@jbrowse/plugin-alignments 2.4.2 → 2.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +0 -1
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +0 -1
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -1
- package/dist/AlignmentsFeatureDetail/index.d.ts +4 -1
- package/dist/AlignmentsTrack/configSchemaF.d.ts +74 -0
- package/dist/AlignmentsTrack/configSchemaF.js +19 -0
- package/dist/AlignmentsTrack/configSchemaF.js.map +1 -0
- package/dist/AlignmentsTrack/index.js +2 -15
- package/dist/AlignmentsTrack/index.js.map +1 -1
- package/dist/BamAdapter/BamAdapter.d.ts +1 -1
- package/dist/BamAdapter/BamAdapter.js +2 -2
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/BamAdapter/configSchema.d.ts +50 -1
- package/dist/CramAdapter/CramAdapter.d.ts +1 -1
- package/dist/CramAdapter/CramAdapter.js +1 -1
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/CramAdapter/CramTestAdapters.js +2 -2
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
- package/dist/CramAdapter/configSchema.d.ts +40 -1
- package/dist/HtsgetBamAdapter/configSchema.d.ts +26 -1
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +0 -1
- package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +39 -1
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +8 -4
- package/dist/LinearAlignmentsDisplay/models/model.js +7 -3
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +0 -1
- package/dist/LinearPileupDisplay/components/ColorByTag.d.ts +0 -1
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +0 -1
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +0 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.d.ts +0 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +3 -5
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SortByTag.d.ts +0 -1
- package/dist/LinearPileupDisplay/configSchema.d.ts +57 -1
- package/dist/LinearPileupDisplay/model.d.ts +107 -50
- package/dist/LinearPileupDisplay/model.js +21 -24
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts +0 -1
- package/dist/LinearReadArcsDisplay/configSchema.d.ts +62 -1
- package/dist/LinearReadArcsDisplay/drawFeats.js +2 -2
- package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +78 -21
- package/dist/LinearReadCloudDisplay/components/ReactComponent.d.ts +0 -1
- package/dist/LinearReadCloudDisplay/configSchema.d.ts +50 -1
- package/dist/LinearReadCloudDisplay/drawFeats.d.ts +2 -0
- package/dist/LinearReadCloudDisplay/drawFeats.js +4 -4
- package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/dist/LinearReadCloudDisplay/model.d.ts +65 -18
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +0 -1
- package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts +79 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +48 -21
- package/dist/LinearSNPCoverageDisplay/models/model.js +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
- package/dist/PileupRenderer/PileupRenderer.js +9 -0
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/PileupRenderer/configSchema.d.ts +87 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +2 -2
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageAdapter/configSchema.d.ts +10 -1
- package/dist/SNPCoverageAdapter/generateCoverageBins.js +50 -46
- package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
- package/dist/SNPCoverageRenderer/configSchema.d.ts +42 -1
- package/dist/shared/FilterByTag.d.ts +0 -1
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +0 -1
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts +0 -1
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts +0 -1
- package/esm/AlignmentsFeatureDetail/index.d.ts +4 -1
- package/esm/AlignmentsTrack/configSchemaF.d.ts +74 -0
- package/esm/AlignmentsTrack/configSchemaF.js +16 -0
- package/esm/AlignmentsTrack/configSchemaF.js.map +1 -0
- package/esm/AlignmentsTrack/index.js +3 -16
- package/esm/AlignmentsTrack/index.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.d.ts +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -2
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/BamAdapter/configSchema.d.ts +50 -1
- package/esm/CramAdapter/CramAdapter.d.ts +1 -1
- package/esm/CramAdapter/CramAdapter.js +1 -1
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/CramAdapter/CramTestAdapters.js +1 -1
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
- package/esm/CramAdapter/configSchema.d.ts +40 -1
- package/esm/HtsgetBamAdapter/configSchema.d.ts +26 -1
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +0 -1
- package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +39 -1
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +8 -4
- package/esm/LinearAlignmentsDisplay/models/model.js +7 -3
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +0 -1
- package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +0 -1
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +0 -1
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +0 -1
- package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +0 -1
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +3 -5
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/esm/LinearPileupDisplay/components/SortByTag.d.ts +0 -1
- package/esm/LinearPileupDisplay/configSchema.d.ts +57 -1
- package/esm/LinearPileupDisplay/model.d.ts +107 -50
- package/esm/LinearPileupDisplay/model.js +21 -24
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearReadArcsDisplay/components/ReactComponent.d.ts +0 -1
- package/esm/LinearReadArcsDisplay/configSchema.d.ts +62 -1
- package/esm/LinearReadArcsDisplay/drawFeats.js +2 -2
- package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +78 -21
- package/esm/LinearReadCloudDisplay/components/ReactComponent.d.ts +0 -1
- package/esm/LinearReadCloudDisplay/configSchema.d.ts +50 -1
- package/esm/LinearReadCloudDisplay/drawFeats.d.ts +2 -0
- package/esm/LinearReadCloudDisplay/drawFeats.js +4 -4
- package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/esm/LinearReadCloudDisplay/model.d.ts +65 -18
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +0 -1
- package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +79 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +48 -21
- package/esm/LinearSNPCoverageDisplay/models/model.js +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
- package/esm/PileupRenderer/PileupRenderer.js +9 -0
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/PileupRenderer/configSchema.d.ts +87 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +2 -2
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageAdapter/configSchema.d.ts +10 -1
- package/esm/SNPCoverageAdapter/generateCoverageBins.js +50 -46
- package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +1 -1
- package/esm/SNPCoverageRenderer/configSchema.d.ts +42 -1
- package/esm/shared/FilterByTag.d.ts +0 -1
- package/package.json +2 -2
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +1 -2
- package/src/AlignmentsTrack/configSchemaF.ts +22 -0
- package/src/AlignmentsTrack/index.ts +3 -24
- package/src/BamAdapter/BamAdapter.ts +5 -2
- package/src/CramAdapter/CramAdapter.ts +4 -1
- package/src/CramAdapter/CramTestAdapters.ts +1 -1
- package/src/LinearAlignmentsDisplay/models/model.tsx +11 -3
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +3 -5
- package/src/LinearPileupDisplay/model.ts +38 -36
- package/src/LinearReadArcsDisplay/drawFeats.ts +2 -2
- package/src/LinearReadCloudDisplay/drawFeats.ts +6 -5
- package/src/LinearSNPCoverageDisplay/models/model.ts +1 -1
- package/src/PileupRenderer/PileupLayoutSession.ts +1 -1
- package/src/PileupRenderer/PileupRenderer.ts +15 -5
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -2
- package/src/SNPCoverageAdapter/generateCoverageBins.ts +58 -55
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import PluginManager from '@jbrowse/core/PluginManager';
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declare const configSchema: import("@jbrowse/core/configuration").
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declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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@@ -13,10 +13,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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} & {
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type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
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}, {
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error: unknown;
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} & {
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setFeatureData(featureData: Record<string, unknown>): void;
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clearFeatureData(): void;
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setFormattedData(feat: Record<string, unknown>): void;
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setExtra(type?: string | undefined, trackId?: string | undefined): void;
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setError(e: unknown): void;
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} & {
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afterCreate(): void;
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}, {
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import PluginManager from '@jbrowse/core/PluginManager';
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export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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name: {
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description: string;
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type: string;
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defaultValue: string;
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};
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assemblyNames: {
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description: string;
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type: string;
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defaultValue: string[];
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};
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description: {
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description: string;
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type: string;
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defaultValue: string;
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};
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category: {
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description: string;
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type: string;
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defaultValue: never[];
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};
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metadata: {
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type: string;
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description: string;
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defaultValue: {};
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};
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adapter: import("mobx-state-tree").IAnyModelType;
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textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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indexingAttributes: {
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type: string;
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description: string;
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defaultValue: string[];
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};
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indexingFeatureTypesToExclude: {
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type: string;
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description: string;
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defaultValue: string[];
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};
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textSearchAdapter: import("mobx-state-tree").IAnyModelType;
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
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formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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feature: {
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type: string;
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description: string;
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defaultValue: {};
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contextVariable: string[];
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};
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subfeatures: {
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type: string;
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description: string;
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defaultValue: {};
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contextVariable: string[];
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};
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depth: {
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defaultValue: number;
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description: string;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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config: {
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description: string;
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defaultValue: {};
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contextVariable: string[];
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};
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hideUris: {
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type: string;
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defaultValue: boolean;
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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const configuration_1 = require("@jbrowse/core/configuration");
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const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
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/**
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* #config AlignmentsTrack
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* has very little config; most config and state logic is on the display
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*/
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function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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function configSchemaFactory(pluginManager) {
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return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
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*/
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baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
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});
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}
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exports.default = configSchemaFactory;
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//# sourceMappingURL=configSchemaF.js.map
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{"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,+EAA2E;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAwB,mBAAmB,CAAC,aAA4B;IACtE,OAAO,IAAA,mCAAmB,EACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,6CAAqB,EAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC;AAXD,sCAWC"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,oEAA2C;AAE3C,SAAwB,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,uBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,mBAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC;AAhBD,2BAgBC"}
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}): import("rxjs").Observable<Feature>;
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|
|
42
|
+
getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
|
|
43
43
|
bytes: number;
|
|
44
44
|
fetchSizeLimit: any;
|
|
45
45
|
}>;
|
|
@@ -161,7 +161,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
161
161
|
observer.complete();
|
|
162
162
|
}, signal);
|
|
163
163
|
}
|
|
164
|
-
async
|
|
164
|
+
async getMultiRegionFeatureDensityStats(regions, opts) {
|
|
165
165
|
const { bam } = await this.configure();
|
|
166
166
|
// this is a method to avoid calling on htsget adapters
|
|
167
167
|
// @ts-expect-error
|
|
@@ -171,7 +171,7 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
171
171
|
return { bytes, fetchSizeLimit };
|
|
172
172
|
}
|
|
173
173
|
else {
|
|
174
|
-
return super.
|
|
174
|
+
return super.getMultiRegionFeatureDensityStats(regions, opts);
|
|
175
175
|
}
|
|
176
176
|
}
|
|
177
177
|
freeResources( /* { region } */) { }
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"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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@@ -1,2 +1,51 @@
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1
|
-
declare const configSchema: import("@jbrowse/core/configuration").
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1
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+
declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
2
|
+
/**
|
|
3
|
+
* #slot
|
|
4
|
+
*/
|
|
5
|
+
bamLocation: {
|
|
6
|
+
type: string;
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7
|
+
defaultValue: {
|
|
8
|
+
uri: string;
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9
|
+
locationType: string;
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|
10
|
+
};
|
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11
|
+
};
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12
|
+
index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
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13
|
+
/**
|
|
14
|
+
* #slot index.indexType
|
|
15
|
+
*/
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16
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+
indexType: {
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17
|
+
model: import("mobx-state-tree").ISimpleType<string>;
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+
type: string;
|
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19
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+
defaultValue: string;
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20
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+
};
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21
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+
/**
|
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22
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+
* #slot index.location
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23
|
+
*/
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+
location: {
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+
type: string;
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26
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+
defaultValue: {
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27
|
+
uri: string;
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28
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+
locationType: string;
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29
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+
};
|
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30
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+
};
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31
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+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
32
|
+
/**
|
|
33
|
+
* #slot
|
|
34
|
+
*/
|
|
35
|
+
fetchSizeLimit: {
|
|
36
|
+
type: string;
|
|
37
|
+
description: string;
|
|
38
|
+
defaultValue: number;
|
|
39
|
+
};
|
|
40
|
+
/**
|
|
41
|
+
* #slot
|
|
42
|
+
* generally refers to the reference genome assembly's sequence adapter
|
|
43
|
+
* currently needs to be manually added
|
|
44
|
+
*/
|
|
45
|
+
sequenceAdapter: {
|
|
46
|
+
type: string;
|
|
47
|
+
description: string;
|
|
48
|
+
defaultValue: null;
|
|
49
|
+
};
|
|
50
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
51
|
export default configSchema;
|
|
@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
|
|
|
45
45
|
}): import("rxjs").Observable<Feature>;
|
|
46
46
|
freeResources(): void;
|
|
47
47
|
cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
|
|
48
|
-
|
|
48
|
+
getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
|
|
49
49
|
bytes: number;
|
|
50
50
|
fetchSizeLimit: any;
|
|
51
51
|
}>;
|
|
@@ -200,7 +200,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
200
200
|
return new CramSlightlyLazyFeature_1.default(record, this);
|
|
201
201
|
}
|
|
202
202
|
// we return the configured fetchSizeLimit, and the bytes for the region
|
|
203
|
-
async
|
|
203
|
+
async getMultiRegionFeatureDensityStats(regions, opts) {
|
|
204
204
|
const bytes = await this.bytesForRegions(regions, opts);
|
|
205
205
|
const fetchSizeLimit = this.getConf('fetchSizeLimit');
|
|
206
206
|
return {
|
|
@@ -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;
|
|
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;IA2Q/C,CAAC;IAzQQ,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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@@ -7,7 +7,7 @@ exports.SequenceAdapter = exports.FetchableSmallFasta = exports.parseSmallFasta
|
|
|
7
7
|
const rxjs_1 = require("rxjs");
|
|
8
8
|
const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
|
|
9
9
|
const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
|
|
10
|
-
const
|
|
10
|
+
const configuration_1 = require("@jbrowse/core/configuration");
|
|
11
11
|
// setup for Cram Adapter Testing
|
|
12
12
|
function parseSmallFasta(text) {
|
|
13
13
|
return text
|
|
@@ -46,7 +46,7 @@ class FetchableSmallFasta {
|
|
|
46
46
|
exports.FetchableSmallFasta = FetchableSmallFasta;
|
|
47
47
|
class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
48
48
|
constructor(filehandle) {
|
|
49
|
-
super((0,
|
|
49
|
+
super((0, configuration_1.ConfigurationSchema)('empty', {}).create());
|
|
50
50
|
this.refNames = [];
|
|
51
51
|
this.fasta = new FetchableSmallFasta(filehandle);
|
|
52
52
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF
|
|
1
|
+
{"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,+DAAiE;AAEjE,iCAAiC;AACjC,SAAgB,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QAC5D,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,GAAG,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,mCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,iBAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC;iBACD,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;YAChC,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAjDD,0CAiDC"}
|
|
@@ -1,2 +1,41 @@
|
|
|
1
|
-
declare const configSchema: import("@jbrowse/core/configuration").
|
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1
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+
declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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2
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/**
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3
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* #slot fetchSizeLimit
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*/
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fetchSizeLimit: {
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type: string;
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description: string;
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defaultValue: number;
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9
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};
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10
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+
/**
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11
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+
* #slot cramLocation
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+
*/
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+
cramLocation: {
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type: string;
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defaultValue: {
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uri: string;
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locationType: string;
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};
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};
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/**
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* #slot craiLocation
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*/
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craiLocation: {
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type: string;
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defaultValue: {
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uri: string;
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locationType: string;
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};
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};
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30
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/**
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* #slot sequenceAdapter
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32
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* generally refers to the reference genome assembly's sequence adapter
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* currently needs to be manually added
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34
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+
*/
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+
sequenceAdapter: {
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type: string;
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description: string;
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defaultValue: null;
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39
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+
};
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40
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+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
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2
41
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export default configSchema;
|
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@@ -1,2 +1,27 @@
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1
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-
declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").
|
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1
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+
declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
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2
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+
/**
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3
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* #slot
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4
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+
*/
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5
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+
htsgetBase: {
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6
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+
type: string;
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7
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+
description: string;
|
|
8
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+
defaultValue: string;
|
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9
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+
};
|
|
10
|
+
/**
|
|
11
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+
* #slot
|
|
12
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+
*/
|
|
13
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+
htsgetTrackId: {
|
|
14
|
+
type: string;
|
|
15
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+
description: string;
|
|
16
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+
defaultValue: string;
|
|
17
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+
};
|
|
18
|
+
/**
|
|
19
|
+
* #slot
|
|
20
|
+
*/
|
|
21
|
+
sequenceAdapter: {
|
|
22
|
+
type: string;
|
|
23
|
+
description: string;
|
|
24
|
+
defaultValue: null;
|
|
25
|
+
};
|
|
26
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
|
|
2
27
|
export default HtsgetBamAdapter;
|
|
@@ -4,4 +4,42 @@ import PluginManager from '@jbrowse/core/PluginManager';
|
|
|
4
4
|
* has a "pileup" sub-display, where you can see individual reads and a
|
|
5
5
|
* quantitative "snpcoverage" sub-display track showing SNP frequencies
|
|
6
6
|
*/
|
|
7
|
-
export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").
|
|
7
|
+
export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
8
|
+
/**
|
|
9
|
+
* #slot
|
|
10
|
+
*/
|
|
11
|
+
pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
|
|
12
|
+
/**
|
|
13
|
+
* #slot
|
|
14
|
+
*/
|
|
15
|
+
snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
|
|
16
|
+
/**
|
|
17
|
+
* #slot
|
|
18
|
+
*/
|
|
19
|
+
height: {
|
|
20
|
+
type: string;
|
|
21
|
+
defaultValue: number;
|
|
22
|
+
};
|
|
23
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
|
|
24
|
+
maxFeatureScreenDensity: {
|
|
25
|
+
type: string;
|
|
26
|
+
description: string;
|
|
27
|
+
defaultValue: number;
|
|
28
|
+
};
|
|
29
|
+
fetchSizeLimit: {
|
|
30
|
+
type: string;
|
|
31
|
+
defaultValue: number;
|
|
32
|
+
description: string;
|
|
33
|
+
};
|
|
34
|
+
height: {
|
|
35
|
+
type: string;
|
|
36
|
+
defaultValue: number;
|
|
37
|
+
description: string;
|
|
38
|
+
};
|
|
39
|
+
mouseover: {
|
|
40
|
+
type: string;
|
|
41
|
+
description: string;
|
|
42
|
+
defaultValue: string;
|
|
43
|
+
contextVariable: string[];
|
|
44
|
+
};
|
|
45
|
+
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
|
|
@@ -3,6 +3,7 @@ import { Instance, IStateTreeNode } from 'mobx-state-tree';
|
|
|
3
3
|
import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
|
|
4
4
|
import PluginManager from '@jbrowse/core/PluginManager';
|
|
5
5
|
import { MenuItem } from '@jbrowse/core/ui';
|
|
6
|
+
import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
|
|
6
7
|
/**
|
|
7
8
|
* #stateModel LinearAlignmentsDisplay
|
|
8
9
|
* extends `BaseDisplay`
|
|
@@ -16,7 +17,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
16
17
|
SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
|
|
17
18
|
snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
18
19
|
type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
|
|
19
|
-
configuration:
|
|
20
|
+
configuration: AnyConfigurationSchemaType;
|
|
20
21
|
heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
21
22
|
userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
22
23
|
lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
@@ -66,7 +67,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
66
67
|
readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
|
|
67
68
|
readonly DisplayMessageComponent: React.FC<any> | undefined;
|
|
68
69
|
trackMenuItems(): MenuItem[];
|
|
69
|
-
readonly viewMenuActions: MenuItem[];
|
|
70
|
+
readonly viewMenuActions: MenuItem[]; /**
|
|
71
|
+
* #action
|
|
72
|
+
*/
|
|
70
73
|
regionCannotBeRendered(): undefined;
|
|
71
74
|
} & {
|
|
72
75
|
setError(error?: unknown): void;
|
|
@@ -88,6 +91,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
88
91
|
* #getter
|
|
89
92
|
*/
|
|
90
93
|
readonly height: any;
|
|
94
|
+
readonly featureIdUnderMouse: any;
|
|
91
95
|
} & {
|
|
92
96
|
/**
|
|
93
97
|
* #getter
|
|
@@ -125,7 +129,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
125
129
|
/**
|
|
126
130
|
* #action
|
|
127
131
|
*/
|
|
128
|
-
|
|
132
|
+
setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
|
|
129
133
|
/**
|
|
130
134
|
* #action
|
|
131
135
|
*/
|
|
@@ -164,7 +168,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
164
168
|
SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
|
|
165
169
|
snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
|
|
166
170
|
type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
|
|
167
|
-
configuration:
|
|
171
|
+
configuration: AnyConfigurationSchemaType;
|
|
168
172
|
heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
169
173
|
userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
170
174
|
lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
|
|
@@ -118,6 +118,10 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
118
118
|
var _a;
|
|
119
119
|
return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'height');
|
|
120
120
|
},
|
|
121
|
+
get featureIdUnderMouse() {
|
|
122
|
+
return (self.PileupDisplay.featureIdUnderMouse ||
|
|
123
|
+
self.SNPCoverageDisplay.featureIdUnderMouse);
|
|
124
|
+
},
|
|
121
125
|
}))
|
|
122
126
|
.views(self => ({
|
|
123
127
|
/**
|
|
@@ -187,9 +191,9 @@ function stateModelFactory(pluginManager, configSchema) {
|
|
|
187
191
|
/**
|
|
188
192
|
* #action
|
|
189
193
|
*/
|
|
190
|
-
|
|
191
|
-
self.PileupDisplay.
|
|
192
|
-
self.SNPCoverageDisplay.
|
|
194
|
+
setFeatureDensityStatsLimit(stats) {
|
|
195
|
+
self.PileupDisplay.setFeatureDensityStatsLimit(stats);
|
|
196
|
+
self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
|
|
193
197
|
},
|
|
194
198
|
/**
|
|
195
199
|
* #action
|
|
@@ -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;
|
|
1
|
+
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