@jbrowse/plugin-alignments 2.0.0 → 2.1.2
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 +61 -90
- package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
- package/dist/AlignmentsFeatureDetail/index.js +14 -16
- package/dist/AlignmentsFeatureDetail/index.js.map +1 -1
- package/dist/AlignmentsTrack/index.js +8 -8
- package/dist/AlignmentsTrack/index.js.map +1 -1
- package/dist/BamAdapter/BamAdapter.d.ts +6 -1
- package/dist/BamAdapter/BamAdapter.js +157 -336
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +68 -103
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/dist/BamAdapter/MismatchParser.d.ts +1 -1
- package/dist/BamAdapter/MismatchParser.js +97 -162
- package/dist/BamAdapter/MismatchParser.js.map +1 -1
- package/dist/BamAdapter/configSchema.js +27 -29
- package/dist/BamAdapter/configSchema.js.map +1 -1
- package/dist/BamAdapter/index.js +9 -11
- package/dist/BamAdapter/index.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +193 -351
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +119 -154
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/CramTestAdapters.js +51 -148
- package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
- package/dist/CramAdapter/configSchema.js +23 -25
- package/dist/CramAdapter/configSchema.js.map +1 -1
- package/dist/CramAdapter/index.js +9 -11
- package/dist/CramAdapter/index.js.map +1 -1
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +25 -87
- package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -1
- package/dist/HtsgetBamAdapter/configSchema.js +16 -18
- package/dist/HtsgetBamAdapter/configSchema.js.map +1 -1
- package/dist/HtsgetBamAdapter/index.js +15 -19
- package/dist/HtsgetBamAdapter/index.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +14 -15
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/index.js +7 -7
- package/dist/LinearAlignmentsDisplay/index.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/configSchema.js +5 -5
- package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/model.js +64 -140
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByModifications.js +24 -53
- package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -1
- package/dist/LinearPileupDisplay/components/ColorByTag.js +14 -30
- package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/FilterByTag.js +33 -49
- package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +7 -7
- package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +17 -33
- package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js +14 -30
- package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -1
- package/dist/LinearPileupDisplay/components/SortByTag.js +14 -30
- package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -1
- package/dist/LinearPileupDisplay/configSchema.js +4 -4
- package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
- package/dist/LinearPileupDisplay/index.js +7 -7
- package/dist/LinearPileupDisplay/index.js.map +1 -1
- package/dist/LinearPileupDisplay/model.js +534 -645
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +5 -2
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +30 -79
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/index.js +7 -7
- package/dist/LinearSNPCoverageDisplay/index.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js +4 -4
- package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +27 -5
- package/dist/LinearSNPCoverageDisplay/models/model.js +171 -244
- package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/dist/NestedFrequencyTable.js +27 -40
- package/dist/NestedFrequencyTable.js.map +1 -1
- package/dist/PileupRPC/rpcMethods.js +63 -191
- package/dist/PileupRPC/rpcMethods.js.map +1 -1
- package/dist/PileupRenderer/PileupLayoutSession.js +25 -47
- package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -1
- package/dist/PileupRenderer/PileupRenderer.d.ts +0 -4
- package/dist/PileupRenderer/PileupRenderer.js +395 -529
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/PileupRenderer/components/PileupRendering.js +41 -68
- package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +2 -2
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/PileupRenderer/index.js +9 -11
- package/dist/PileupRenderer/index.js.map +1 -1
- package/dist/PileupRenderer/sortUtil.js +36 -40
- package/dist/PileupRenderer/sortUtil.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +229 -414
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/SNPCoverageAdapter/configSchema.js +5 -9
- package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
- package/dist/SNPCoverageAdapter/index.js +17 -21
- package/dist/SNPCoverageAdapter/index.js.map +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +175 -259
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/dist/SNPCoverageRenderer/configSchema.js +1 -1
- package/dist/SNPCoverageRenderer/configSchema.js.map +1 -1
- package/dist/SNPCoverageRenderer/index.js +10 -12
- package/dist/SNPCoverageRenderer/index.js.map +1 -1
- package/dist/index.js +40 -58
- package/dist/index.js.map +1 -1
- package/dist/shared.js +23 -78
- package/dist/shared.js.map +1 -1
- package/dist/util.js +13 -66
- package/dist/util.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.d.ts +6 -1
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/BamAdapter/MismatchParser.d.ts +1 -1
- package/esm/BamAdapter/MismatchParser.js +2 -2
- package/esm/BamAdapter/MismatchParser.js.map +1 -1
- package/esm/LinearPileupDisplay/model.js +0 -1
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +4 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +0 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +27 -5
- package/esm/LinearSNPCoverageDisplay/models/model.js +1 -0
- package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
- package/esm/PileupRenderer/PileupRenderer.d.ts +0 -4
- package/esm/PileupRenderer/PileupRenderer.js +1 -3
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +4 -3
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +0 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/package.json +6 -7
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +12 -12
- package/src/BamAdapter/BamAdapter.ts +1 -1
- package/src/BamAdapter/MismatchParser.ts +2 -2
- package/src/LinearPileupDisplay/model.ts +2 -2
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +3 -4
- package/src/LinearSNPCoverageDisplay/models/model.ts +3 -1
- package/src/PileupRenderer/PileupRenderer.tsx +13 -19
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +4 -3
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +1 -3
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1
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+
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AW,CAAC,YAAY,CAAC,EAAE,CAAC;oCAC3C,gBAAgB;oCAChB,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,YAAY,EAAE;iCAC3C,CAAC,CAAA;4BACJ,CAAC;yBACF;wBACD;4BACE,KAAK,EAAE,aAAa;4BACpB,OAAO,EAAE,GAAG,EAAE;gCACZ,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;4BAC7C,CAAC;yBACF;wBACD;4BACE,KAAK,EAAE,qBAAqB;4BAC5B,OAAO,EAAE,GAAG,EAAE;gCACZ,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,iBAAiB,EAAE,CAAC,CAAA;4BAClD,CAAC;yBACF;wBACD;4BACE,KAAK,EAAE,iBAAiB;4BACxB,OAAO,EAAE,GAAG,EAAE;gCACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAAC;oCAC3C,aAAa;oCACb,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,YAAY,EAAE;iCAC3C,CAAC,CAAA;4BACJ,CAAC;yBACF;qBACF;iBACF;gBACD;oBACE,KAAK,EAAE,WAAW;oBAClB,IAAI,EAAE,cAAc;oBACpB,OAAO,EAAE,GAAG,EAAE;wBACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAAC;4BAC3C,cAAc;4BACd,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,YAAY,EAAE;yBAC3C,CAAC,CAAA;oBACJ,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,oBAAoB;oBAC3B,OAAO,EAAE,GAAG,EAAE;wBACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAAC;4BAC3C,mBAAmB;4BACnB,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,YAAY,EAAE;yBAC3C,CAAC,CAAA;oBACJ,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,gBAAgB;oBACvB,OAAO,EAAE,GAAG,EAAE;wBACZ,UAAU,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAAC;4BAC3C,eAAe;4BACf,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,YAAY,EAAE;yBAC3C,CAAC,CAAA;oBACJ,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,4BAA4B;oBACnC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,oBAAoB;oBAClC,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC,mBAAmB,EAAE,CAAA;oBAC5B,CAAC;iBACF;aACF,CAAA;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAKN,eAAe,iBAAiB,CAAA"}
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@@ -1,7 +1,10 @@
|
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1
1
|
/// <reference types="react" />
|
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2
|
+
import { Feature } from '@jbrowse/core/util/simpleFeature';
|
|
2
3
|
declare type Coord = [number, number];
|
|
3
4
|
declare const SNPCoverageTooltip: (props: {
|
|
4
|
-
model:
|
|
5
|
+
model: {
|
|
6
|
+
featureUnderMouse: Feature;
|
|
7
|
+
};
|
|
5
8
|
height: number;
|
|
6
9
|
offsetMouseCoord: Coord;
|
|
7
10
|
clientMouseCoord: Coord;
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":"AAAA,
|
|
1
|
+
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAyBhD,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AACnD,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AACvC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,KAAa,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;AAE7E,MAAM,eAAe,GAAG,KAAK,CAAC,UAAU,CACtC,CAAC,EAAE,OAAO,EAAE,EAAE,QAAQ,EAAE,EAAE;IACxB,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,MAAM,EACJ,OAAO,EACP,GAAG,EACH,KAAK,EACL,GAAG,EACH,IAAI,EAAE,GAAG,EACT,GAAG,EAAE,EAAE,EACP,GAAG,EAAE,EAAE,EACP,GAAG,IAAI,EACR,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;IACrC,MAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SACvE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,CACL,6BAAK,GAAG,EAAE,QAAQ;QAChB;YACE,qCAAU,GAAG,CAAW;YACxB;gBACE;oBACE,uCAAa;oBACb,wCAAc;oBACd,6CAAmB;oBACnB,0CAAgB;oBAChB,yCAAe,CACZ,CACC;YACR;gBACE;oBACE,wCAAc;oBACd,gCAAK,GAAG,CAAM,CACX;gBACL;oBACE;;wBAAS,OAAO,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAM;oBAC1D,gCAAK,GAAG,CAAM;oBACd,gCAAK,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAM;oBACxB;wBACG,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtB,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAClB;oBACL,+BAAM,CACH;gBAEJ,MAAM,CAAC,OAAO,CAAC,IAAwC,CAAC,CAAC,GAAG,CAC3D,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CACf,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAC3C,4BAAI,GAAG,EAAE,IAAI;oBACX,gCAAK,IAAI,CAAC,WAAW,EAAE,CAAM;oBAC7B,gCAAK,KAAK,CAAC,KAAK,CAAM;oBACtB,gCACG,IAAI,KAAK,OAAO,IAAI,IAAI,KAAK,MAAM;wBAClC,CAAC,CAAC,KAAK;wBACP,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CACtB;oBACL;wBACG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAClC;oBACL,gCAAK,GAAG,CAAM,CACX,CACN,CAAC,CACL,CACK,CACF,CACJ,CACP,CAAA;AACH,CAAC,CACF,CAAA;AAID,MAAM,kBAAkB,GAAG,QAAQ,CACjC,CAAC,KAMA,EAAE,EAAE;IACH,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACzC,OAAO,IAAI,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAClD,oBAAC,OAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CACzD,CAAA;AACH,CAAC,CACF,CAAA;AAED,eAAe,kBAAkB,CAAA"}
|
|
@@ -61,6 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
|
|
|
61
61
|
selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
62
62
|
resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
63
63
|
fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
|
|
64
|
+
minSize: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
|
|
64
65
|
color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
65
66
|
posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
66
67
|
negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
@@ -224,7 +225,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
|
|
|
224
225
|
};
|
|
225
226
|
statsFetchInProgress: AbortController | undefined;
|
|
226
227
|
} & {
|
|
227
|
-
updateStats(
|
|
228
|
+
updateStats(stats: {
|
|
228
229
|
scoreMin: number;
|
|
229
230
|
scoreMax: number;
|
|
230
231
|
}): void;
|
|
@@ -234,7 +235,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
|
|
|
234
235
|
setLoading(aborter: AbortController): void;
|
|
235
236
|
selectFeature(feature: import("@jbrowse/core/util").Feature): void;
|
|
236
237
|
setResolution(res: number): void;
|
|
237
|
-
setFill(fill:
|
|
238
|
+
setFill(fill: number): void;
|
|
238
239
|
toggleLogScale(): void;
|
|
239
240
|
setScaleType(scale?: string | undefined): void;
|
|
240
241
|
setSummaryScoreMode(val: string): void;
|
|
@@ -247,6 +248,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
|
|
|
247
248
|
} & {
|
|
248
249
|
readonly TooltipComponent: import("react").FC<{}>;
|
|
249
250
|
readonly adapterTypeName: any;
|
|
251
|
+
readonly rendererTypeNameSimple: any;
|
|
250
252
|
readonly rendererTypeName: string;
|
|
251
253
|
readonly filters: undefined;
|
|
252
254
|
readonly scaleType: any;
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readonly ticks:
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};
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renderProps(): any;
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trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
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label: string;
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}[];
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type: string;
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@@ -324,7 +344,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
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afterAttach(): void;
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model:
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model: {
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};
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height: number;
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offsetMouseCoord: [number, number];
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clientMouseCoord: [number, number];
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@@ -3,6 +3,7 @@ import { observable, autorun } from 'mobx';
|
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3
3
|
import { getConf, readConfObject, } from '@jbrowse/core/configuration';
|
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4
4
|
import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
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|
import { getContainingView } from '@jbrowse/core/util';
|
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|
+
// locals
|
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|
import Tooltip from '../components/Tooltip';
|
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7
8
|
import { getUniqueModificationValues } from '../../shared';
|
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8
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|
// using a map because it preserves order
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,IAAI,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC/E,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC1C,OAAO,EACL,OAAO,EACP,cAAc,GAGf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,+BAA+B,EAAE,MAAM,wBAAwB,CAAA;
|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,IAAI,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC/E,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC1C,OAAO,EACL,OAAO,EACP,cAAc,GAGf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,+BAA+B,EAAE,MAAM,wBAAwB,CAAA;AAIxE,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,SAAS;AACT,OAAO,OAAO,MAAM,uBAAuB,CAAA;AAC3C,OAAO,EAAE,2BAA2B,EAAE,MAAM,cAAc,CAAA;AAE1D,yCAAyC;AACzC,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,aAAa,EAAE,qBAAqB,CAAC,CAAC,CAAC,CAAA;AAIvE,MAAM,iBAAiB,GAAG,CACxB,aAA4B,EAC5B,YAAwC,EACxC,EAAE,CACF,KAAK;KACF,OAAO,CACN,0BAA0B,EAC1B,+BAA+B,CAAC,aAAa,EAAE,YAAY,CAAC,EAC5D,KAAK,CAAC,KAAK,CAAC;IACV,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,0BAA0B,CAAC;IAC/C,mBAAmB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;IAC/C,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;IAC1C,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC;IACpC,QAAQ,EAAE,KAAK,CAAC,QAAQ,CACtB,KAAK,CAAC,KAAK,CAAC;QACV,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QAC5C,WAAW,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC/C,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACnC,SAAS,EAAE,KAAK,CAAC,KAAK,CACpB,KAAK,CAAC,KAAK,CAAC,EAAE,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CACxD;KACF,CAAC,EACF,EAAE,CACH;IACD,OAAO,EAAE,KAAK,CAAC,KAAK,CAClB,KAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,KAAK,CAAC,MAAM;QAClB,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC,CACH;CACF,CAAC,CACH;KACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,kBAAkB,EAAE,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;CACvC,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,SAAS,CAAC,aAAoC;QAC5C,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;IACpC,CAAC;IACD,WAAW,CAAC,MAKX;QACC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,MAAM,CAAC,CAAA;IAC9B,CAAC;IACD,UAAU,CAAC,OAAwC;QACjD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,CAAA;IAC9B,CAAC;IAED,0BAA0B,CAAC,mBAA6B;QACtD,MAAM,YAAY,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QACjE,IAAI,CAAC,GAAG,CAAC,CAAA;QAET,mBAAmB,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;YAClC,IAAI,CAAC,IAAI,CAAC,kBAAkB,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE;gBACvC,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,EAAE,CAAC,CAAA;gBAClC,IAAI,CAAC,kBAAkB,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAA;aAC7C;QACH,CAAC,CAAC,CAAA;IACJ,CAAC;CACF,CAAC,CAAC;KACF,KAAK,CAAC,IAAI,CAAC,EAAE;IACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;IAC9C,OAAO;QACL,IAAI,cAAc;;YAChB,MAAM,UAAU,GACd,OAAO,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,IAAI,EAAE,CAAA;YAE3D,OAAO,IAAI,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,CAC1C;gBACE,GAAG,UAAU;gBACb,mBAAmB,EACjB,MAAA,IAAI,CAAC,mBAAmB,mCAAI,UAAU,CAAC,mBAAmB;gBAC5D,cAAc,EAAE,MAAA,IAAI,CAAC,cAAc,mCAAI,UAAU,CAAC,cAAc;gBAChE,QAAQ,EAAE,MAAA,IAAI,CAAC,QAAQ,mCAAI,UAAU,CAAC,QAAQ;aAC/C,EACD,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QACH,CAAC;QACD,IAAI,eAAe;;YACjB,OAAO,CACL,MAAA,IAAI,CAAC,QAAQ,mCAAI,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,UAAU,CAAC,CACjE,CAAA;QACH,CAAC;QACD,IAAI,0BAA0B;;YAC5B,OAAO,CACL,MAAA,IAAI,CAAC,mBAAmB,mCACxB,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,qBAAqB,CAAC,CAC3D,CAAA;QACH,CAAC;QACD,IAAI,qBAAqB;;YACvB,OAAO,CACL,MAAA,IAAI,CAAC,cAAc,mCACnB,cAAc,CAAC,IAAI,CAAC,cAAc,EAAE,gBAAgB,CAAC,CACtD,CAAA;QACH,CAAC;QAED,IAAI,kBAAkB;;YACpB,OAAO,CAAA,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,MAAK,eAAe;gBAC3C,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,CAAC;qBAC7D,MAAM,GAAG,CAAC;gBACf,CAAC,CAAC,IAAI,CAAA;QACV,CAAC;QAED,WAAW;YACT,MAAM,UAAU,GAAG,gBAAgB,EAAE,CAAA;YACrC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;YACtD,OAAO;gBACL,GAAG,UAAU;gBACb,QAAQ,EAAE,UAAU,CAAC,QAAQ,IAAI,CAAC,IAAI,CAAC,kBAAkB;gBACzD,kBAAkB,EAAE,MAAM,CAAC,WAAW,CAAC,kBAAkB,CAAC,MAAM,EAAE,CAAC;gBAEnE,kEAAkE;gBAClE,4BAA4B;gBAC5B,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS;gBACnD,QAAQ,EAAE,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS;aACvD,CAAA;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC;KACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,oBAAoB;QAClB,IAAI,CAAC,cAAc,GAAG,CAAC,IAAI,CAAC,qBAAqB,CAAA;IACnD,CAAC;IACD,yBAAyB;QACvB,IAAI,CAAC,mBAAmB,GAAG,CAAC,IAAI,CAAC,0BAA0B,CAAA;IAC7D,CAAC;IACD,cAAc;QACZ,IAAI,CAAC,QAAQ,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;IACvC,CAAC;IACD,WAAW;QACT,WAAW,CACT,IAAI,EACJ,OAAO,CACL,KAAK,IAAI,EAAE;YACT,IAAI;gBACF,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;gBACxB,MAAM,EAAE,YAAY,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAAQ,CAAA;gBAEvD,IAAI,CAAC,IAAI,CAAC,mBAAmB,EAAE;oBAC7B,OAAM;iBACP;gBACD,IAAI,IAAI,CAAC,cAAc,EAAE;oBACvB,OAAM;iBACP;gBACD,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;oBACrC,MAAM,IAAI,GAAG,MAAM,2BAA2B,CAC5C,IAAI,EACJ,OAAO,CAAC,IAAI,CAAC,WAAW,EAAE,SAAS,CAAC,EACpC,OAAO,EACP,YAAY,CACb,CAAA;oBACD,IAAI,CAAC,0BAA0B,CAAC,IAAI,CAAC,CAAA;iBACtC;aACF;YAAC,OAAO,KAAK,EAAE;gBACd,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;aACrB;QACH,CAAC,EACD,EAAE,KAAK,EAAE,IAAI,EAAE,CAChB,CACF,CAAA;IACH,CAAC;CACF,CAAC,CAAC;KAEF,KAAK,CAAC,IAAI,CAAC,EAAE;IACZ,MAAM,EAAE,cAAc,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;IACpD,OAAO;QACL,IAAI,gBAAgB;YAClB,OAAO,OAAO,CAAA;QAChB,CAAC;QAED,IAAI,aAAa;YACf,MAAM,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,WAAW,EAAE,SAAS,CAAC,CAAA;YACvD,OAAO;gBACL,IAAI,EAAE,oBAAoB;gBAC1B,UAAU;aACX,CAAA;QACH,CAAC;QAED,IAAI,gBAAgB;YAClB,OAAO,aAAa,CAAC,GAAG,CAAC,aAAa,CAAC,CAAA;QACzC,CAAC;QAED,IAAI,aAAa;YACf,OAAO,IAAI,CAAA;QACb,CAAC;QAED,gBAAgB;YACd,OAAO,EAAE,CAAA;QACX,CAAC;QAED,cAAc;YACZ,OAAO;gBACL,GAAG,mBAAmB,EAAE;gBACxB;oBACE,KAAK,EAAE,oCAAoC;oBAC3C,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,qBAAqB;oBACnC,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC,oBAAoB,EAAE,CAAA;oBAC7B,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,gCAAgC;oBACvC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,0BAA0B;oBACxC,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC,yBAAyB,EAAE,CAAA;oBAClC,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,WAAW;oBAClB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC,cAAc,EAAE,CAAA;oBACvB,CAAC;iBACF;aACF,CAAA;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAIN,eAAe,iBAAiB,CAAA"}
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@@ -154,7 +154,6 @@ export default class PileupRenderer extends BoxRendererType {
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imageData?: undefined;
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} | {
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features: Map<any, any>;
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@@ -163,8 +162,6 @@ export default class PileupRenderer extends BoxRendererType {
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}>;
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}
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|
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|
function getColorBaseMap(theme) {
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|
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// @ts-ignore
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|
const { bases } = theme.palette;
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|
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|
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A: bases.A.main,
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|
@@ -636,7 +635,6 @@ export default class PileupRenderer extends BoxRendererType {
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|
636
635
|
const mismatches = feature.get('mismatches');
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|
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636
|
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|
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637
|
const { charWidth, charHeight } = this.getCharWidthHeight(ctx);
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|
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// @ts-ignore
|
|
640
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|
const { bases } = theme.palette;
|
|
641
639
|
const colorForBase = {
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A: bases.A.main,
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|
@@ -793,7 +791,7 @@ export default class PileupRenderer extends BoxRendererType {
|
|
|
793
791
|
const width = (end - start) / bpPerPx;
|
|
794
792
|
const height = Math.max(layout.getTotalHeight(), 1);
|
|
795
793
|
const Color = await import('color').then(f => f.default);
|
|
796
|
-
const res = await renderToAbstractCanvas(width, height, renderProps,
|
|
794
|
+
const res = await renderToAbstractCanvas(width, height, renderProps, ctx => this.makeImageData({
|
|
797
795
|
ctx,
|
|
798
796
|
layoutRecords,
|
|
799
797
|
canvasWidth: width,
|
|
@@ -1 +1 @@
|
|
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1
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-
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1
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+
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@@ -57,13 +57,14 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
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57
57
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.toPromise();
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|
58
58
|
const { bins, skipmap } = await this.generateCoverageBins(feats, region, opts);
|
|
59
59
|
bins.forEach((bin, index) => {
|
|
60
|
+
const start = region.start + index;
|
|
60
61
|
observer.next(new SimpleFeature({
|
|
61
|
-
id: `${this.id}-${
|
|
62
|
+
id: `${this.id}-${start}`,
|
|
62
63
|
data: {
|
|
63
64
|
score: bin.total,
|
|
64
65
|
snpinfo: bin,
|
|
65
|
-
start
|
|
66
|
-
end:
|
|
66
|
+
start,
|
|
67
|
+
end: start + 1,
|
|
67
68
|
refName: region.refName,
|
|
68
69
|
},
|
|
69
70
|
}));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EACL,MAAM,EACN,SAAS,EACT,aAAa,EACb,4BAA4B,GAC7B,MAAM,SAAS,CAAA;AAChB,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAA;QACpE,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACvD,KAAK,EACL,MAAM,EACN,IAAI,CACL,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EACL,MAAM,EACN,SAAS,EACT,aAAa,EACb,4BAA4B,GAC7B,MAAM,SAAS,CAAA;AAChB,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,8BAA8B,CAAA;AAErC,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,YAAY,EAAE,iBAAiB,CAAC,CAAC,CAAA;QACpE,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACvD,KAAK,EACL,MAAM,EACN,IAAI,CACL,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;IAExC,KAAK,CAAC,oBAAoB,CACxB,QAAmB,EACnB,MAAc,EACd,IAAoE;;QAEpE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;QAEnD,MAAM,OAAO,GAAG,EASf,CAAA;QAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,4BAA4B,CAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;YACjE,CAAC,CAAC,MAAM,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC;YAClC,CAAC,CAAC,SAAS,CAAA;QAEf,MAAM,IAAI,GAAG,EAYV,CAAA;QAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;YAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;YAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;gBACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;oBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;wBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;4BACR,KAAK,EAAE,CAAC;4BACR,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,IAAI,EAAE,CAAC;4BACP,GAAG,EAAE,CAAC;4BACN,GAAG,EAAE,CAAC;4BACN,OAAO,EAAE,EAAa;4BACtB,GAAG,EAAE,EAAa;4BAClB,QAAQ,EAAE,EAAa;4BACvB,MAAM,EAAE,EAAa;yBACtB,CAAA;qBACF;oBACD,IAAI,CAAC,KAAK,IAAI,EAAE;wBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;wBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;wBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;qBACnB;iBACF;aACF;YAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;gBACrC,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@@ -1,4 +1,4 @@
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1
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-
import { Feature } from '@jbrowse/core/util
|
|
1
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+
import { Feature } from '@jbrowse/core/util';
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|
2
2
|
import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
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|
3
3
|
import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
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|
4
4
|
export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
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@@ -37,7 +37,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
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|
37
37
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const toHeight = (n) => toY(originY) - toY(n);
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|
38
38
|
const indicatorToY = (n) => height - (indicatorViewScale(n) || 0) + offset;
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|
39
39
|
const indicatorToHeight = (n) => indicatorToY(getOrigin('linear')) - indicatorToY(n);
|
|
40
|
-
// @ts-ignore
|
|
41
40
|
const { bases } = theme.palette;
|
|
42
41
|
const colorForBase = {
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|
43
42
|
A: bases.A.main,
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