@jbrowse/plugin-alignments 1.7.9 → 2.0.0
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.js +192 -207
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
- package/dist/AlignmentsFeatureDetail/index.d.ts +28 -3
- package/dist/AlignmentsFeatureDetail/index.js +48 -55
- package/dist/AlignmentsFeatureDetail/index.js.map +1 -0
- package/dist/AlignmentsTrack/index.js +24 -32
- package/dist/AlignmentsTrack/index.js.map +1 -0
- package/dist/BamAdapter/BamAdapter.js +345 -585
- package/dist/BamAdapter/BamAdapter.js.map +1 -0
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +143 -174
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
- package/dist/BamAdapter/MismatchParser.js +340 -416
- package/dist/BamAdapter/MismatchParser.js.map +1 -0
- package/dist/BamAdapter/configSchema.js +33 -46
- package/dist/BamAdapter/configSchema.js.map +1 -0
- package/dist/BamAdapter/index.js +36 -32
- package/dist/BamAdapter/index.js.map +1 -0
- package/dist/CramAdapter/CramAdapter.js +376 -644
- package/dist/CramAdapter/CramAdapter.js.map +1 -0
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +374 -439
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
- package/dist/CramAdapter/CramTestAdapters.js +169 -227
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -0
- package/dist/CramAdapter/configSchema.js +28 -38
- package/dist/CramAdapter/configSchema.js.map +1 -0
- package/dist/CramAdapter/index.js +37 -32
- package/dist/CramAdapter/index.js.map +1 -0
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +91 -93
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
- package/dist/HtsgetBamAdapter/configSchema.js +19 -29
- package/dist/HtsgetBamAdapter/configSchema.js.map +1 -0
- package/dist/HtsgetBamAdapter/index.js +44 -38
- package/dist/HtsgetBamAdapter/index.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +36 -65
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/index.js +22 -28
- package/dist/LinearAlignmentsDisplay/index.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/models/configSchema.js +12 -23
- package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +10 -10
- package/dist/LinearAlignmentsDisplay/models/model.js +257 -245
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -0
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +98 -116
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
- package/dist/LinearPileupDisplay/components/ColorByTag.js +82 -91
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/components/FilterByTag.js +156 -192
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +15 -29
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +79 -93
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +78 -81
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
- package/dist/LinearPileupDisplay/components/SortByTag.js +80 -88
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -0
- package/dist/LinearPileupDisplay/configSchema.js +40 -42
- package/dist/LinearPileupDisplay/configSchema.js.map +1 -0
- package/dist/LinearPileupDisplay/index.js +21 -27
- package/dist/LinearPileupDisplay/index.js.map +1 -0
- package/dist/LinearPileupDisplay/model.d.ts +33 -20
- package/dist/LinearPileupDisplay/model.js +702 -716
- package/dist/LinearPileupDisplay/model.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +105 -57
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/index.js +21 -27
- package/dist/LinearSNPCoverageDisplay/index.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js +45 -55
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +14 -12
- package/dist/LinearSNPCoverageDisplay/models/model.js +257 -230
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -0
- package/dist/NestedFrequencyTable.js +104 -139
- package/dist/NestedFrequencyTable.js.map +1 -0
- package/dist/PileupRPC/rpcMethods.js +199 -278
- package/dist/PileupRPC/rpcMethods.js.map +1 -0
- package/dist/PileupRenderer/PileupLayoutSession.js +56 -76
- package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -0
- package/dist/PileupRenderer/PileupRenderer.d.ts +56 -11
- package/dist/PileupRenderer/PileupRenderer.js +942 -1134
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -0
- package/dist/PileupRenderer/components/PileupRendering.d.ts +1 -1
- package/dist/PileupRenderer/components/PileupRendering.js +173 -253
- package/dist/PileupRenderer/components/PileupRendering.js.map +1 -0
- package/dist/PileupRenderer/configSchema.js +65 -71
- package/dist/PileupRenderer/configSchema.js.map +1 -0
- package/dist/PileupRenderer/index.js +17 -22
- package/dist/PileupRenderer/index.js.map +1 -0
- package/dist/PileupRenderer/sortUtil.js +83 -107
- package/dist/PileupRenderer/sortUtil.js.map +1 -0
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +2 -0
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +436 -586
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
- package/dist/SNPCoverageAdapter/configSchema.js +10 -20
- package/dist/SNPCoverageAdapter/configSchema.js.map +1 -0
- package/dist/SNPCoverageAdapter/index.js +46 -41
- package/dist/SNPCoverageAdapter/index.js.map +1 -0
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +265 -290
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
- package/dist/SNPCoverageRenderer/configSchema.js +30 -39
- package/dist/SNPCoverageRenderer/configSchema.js.map +1 -0
- package/dist/SNPCoverageRenderer/index.js +19 -30
- package/dist/SNPCoverageRenderer/index.js.map +1 -0
- package/dist/index.js +135 -152
- package/dist/index.js.map +1 -0
- package/dist/shared.js +84 -92
- package/dist/shared.js.map +1 -0
- package/dist/util.js +130 -121
- package/dist/util.js.map +1 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +6 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +145 -0
- package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
- package/esm/AlignmentsFeatureDetail/index.d.ts +38 -0
- package/esm/AlignmentsFeatureDetail/index.js +23 -0
- package/esm/AlignmentsFeatureDetail/index.js.map +1 -0
- package/esm/AlignmentsTrack/index.d.ts +2 -0
- package/esm/AlignmentsTrack/index.js +23 -0
- package/esm/AlignmentsTrack/index.js.map +1 -0
- package/esm/BamAdapter/BamAdapter.d.ts +40 -0
- package/esm/BamAdapter/BamAdapter.js +173 -0
- package/esm/BamAdapter/BamAdapter.js.map +1 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +33 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +107 -0
- package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
- package/esm/BamAdapter/MismatchParser.d.ts +25 -0
- package/esm/BamAdapter/MismatchParser.js +294 -0
- package/esm/BamAdapter/MismatchParser.js.map +1 -0
- package/esm/BamAdapter/configSchema.d.ts +2 -0
- package/esm/BamAdapter/configSchema.js +31 -0
- package/esm/BamAdapter/configSchema.js.map +1 -0
- package/esm/BamAdapter/index.d.ts +3 -0
- package/esm/BamAdapter/index.js +10 -0
- package/esm/BamAdapter/index.js.map +1 -0
- package/esm/CramAdapter/CramAdapter.d.ts +53 -0
- package/esm/CramAdapter/CramAdapter.js +228 -0
- package/esm/CramAdapter/CramAdapter.js.map +1 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +49 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +349 -0
- package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
- package/esm/CramAdapter/CramTestAdapters.d.ts +29 -0
- package/esm/CramAdapter/CramTestAdapters.js +70 -0
- package/esm/CramAdapter/CramTestAdapters.js.map +1 -0
- package/esm/CramAdapter/configSchema.d.ts +3 -0
- package/esm/CramAdapter/configSchema.js +26 -0
- package/esm/CramAdapter/configSchema.js.map +1 -0
- package/esm/CramAdapter/index.d.ts +3 -0
- package/esm/CramAdapter/index.js +11 -0
- package/esm/CramAdapter/index.js.map +1 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +9 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +27 -0
- package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
- package/esm/HtsgetBamAdapter/configSchema.d.ts +2 -0
- package/esm/HtsgetBamAdapter/configSchema.js +17 -0
- package/esm/HtsgetBamAdapter/configSchema.js.map +1 -0
- package/esm/HtsgetBamAdapter/index.d.ts +3 -0
- package/esm/HtsgetBamAdapter/index.js +16 -0
- package/esm/HtsgetBamAdapter/index.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +7 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +34 -0
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/index.d.ts +2 -0
- package/esm/LinearAlignmentsDisplay/index.js +19 -0
- package/esm/LinearAlignmentsDisplay/index.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +4 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.js +12 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +105 -0
- package/esm/LinearAlignmentsDisplay/models/model.js +181 -0
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +14 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.js +71 -0
- package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +9 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.js +45 -0
- package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.d.ts +18 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.js +123 -0
- package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +13 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +13 -0
- package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +16 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +41 -0
- package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +10 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js +43 -0
- package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
- package/esm/LinearPileupDisplay/components/SortByTag.d.ts +9 -0
- package/esm/LinearPileupDisplay/components/SortByTag.js +43 -0
- package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -0
- package/esm/LinearPileupDisplay/configSchema.d.ts +6 -0
- package/esm/LinearPileupDisplay/configSchema.js +41 -0
- package/esm/LinearPileupDisplay/configSchema.js.map +1 -0
- package/esm/LinearPileupDisplay/index.d.ts +2 -0
- package/esm/LinearPileupDisplay/index.js +18 -0
- package/esm/LinearPileupDisplay/index.js.map +1 -0
- package/esm/LinearPileupDisplay/model.d.ts +332 -0
- package/esm/LinearPileupDisplay/model.js +576 -0
- package/esm/LinearPileupDisplay/model.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +10 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +57 -0
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/index.d.ts +2 -0
- package/esm/LinearSNPCoverageDisplay/index.js +18 -0
- package/esm/LinearSNPCoverageDisplay/index.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +2 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.js +44 -0
- package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +348 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js +185 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -0
- package/esm/NestedFrequencyTable.d.ts +14 -0
- package/esm/NestedFrequencyTable.js +101 -0
- package/esm/NestedFrequencyTable.js.map +1 -0
- package/esm/PileupRPC/rpcMethods.d.ts +34 -0
- package/esm/PileupRPC/rpcMethods.js +70 -0
- package/esm/PileupRPC/rpcMethods.js.map +1 -0
- package/esm/PileupRenderer/PileupLayoutSession.d.ts +32 -0
- package/esm/PileupRenderer/PileupLayoutSession.js +32 -0
- package/esm/PileupRenderer/PileupLayoutSession.js.map +1 -0
- package/esm/PileupRenderer/PileupRenderer.d.ts +182 -0
- package/esm/PileupRenderer/PileupRenderer.js +830 -0
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -0
- package/esm/PileupRenderer/components/PileupRendering.d.ts +23 -0
- package/esm/PileupRenderer/components/PileupRendering.js +138 -0
- package/esm/PileupRenderer/components/PileupRendering.js.map +1 -0
- package/esm/PileupRenderer/configSchema.d.ts +2 -0
- package/esm/PileupRenderer/configSchema.js +64 -0
- package/esm/PileupRenderer/configSchema.js.map +1 -0
- package/esm/PileupRenderer/index.d.ts +2 -0
- package/esm/PileupRenderer/index.js +12 -0
- package/esm/PileupRenderer/index.js.map +1 -0
- package/esm/PileupRenderer/sortUtil.d.ts +8 -0
- package/esm/PileupRenderer/sortUtil.js +80 -0
- package/esm/PileupRenderer/sortUtil.js.map +1 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +67 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +259 -0
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
- package/esm/SNPCoverageAdapter/configSchema.d.ts +3 -0
- package/esm/SNPCoverageAdapter/configSchema.js +6 -0
- package/esm/SNPCoverageAdapter/configSchema.js.map +1 -0
- package/esm/SNPCoverageAdapter/index.d.ts +3 -0
- package/esm/SNPCoverageAdapter/index.js +18 -0
- package/esm/SNPCoverageAdapter/index.js.map +1 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +20 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +185 -0
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
- package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -0
- package/esm/SNPCoverageRenderer/configSchema.js +29 -0
- package/esm/SNPCoverageRenderer/configSchema.js.map +1 -0
- package/esm/SNPCoverageRenderer/index.d.ts +3 -0
- package/esm/SNPCoverageRenderer/index.js +14 -0
- package/esm/SNPCoverageRenderer/index.js.map +1 -0
- package/esm/index.d.ts +10 -0
- package/esm/index.js +91 -0
- package/esm/index.js.map +1 -0
- package/esm/shared.d.ts +25 -0
- package/esm/shared.js +28 -0
- package/esm/shared.js.map +1 -0
- package/esm/util.d.ts +19 -0
- package/esm/util.js +83 -0
- package/esm/util.js.map +1 -0
- package/package.json +19 -11
- package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +16 -6
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +321 -397
- package/src/AlignmentsFeatureDetail/index.ts +7 -17
- package/src/BamAdapter/MismatchParser.ts +1 -0
- package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -3
- package/src/LinearPileupDisplay/components/ColorByModifications.tsx +7 -7
- package/src/LinearPileupDisplay/components/ColorByTag.tsx +5 -5
- package/src/LinearPileupDisplay/components/FilterByTag.tsx +5 -5
- package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
- package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +9 -9
- package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +5 -5
- package/src/LinearPileupDisplay/components/SortByTag.tsx +5 -5
- package/src/LinearPileupDisplay/model.ts +90 -32
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +44 -30
- package/src/LinearSNPCoverageDisplay/models/model.ts +25 -25
- package/src/PileupRenderer/PileupRenderer.tsx +399 -198
- package/src/PileupRenderer/components/PileupRendering.tsx +11 -11
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -0
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +7 -5
- package/dist/AlignmentsFeatureDetail/index.test.js +0 -60
- package/dist/BamAdapter/BamAdapter.test.js +0 -177
- package/dist/BamAdapter/MismatchParser.test.js +0 -251
- package/dist/CramAdapter/CramAdapter.test.js +0 -138
- package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +0 -83
- package/dist/LinearPileupDisplay/configSchema.test.js +0 -92
- package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +0 -62
- package/dist/PileupRenderer/components/PileupRendering.test.js +0 -36
- package/dist/declare.d.js +0 -1
- package/dist/index.test.js +0 -26
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import React from 'react';
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2
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import { Region } from '@jbrowse/core/util/types';
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3
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import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
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4
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declare function PileupRendering(props: {
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blockKey: string;
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displayModel: BaseLinearDisplayModel;
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width: number;
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height: number;
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regions: Region[];
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bpPerPx: number;
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sortedBy?: {
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type: string;
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pos: number;
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refName: string;
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};
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colorBy?: {
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type: string;
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tag?: string;
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};
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onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void;
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+
}): JSX.Element;
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22
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declare const _default: typeof PileupRendering;
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export default _default;
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@@ -0,0 +1,138 @@
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1
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import React, { useRef, useState, useEffect } from 'react';
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2
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import { PrerenderedCanvas } from '@jbrowse/core/ui';
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3
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+
import { bpSpanPx } from '@jbrowse/core/util';
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4
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+
import { observer } from 'mobx-react';
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5
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+
// used so that user can click-away-from-feature below the laid out features
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6
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// (issue #1248)
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7
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const canvasPadding = 100;
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8
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+
function PileupRendering(props) {
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9
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+
const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, } = props;
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10
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+
const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } = displayModel;
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11
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+
const [region] = regions;
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12
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+
const highlightOverlayCanvas = useRef(null);
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13
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+
const [mouseIsDown, setMouseIsDown] = useState(false);
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14
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+
const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] = useState(false);
|
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15
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+
useEffect(() => {
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16
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+
var _a, _b;
|
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17
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+
const canvas = highlightOverlayCanvas.current;
|
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18
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+
if (!canvas) {
|
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19
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+
return;
|
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20
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+
}
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21
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+
const ctx = canvas.getContext('2d');
|
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22
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+
if (!ctx) {
|
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23
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+
return;
|
|
24
|
+
}
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|
25
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+
ctx.clearRect(0, 0, canvas.width, canvas.height);
|
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26
|
+
const selectedRect = selectedFeatureId
|
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27
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+
? (_a = displayModel.getFeatureByID) === null || _a === void 0 ? void 0 : _a.call(displayModel, blockKey, selectedFeatureId)
|
|
28
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+
: undefined;
|
|
29
|
+
if (selectedRect) {
|
|
30
|
+
const [leftBp, topPx, rightBp, bottomPx] = selectedRect;
|
|
31
|
+
const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx);
|
|
32
|
+
const rectTop = Math.round(topPx);
|
|
33
|
+
const rectHeight = Math.round(bottomPx - topPx);
|
|
34
|
+
ctx.shadowColor = '#222266';
|
|
35
|
+
ctx.shadowBlur = 10;
|
|
36
|
+
ctx.lineJoin = 'bevel';
|
|
37
|
+
ctx.lineWidth = 2;
|
|
38
|
+
ctx.strokeStyle = '#00b8ff';
|
|
39
|
+
ctx.strokeRect(leftPx - 2, rectTop - 2, rightPx - leftPx + 4, rectHeight + 4);
|
|
40
|
+
ctx.clearRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
|
|
41
|
+
}
|
|
42
|
+
const highlightedFeature = featureIdUnderMouse || (contextMenuFeature === null || contextMenuFeature === void 0 ? void 0 : contextMenuFeature.id());
|
|
43
|
+
const highlightedRect = highlightedFeature
|
|
44
|
+
? (_b = displayModel.getFeatureByID) === null || _b === void 0 ? void 0 : _b.call(displayModel, blockKey, highlightedFeature)
|
|
45
|
+
: undefined;
|
|
46
|
+
if (highlightedRect) {
|
|
47
|
+
const [leftBp, topPx, rightBp, bottomPx] = highlightedRect;
|
|
48
|
+
const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx);
|
|
49
|
+
const rectTop = Math.round(topPx);
|
|
50
|
+
const rectHeight = Math.round(bottomPx - topPx);
|
|
51
|
+
ctx.fillStyle = '#0003';
|
|
52
|
+
ctx.fillRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
|
|
53
|
+
}
|
|
54
|
+
}, [
|
|
55
|
+
bpPerPx,
|
|
56
|
+
region,
|
|
57
|
+
blockKey,
|
|
58
|
+
selectedFeatureId,
|
|
59
|
+
displayModel,
|
|
60
|
+
featureIdUnderMouse,
|
|
61
|
+
contextMenuFeature,
|
|
62
|
+
]);
|
|
63
|
+
function onMouseDown(event) {
|
|
64
|
+
setMouseIsDown(true);
|
|
65
|
+
setMovedDuringLastMouseDown(false);
|
|
66
|
+
callMouseHandler('MouseDown', event);
|
|
67
|
+
}
|
|
68
|
+
function onMouseEnter(event) {
|
|
69
|
+
callMouseHandler('MouseEnter', event);
|
|
70
|
+
}
|
|
71
|
+
function onMouseOut(event) {
|
|
72
|
+
callMouseHandler('MouseOut', event);
|
|
73
|
+
callMouseHandler('MouseLeave', event);
|
|
74
|
+
}
|
|
75
|
+
function onMouseOver(event) {
|
|
76
|
+
callMouseHandler('MouseOver', event);
|
|
77
|
+
}
|
|
78
|
+
function onMouseUp(event) {
|
|
79
|
+
setMouseIsDown(false);
|
|
80
|
+
callMouseHandler('MouseUp', event);
|
|
81
|
+
}
|
|
82
|
+
function onClick(event) {
|
|
83
|
+
if (!movedDuringLastMouseDown) {
|
|
84
|
+
callMouseHandler('Click', event);
|
|
85
|
+
}
|
|
86
|
+
}
|
|
87
|
+
function onMouseLeave(event) {
|
|
88
|
+
callMouseHandler('MouseOut', event);
|
|
89
|
+
callMouseHandler('MouseLeave', event);
|
|
90
|
+
}
|
|
91
|
+
function onContextMenu(event) {
|
|
92
|
+
callMouseHandler('ContextMenu', event);
|
|
93
|
+
}
|
|
94
|
+
function mouseMove(event) {
|
|
95
|
+
if (mouseIsDown) {
|
|
96
|
+
setMovedDuringLastMouseDown(true);
|
|
97
|
+
}
|
|
98
|
+
let offsetX = 0;
|
|
99
|
+
let offsetY = 0;
|
|
100
|
+
const canvas = highlightOverlayCanvas.current;
|
|
101
|
+
if (canvas) {
|
|
102
|
+
const { left, top } = canvas.getBoundingClientRect();
|
|
103
|
+
offsetX = left;
|
|
104
|
+
offsetY = top;
|
|
105
|
+
}
|
|
106
|
+
offsetX = event.clientX - offsetX;
|
|
107
|
+
offsetY = event.clientY - offsetY;
|
|
108
|
+
const px = region.reversed ? width - offsetX : offsetX;
|
|
109
|
+
const clientBp = region.start + bpPerPx * px;
|
|
110
|
+
const featIdUnderMouse = displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY);
|
|
111
|
+
if (onMouseMove) {
|
|
112
|
+
onMouseMove(event, featIdUnderMouse);
|
|
113
|
+
}
|
|
114
|
+
}
|
|
115
|
+
function callMouseHandler(handlerName, event) {
|
|
116
|
+
// @ts-ignore
|
|
117
|
+
// eslint-disable-next-line react/destructuring-assignment
|
|
118
|
+
const featureHandler = props[`onFeature${handlerName}`];
|
|
119
|
+
// @ts-ignore
|
|
120
|
+
// eslint-disable-next-line react/destructuring-assignment
|
|
121
|
+
const canvasHandler = props[`on${handlerName}`];
|
|
122
|
+
if (featureHandler && featureIdUnderMouse) {
|
|
123
|
+
featureHandler(event, featureIdUnderMouse);
|
|
124
|
+
}
|
|
125
|
+
else if (canvasHandler) {
|
|
126
|
+
canvasHandler(event, featureIdUnderMouse);
|
|
127
|
+
}
|
|
128
|
+
}
|
|
129
|
+
const canvasWidth = Math.ceil(width);
|
|
130
|
+
// need to call this in render so we get the right observer behavior
|
|
131
|
+
return (React.createElement("div", { className: "PileupRendering", "data-testid": `pileup-${sortedBy || colorBy
|
|
132
|
+
? `${(sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) || ''}`
|
|
133
|
+
: 'normal'}`, style: { position: 'relative', width: canvasWidth, height } },
|
|
134
|
+
React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }),
|
|
135
|
+
React.createElement("canvas", { "data-testid": "pileup_overlay_canvas", width: canvasWidth, height: height + canvasPadding, style: { position: 'absolute', left: 0, top: 0 }, className: "highlightOverlayCanvas", ref: highlightOverlayCanvas, onMouseDown: event => onMouseDown(event), onMouseEnter: event => onMouseEnter(event), onMouseOut: event => onMouseOut(event), onMouseOver: event => onMouseOver(event), onMouseUp: event => onMouseUp(event), onMouseLeave: event => onMouseLeave(event), onMouseMove: event => mouseMove(event), onClick: event => onClick(event), onContextMenu: event => onContextMenu(event), onFocus: () => { }, onBlur: () => { } })));
|
|
136
|
+
}
|
|
137
|
+
export default observer(PileupRendering);
|
|
138
|
+
//# sourceMappingURL=PileupRendering.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|
|
@@ -0,0 +1,64 @@
|
|
|
1
|
+
import { ConfigurationSchema } from '@jbrowse/core/configuration';
|
|
2
|
+
import { types } from 'mobx-state-tree';
|
|
3
|
+
export default ConfigurationSchema('PileupRenderer', {
|
|
4
|
+
// default magenta here is used to detect the user has not customized this
|
|
5
|
+
color: {
|
|
6
|
+
type: 'color',
|
|
7
|
+
description: 'the color of each feature in a pileup alignment',
|
|
8
|
+
defaultValue: '#f0f',
|
|
9
|
+
contextVariable: ['feature'],
|
|
10
|
+
},
|
|
11
|
+
orientationType: {
|
|
12
|
+
type: 'stringEnum',
|
|
13
|
+
model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
|
|
14
|
+
defaultValue: 'fr',
|
|
15
|
+
description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
|
|
16
|
+
},
|
|
17
|
+
displayMode: {
|
|
18
|
+
type: 'stringEnum',
|
|
19
|
+
model: types.enumeration('displayMode', [
|
|
20
|
+
'normal',
|
|
21
|
+
'compact',
|
|
22
|
+
'collapse',
|
|
23
|
+
]),
|
|
24
|
+
description: 'Alternative display modes',
|
|
25
|
+
defaultValue: 'normal',
|
|
26
|
+
},
|
|
27
|
+
minSubfeatureWidth: {
|
|
28
|
+
type: 'number',
|
|
29
|
+
description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
|
|
30
|
+
defaultValue: 0.7,
|
|
31
|
+
},
|
|
32
|
+
maxHeight: {
|
|
33
|
+
type: 'integer',
|
|
34
|
+
description: 'the maximum height to be used in a pileup rendering',
|
|
35
|
+
defaultValue: 1200,
|
|
36
|
+
},
|
|
37
|
+
maxClippingSize: {
|
|
38
|
+
type: 'integer',
|
|
39
|
+
description: 'the max clip size to be used in a pileup rendering',
|
|
40
|
+
defaultValue: 10000,
|
|
41
|
+
},
|
|
42
|
+
height: {
|
|
43
|
+
type: 'number',
|
|
44
|
+
description: 'the height of each feature in a pileup alignment',
|
|
45
|
+
defaultValue: 7,
|
|
46
|
+
contextVariable: ['feature'],
|
|
47
|
+
},
|
|
48
|
+
noSpacing: {
|
|
49
|
+
type: 'boolean',
|
|
50
|
+
description: 'remove spacing between features',
|
|
51
|
+
defaultValue: false,
|
|
52
|
+
},
|
|
53
|
+
largeInsertionIndicatorScale: {
|
|
54
|
+
type: 'number',
|
|
55
|
+
description: 'scale at which to draw the large insertion indicators (bp/pixel)',
|
|
56
|
+
defaultValue: 10,
|
|
57
|
+
},
|
|
58
|
+
mismatchAlpha: {
|
|
59
|
+
type: 'boolean',
|
|
60
|
+
defaultValue: false,
|
|
61
|
+
description: 'Fade low quality mismatches',
|
|
62
|
+
},
|
|
63
|
+
}, { explicitlyTyped: true });
|
|
64
|
+
//# sourceMappingURL=configSchema.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,mBAAmB,CAChC,gBAAgB,EAChB;IACE,0EAA0E;IAC1E,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,mIAAmI;KACtI;IACD,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
import PileupRenderer from './PileupRenderer';
|
|
2
|
+
import ReactComponent from './components/PileupRendering';
|
|
3
|
+
import configSchema from './configSchema';
|
|
4
|
+
export default function register(pluginManager) {
|
|
5
|
+
pluginManager.addRendererType(() => new PileupRenderer({
|
|
6
|
+
name: 'PileupRenderer',
|
|
7
|
+
ReactComponent,
|
|
8
|
+
configSchema,
|
|
9
|
+
pluginManager,
|
|
10
|
+
}));
|
|
11
|
+
}
|
|
12
|
+
//# sourceMappingURL=index.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,cAAc,MAAM,8BAA8B,CAAA;AACzD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,cAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}
|
|
@@ -0,0 +1,80 @@
|
|
|
1
|
+
import { doesIntersect2 } from '@jbrowse/core/util/range';
|
|
2
|
+
export const sortFeature = (features, sortedBy) => {
|
|
3
|
+
const featureArray = Array.from(features.values());
|
|
4
|
+
const featuresInCenterLine = [];
|
|
5
|
+
const featuresOutsideCenter = [];
|
|
6
|
+
const { pos, type } = sortedBy;
|
|
7
|
+
// only sort on features that intersect center line, append those outside post-sort
|
|
8
|
+
featureArray.forEach(innerArray => {
|
|
9
|
+
const feature = innerArray;
|
|
10
|
+
const start = feature.get('start');
|
|
11
|
+
const end = feature.get('end');
|
|
12
|
+
if (doesIntersect2(pos - 1, pos, start, end)) {
|
|
13
|
+
featuresInCenterLine.push(innerArray);
|
|
14
|
+
}
|
|
15
|
+
else {
|
|
16
|
+
featuresOutsideCenter.push(innerArray);
|
|
17
|
+
}
|
|
18
|
+
});
|
|
19
|
+
const isCram = featureArray.length ? featureArray[0].get('tags') : false;
|
|
20
|
+
switch (type) {
|
|
21
|
+
case 'Start location': {
|
|
22
|
+
featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'));
|
|
23
|
+
break;
|
|
24
|
+
}
|
|
25
|
+
case 'tag': {
|
|
26
|
+
const tag = sortedBy.tag;
|
|
27
|
+
const getTag = (f, t) => {
|
|
28
|
+
return isCram ? f.get('tags')[t] : f.get(t);
|
|
29
|
+
};
|
|
30
|
+
const isString = featuresInCenterLine[0] &&
|
|
31
|
+
typeof getTag(featuresInCenterLine[0], tag) === 'string';
|
|
32
|
+
if (isString) {
|
|
33
|
+
featuresInCenterLine.sort((a, b) => getTag(b, tag).localeCompare(getTag(a, tag)));
|
|
34
|
+
}
|
|
35
|
+
else {
|
|
36
|
+
featuresInCenterLine.sort((a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0));
|
|
37
|
+
}
|
|
38
|
+
break;
|
|
39
|
+
}
|
|
40
|
+
// first sort all mismatches, then all reference bases at the end
|
|
41
|
+
case 'Base pair': {
|
|
42
|
+
const baseSortArray = [];
|
|
43
|
+
featuresInCenterLine.forEach(feature => {
|
|
44
|
+
const mismatches = feature.get('mismatches');
|
|
45
|
+
mismatches.forEach(mismatch => {
|
|
46
|
+
const start = feature.get('start');
|
|
47
|
+
const offset = start + mismatch.start + 1;
|
|
48
|
+
const consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
|
|
49
|
+
const len = consuming ? 0 : mismatch.length;
|
|
50
|
+
if (pos >= offset && pos < offset + len) {
|
|
51
|
+
baseSortArray.push([feature.id(), mismatch]);
|
|
52
|
+
}
|
|
53
|
+
});
|
|
54
|
+
});
|
|
55
|
+
const baseMap = new Map(baseSortArray);
|
|
56
|
+
featuresInCenterLine.sort((a, b) => {
|
|
57
|
+
const aMismatch = baseMap.get(a.id());
|
|
58
|
+
const bMismatch = baseMap.get(b.id());
|
|
59
|
+
const acode = bMismatch && bMismatch.base.toUpperCase();
|
|
60
|
+
const bcode = aMismatch && aMismatch.base.toUpperCase();
|
|
61
|
+
if (acode === bcode && acode === '*') {
|
|
62
|
+
// @ts-ignore
|
|
63
|
+
return aMismatch.length - bMismatch.length;
|
|
64
|
+
}
|
|
65
|
+
return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
|
|
66
|
+
});
|
|
67
|
+
break;
|
|
68
|
+
}
|
|
69
|
+
// sorts positive strands then negative strands
|
|
70
|
+
case 'Read strand': {
|
|
71
|
+
featuresInCenterLine.sort((a, b) => a.get('strand') <= b.get('strand') ? 1 : -1);
|
|
72
|
+
break;
|
|
73
|
+
}
|
|
74
|
+
}
|
|
75
|
+
const sortedMap = new Map(featuresInCenterLine
|
|
76
|
+
.concat(featuresOutsideCenter)
|
|
77
|
+
.map(feature => [feature.id(), feature]));
|
|
78
|
+
return sortedMap;
|
|
79
|
+
};
|
|
80
|
+
//# sourceMappingURL=sortUtil.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"sortUtil.js","sourceRoot":"","sources":["../../src/PileupRenderer/sortUtil.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAA;AAQzD,MAAM,CAAC,MAAM,WAAW,GAAG,CACzB,QAA8B,EAC9B,QAAoB,EACpB,EAAE;IACF,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IAClD,MAAM,oBAAoB,GAAc,EAAE,CAAA;IAC1C,MAAM,qBAAqB,GAAc,EAAE,CAAA;IAC3C,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;IAE9B,mFAAmF;IACnF,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;QAChC,MAAM,OAAO,GAAG,UAAU,CAAA;QAC1B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC9B,IAAI,cAAc,CAAC,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE;YAC5C,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACtC;aAAM;YACL,qBAAqB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACvC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IACxE,QAAQ,IAAI,EAAE;QACZ,KAAK,gBAAgB,CAAC,CAAC;YACrB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YACpE,MAAK;SACN;QAED,KAAK,KAAK,CAAC,CAAC;YACV,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAa,CAAA;YAClC,MAAM,MAAM,GAAG,CAAC,CAAU,EAAE,CAAS,EAAE,EAAE;gBACvC,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAC7C,CAAC,CAAA;YACD,MAAM,QAAQ,GACZ,oBAAoB,CAAC,CAAC,CAAC;gBACvB,OAAO,MAAM,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,QAAQ,CAAA;YAC1D,IAAI,QAAQ,EAAE;gBACZ,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAC7C,CAAA;aACF;iBAAM;gBACL,oBAAoB,CAAC,IAAI,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,CACxD,CAAA;aACF;YACD,MAAK;SACN;QAED,iEAAiE;QACjE,KAAK,WAAW,CAAC,CAAC;YAChB,MAAM,aAAa,GAAyB,EAAE,CAAA;YAC9C,oBAAoB,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;gBACrC,MAAM,UAAU,GAAe,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBACxD,UAAU,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE;oBAC5B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;oBAClC,MAAM,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAA;oBACzC,MAAM,SAAS,GACb,QAAQ,CAAC,IAAI,KAAK,WAAW,IAAI,QAAQ,CAAC,IAAI,KAAK,UAAU,CAAA;oBAC/D,MAAM,GAAG,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAA;oBAC3C,IAAI,GAAG,IAAI,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,GAAG,EAAE;wBACvC,aAAa,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAA;qBAC7C;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEF,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;YACtC,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;gBACjC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,IAAI,KAAK,KAAK,KAAK,IAAI,KAAK,KAAK,GAAG,EAAE;oBACpC,aAAa;oBACb,OAAO,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;iBAC3C;gBACD,OAAO,CACL,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACtE,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,MAAK;SACN;QAED,+CAA+C;QAC/C,KAAK,aAAa,CAAC,CAAC;YAClB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC5C,CAAA;YACD,MAAK;SACN;KACF;IAED,MAAM,SAAS,GAAG,IAAI,GAAG,CACvB,oBAAoB;SACjB,MAAM,CAAC,qBAAqB,CAAC;SAC7B,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC,CAC3C,CAAA;IAED,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA"}
|
|
@@ -0,0 +1,67 @@
|
|
|
1
|
+
import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
|
|
2
|
+
import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
|
|
3
|
+
import { Feature } from '@jbrowse/core/util/simpleFeature';
|
|
4
|
+
export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
|
|
5
|
+
protected configure(): Promise<{
|
|
6
|
+
subadapter: BaseFeatureDataAdapter;
|
|
7
|
+
sequenceAdapter: BaseFeatureDataAdapter | undefined;
|
|
8
|
+
}>;
|
|
9
|
+
fetchSequence(region: Region): Promise<any>;
|
|
10
|
+
getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
|
|
11
|
+
estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
|
|
12
|
+
getRefNames(opts?: BaseOptions): Promise<string[]>;
|
|
13
|
+
freeResources(): void;
|
|
14
|
+
generateCoverageBins(features: Feature[], region: Region, opts: {
|
|
15
|
+
bpPerPx?: number;
|
|
16
|
+
colorBy?: {
|
|
17
|
+
type: string;
|
|
18
|
+
tag?: string;
|
|
19
|
+
};
|
|
20
|
+
}): Promise<{
|
|
21
|
+
bins: {
|
|
22
|
+
refbase?: string | undefined;
|
|
23
|
+
total: number;
|
|
24
|
+
all: number;
|
|
25
|
+
ref: number;
|
|
26
|
+
'-1': 0;
|
|
27
|
+
'0': 0;
|
|
28
|
+
'1': 0;
|
|
29
|
+
lowqual: {
|
|
30
|
+
total: number;
|
|
31
|
+
strands: {
|
|
32
|
+
[key: string]: number;
|
|
33
|
+
};
|
|
34
|
+
};
|
|
35
|
+
cov: {
|
|
36
|
+
total: number;
|
|
37
|
+
strands: {
|
|
38
|
+
[key: string]: number;
|
|
39
|
+
};
|
|
40
|
+
};
|
|
41
|
+
delskips: {
|
|
42
|
+
total: number;
|
|
43
|
+
strands: {
|
|
44
|
+
[key: string]: number;
|
|
45
|
+
};
|
|
46
|
+
};
|
|
47
|
+
noncov: {
|
|
48
|
+
total: number;
|
|
49
|
+
strands: {
|
|
50
|
+
[key: string]: number;
|
|
51
|
+
};
|
|
52
|
+
};
|
|
53
|
+
}[];
|
|
54
|
+
skipmap: {
|
|
55
|
+
[key: string]: {
|
|
56
|
+
score: number;
|
|
57
|
+
feature: unknown;
|
|
58
|
+
start: number;
|
|
59
|
+
end: number;
|
|
60
|
+
strand: number;
|
|
61
|
+
xs: string;
|
|
62
|
+
};
|
|
63
|
+
};
|
|
64
|
+
}>;
|
|
65
|
+
}
|
|
66
|
+
declare const capabilities: string[];
|
|
67
|
+
export { capabilities };
|