@jbrowse/plugin-alignments 2.4.0 → 2.4.1
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 -2
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +2 -2
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/util.js +10 -10
- package/dist/CramAdapter/util.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -3
- package/dist/LinearAlignmentsDisplay/models/model.js +3 -4
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/dist/LinearPileupDisplay/index.d.ts +2 -3
- package/dist/LinearPileupDisplay/index.js +4 -2
- package/dist/LinearPileupDisplay/index.js.map +1 -1
- package/dist/LinearPileupDisplay/model.d.ts +7 -9
- package/dist/LinearPileupDisplay/model.js +4 -4
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +2 -2
- package/dist/LinearReadCloudDisplay/model.d.ts +2 -2
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
- package/dist/MismatchParser/index.js +4 -6
- package/dist/MismatchParser/index.js.map +1 -1
- package/dist/NestedFrequencyTable.js +3 -13
- package/dist/NestedFrequencyTable.js.map +1 -1
- package/dist/PileupRPC/rpcMethods.d.ts +3 -4
- package/dist/PileupRPC/rpcMethods.js +6 -6
- package/dist/PileupRPC/rpcMethods.js.map +1 -1
- package/dist/PileupRenderer/PileupRenderer.d.ts +6 -4
- package/dist/PileupRenderer/PileupRenderer.js +30 -34
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/PileupRenderer/components/PileupRendering.js +2 -2
- package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +1 -1
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/PileupRenderer/sortUtil.js +5 -4
- package/dist/PileupRenderer/sortUtil.js.map +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/dist/index.d.ts +3 -5
- package/dist/index.js +6 -6
- package/dist/index.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -2
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
- package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/esm/CramAdapter/CramAdapter.js +2 -2
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
- package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/esm/CramAdapter/util.js +10 -10
- package/esm/CramAdapter/util.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -3
- package/esm/LinearAlignmentsDisplay/models/model.js +3 -4
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/esm/LinearPileupDisplay/index.d.ts +2 -3
- package/esm/LinearPileupDisplay/index.js +2 -1
- package/esm/LinearPileupDisplay/index.js.map +1 -1
- package/esm/LinearPileupDisplay/model.d.ts +7 -9
- package/esm/LinearPileupDisplay/model.js +4 -4
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +2 -2
- package/esm/LinearReadCloudDisplay/model.d.ts +2 -2
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
- package/esm/MismatchParser/index.js +4 -6
- package/esm/MismatchParser/index.js.map +1 -1
- package/esm/NestedFrequencyTable.js +3 -13
- package/esm/NestedFrequencyTable.js.map +1 -1
- package/esm/PileupRPC/rpcMethods.d.ts +3 -4
- package/esm/PileupRPC/rpcMethods.js +3 -4
- package/esm/PileupRPC/rpcMethods.js.map +1 -1
- package/esm/PileupRenderer/PileupRenderer.d.ts +6 -4
- package/esm/PileupRenderer/PileupRenderer.js +30 -34
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/PileupRenderer/components/PileupRendering.js +2 -2
- package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
- package/esm/PileupRenderer/configSchema.js +1 -1
- package/esm/PileupRenderer/configSchema.js.map +1 -1
- package/esm/PileupRenderer/sortUtil.js +5 -4
- package/esm/PileupRenderer/sortUtil.js.map +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/esm/index.d.ts +3 -5
- package/esm/index.js +3 -3
- package/esm/index.js.map +1 -1
- package/package.json +2 -2
- package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
- package/src/BamAdapter/BamAdapter.ts +2 -2
- package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
- package/src/CramAdapter/CramAdapter.ts +2 -2
- package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
- package/src/CramAdapter/util.ts +10 -10
- package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +2 -2
- package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
- package/src/LinearAlignmentsDisplay/models/model.tsx +3 -4
- package/src/LinearPileupDisplay/index.ts +2 -4
- package/src/LinearPileupDisplay/model.ts +4 -4
- package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
- package/src/MismatchParser/index.ts +3 -5
- package/src/NestedFrequencyTable.ts +3 -11
- package/src/PileupRPC/rpcMethods.ts +3 -9
- package/src/PileupRenderer/PileupRenderer.ts +47 -61
- package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
- package/src/PileupRenderer/configSchema.ts +1 -1
- package/src/PileupRenderer/sortUtil.ts +5 -4
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
- package/src/index.ts +5 -10
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@@ -121,7 +121,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
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const trimLength = trimEnd - trimStart;
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const chunkSeq = chunk.get('seq') || chunk.get('residues');
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-
sequence += chunkSeq.
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sequence += chunkSeq.slice(trimStart, trimStart + trimLength);
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});
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if (sequence.length !== end - start) {
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throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
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@@ -164,7 +164,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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async estimateRegionsStats(regions, opts) {
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const { bam } = await this.configure();
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// this is a method to avoid calling on htsget adapters
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// @ts-
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// @ts-expect-error
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if (bam.index.filehandle !== '?') {
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const bytes = await (0, util_1.bytesForRegions)(regions, bam);
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const fetchSizeLimit = this.getConf('fetchSizeLimit');
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@@ -1 +1 @@
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1
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-
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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,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC/D,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,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@@ -65,9 +65,9 @@ class BamSlightlyLazyFeature {
|
|
|
65
65
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
66
66
|
get(field) {
|
|
67
67
|
const methodName = `_get_${field}`;
|
|
68
|
-
// @ts-
|
|
68
|
+
// @ts-expect-error
|
|
69
69
|
if (this[methodName]) {
|
|
70
|
-
// @ts-
|
|
70
|
+
// @ts-expect-error
|
|
71
71
|
return this[methodName]();
|
|
72
72
|
}
|
|
73
73
|
return this.record.get(field);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,SAAS;AACT,sDAA0D;AAG1D,MAAqB,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,
|
|
1
|
+
{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAOA,SAAS;AACT,sDAA0D;AAG1D,MAAqB,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,IAAA,8BAAa,EAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAA,wBAAO,EAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;IAC3C,CAAC;CACF;AAzID,yCAyIC"}
|
|
@@ -82,7 +82,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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|
82
82
|
const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
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|
const trimLength = trimEnd - trimStart;
|
|
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|
const chunkSeq = chunk.get('seq') || chunk.get('residues');
|
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85
|
-
return chunkSeq.
|
|
85
|
+
return chunkSeq.slice(trimStart, trimStart + trimLength);
|
|
86
86
|
})
|
|
87
87
|
.join('');
|
|
88
88
|
if (sequence.length !== end - start) {
|
|
@@ -180,7 +180,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
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|
180
180
|
});
|
|
181
181
|
if (tagFilter) {
|
|
182
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|
filtered = filtered.filter(record => {
|
|
183
|
-
// @ts-
|
|
183
|
+
// @ts-expect-error
|
|
184
184
|
const val = record[tagFilter.tag];
|
|
185
185
|
return val === '*' ? val !== undefined : val === tagFilter.value;
|
|
186
186
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC1D,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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@@ -94,9 +94,9 @@ class CramSlightlyLazyFeature {
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94
94
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}
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|
95
95
|
get(field) {
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96
96
|
const methodName = `_get_${field}`;
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97
|
-
// @ts-
|
|
97
|
+
// @ts-expect-error
|
|
98
98
|
if (this[methodName]) {
|
|
99
|
-
// @ts-
|
|
99
|
+
// @ts-expect-error
|
|
100
100
|
return this[methodName]();
|
|
101
101
|
}
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|
102
102
|
return undefined;
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AASA,iCAAsE;AAEtE,MAAqB,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,IAAA,0BAAmB,EACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,
|
|
1
|
+
{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":";;AASA,iCAAsE;AAEtE,MAAqB,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,IAAA,0BAAmB,EACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAI,CAAC;IAER,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,IAAA,+BAAwB,EAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF;AAhLD,0CAgLC"}
|
package/dist/CramAdapter/util.js
CHANGED
|
@@ -137,14 +137,14 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
137
137
|
for (let i = 0; i < readFeatures.length; i++) {
|
|
138
138
|
const { code, refPos, sub, data } = readFeatures[i];
|
|
139
139
|
sublen = refPos - lastPos;
|
|
140
|
-
seq += ref.
|
|
140
|
+
seq += ref.slice(lastPos - refStart, refPos - refStart);
|
|
141
141
|
lastPos = refPos;
|
|
142
142
|
if (insLen > 0 && sublen) {
|
|
143
143
|
cigar += `${insLen}I`;
|
|
144
144
|
insLen = 0;
|
|
145
145
|
}
|
|
146
146
|
if (oplen && op !== 'M') {
|
|
147
|
-
cigar += oplen
|
|
147
|
+
cigar += `${oplen}${op}`;
|
|
148
148
|
oplen = 0;
|
|
149
149
|
}
|
|
150
150
|
if (sublen) {
|
|
@@ -175,7 +175,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
175
175
|
// Deletion or Ref Skip
|
|
176
176
|
lastPos += data;
|
|
177
177
|
if (oplen) {
|
|
178
|
-
cigar += oplen
|
|
178
|
+
cigar += `${oplen}${op}`;
|
|
179
179
|
}
|
|
180
180
|
cigar += data + code;
|
|
181
181
|
oplen = 0;
|
|
@@ -184,7 +184,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
184
184
|
// Insertion or soft-clip
|
|
185
185
|
seq += data;
|
|
186
186
|
if (oplen) {
|
|
187
|
-
cigar += oplen
|
|
187
|
+
cigar += `${oplen}${op}`;
|
|
188
188
|
}
|
|
189
189
|
cigar += data.length + code;
|
|
190
190
|
oplen = 0;
|
|
@@ -193,7 +193,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
193
193
|
// Single base insertion
|
|
194
194
|
// seq += data
|
|
195
195
|
if (oplen) {
|
|
196
|
-
cigar += oplen
|
|
196
|
+
cigar += `${oplen}${op}`;
|
|
197
197
|
}
|
|
198
198
|
insLen++;
|
|
199
199
|
seq += data;
|
|
@@ -202,14 +202,14 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
202
202
|
else if (code === 'P') {
|
|
203
203
|
// Padding
|
|
204
204
|
if (oplen) {
|
|
205
|
-
cigar += oplen
|
|
205
|
+
cigar += `${oplen}${op}`;
|
|
206
206
|
}
|
|
207
207
|
cigar += `${data}P`;
|
|
208
208
|
}
|
|
209
209
|
else if (code === 'H') {
|
|
210
210
|
// Hard clip
|
|
211
211
|
if (oplen) {
|
|
212
|
-
cigar += oplen
|
|
212
|
+
cigar += `${oplen}${op}`;
|
|
213
213
|
}
|
|
214
214
|
cigar += `${data}H`;
|
|
215
215
|
oplen = 0;
|
|
@@ -221,9 +221,9 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
221
221
|
}
|
|
222
222
|
if (seq.length !== readLen) {
|
|
223
223
|
sublen = readLen - seq.length;
|
|
224
|
-
seq += ref.
|
|
224
|
+
seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
|
|
225
225
|
if (oplen && op !== 'M') {
|
|
226
|
-
cigar += oplen
|
|
226
|
+
cigar += `${oplen}${op}`;
|
|
227
227
|
oplen = 0;
|
|
228
228
|
}
|
|
229
229
|
op = 'M';
|
|
@@ -233,7 +233,7 @@ function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRegion) {
|
|
|
233
233
|
cigar += `${insLen}I`;
|
|
234
234
|
}
|
|
235
235
|
if (oplen) {
|
|
236
|
-
cigar += oplen
|
|
236
|
+
cigar += `${oplen}${op}`;
|
|
237
237
|
}
|
|
238
238
|
return cigar;
|
|
239
239
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/CramAdapter/util.ts"],"names":[],"mappings":";;;AAeA,SAAgB,wBAAwB,CACtC,YAA0B,EAC1B,KAAa,EACb,IAAsB;IAEtB,IAAI,CAAC,YAAY,EAAE;QACjB,OAAO,EAAE,CAAA;KACV;IACD,MAAM,UAAU,GAAe,IAAI,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;IAC7D,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,OAAO,GAAG,KAAK,CAAA;IAEnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC5C,MAAM,CAAC,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QACzB,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;QACvC,MAAM,GAAG,MAAM,GAAG,OAAO,CAAA;QACzB,OAAO,GAAG,MAAM,CAAA;QAEhB,IAAI,MAAM,IAAI,MAAM,GAAG,CAAC,EAAE;YACxB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,GAAG,MAAM,EAAE;gBACjB,MAAM,EAAE,CAAC;aACV,CAAA;YACD,MAAM,GAAG,CAAC,CAAA;SACX;QACD,MAAM,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC,GAAG,KAAK,CAAA;QAE7B,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,eAAe;YACf,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,MAAM,EAAE,CAAC;gBACT,IAAI,EAAE,GAAG;gBACT,IAAI,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,GAAG,GAAG,CAAC,CAAC;gBACrB,OAAO,EAAE,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,WAAW,EAAE;gBAC3B,IAAI,EAAE,UAAU;aACjB,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE;gBACtB,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,iBAAiB;YACjB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,GAAG;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;YACvB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,UAAU;SACX;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,MAAM,GAAG,GAAG,IAAI,CAAA;YAChB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,WAAW;YACX,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,IAAI,EAAE,UAAU;gBAChB,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,GAAG;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,mBAAmB;SACpB;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yBAAyB;SAC1B;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yBAAyB;SAC1B;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yEAAyE;YACzE,gCAAgC;YAChC,MAAM,EAAE,CAAA;SACT;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,uBAAuB;SACxB;KACF;IAED,IAAI,MAAM,IAAI,MAAM,GAAG,CAAC,EAAE;QACxB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;YAChB,KAAK,EAAE,MAAM;YACb,IAAI,EAAE,WAAW;YACjB,IAAI,EAAE,GAAG,MAAM,EAAE;YACjB,MAAM,EAAE,CAAC;SACV,CAAA;QACD,MAAM,GAAG,CAAC,CAAA;KACX;IAED,OAAO,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC/B,CAAC;AAlHD,4DAkHC;AAED,SAAgB,mBAAmB,CACjC,YAA0B,EAC1B,cAAsB,EACtB,OAAe,EACf,SAA0C;IAE1C,IAAI,GAAG,GAAG,EAAE,CAAA;IACZ,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,EAAE,GAAG,GAAG,CAAA;IACZ,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,CAAC,SAAS,EAAE;QACd,OAAO,EAAE,CAAA;KACV;IAED,yCAAyC;IACzC,MAAM,GAAG,GAAG,SAAS,CAAC,GAAG,CAAA;IACzB,MAAM,QAAQ,GAAG,SAAS,CAAC,KAAK,CAAA;IAChC,IAAI,OAAO,GAAG,cAAc,CAAA;IAC5B,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,YAAY,KAAK,SAAS,EAAE;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5C,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;YACnD,MAAM,GAAG,MAAM,GAAG,OAAO,CAAA;YACzB,GAAG,IAAI,GAAG,CAAC,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/CramAdapter/util.ts"],"names":[],"mappings":";;;AAeA,SAAgB,wBAAwB,CACtC,YAA0B,EAC1B,KAAa,EACb,IAAsB;IAEtB,IAAI,CAAC,YAAY,EAAE;QACjB,OAAO,EAAE,CAAA;KACV;IACD,MAAM,UAAU,GAAe,IAAI,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;IAC7D,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,OAAO,GAAG,KAAK,CAAA;IAEnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC5C,MAAM,CAAC,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QACzB,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;QACvC,MAAM,GAAG,MAAM,GAAG,OAAO,CAAA;QACzB,OAAO,GAAG,MAAM,CAAA;QAEhB,IAAI,MAAM,IAAI,MAAM,GAAG,CAAC,EAAE;YACxB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,GAAG,MAAM,EAAE;gBACjB,MAAM,EAAE,CAAC;aACV,CAAA;YACD,MAAM,GAAG,CAAC,CAAA;SACX;QACD,MAAM,GAAG,CAAC,CAAC,MAAM,GAAG,CAAC,GAAG,KAAK,CAAA;QAE7B,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,eAAe;YACf,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,MAAM,EAAE,CAAC;gBACT,IAAI,EAAE,GAAG;gBACT,IAAI,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,GAAG,GAAG,CAAC,CAAC;gBACrB,OAAO,EAAE,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,WAAW,EAAE;gBAC3B,IAAI,EAAE,UAAU;aACjB,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,WAAW;gBACjB,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,EAAE;gBACtB,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,iBAAiB;YACjB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,GAAG;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAA;YACvB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,UAAU;SACX;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,YAAY;YACZ,MAAM,GAAG,GAAG,IAAI,CAAA;YAChB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,IAAI,GAAG,EAAE;gBACf,OAAO,EAAE,GAAG;gBACZ,MAAM,EAAE,CAAC;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,WAAW;YACX,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;gBAChB,IAAI,EAAE,UAAU;gBAChB,MAAM,EAAE,IAAI;gBACZ,KAAK,EAAE,MAAM;gBACb,IAAI,EAAE,GAAG;aACV,CAAA;SACF;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,mBAAmB;SACpB;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yBAAyB;SAC1B;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yBAAyB;SAC1B;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,yEAAyE;YACzE,gCAAgC;YAChC,MAAM,EAAE,CAAA;SACT;aAAM,IAAI,IAAI,KAAK,GAAG,EAAE;YACvB,uBAAuB;SACxB;KACF;IAED,IAAI,MAAM,IAAI,MAAM,GAAG,CAAC,EAAE;QACxB,UAAU,CAAC,CAAC,EAAE,CAAC,GAAG;YAChB,KAAK,EAAE,MAAM;YACb,IAAI,EAAE,WAAW;YACjB,IAAI,EAAE,GAAG,MAAM,EAAE;YACjB,MAAM,EAAE,CAAC;SACV,CAAA;QACD,MAAM,GAAG,CAAC,CAAA;KACX;IAED,OAAO,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC/B,CAAC;AAlHD,4DAkHC;AAED,SAAgB,mBAAmB,CACjC,YAA0B,EAC1B,cAAsB,EACtB,OAAe,EACf,SAA0C;IAE1C,IAAI,GAAG,GAAG,EAAE,CAAA;IACZ,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,EAAE,GAAG,GAAG,CAAA;IACZ,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,IAAI,CAAC,SAAS,EAAE;QACd,OAAO,EAAE,CAAA;KACV;IAED,yCAAyC;IACzC,MAAM,GAAG,GAAG,SAAS,CAAC,GAAG,CAAA;IACzB,MAAM,QAAQ,GAAG,SAAS,CAAC,KAAK,CAAA;IAChC,IAAI,OAAO,GAAG,cAAc,CAAA;IAC5B,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,IAAI,YAAY,KAAK,SAAS,EAAE;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC5C,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;YACnD,MAAM,GAAG,MAAM,GAAG,OAAO,CAAA;YACzB,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,EAAE,MAAM,GAAG,QAAQ,CAAC,CAAA;YACvD,OAAO,GAAG,MAAM,CAAA;YAEhB,IAAI,MAAM,GAAG,CAAC,IAAI,MAAM,EAAE;gBACxB,KAAK,IAAI,GAAG,MAAM,GAAG,CAAA;gBACrB,MAAM,GAAG,CAAC,CAAA;aACX;YACD,IAAI,KAAK,IAAI,EAAE,KAAK,GAAG,EAAE;gBACvB,KAAK,IAAI,GAAG,KAAK,GAAG,EAAE,EAAE,CAAA;gBACxB,KAAK,GAAG,CAAC,CAAA;aACV;YACD,IAAI,MAAM,EAAE;gBACV,EAAE,GAAG,GAAG,CAAA;gBACR,KAAK,IAAI,MAAM,CAAA;aAChB;YAED,IAAI,IAAI,KAAK,GAAG,EAAE;gBAChB,oCAAoC;gBACpC,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,YAAY,CAAC,GAAG,GAAG,CAAC,CAAA;gBACzC,GAAG,IAAI,KAAK,CAAA;gBACZ,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;gBACvB,KAAK,IAAI,KAAK,CAAC,MAAM,CAAA;aACtB;iBAAM,IAAI,IAAI,KAAK,GAAG,EAAE;gBACvB,6BAA6B;gBAC7B,GAAG,IAAI,GAAG,CAAA;gBACV,OAAO,EAAE,CAAA;gBACT,KAAK,EAAE,CAAA;aACR;iBAAM,IAAI,IAAI,KAAK,GAAG,EAAE;gBACvB,eAAe;gBACf,GAAG,IAAI,GAAG,CAAA;gBACV,OAAO,EAAE,CAAA;gBACT,KAAK,EAAE,CAAA;aACR;iBAAM,IAAI,IAAI,KAAK,GAAG,IAAI,IAAI,KAAK,GAAG,EAAE;gBACvC,uBAAuB;gBACvB,OAAO,IAAI,IAAI,CAAA;gBACf,IAAI,KAAK,EAAE;oBACT,KAAK,IAAI,GAAG,KAAK,GAAG,EAAE,EAAE,CAAA;iBACzB;gBACD,KAAK,IAAI,IAAI,GAAG,IAAI,CAAA;gBACpB,KAAK,GAAG,CAAC,CAAA;aACV;iBAAM,IAAI,IAAI,KAAK,GAAG,IAAI,IAAI,KAAK,GAAG,EAAE;gBACvC,yBAAyB;gBACzB,GAAG,IAAI,IAAI,CAAA;gBACX,IAAI,KAAK,EAAE;oBACT,KAAK,IAAI,GAAG,KAAK,GAAG,EAAE,EAAE,CAAA;iBACzB;gBACD,KAAK,IAAI,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;gBAC3B,KAAK,GAAG,CAAC,CAAA;aACV;iBAAM,IAAI,IAAI,K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@@ -8,13 +8,13 @@ const mobx_react_1 = require("mobx-react");
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const mui_1 = require("tss-react/mui");
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const useStyles = (0, mui_1.makeStyles)()(
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const useStyles = (0, mui_1.makeStyles)()({
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resizeHandle: {
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height: 2,
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position: 'absolute',
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})
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});
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function AlignmentsDisplay({ model }) {
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const { PileupDisplay, SNPCoverageDisplay } = model;
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const { classes } = useStyles();
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC
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1
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+
{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,uCAA0C;AAC1C,+DAAqD;AACrD,yCAA+C;AAK/C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAEF,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,sDACe,WAAW,IAAA,uBAAO,EAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,sDAAiB,sBAAsB;YACrC,8BAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,8BAAC,iBAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GACd;QAEF,sDACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,8BAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,iBAAiB,CAAC,CAAA"}
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@@ -65,9 +65,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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renderProps(): any;
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readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
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readonly DisplayMessageComponent: React.FC<any> | undefined;
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-
trackMenuItems(): MenuItem[];
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-
* #action
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*/
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+
trackMenuItems(): MenuItem[];
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readonly viewMenuActions: MenuItem[];
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regionCannotBeRendered(): undefined;
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} & {
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@@ -14,9 +14,9 @@ const minDisplayHeight = 20;
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function getLowerPanelDisplays(pluginManager) {
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return (pluginManager
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|
.getDisplayElements()
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// @ts-
|
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+
// @ts-expect-error
|
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18
|
.filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
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// @ts-
|
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+
// @ts-expect-error
|
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20
|
.filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
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}
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function deepSnap(x1, x2) {
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@@ -54,7 +54,6 @@ function AlignmentsModel(pluginManager, configSchema) {
|
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|
* #property
|
|
55
55
|
* refers to LinearPileupDisplay sub-display model
|
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|
*/
|
|
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-
// @ts-ignore
|
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|
PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...lowerPanelDisplays)),
|
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|
/**
|
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* #property
|
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@@ -302,7 +301,7 @@ function stateModelFactory(pluginManager, configSchema) {
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|
if (!snap) {
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|
return snap;
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}
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// @ts-
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+
// @ts-expect-error
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306
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|
const { height, ...rest } = snap;
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|
return { heightPreConfig: height, ...rest };
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|
});
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+BAAoC;AACpC,qDAOwB;AACxB,sEAAuC;AAEvC,UAAU;AACV,+DAKoC;AACpC,uEAAwE;AAIxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,
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1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,+BAAoC;AACpC,qDAOwB;AACxB,sEAAuC;AAEvC,UAAU;AACV,+DAKoC;AACpC,uEAAwE;AAIxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,IAAI,MAAK,yBAAyB,CAAA,EAAA,CAAC;QAC9D,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,UAAU,CAAA,EAAA,CAAC,CACzC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CACf,EAAK,EACL,EAAK;IAEL,OAAO,IAAA,yBAAS,EACd,EAAE,CAAC,CAAC,CAAC,IAAA,6BAAW,EAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,EAChC,EAAE,CAAC,CAAC,CAAC,IAAA,6BAAW,EAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CACjC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,IAA4B;IAC5C,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,OAAO,CACL,aAAa;QACb,IAAA,yBAAO,EAAC,aAAa,CAAC;QACtB,kBAAkB;QAClB,IAAA,yBAAO,EAAC,kBAAkB,CAAC,CAC5B,CAAA;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,IAA4B;IACpD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,EAAE;QAC7C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,kBAAkB,CAAC,OAAO,CAAC,EAAE;QAChE,kBAAkB,CAAC,UAAU,CAAC,IAAA,6BAAW,EAAC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;KAClE;AACH,CAAC;AAED,SAAS,iBAAiB,CAAC,IAA4B;IACrD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,EAAE;QAC9C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,QAAQ,EAAE,kBAAkB,CAAC,QAAQ,CAAC,EAAE;QAClE,kBAAkB,CAAC,WAAW,CAAC,IAAA,6BAAW,EAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAA;KACpE;AACH,CAAC;AAED,SAAS,eAAe,CACtB,aAA4B,EAC5B,YAAwC;IAExC,MAAM,kBAAkB,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CACjE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAClB,CAAA;IAED,OAAO,uBAAK,CAAC,KAAK,CAAC;QACjB;;;WAGG;QACH,aAAa,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,KAAK,CAAC,GAAG,kBAAkB,CAAC,CAAC;QAC9D;;;WAGG;QACH,kBAAkB,EAAE,uBAAK,CAAC,KAAK,CAC7B,aAAa,CAAC,cAAc,CAAC,0BAA0B,CAAC,CAAC,UAAU,CACpE;QACD;;WAEG;QACH,YAAY,EAAE,EAAE;QAChB;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;QAC9C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QACnD;;WAEG;QACH,eAAe,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,wBAAwB,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QACnD;;WAEG;QACH,cAAc,EAAE,qBAAqB;KACtC,CAAC,CAAA;AACJ,CAAC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CACxB,aAA4B,EAC5B,YAAwC;IAExC,OAAO,uBAAK;SACT,OAAO,CACN,yBAAyB,EACzB,oBAAW,EACX,eAAe,CAAC,aAAa,EAAE,YAAY,CAAC,CAC7C;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,MAAM;;YACR,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;QACxD,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,UAAU;YACZ,MAAM,IAAI,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,eAAe,CAAC,CAAA;YAC3C,OAAO;gBACL,GAAG,IAAI;gBACP,IAAI,EAAE,IAAI,CAAC,cAAc;gBACzB,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,IAAI,IAAI,CAAC,cAAc,MAAM,EAAE,yEAAyE;aACnJ,CAAA;QACH,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,QAAgB,EAAE,EAAU;YACzC,OAAO,IAAI,CAAC,aAAa,CAAC,cAAc,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;QACxD,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,EAAU;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;;YACd,OAAO,MAAA,IAAI,CAAC,aAAa,0CAAE,YAAY,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;YACd,MAAM,IAAI,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,oBAAoB,CAAC,CAAA;YAChD,OAAO;gBACL,GAAG,IAAI;gBACP,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,kBAAkB,EAAE,yEAAyE;aACxI,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,qBAAqB,CAAC,aAAoC;YACxD,IAAI,CAAC,kBAAkB,GAAG;gBACxB,IAAI,EAAE,0BAA0B;gBAChC,aAAa;gBACb,MAAM,EAAE,IAAI,CAAC,YAAY;aAC1B,CAAA;QACH,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,KAAc;YAC7B,IAAI,CAAC,aAAa,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,CAAC,kBAAkB,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,aAAoC;YACnD,IAAI,CAAC,aAAa,GAAG;gBACnB,IAAI,EAAE,aAAa,CAAC,IAAI,IAAI,qBAAqB;gBACjD,aAAa;aACd,CAAA;QACH,CAAC;QACD;;WAEG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,gBAAgB,CAAC,CAAA;YACpD,OAAO,IAAI,CAAC,eAAe,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,IAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,IAAA,6BAAW,EACT,IAAI,EACJ,IAAA,cAAO,EAAC,GAAG,EAAE;gBACX,MAAM,EACJ,kBAAkB,EAClB,aAAa,EACb,YAAY,EACZ,UAAU,GACX,GAAG,I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import configSchemaFactory from './configSchema';
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import modelFactory from './model';
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export default function register(pluginManager: PluginManager): void;
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export {
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export { default as linearPileupDisplayStateModelFactory } from './model';
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export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.linearPileupDisplayConfigSchemaFactory = exports.linearPileupDisplayStateModelFactory = void 0;
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const configSchema_1 = __importDefault(require("./configSchema"));
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exports.linearPileupDisplayConfigSchemaFactory = configSchema_1.default;
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const model_1 = __importDefault(require("./model"));
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exports.linearPileupDisplayStateModelFactory = model_1.default;
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const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
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const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
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function register(pluginManager) {
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@@ -26,4 +24,8 @@ function register(pluginManager) {
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}
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exports.default = register;
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var model_2 = require("./model");
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Object.defineProperty(exports, "linearPileupDisplayStateModelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
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var configSchema_2 = require("./configSchema");
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Object.defineProperty(exports, "linearPileupDisplayConfigSchemaFactory", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
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//# sourceMappingURL=index.js.map
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@@ -1 +1 @@
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1
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAChD,oDAAkC;AAClC,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,2BAcC;AAED,iCAAyE;AAAhE,8IAAA,OAAO,OAAwC;AACxD,+CAAkF;AAAzE,uJAAA,OAAO,OAA0C"}
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@@ -157,7 +157,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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readonly height:
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@@ -187,7 +187,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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clearRegionStats(): void;
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setHeight(displayHeight: number):
|
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setHeight(displayHeight: number): number;
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setScrollTop(scrollTop: number): void;
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updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
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@@ -206,9 +206,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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reload(): Promise<void>;
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afterAttach(): void;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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* #action
|
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*/
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
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trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
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contextMenuItems(): {
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@@ -470,7 +468,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
|
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|
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setMessage(messageText: string): void;
|
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setRendered(props: {
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|
reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
|
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|
-
features: Map<string, Feature>;
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|
+
features: Map<string, Feature>; /**
|
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* #getter
|
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+
*/
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|
layout: any;
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|
maxHeightReached: boolean;
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|
renderProps: any;
|
|
@@ -486,9 +486,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
|
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|
id: string;
|
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|
rpcDriverName: string | undefined;
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|
heightPreConfig: number | undefined;
|
|
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|
-
userBpPerPxLimit: number | undefined;
|
|
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|
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* #method
|
|
491
|
-
*/
|
|
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|
+
userBpPerPxLimit: number | undefined;
|
|
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|
userByteSizeLimit: number | undefined;
|
|
493
491
|
} & import("mobx-state-tree")._NotCustomized>;
|
|
494
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|
export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
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@@ -236,7 +236,7 @@ function stateModelFactory(configSchema) {
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236
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if (sortedBy) {
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237
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const { pos, refName, assemblyName } = sortedBy;
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238
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// render just the sorted region first
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|
239
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-
// @ts-
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239
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+
// @ts-expect-error
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240
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await self.rendererType.renderInClient(rpcManager, {
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241
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assemblyName,
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242
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regions: [
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@@ -291,9 +291,9 @@ function stateModelFactory(configSchema) {
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291
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// feature.id that was returned e.g. that the user hasn't
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292
292
|
// moused over to a new position during the async operation
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293
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|
// above
|
|
294
|
-
// @ts-
|
|
294
|
+
// @ts-expect-error
|
|
295
295
|
if (self.featureIdUnderMouse === feature.uniqueId) {
|
|
296
|
-
// @ts-
|
|
296
|
+
// @ts-expect-error
|
|
297
297
|
self.setFeatureUnderMouse(new util_1.SimpleFeature(feature));
|
|
298
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|
}
|
|
299
299
|
}
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|
@@ -521,7 +521,7 @@ function stateModelFactory(configSchema) {
|
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|
521
521
|
rendererType: 'PileupRenderer',
|
|
522
522
|
}));
|
|
523
523
|
if (feature) {
|
|
524
|
-
// @ts-
|
|
524
|
+
// @ts-expect-error
|
|
525
525
|
self.selectFeature(new util_1.SimpleFeature(feature));
|
|
526
526
|
}
|
|
527
527
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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