@jbrowse/plugin-variants 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/ChordVariantDisplay/models/stateModelFactory.d.ts +5 -2
- package/dist/ChordVariantDisplay/models/stateModelFactory.js +1 -1
- package/dist/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
- package/dist/LinearVariantDisplay/model.d.ts +2 -2
- package/dist/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
- package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
- package/dist/VcfAdapter/VcfAdapter.d.ts +3 -1
- package/dist/VcfAdapter/VcfAdapter.js +9 -10
- package/dist/VcfAdapter/VcfAdapter.js.map +1 -1
- package/dist/VcfFeature/index.js +1 -1
- package/dist/VcfFeature/index.js.map +1 -1
- package/dist/VcfFeature/util.js +4 -7
- package/dist/VcfFeature/util.js.map +1 -1
- package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +5 -2
- package/esm/ChordVariantDisplay/models/stateModelFactory.js +1 -1
- package/esm/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
- package/esm/LinearVariantDisplay/model.d.ts +2 -2
- package/esm/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
- package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
- package/esm/VcfAdapter/VcfAdapter.d.ts +3 -1
- package/esm/VcfAdapter/VcfAdapter.js +9 -10
- package/esm/VcfAdapter/VcfAdapter.js.map +1 -1
- package/esm/VcfFeature/index.js +1 -1
- package/esm/VcfFeature/index.js.map +1 -1
- package/esm/VcfFeature/util.js +4 -7
- package/esm/VcfFeature/util.js.map +1 -1
- package/package.json +3 -3
- package/src/ChordVariantDisplay/models/stateModelFactory.ts +2 -2
- package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +11 -5
- package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx +1 -1
- package/src/VcfAdapter/VcfAdapter.ts +15 -16
- package/src/VcfFeature/index.ts +1 -1
- package/src/VcfFeature/util.ts +4 -6
- package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap +5 -5
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@@ -1,5 +1,6 @@
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/// <reference types="react" />
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import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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3
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+
import { Feature } from '@jbrowse/core/util';
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/**
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* #stateModel ChordVariantDisplay
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* extends `BaseChordDisplay`
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@@ -22,7 +23,9 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
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configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
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}, {
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rendererTypeName: string;
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error: unknown;
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error: unknown; /**
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* #property
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*/
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} & {
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readonly RenderingComponent: import("react").FC<{
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model: {
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@@ -81,7 +84,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
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renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
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refNameMap: Record<string, string> | undefined;
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} & {
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-
onChordClick(feature:
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+
onChordClick(feature: Feature): void;
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} & {
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readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
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renderProps(): any;
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@@ -41,7 +41,7 @@ const stateModelFactory = (configSchema) => {
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radius: view.radiusPx,
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blockDefinitions: self.blockDefinitions,
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config: self.configuration.renderer,
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onChordClick: self.onChordClick,
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onChordClick: (arg) => self.onChordClick(arg),
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};
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},
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}));
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,
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{"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,6CAA+D;AAC/D,sDAAgE;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,uBAAK;SACT,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,CAAC,GAAY,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC;aACvD,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,iBAAiB,CAAA"}
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@@ -137,7 +137,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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} & {
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readonly height:
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readonly height: number;
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readonly blockType: "dynamicBlocks" | "staticBlocks";
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readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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} & {
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@@ -167,7 +167,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
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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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resizeHeight(distance: 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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@@ -52,17 +52,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
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try {
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const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
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function remapIds(arr) {
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return arr.map(
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return arr.map(v => ({
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...v,
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id: v.trackId
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id: `${v.trackId}-${Math.random()}`,
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}));
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}
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viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
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viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
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viewSnapshot.featureData = feature;
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// eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
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const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
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viewSnapshot.views[0].tracks = remapIds(viewTracks);
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viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? viewTracks.
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viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
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session.addView('BreakpointSplitView', viewSnapshot);
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}
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catch (e) {
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@@ -1 +1 @@
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-
{"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,uCAA0C;AAC1C,qDAA6C;AAC7C,UAAU;AACV,yCAAyC;AACzC,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;
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{"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,uCAA0C;AAC1C,qDAA6C;AAC7C,UAAU;AACV,yCAAyC;AACzC,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBAMD,SAAS,QAAQ,CAAC,GAAY;4BAC5B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gCACnB,GAAG,CAAC;gCACJ,EAAE,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,4EAA4E;wBAC5E,MAAM,UAAU,GAAG,IAAA,6BAAW,EAAC,IAAI,CAAC,MAAM,CAAY,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACtD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,oBAAoB,CAAC,CAAA"}
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@@ -11,7 +11,9 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
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getMetadata(): Promise<any>;
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setupP(): Promise<{
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intervalTree:
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intervalTree: {
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[key: string]: IntervalTree<any>;
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};
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}>;
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}
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const str = new TextDecoder().decode(buffer);
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const { header, lines } = readVcf(str);
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const intervalTree =
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const intervalTree = {};
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for (const obj of lines.map((line, id) => {
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var _a;
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const [refName, startP, , ref, , , , info] = line.split('\t');
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const start = +startP - 1;
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const
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const def = start + ref.length;
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const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
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return { line, refName, start, end, id };
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})
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.reduce((acc, obj) => {
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})) {
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const key = obj.refName;
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if (!
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if (!intervalTree[key]) {
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intervalTree[key] = new interval_tree_1.default();
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}
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}, {});
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intervalTree[key].insert([obj.start, obj.end], obj);
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}
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return { header, intervalTree };
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}
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async setup() {
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|
-
{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzFjC,6BA0FC;AAzFe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
|
package/dist/VcfFeature/index.js
CHANGED
|
@@ -34,7 +34,7 @@ class VCFFeature {
|
|
|
34
34
|
const start = POS - 1;
|
|
35
35
|
const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, this.parser);
|
|
36
36
|
const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
|
|
37
|
-
const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.
|
|
37
|
+
const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
|
|
38
38
|
return {
|
|
39
39
|
refName: CHROM,
|
|
40
40
|
start,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfFeature/index.ts"],"names":[],"mappings":";;AAGA,SAAS;AACT,iCAAgD;AAsBhD,MAAqB,UAAU;IAU7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAI,CAAC;IAER,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,OAAO,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,IAAI,EAAE,WAAW,CAAC,GAAG,IAAA,8BAAuB,EAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QAC1E,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfFeature/index.ts"],"names":[],"mappings":";;AAGA,SAAS;AACT,iCAAgD;AAsBhD,MAAqB,UAAU;IAU7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAI,CAAC;IAER,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,OAAO,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,IAAI,EAAE,WAAW,CAAC,GAAG,IAAA,8BAAuB,EAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QAC1E,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAA;QAElD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI;YACJ,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED,8DAA8D;IAC9D,MAAM;QACJ,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,GAAG;YAClB,GAAG,IAAI,CAAC,OAAO;YACf,GAAG,IAAI,CAAC,IAAI;YACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO;SAC9B,CAAA;IACH,CAAC;CACF;AA7ED,6BA6EC"}
|
package/dist/VcfFeature/util.js
CHANGED
|
@@ -74,7 +74,7 @@ function getSOAndDescFromAltDefs(ref, alt, parser) {
|
|
|
74
74
|
// try to look for a definition for a parent term if we can
|
|
75
75
|
const modAlt = alt.split(':');
|
|
76
76
|
if (modAlt.length > 1) {
|
|
77
|
-
return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0,
|
|
77
|
+
return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
|
|
78
78
|
}
|
|
79
79
|
// no parent
|
|
80
80
|
return [];
|
|
@@ -107,12 +107,9 @@ function getSOAndDescByExamination(ref, alt) {
|
|
|
107
107
|
return ['sv', alt];
|
|
108
108
|
}
|
|
109
109
|
else if (ref.length === alt.length) {
|
|
110
|
-
|
|
111
|
-
|
|
112
|
-
|
|
113
|
-
else {
|
|
114
|
-
return ['substitution', makeDescriptionString('substitution', ref, alt)];
|
|
115
|
-
}
|
|
110
|
+
return ref.split('').reverse().join('') === alt
|
|
111
|
+
? ['inversion', makeDescriptionString('inversion', ref, alt)]
|
|
112
|
+
: ['substitution', makeDescriptionString('substitution', ref, alt)];
|
|
116
113
|
}
|
|
117
114
|
else if (ref.length <= alt.length) {
|
|
118
115
|
return ['insertion', makeDescriptionString('insertion', ref, alt)];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/VcfFeature/util.ts"],"names":[],"mappings":";;;AAAA,mCAA8C;AAE9C,MAAM,WAAW,GAA0C;IACzD,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA;AAED;;GAEG;AACH,SAAgB,uBAAuB,CACrC,GAAW,EACX,GAAa,EACb,MAAW;IAEX,uDAAuD;IACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;KAC5C;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;IACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACnE,IAAI,CAAC,MAAM,EAAE;YACX,CAAC;YAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,yBAAyB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;SAC3D;QACD,IAAI,MAAM,IAAI,WAAW,EAAE;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;SAC9B;IACH,CAAC,CAAC,CAAA;IAEF,6EAA6E;IAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACf,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QACrC,CAAC,CAAC,CACH,CAAA;QAED,YAAY,GAAG,IAAI,GAAG,CACpB,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,KAAK;iBACnB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;YACrD,CAAC,CAAC;iBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnB,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACvE,CAAC,CAAC,CACH,CAAA;KACF;IACD,IAAI,OAAO,CAAC,IAAI,EAAE;QAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;KAC7D;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAlDD,0DAkDC;AAED,SAAgB,uBAAuB,CACrC,GAAW,EACX,GAAW,EACX,MAAW;IAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;QACnD,OAAO,EAAE,CAAA;KACV;IAED,iDAAiD;IACjD,IAAI,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC7B,gEAAgE;IAChE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;QAC7C,MAAM,GAAG,kBAAkB,CAAA;KAC5B;IACD,IAAI,MAAM,EAAE;QACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;KACrB;IAED,2DAA2D;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,OAAO,uBAAuB,CAC5B,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/VcfFeature/util.ts"],"names":[],"mappings":";;;AAAA,mCAA8C;AAE9C,MAAM,WAAW,GAA0C;IACzD,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA;AAED;;GAEG;AACH,SAAgB,uBAAuB,CACrC,GAAW,EACX,GAAa,EACb,MAAW;IAEX,uDAAuD;IACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;KAC5C;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;IACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACnE,IAAI,CAAC,MAAM,EAAE;YACX,CAAC;YAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,yBAAyB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;SAC3D;QACD,IAAI,MAAM,IAAI,WAAW,EAAE;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;SAC9B;IACH,CAAC,CAAC,CAAA;IAEF,6EAA6E;IAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACf,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QACrC,CAAC,CAAC,CACH,CAAA;QAED,YAAY,GAAG,IAAI,GAAG,CACpB,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,KAAK;iBACnB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;YACrD,CAAC,CAAC;iBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnB,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACvE,CAAC,CAAC,CACH,CAAA;KACF;IACD,IAAI,OAAO,CAAC,IAAI,EAAE;QAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;KAC7D;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAlDD,0DAkDC;AAED,SAAgB,uBAAuB,CACrC,GAAW,EACX,GAAW,EACX,MAAW;IAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;QACnD,OAAO,EAAE,CAAA;KACV;IAED,iDAAiD;IACjD,IAAI,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC7B,gEAAgE;IAChE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;QAC7C,MAAM,GAAG,kBAAkB,CAAA;KAC5B;IACD,IAAI,MAAM,EAAE;QACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;KACrB;IAED,2DAA2D;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,OAAO,uBAAuB,CAC5B,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EACpC,MAAM,CACP,CAAA;KACF;IAED,YAAY;IACZ,OAAO,EAAE,CAAA;AACX,CAAC;AA/BD,0DA+BC;AAED,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO;AACP,SAAgB,yBAAyB,CAAC,GAAW,EAAE,GAAW;IAChE,MAAM,GAAG,GAAG,IAAA,mBAAa,EAAC,GAAG,CAAC,CAAA;IAC9B,IAAI,GAAG,EAAE;QACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC/C,OAAO,CAAC,KAAK,EAAE,qBAAqB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACvD;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;KAC1B;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;KAC9B;SAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;QAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;KACnB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;QACpC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG;YAC7C,CAAC,CAAC,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC7D,CAAC,CAAC,CAAC,cAAc,EAAE,qBAAqB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACtE;SAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;QACnC,OAAO,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACnE;SAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;QAClC,OAAO,CAAC,UAAU,EAAE,qBAAqB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACjE;IAED,OAAO,CAAC,OAAO,EAAE,qBAAqB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;AAC5D,CAAC;AA3BD,8DA2BC;AAED,SAAS,qBAAqB,CAAC,MAAc,EAAE,GAAW,EAAE,GAAW;IACrE,OAAO,GAAG,MAAM,IAAI,GAAG,OAAO,GAAG,EAAE,CAAA;AACrC,CAAC"}
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@@ -1,5 +1,6 @@
|
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1
1
|
/// <reference types="react" />
|
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2
2
|
import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
|
|
3
|
+
import { Feature } from '@jbrowse/core/util';
|
|
3
4
|
/**
|
|
4
5
|
* #stateModel ChordVariantDisplay
|
|
5
6
|
* extends `BaseChordDisplay`
|
|
@@ -22,7 +23,9 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
|
|
|
22
23
|
configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
|
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23
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|
}, {
|
|
24
25
|
rendererTypeName: string;
|
|
25
|
-
error: unknown;
|
|
26
|
+
error: unknown; /**
|
|
27
|
+
* #property
|
|
28
|
+
*/
|
|
26
29
|
} & {
|
|
27
30
|
readonly RenderingComponent: import("react").FC<{
|
|
28
31
|
model: {
|
|
@@ -81,7 +84,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
|
|
|
81
84
|
renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
|
|
82
85
|
refNameMap: Record<string, string> | undefined;
|
|
83
86
|
} & {
|
|
84
|
-
onChordClick(feature:
|
|
87
|
+
onChordClick(feature: Feature): void;
|
|
85
88
|
} & {
|
|
86
89
|
readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
|
|
87
90
|
renderProps(): any;
|
|
@@ -39,7 +39,7 @@ const stateModelFactory = (configSchema) => {
|
|
|
39
39
|
radius: view.radiusPx,
|
|
40
40
|
blockDefinitions: self.blockDefinitions,
|
|
41
41
|
config: self.configuration.renderer,
|
|
42
|
-
onChordClick: self.onChordClick,
|
|
42
|
+
onChordClick: (arg) => self.onChordClick(arg),
|
|
43
43
|
};
|
|
44
44
|
},
|
|
45
45
|
}));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,qBAAqB,EAAE,MAAM,+BAA+B,CAAA;AACrE,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,
|
|
1
|
+
{"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,qBAAqB,EAAE,MAAM,+BAA+B,CAAA;AACrE,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAW,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAC/D,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,KAAK;SACT,OAAO,CACN,qBAAqB,EACrB,qBAAqB,EACrB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,oBAAoB,CAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,CAAC,GAAY,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC;aACvD,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,eAAe,iBAAiB,CAAA"}
|
|
@@ -137,7 +137,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
|
|
|
137
137
|
estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
|
|
138
138
|
estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
|
|
139
139
|
} & {
|
|
140
|
-
readonly height:
|
|
140
|
+
readonly height: number;
|
|
141
141
|
readonly blockType: "dynamicBlocks" | "staticBlocks";
|
|
142
142
|
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
143
143
|
} & {
|
|
@@ -167,7 +167,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
|
|
|
167
167
|
setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
|
|
168
168
|
setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
|
|
169
169
|
clearRegionStats(): void;
|
|
170
|
-
setHeight(displayHeight: number):
|
|
170
|
+
setHeight(displayHeight: number): number;
|
|
171
171
|
resizeHeight(distance: number): number;
|
|
172
172
|
setScrollTop(scrollTop: number): void;
|
|
173
173
|
updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
|
|
@@ -27,17 +27,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
|
|
|
27
27
|
try {
|
|
28
28
|
const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
|
|
29
29
|
function remapIds(arr) {
|
|
30
|
-
return arr.map(
|
|
30
|
+
return arr.map(v => ({
|
|
31
31
|
...v,
|
|
32
|
-
id: v.trackId
|
|
32
|
+
id: `${v.trackId}-${Math.random()}`,
|
|
33
33
|
}));
|
|
34
34
|
}
|
|
35
35
|
viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
|
|
36
36
|
viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
|
|
37
37
|
viewSnapshot.featureData = feature;
|
|
38
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
|
|
38
39
|
const viewTracks = getSnapshot(view.tracks);
|
|
39
40
|
viewSnapshot.views[0].tracks = remapIds(viewTracks);
|
|
40
|
-
viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? viewTracks.
|
|
41
|
+
viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
|
|
41
42
|
session.addView('BreakpointSplitView', viewSnapshot);
|
|
42
43
|
}
|
|
43
44
|
catch (e) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,UAAU;AACV,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;
|
|
1
|
+
{"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,UAAU;AACV,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBAMD,SAAS,QAAQ,CAAC,GAAY;4BAC5B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gCACnB,GAAG,CAAC;gCACJ,EAAE,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,4EAA4E;wBAC5E,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAY,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACtD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
|
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@@ -11,7 +11,9 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
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11
11
|
getMetadata(): Promise<any>;
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12
12
|
setupP(): Promise<{
|
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13
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|
header: string;
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14
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-
intervalTree:
|
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14
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+
intervalTree: {
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15
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+
[key: string]: IntervalTree<any>;
|
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16
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+
};
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15
17
|
}>;
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16
18
|
setup(): Promise<{
|
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17
19
|
header: string;
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@@ -46,22 +46,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
|
|
|
46
46
|
}
|
|
47
47
|
const str = new TextDecoder().decode(buffer);
|
|
48
48
|
const { header, lines } = readVcf(str);
|
|
49
|
-
const intervalTree =
|
|
50
|
-
|
|
49
|
+
const intervalTree = {};
|
|
50
|
+
for (const obj of lines.map((line, id) => {
|
|
51
51
|
var _a;
|
|
52
52
|
const [refName, startP, , ref, , , , info] = line.split('\t');
|
|
53
53
|
const start = +startP - 1;
|
|
54
|
-
const
|
|
54
|
+
const def = start + ref.length;
|
|
55
|
+
const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
|
|
55
56
|
return { line, refName, start, end, id };
|
|
56
|
-
})
|
|
57
|
-
.reduce((acc, obj) => {
|
|
57
|
+
})) {
|
|
58
58
|
const key = obj.refName;
|
|
59
|
-
if (!
|
|
60
|
-
|
|
59
|
+
if (!intervalTree[key]) {
|
|
60
|
+
intervalTree[key] = new IntervalTree();
|
|
61
61
|
}
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
}, {});
|
|
62
|
+
intervalTree[key].insert([obj.start, obj.end], obj);
|
|
63
|
+
}
|
|
65
64
|
return { header, intervalTree };
|
|
66
65
|
}
|
|
67
66
|
async setup() {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
|
package/esm/VcfFeature/index.js
CHANGED
|
@@ -32,7 +32,7 @@ export default class VCFFeature {
|
|
|
32
32
|
const start = POS - 1;
|
|
33
33
|
const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
|
|
34
34
|
const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
|
|
35
|
-
const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.
|
|
35
|
+
const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
|
|
36
36
|
return {
|
|
37
37
|
refName: CHROM,
|
|
38
38
|
start,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfFeature/index.ts"],"names":[],"mappings":"AAGA,SAAS;AACT,OAAO,EAAE,uBAAuB,EAAE,MAAM,QAAQ,CAAA;AAsBhD,MAAM,CAAC,OAAO,OAAO,UAAU;IAU7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAI,CAAC;IAER,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,OAAO,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,IAAI,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QAC1E,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfFeature/index.ts"],"names":[],"mappings":"AAGA,SAAS;AACT,OAAO,EAAE,uBAAuB,EAAE,MAAM,QAAQ,CAAA;AAsBhD,MAAM,CAAC,OAAO,OAAO,UAAU;IAU7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAI,CAAC;IAER,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,OAAO,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,IAAI,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;QAC1E,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAA;QAElD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI;YACJ,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED,8DAA8D;IAC9D,MAAM;QACJ,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,GAAG;YAClB,GAAG,IAAI,CAAC,OAAO;YACf,GAAG,IAAI,CAAC,IAAI;YACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO;SAC9B,CAAA;IACH,CAAC;CACF"}
|
package/esm/VcfFeature/util.js
CHANGED
|
@@ -70,7 +70,7 @@ export function getSOAndDescFromAltDefs(ref, alt, parser) {
|
|
|
70
70
|
// try to look for a definition for a parent term if we can
|
|
71
71
|
const modAlt = alt.split(':');
|
|
72
72
|
if (modAlt.length > 1) {
|
|
73
|
-
return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0,
|
|
73
|
+
return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
|
|
74
74
|
}
|
|
75
75
|
// no parent
|
|
76
76
|
return [];
|
|
@@ -102,12 +102,9 @@ export function getSOAndDescByExamination(ref, alt) {
|
|
|
102
102
|
return ['sv', alt];
|
|
103
103
|
}
|
|
104
104
|
else if (ref.length === alt.length) {
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
|
|
108
|
-
else {
|
|
109
|
-
return ['substitution', makeDescriptionString('substitution', ref, alt)];
|
|
110
|
-
}
|
|
105
|
+
return ref.split('').reverse().join('') === alt
|
|
106
|
+
? ['inversion', makeDescriptionString('inversion', ref, alt)]
|
|
107
|
+
: ['substitution', makeDescriptionString('substitution', ref, alt)];
|
|
111
108
|
}
|
|
112
109
|
else if (ref.length <= alt.length) {
|
|
113
110
|
return ['insertion', makeDescriptionString('insertion', ref, alt)];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/VcfFeature/util.ts"],"names":[],"mappings":"AAAA,OAAY,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAE9C,MAAM,WAAW,GAA0C;IACzD,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA;AAED;;GAEG;AACH,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAa,EACb,MAAW;IAEX,uDAAuD;IACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;KAC5C;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;IACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACnE,IAAI,CAAC,MAAM,EAAE;YACX,CAAC;YAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,yBAAyB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;SAC3D;QACD,IAAI,MAAM,IAAI,WAAW,EAAE;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;SAC9B;IACH,CAAC,CAAC,CAAA;IAEF,6EAA6E;IAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACf,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QACrC,CAAC,CAAC,CACH,CAAA;QAED,YAAY,GAAG,IAAI,GAAG,CACpB,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,KAAK;iBACnB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;YACrD,CAAC,CAAC;iBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnB,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACvE,CAAC,CAAC,CACH,CAAA;KACF;IACD,IAAI,OAAO,CAAC,IAAI,EAAE;QAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;KAC7D;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAW,EACX,MAAW;IAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;QACnD,OAAO,EAAE,CAAA;KACV;IAED,iDAAiD;IACjD,IAAI,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC7B,gEAAgE;IAChE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;QAC7C,MAAM,GAAG,kBAAkB,CAAA;KAC5B;IACD,IAAI,MAAM,EAAE;QACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;KACrB;IAED,2DAA2D;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,OAAO,uBAAuB,CAC5B,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/VcfFeature/util.ts"],"names":[],"mappings":"AAAA,OAAY,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAE9C,MAAM,WAAW,GAA0C;IACzD,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA;AAED;;GAEG;AACH,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAa,EACb,MAAW;IAEX,uDAAuD;IACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;KAC5C;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;IACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACnE,IAAI,CAAC,MAAM,EAAE;YACX,CAAC;YAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,yBAAyB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;SAC3D;QACD,IAAI,MAAM,IAAI,WAAW,EAAE;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;SAC9B;IACH,CAAC,CAAC,CAAA;IAEF,6EAA6E;IAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACf,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QACrC,CAAC,CAAC,CACH,CAAA;QAED,YAAY,GAAG,IAAI,GAAG,CACpB,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,KAAK;iBACnB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;YACrD,CAAC,CAAC;iBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnB,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACvE,CAAC,CAAC,CACH,CAAA;KACF;IACD,IAAI,OAAO,CAAC,IAAI,EAAE;QAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;KAC7D;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAW,EACX,MAAW;IAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;QACnD,OAAO,EAAE,CAAA;KACV;IAED,iDAAiD;IACjD,IAAI,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC7B,gEAAgE;IAChE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;QAC7C,MAAM,GAAG,kBAAkB,CAAA;KAC5B;IACD,IAAI,MAAM,EAAE;QACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;KACrB;IAED,2DAA2D;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,OAAO,uBAAuB,CAC5B,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EACpC,MAAM,CACP,CAAA;KACF;IAED,YAAY;IACZ,OAAO,EAAE,CAAA;AACX,CAAC;AAED,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO;AACP,MAAM,UAAU,yBAAyB,CAAC,GAAW,EAAE,GAAW;IAChE,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,CAAA;IAC9B,IAAI,GAAG,EAAE;QACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC/C,OAAO,CAAC,KAAK,EAAE,qBAAqB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACvD;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;KAC1B;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;KAC9B;SAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;QAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;KACnB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;QACpC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG;YAC7C,CAAC,CAAC,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC7D,CAAC,CAAC,CAAC,cAAc,EAAE,qBAAqB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACtE;SAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;QACnC,OAAO,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACnE;SAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;QAClC,OAAO,CAAC,UAAU,EAAE,qBAAqB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACjE;IAED,OAAO,CAAC,OAAO,EAAE,qBAAqB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;AAC5D,CAAC;AAED,SAAS,qBAAqB,CAAC,MAAc,EAAE,GAAW,EAAE,GAAW;IACrE,OAAO,GAAG,MAAM,IAAI,GAAG,OAAO,GAAG,EAAE,CAAA;AACrC,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-variants",
|
|
3
|
-
"version": "2.4.
|
|
3
|
+
"version": "2.4.1",
|
|
4
4
|
"description": "JBrowse 2 variant adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -39,7 +39,7 @@
|
|
|
39
39
|
"dependencies": {
|
|
40
40
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
41
41
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
42
|
-
"@gmod/tabix": "^1.5.
|
|
42
|
+
"@gmod/tabix": "^1.5.6",
|
|
43
43
|
"@gmod/vcf": "^5.0.9",
|
|
44
44
|
"@mui/icons-material": "^5.0.2",
|
|
45
45
|
"@mui/x-data-grid": "^5.0.1",
|
|
@@ -64,5 +64,5 @@
|
|
|
64
64
|
"distModule": "esm/index.js",
|
|
65
65
|
"srcModule": "src/index.ts",
|
|
66
66
|
"module": "esm/index.js",
|
|
67
|
-
"gitHead": "
|
|
67
|
+
"gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
|
|
68
68
|
}
|
|
@@ -4,7 +4,7 @@ import {
|
|
|
4
4
|
ConfigurationReference,
|
|
5
5
|
} from '@jbrowse/core/configuration'
|
|
6
6
|
import { types } from 'mobx-state-tree'
|
|
7
|
-
import { getContainingView } from '@jbrowse/core/util'
|
|
7
|
+
import { Feature, getContainingView } from '@jbrowse/core/util'
|
|
8
8
|
import { getParentRenderProps } from '@jbrowse/core/util/tracks'
|
|
9
9
|
|
|
10
10
|
/**
|
|
@@ -48,7 +48,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
|
|
|
48
48
|
radius: view.radiusPx,
|
|
49
49
|
blockDefinitions: self.blockDefinitions,
|
|
50
50
|
config: self.configuration.renderer,
|
|
51
|
-
onChordClick: self.onChordClick,
|
|
51
|
+
onChordClick: (arg: Feature) => self.onChordClick(arg),
|
|
52
52
|
}
|
|
53
53
|
},
|
|
54
54
|
}))
|
|
@@ -70,19 +70,25 @@ function BreakendOptionDialog({
|
|
|
70
70
|
feature,
|
|
71
71
|
view,
|
|
72
72
|
)
|
|
73
|
-
|
|
74
|
-
|
|
73
|
+
|
|
74
|
+
interface Track {
|
|
75
|
+
trackId: string
|
|
76
|
+
[key: string]: unknown
|
|
77
|
+
}
|
|
78
|
+
function remapIds(arr: Track[]) {
|
|
79
|
+
return arr.map(v => ({
|
|
75
80
|
...v,
|
|
76
|
-
id: v.trackId
|
|
81
|
+
id: `${v.trackId}-${Math.random()}`,
|
|
77
82
|
}))
|
|
78
83
|
}
|
|
79
84
|
viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
|
|
80
85
|
viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
|
|
81
86
|
viewSnapshot.featureData = feature
|
|
82
|
-
|
|
87
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
|
|
88
|
+
const viewTracks = getSnapshot(view.tracks) as Track[]
|
|
83
89
|
viewSnapshot.views[0].tracks = remapIds(viewTracks)
|
|
84
90
|
viewSnapshot.views[1].tracks = remapIds(
|
|
85
|
-
mirrorTracks ? viewTracks.
|
|
91
|
+
mirrorTracks ? [...viewTracks].reverse() : viewTracks,
|
|
86
92
|
)
|
|
87
93
|
|
|
88
94
|
session.addView('BreakpointSplitView', viewSnapshot)
|
|
@@ -65,22 +65,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
|
|
|
65
65
|
|
|
66
66
|
const str = new TextDecoder().decode(buffer)
|
|
67
67
|
const { header, lines } = readVcf(str)
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
}
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
}, {} as Record<string, IntervalTree>)
|
|
68
|
+
const intervalTree = {} as { [key: string]: IntervalTree }
|
|
69
|
+
|
|
70
|
+
for (const obj of lines.map((line, id) => {
|
|
71
|
+
const [refName, startP, , ref, , , , info] = line.split('\t')
|
|
72
|
+
const start = +startP - 1
|
|
73
|
+
const def = start + ref.length
|
|
74
|
+
const end = +(info.match(/END=(\d+)/)?.[1].trim() || def)
|
|
75
|
+
return { line, refName, start, end, id }
|
|
76
|
+
})) {
|
|
77
|
+
const key = obj.refName
|
|
78
|
+
if (!intervalTree[key]) {
|
|
79
|
+
intervalTree[key] = new IntervalTree()
|
|
80
|
+
}
|
|
81
|
+
intervalTree[key].insert([obj.start, obj.end], obj)
|
|
82
|
+
}
|
|
84
83
|
|
|
85
84
|
return { header, intervalTree }
|
|
86
85
|
}
|
package/src/VcfFeature/index.ts
CHANGED
|
@@ -79,7 +79,7 @@ export default class VCFFeature implements Feature {
|
|
|
79
79
|
const start = POS - 1
|
|
80
80
|
const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
|
|
81
81
|
const isTRA = ALT?.some(f => f === '<TRA>')
|
|
82
|
-
const isSymbolic = ALT?.some(f => f.
|
|
82
|
+
const isSymbolic = ALT?.some(f => f.includes('<'))
|
|
83
83
|
|
|
84
84
|
return {
|
|
85
85
|
refName: CHROM,
|
package/src/VcfFeature/util.ts
CHANGED
|
@@ -92,7 +92,7 @@ export function getSOAndDescFromAltDefs(
|
|
|
92
92
|
if (modAlt.length > 1) {
|
|
93
93
|
return getSOAndDescFromAltDefs(
|
|
94
94
|
ref,
|
|
95
|
-
`<${modAlt.slice(0,
|
|
95
|
+
`<${modAlt.slice(0, -1).join(':')}>`,
|
|
96
96
|
parser,
|
|
97
97
|
)
|
|
98
98
|
}
|
|
@@ -121,11 +121,9 @@ export function getSOAndDescByExamination(ref: string, alt: string) {
|
|
|
121
121
|
} else if (alt.includes('<')) {
|
|
122
122
|
return ['sv', alt]
|
|
123
123
|
} else if (ref.length === alt.length) {
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
return ['substitution', makeDescriptionString('substitution', ref, alt)]
|
|
128
|
-
}
|
|
124
|
+
return ref.split('').reverse().join('') === alt
|
|
125
|
+
? ['inversion', makeDescriptionString('inversion', ref, alt)]
|
|
126
|
+
: ['substitution', makeDescriptionString('substitution', ref, alt)]
|
|
129
127
|
} else if (ref.length <= alt.length) {
|
|
130
128
|
return ['insertion', makeDescriptionString('insertion', ref, alt)]
|
|
131
129
|
} else if (ref.length > alt.length) {
|
|
@@ -66,7 +66,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
|
|
|
66
66
|
},
|
|
67
67
|
"start": 276,
|
|
68
68
|
"type": "SNV",
|
|
69
|
-
"uniqueId": "test-vcf-
|
|
69
|
+
"uniqueId": "test-vcf-604453",
|
|
70
70
|
},
|
|
71
71
|
{
|
|
72
72
|
"ALT": [
|
|
@@ -132,7 +132,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
|
|
|
132
132
|
},
|
|
133
133
|
"start": 1693,
|
|
134
134
|
"type": "SNV",
|
|
135
|
-
"uniqueId": "test-vcf-
|
|
135
|
+
"uniqueId": "test-vcf-604551",
|
|
136
136
|
},
|
|
137
137
|
{
|
|
138
138
|
"ALT": [
|
|
@@ -198,7 +198,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
|
|
|
198
198
|
},
|
|
199
199
|
"start": 2643,
|
|
200
200
|
"type": "SNV",
|
|
201
|
-
"uniqueId": "test-vcf-
|
|
201
|
+
"uniqueId": "test-vcf-604668",
|
|
202
202
|
},
|
|
203
203
|
{
|
|
204
204
|
"ALT": [
|
|
@@ -258,7 +258,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
|
|
|
258
258
|
},
|
|
259
259
|
"start": 3212,
|
|
260
260
|
"type": "SNV",
|
|
261
|
-
"uniqueId": "test-vcf-
|
|
261
|
+
"uniqueId": "test-vcf-604785",
|
|
262
262
|
},
|
|
263
263
|
{
|
|
264
264
|
"ALT": [
|
|
@@ -319,7 +319,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
|
|
|
319
319
|
},
|
|
320
320
|
"start": 3857,
|
|
321
321
|
"type": "deletion",
|
|
322
|
-
"uniqueId": "test-vcf-
|
|
322
|
+
"uniqueId": "test-vcf-604887",
|
|
323
323
|
},
|
|
324
324
|
]
|
|
325
325
|
`;
|