afterEach(() => {
|
|
12
|
+
// @ts-ignore
|
|
12
13
|
console.warn.mockRestore()
|
|
13
14
|
})
|
|
14
15
|
// change renderer
|
|
15
16
|
class SNPCoverageRendererPlugin extends Plugin {
|
|
16
|
-
|
|
17
|
+
name = 'SNPCoverageRendererPlugin'
|
|
18
|
+
install(pluginManager: PluginManager) {
|
|
17
19
|
SNPCoverageRenderer(pluginManager)
|
|
18
20
|
}
|
|
19
21
|
}
|
|
@@ -3,6 +3,9 @@ import { Region } from '@jbrowse/core/util'
|
|
|
3
3
|
import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
|
|
4
4
|
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
|
|
5
5
|
import { toArray } from 'rxjs/operators'
|
|
6
|
+
import { firstValueFrom } from 'rxjs'
|
|
7
|
+
|
|
8
|
+
// locals
|
|
6
9
|
import PileupBaseRPC from '../base'
|
|
7
10
|
import { getTag } from '../../util'
|
|
8
11
|
|
|
@@ -28,7 +31,7 @@ export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
|
|
|
28
31
|
).dataAdapter as BaseFeatureDataAdapter
|
|
29
32
|
|
|
30
33
|
const features = dataAdapter.getFeaturesInMultipleRegions(regions)
|
|
31
|
-
const featuresArray = await features.pipe(toArray())
|
|
34
|
+
const featuresArray = await firstValueFrom(features.pipe(toArray()))
|
|
32
35
|
return [
|
|
33
36
|
...new Set(
|
|
34
37
|
featuresArray
|
|
@@ -3,7 +3,7 @@ import { Region, dedupe } from '@jbrowse/core/util'
|
|
|
3
3
|
import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
|
|
4
4
|
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
|
|
5
5
|
import { toArray } from 'rxjs/operators'
|
|
6
|
-
|
|
6
|
+
import { firstValueFrom } from 'rxjs'
|
|
7
7
|
// locals
|
|
8
8
|
import { filterForPairs, getInsertSizeStats } from '../util'
|
|
9
9
|
import { ReducedFeature } from '../../shared/fetchChains'
|
|
@@ -31,10 +31,9 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
|
|
|
31
31
|
await getAdapter(this.pluginManager, sessionId, adapterConfig)
|
|
32
32
|
).dataAdapter as BaseFeatureDataAdapter
|
|
33
33
|
|
|
34
|
-
const featuresArray = await
|
|
35
|
-
.getFeaturesInMultipleRegions(regions, des)
|
|
36
|
-
|
|
37
|
-
.toPromise()
|
|
34
|
+
const featuresArray = await firstValueFrom(
|
|
35
|
+
dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe(toArray()),
|
|
36
|
+
)
|
|
38
37
|
|
|
39
38
|
const reduced = dedupe(
|
|
40
39
|
featuresArray.map(f => ({
|
|
@@ -3,6 +3,7 @@ import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
|
|
|
3
3
|
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
|
|
4
4
|
import { Region } from '@jbrowse/core/util'
|
|
5
5
|
import { toArray } from 'rxjs/operators'
|
|
6
|
+
import { firstValueFrom } from 'rxjs'
|
|
6
7
|
|
|
7
8
|
// locals
|
|
8
9
|
import { getModificationTypes } from '../../MismatchParser'
|
|
@@ -29,10 +30,9 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
|
|
|
29
30
|
await getAdapter(this.pluginManager, sessionId, adapterConfig)
|
|
30
31
|
).dataAdapter as BaseFeatureDataAdapter
|
|
31
32
|
|
|
32
|
-
const featuresArray = await
|
|
33
|
-
.getFeaturesInMultipleRegions(regions)
|
|
34
|
-
|
|
35
|
-
.toPromise()
|
|
33
|
+
const featuresArray = await firstValueFrom(
|
|
34
|
+
dataAdapter.getFeaturesInMultipleRegions(regions).pipe(toArray()),
|
|
35
|
+
)
|
|
36
36
|
|
|
37
37
|
const uniqueValues = new Set<string>()
|
|
38
38
|
featuresArray.forEach(f => {
|
|
@@ -6,6 +6,9 @@ import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
|
|
|
6
6
|
import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
|
|
7
7
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
|
|
8
8
|
import { toArray } from 'rxjs/operators'
|
|
9
|
+
import { firstValueFrom } from 'rxjs'
|
|
10
|
+
|
|
11
|
+
// locals
|
|
9
12
|
import generateCoverageBins from './generateCoverageBins'
|
|
10
13
|
import { fetchSequence } from '../util'
|
|
11
14
|
|
|
@@ -43,10 +46,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
|
43
46
|
getFeatures(region: Region, opts: BaseOptions = {}) {
|
|
44
47
|
return ObservableCreate<Feature>(async observer => {
|
|
45
48
|
const { subadapter } = await this.configure()
|
|
46
|
-
const feats = await
|
|
47
|
-
.getFeatures(region, opts)
|
|
48
|
-
|
|
49
|
-
.toPromise()
|
|
49
|
+
const feats = await firstValueFrom(
|
|
50
|
+
subadapter.getFeatures(region, opts).pipe(toArray()),
|
|
51
|
+
)
|
|
50
52
|
|
|
51
53
|
const { bins, skipmap } = await generateCoverageBins(
|
|
52
54
|
feats,
|
package/src/index.test.ts
CHANGED
|
@@ -4,7 +4,6 @@ import { getSnapshot } from 'mobx-state-tree'
|
|
|
4
4
|
import ThisPlugin from '.'
|
|
5
5
|
|
|
6
6
|
test('plugin in a stock JBrowse', () => {
|
|
7
|
-
console.warn = jest.fn()
|
|
8
7
|
const pluginManager = new PluginManager([new ThisPlugin(), new SVG()])
|
|
9
8
|
pluginManager.createPluggableElements()
|
|
10
9
|
pluginManager.configure()
|
package/src/util.ts
CHANGED
|
@@ -2,6 +2,7 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
|
|
|
2
2
|
import { toArray } from 'rxjs/operators'
|
|
3
3
|
import { Feature } from '@jbrowse/core/util/simpleFeature'
|
|
4
4
|
import { AugmentedRegion } from '@jbrowse/core/util'
|
|
5
|
+
import { firstValueFrom } from 'rxjs'
|
|
5
6
|
// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
|
|
6
7
|
// BAM does not
|
|
7
8
|
export function getTag(feature: Feature, tag: string) {
|
|
@@ -86,14 +87,15 @@ export async function fetchSequence(
|
|
|
86
87
|
) {
|
|
87
88
|
const { end, originalRefName, refName } = region
|
|
88
89
|
|
|
89
|
-
const feats = await
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
90
|
+
const feats = await firstValueFrom(
|
|
91
|
+
adapter
|
|
92
|
+
.getFeatures({
|
|
93
|
+
...region,
|
|
94
|
+
refName: originalRefName || refName,
|
|
95
|
+
end: end + 1,
|
|
96
|
+
})
|
|
97
|
+
.pipe(toArray()),
|
|
98
|
+
)
|
|
97
99
|
return feats[0]?.get('seq')
|
|
98
100
|
}
|
|
99
101
|
|
|
@@ -1,21 +0,0 @@
|
|
|
1
|
-
import PrecomputedLayout from '@jbrowse/core/util/layouts/PrecomputedLayout'
|
|
2
|
-
import React from 'react'
|
|
3
|
-
import { render } from '@testing-library/react'
|
|
4
|
-
import PileupRendering from './PileupRendering'
|
|
5
|
-
|
|
6
|
-
// these tests do very little, let's try to expand them at some point
|
|
7
|
-
test('one', () => {
|
|
8
|
-
const { container } = render(
|
|
9
|
-
<PileupRendering
|
|
10
|
-
width={500}
|
|
11
|
-
height={500}
|
|
12
|
-
regions={[{ refName: 'zonk', start: 1, end: 3 }]}
|
|
13
|
-
layout={new PrecomputedLayout({ rectangles: {}, totalHeight: 20 })}
|
|
14
|
-
displayModel={{}}
|
|
15
|
-
bpPerPx={3}
|
|
16
|
-
config={{ type: 'DummyRenderer' }}
|
|
17
|
-
/>,
|
|
18
|
-
)
|
|
19
|
-
|
|
20
|
-
expect(container.firstChild).toMatchSnapshot()
|
|
21
|
-
})
|
|
@@ -1,23 +0,0 @@
|
|
|
1
|
-
// Jest Snapshot v1, https://goo.gl/fbAQLP
|
|
2
|
-
|
|
3
|
-
exports[`one 1`] = `
|
|
4
|
-
<div
|
|
5
|
-
class="PileupRendering"
|
|
6
|
-
data-testid="pileup-normal"
|
|
7
|
-
style="position: relative; width: 500px; height: 500px;"
|
|
8
|
-
>
|
|
9
|
-
<canvas
|
|
10
|
-
data-testid="prerendered_canvas"
|
|
11
|
-
height="500"
|
|
12
|
-
style="width: 500px; height: 500px; position: absolute; left: 0px; top: 0px;"
|
|
13
|
-
width="500"
|
|
14
|
-
/>
|
|
15
|
-
<canvas
|
|
16
|
-
class="highlightOverlayCanvas"
|
|
17
|
-
data-testid="pileup_overlay_canvas"
|
|
18
|
-
height="600"
|
|
19
|
-
style="position: absolute; left: 0px; top: 0px;"
|
|
20
|
-
width="500"
|
|
21
|
-
/>
|
|
22
|
-
</div>
|
|
23
|
-
`;
|