@jbrowse/plugin-alignments 2.3.1 → 2.3.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BamAdapter/BamAdapter.js +2 -1
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +3 -3
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/LinearReadArcsDisplay/configSchema.js +8 -0
- package/dist/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/dist/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/dist/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +46 -15
- package/dist/LinearReadArcsDisplay/model.js +42 -0
- package/dist/LinearReadArcsDisplay/model.js.map +1 -1
- package/dist/LinearReadCloudDisplay/drawFeats.js +18 -32
- package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/dist/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/dist/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/dist/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/dist/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/dist/util.js +3 -3
- package/dist/util.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -1
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/CramAdapter/CramAdapter.js +3 -3
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/LinearReadArcsDisplay/configSchema.js +8 -0
- package/esm/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/esm/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/esm/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +46 -15
- package/esm/LinearReadArcsDisplay/model.js +42 -0
- package/esm/LinearReadArcsDisplay/model.js.map +1 -1
- package/esm/LinearReadCloudDisplay/drawFeats.js +19 -33
- package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +8 -8
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js +3 -1
- package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +1 -1
- package/esm/PileupRPC/methods/GetReducedFeatures.js +2 -4
- package/esm/PileupRPC/methods/GetReducedFeatures.js.map +1 -1
- package/esm/PileupRPC/methods/GetVisibleModifications.js +2 -4
- package/esm/PileupRPC/methods/GetVisibleModifications.js.map +1 -1
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +3 -4
- package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -1
- package/esm/util.js +3 -3
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/AlignmentsFeatureDetail/__snapshots__/{index.test.js.snap → index.test.tsx.snap} +0 -0
- package/src/AlignmentsFeatureDetail/{index.test.js → index.test.tsx} +4 -2
- package/src/BamAdapter/BamAdapter.test.ts +5 -4
- package/src/BamAdapter/BamAdapter.ts +2 -1
- package/src/CombinationTest.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.test.ts +3 -2
- package/src/CramAdapter/CramAdapter.ts +11 -9
- package/src/LinearAlignmentsDisplay/models/{configSchema.test.js → configSchema.test.ts} +5 -1
- package/src/LinearReadArcsDisplay/configSchema.ts +10 -0
- package/src/LinearReadArcsDisplay/drawFeats.ts +73 -54
- package/src/LinearReadArcsDisplay/model.tsx +45 -0
- package/src/LinearReadCloudDisplay/drawFeats.ts +21 -33
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +76 -73
- package/src/LinearSNPCoverageDisplay/models/{configSchema.test.js → configSchema.test.ts} +3 -1
- package/src/PileupRPC/methods/GetGlobalValueForTag.ts +4 -1
- package/src/PileupRPC/methods/GetReducedFeatures.ts +4 -5
- package/src/PileupRPC/methods/GetVisibleModifications.ts +4 -4
- package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +6 -4
- package/src/index.test.ts +0 -1
- package/src/util.ts +10 -8
- package/src/PileupRenderer/components/PileupRendering.test.js +0 -21
- package/src/PileupRenderer/components/__snapshots__/PileupRendering.test.js.snap +0 -23
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@@ -25,9 +25,15 @@ async function drawFeats(self, ctx) {
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if (!chainData) {
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return;
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}
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const { assemblyManager } = (0, util_1.getSession)(self);
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const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
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const displayHeight = self.height;
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const view = (0, util_1.getContainingView)(self);
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const assemblyName = view.assemblyNames[0];
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const asm = assemblyManager.get(assemblyName);
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if (!asm) {
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return;
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}
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self.setLastDrawnOffsetPx(view.offsetPx);
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const { chains, stats } = chainData;
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const coords = [];
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if (chain[0].flags & 1 && chain.length > 1) {
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const v0 = chain[0];
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const v1 = chain[1];
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const
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});
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const
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coord: v0.end,
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});
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const r2s = view.bpToPx({
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refName: v1.refName,
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coord: v1.start,
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});
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const r2e = view.bpToPx({
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refName: v1.refName,
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coord: v1.end,
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});
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const ra1 = asm.getCanonicalRefName(v0.refName);
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const ra2 = asm.getCanonicalRefName(v1.refName);
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const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
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const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
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const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
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const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
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let distance = 0;
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if (r1s !== undefined &&
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for (let i = 1; i < chain.length; i++) {
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});
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const r2e = view.bpToPx({
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coord: v1.end,
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});
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const ra1 = asm.getCanonicalRefName(v0.refName);
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const ra2 = asm.getCanonicalRefName(v1.refName);
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const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
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const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
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const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
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const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
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if (r1s !== undefined &&
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@@ -1 +1 @@
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{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":";;AAAA,+DAAqD;AACrD,
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@@ -9,7 +9,7 @@ const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
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9
9
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const en = (n) => n.toLocaleString('en-US');
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const toP = (s = 0) => +(+s).toFixed(1);
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const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
|
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-
const TooltipContents = react_1.default.forwardRef(({ feature }, reactRef)
|
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+
const TooltipContents = react_1.default.forwardRef(function ({ feature }, reactRef) {
|
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const start = feature.get('start');
|
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|
const end = feature.get('end');
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const name = feature.get('refName');
|
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,0DAAgD;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;
|
|
1
|
+
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,0DAAgD;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;AAI7E,MAAM,eAAe,GAAG,eAAK,CAAC,UAAU,CAAwB,UAC9D,EAAE,OAAO,EAAE,EACX,QAAQ;IAER,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,uCAAK,GAAG,EAAE,QAAQ;QAChB;YACE,+CAAU,GAAG,CAAW;YACxB;gBACE;oBACE,iDAAa;oBACb,kDAAc;oBACd,uDAAmB;oBACnB,oDAAgB;oBAChB,mDAAe,CACZ,CACC;YACR;gBACE;oBACE,kDAAc;oBACd,0CAAK,GAAG,CAAM,CACX;gBACL;oBACE;;wBAAS,OAAO,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAM;oBAC1D,0CAAK,GAAG,CAAM;oBACd,0CAAK,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,yCAAM,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,sCAAI,GAAG,EAAE,IAAI;oBACX,0CAAK,IAAI,CAAC,WAAW,EAAE,CAAM;oBAC7B,0CAAK,KAAK,CAAC,KAAK,CAAM;oBACtB,0CACG,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,0CAAK,GAAG,CAAM,CACX,CACN,CAAC,CACL,CACK,CACF,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAIF,MAAM,kBAAkB,GAAG,IAAA,qBAAQ,EACjC,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,8BAAC,uBAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CACzD,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,kBAAkB,CAAA"}
|
|
@@ -45,7 +45,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
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|
45
45
|
}) => any;
|
|
46
46
|
renderProps: any;
|
|
47
47
|
} & {
|
|
48
|
-
doReload(): void;
|
|
48
|
+
doReload(): void; /**
|
|
49
|
+
* #action
|
|
50
|
+
*/
|
|
49
51
|
afterAttach(): void;
|
|
50
52
|
setStatus(message: string): void;
|
|
51
53
|
setLoading(abortController: AbortController): void;
|
|
@@ -56,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
56
58
|
layout: any;
|
|
57
59
|
maxHeightReached: boolean;
|
|
58
60
|
renderProps: any;
|
|
59
|
-
} | undefined): void;
|
|
60
|
-
* #getter
|
|
61
|
-
*/
|
|
61
|
+
} | undefined): void;
|
|
62
62
|
setError(error: unknown): void;
|
|
63
63
|
reload(): void;
|
|
64
64
|
beforeDestroy(): void;
|
|
@@ -152,13 +152,13 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
|
|
|
152
152
|
rendererTypeName: string;
|
|
153
153
|
error: unknown;
|
|
154
154
|
} & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
|
|
155
|
-
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
156
|
-
* #getter
|
|
157
|
-
*/
|
|
155
|
+
id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
|
|
158
156
|
type: import("mobx-state-tree").ISimpleType<string>;
|
|
159
157
|
rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
160
158
|
}, {
|
|
161
|
-
rendererTypeName: string;
|
|
159
|
+
rendererTypeName: string; /**
|
|
160
|
+
* #method
|
|
161
|
+
*/
|
|
162
162
|
error: unknown;
|
|
163
163
|
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
|
164
164
|
}> | null;
|
|
@@ -5,6 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
|
|
7
7
|
const operators_1 = require("rxjs/operators");
|
|
8
|
+
const rxjs_1 = require("rxjs");
|
|
9
|
+
// locals
|
|
8
10
|
const base_1 = __importDefault(require("../base"));
|
|
9
11
|
const util_1 = require("../../util");
|
|
10
12
|
class PileupGetGlobalValueForTag extends base_1.default {
|
|
@@ -16,7 +18,7 @@ class PileupGetGlobalValueForTag extends base_1.default {
|
|
|
16
18
|
const { adapterConfig, sessionId, regions, tag } = await this.deserializeArguments(args, rpcDriver);
|
|
17
19
|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
18
20
|
const features = dataAdapter.getFeaturesInMultipleRegions(regions);
|
|
19
|
-
const featuresArray = await features.pipe((0, operators_1.toArray)())
|
|
21
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(features.pipe((0, operators_1.toArray)()));
|
|
20
22
|
return [
|
|
21
23
|
...new Set(featuresArray
|
|
22
24
|
.map(feature => (0, util_1.getTag)(feature, tag))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,mDAAmC;AACnC,qCAAmC;AAEnC,MAAqB,0BAA2B,SAAQ,cAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,
|
|
1
|
+
{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,mDAAmC;AACnC,qCAAmC;AAEnC,MAAqB,0BAA2B,SAAQ,cAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EAAC,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,CAAA;QACpE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,IAAA,aAAM,EAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF;AAhCD,6CAgCC"}
|
|
@@ -6,6 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
6
6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
|
|
7
7
|
const util_1 = require("@jbrowse/core/util");
|
|
8
8
|
const operators_1 = require("rxjs/operators");
|
|
9
|
+
const rxjs_1 = require("rxjs");
|
|
9
10
|
// locals
|
|
10
11
|
const util_2 = require("../util");
|
|
11
12
|
const base_1 = __importDefault(require("../base"));
|
|
@@ -20,10 +21,7 @@ class PileupGetReducedFeatures extends base_1.default {
|
|
|
20
21
|
const des = await this.deserializeArguments(args, rpcDriver);
|
|
21
22
|
const { adapterConfig, sessionId, regions } = des;
|
|
22
23
|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
23
|
-
const featuresArray = await dataAdapter
|
|
24
|
-
.getFeaturesInMultipleRegions(regions, des)
|
|
25
|
-
.pipe((0, operators_1.toArray)())
|
|
26
|
-
.toPromise();
|
|
24
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe((0, operators_1.toArray)()));
|
|
27
25
|
const reduced = (0, util_1.dedupe)(featuresArray.map(f => ({
|
|
28
26
|
id: f.id(),
|
|
29
27
|
refName: f.get('refName'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AACzE,6CAAmD;AAGnD,8CAAwC;
|
|
1
|
+
{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AACzE,6CAAmD;AAGnD,8CAAwC;AACxC,+BAAqC;AACrC,SAAS;AACT,kCAA4D;AAE5D,mDAAmC;AACnC,qCAAmC;AAEnC,mEAAmE;AACnE,MAAqB,wBAAyB,SAAQ,cAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA4DnC,CAAC;IA1DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACvE,CAAA;QAED,MAAM,OAAO,GAAG,IAAA,aAAM,EACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,IAAA,aAAM,EAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,IAAA,qBAAc,EAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,IAAA,yBAAkB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF;AA7DD,2CA6DC"}
|
|
@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
|
|
7
7
|
const operators_1 = require("rxjs/operators");
|
|
8
|
+
const rxjs_1 = require("rxjs");
|
|
8
9
|
// locals
|
|
9
10
|
const MismatchParser_1 = require("../../MismatchParser");
|
|
10
11
|
const base_1 = __importDefault(require("../base"));
|
|
@@ -17,10 +18,7 @@ class PileupGetVisibleModifications extends base_1.default {
|
|
|
17
18
|
async execute(args, rpcDriver) {
|
|
18
19
|
const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
|
|
19
20
|
const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
|
|
20
|
-
const featuresArray = await dataAdapter
|
|
21
|
-
.getFeaturesInMultipleRegions(regions)
|
|
22
|
-
.pipe((0, operators_1.toArray)())
|
|
23
|
-
.toPromise();
|
|
21
|
+
const featuresArray = await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions).pipe((0, operators_1.toArray)()));
|
|
24
22
|
const uniqueValues = new Set();
|
|
25
23
|
featuresArray.forEach(f => {
|
|
26
24
|
(0, MismatchParser_1.getModificationTypes)((0, util_1.getTagAlt)(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;
|
|
1
|
+
{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":";;;;;AAAA,mFAAyE;AAIzE,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,yDAA2D;AAC3D,mDAAmC;AACnC,qCAAsC;AAEtC,MAAqB,6BAA8B,SAAQ,cAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IA+BxC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,MAAM,WAAW,GAAG,CAClB,MAAM,IAAA,6BAAU,EAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,IAAA,qBAAc,EACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAClE,CAAA;QAED,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,IAAA,qCAAoB,EAAC,IAAA,gBAAS,EAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF;AAhCD,gDAgCC"}
|
|
@@ -8,6 +8,8 @@ const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
|
|
|
8
8
|
const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
|
|
9
9
|
const rxjs_1 = require("@jbrowse/core/util/rxjs");
|
|
10
10
|
const operators_1 = require("rxjs/operators");
|
|
11
|
+
const rxjs_2 = require("rxjs");
|
|
12
|
+
// locals
|
|
11
13
|
const generateCoverageBins_1 = __importDefault(require("./generateCoverageBins"));
|
|
12
14
|
const util_1 = require("../util");
|
|
13
15
|
class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
@@ -37,10 +39,7 @@ class SNPCoverageAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
37
39
|
getFeatures(region, opts = {}) {
|
|
38
40
|
return (0, rxjs_1.ObservableCreate)(async (observer) => {
|
|
39
41
|
const { subadapter } = await this.configure();
|
|
40
|
-
const feats = await subadapter
|
|
41
|
-
.getFeatures(region, opts)
|
|
42
|
-
.pipe((0, operators_1.toArray)())
|
|
43
|
-
.toPromise();
|
|
42
|
+
const feats = await (0, rxjs_2.firstValueFrom)(subadapter.getFeatures(region, opts).pipe((0, operators_1.toArray)()));
|
|
44
43
|
const { bins, skipmap } = await (0, generateCoverageBins_1.default)(feats, region, opts, arg => this.fetchSequence(arg));
|
|
45
44
|
bins.forEach((bin, index) => {
|
|
46
45
|
const start = region.start + index;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,kFAAyD;AACzD,kCAAuC;AAEvC,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,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,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU
|
|
1
|
+
{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":";;;;;;AAAA,yEAGgD;AAEhD,qFAAyE;AACzE,kDAA0D;AAC1D,8CAAwC;AACxC,+BAAqC;AAErC,SAAS;AACT,kFAAyD;AACzD,kCAAuC;AAEvC,MAAqB,kBAAmB,SAAQ,oCAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,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,IAAA,oBAAa,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,UAAU,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACrD,CAAA;YAED,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,IAAA,8BAAoB,EAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,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,uBAAa,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,uBAAa,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;CACzC;AA7FD,qCA6FC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAClC,oCAAY"}
|
package/dist/util.js
CHANGED
|
@@ -2,6 +2,7 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.shouldFetchReferenceSequence = exports.fetchSequence = exports.getColorWGBS = exports.orientationTypes = exports.getTagAlt = exports.getTag = void 0;
|
|
4
4
|
const operators_1 = require("rxjs/operators");
|
|
5
|
+
const rxjs_1 = require("rxjs");
|
|
5
6
|
// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
|
|
6
7
|
// BAM does not
|
|
7
8
|
function getTag(feature, tag) {
|
|
@@ -72,14 +73,13 @@ exports.getColorWGBS = getColorWGBS;
|
|
|
72
73
|
async function fetchSequence(region, adapter) {
|
|
73
74
|
var _a;
|
|
74
75
|
const { end, originalRefName, refName } = region;
|
|
75
|
-
const feats = await adapter
|
|
76
|
+
const feats = await (0, rxjs_1.firstValueFrom)(adapter
|
|
76
77
|
.getFeatures({
|
|
77
78
|
...region,
|
|
78
79
|
refName: originalRefName || refName,
|
|
79
80
|
end: end + 1,
|
|
80
81
|
})
|
|
81
|
-
.pipe((0, operators_1.toArray)())
|
|
82
|
-
.toPromise();
|
|
82
|
+
.pipe((0, operators_1.toArray)()));
|
|
83
83
|
return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
|
|
84
84
|
}
|
|
85
85
|
exports.fetchSequence = fetchSequence;
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AACA,8CAAwC;AAGxC,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAEM,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,OAAO;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AACA,8CAAwC;AAGxC,+BAAqC;AACrC,4EAA4E;AAC5E,eAAe;AACf,SAAgB,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAHD,wBAGC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,SAAgB,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAFD,8BAEC;AAED,gDAAgD;AAChD,kFAAkF;AACrE,QAAA,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,SAAgB,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAjBD,oCAiBC;AAEM,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,IAAA,qBAAc,EAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;KACb,CAAC;SACD,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAhBD,sCAgBC;AAED,kEAAkE;AAClE,SAAgB,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC;AAFD,oEAEC"}
|
|
@@ -6,6 +6,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
|
6
6
|
import { toArray } from 'rxjs/operators';
|
|
7
7
|
// locals
|
|
8
8
|
import BamSlightlyLazyFeature from './BamSlightlyLazyFeature';
|
|
9
|
+
import { firstValueFrom } from 'rxjs';
|
|
9
10
|
export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
10
11
|
// derived classes may not use the same configuration so a custom
|
|
11
12
|
// configure method allows derived classes to override this behavior
|
|
@@ -104,7 +105,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
|
|
|
104
105
|
end,
|
|
105
106
|
assemblyName: '',
|
|
106
107
|
});
|
|
107
|
-
const seqChunks = await features.pipe(toArray())
|
|
108
|
+
const seqChunks = await firstValueFrom(features.pipe(toArray()));
|
|
108
109
|
let sequence = '';
|
|
109
110
|
seqChunks
|
|
110
111
|
.sort((a, b) => a.get('start') - b.get('start'))
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,eAAe,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC3E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;
|
|
1
|
+
{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,eAAe,EAAE,YAAY,EAAW,MAAM,oBAAoB,CAAA;AAC3E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAOrC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;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,OAAO,CAAC;YACtB,aAAa,EAAE,YAAY,CAAC,WAAW,EAAE,EAAE,CAAC;YAC5C,aAAa,EAAE,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC3D,aAAa,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,YAAY,CAAC,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,YAAY,CACjC,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,cAAc,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,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,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;QACpD,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,gBAAgB,CAAU,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;Y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@@ -4,6 +4,7 @@ import { checkAbortSignal } from '@jbrowse/core/util';
|
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|
4
4
|
import { openLocation } from '@jbrowse/core/util/io';
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|
5
5
|
import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
6
6
|
import { toArray } from 'rxjs/operators';
|
|
7
|
+
import { firstValueFrom } from 'rxjs';
|
|
7
8
|
import CramSlightlyLazyFeature from './CramSlightlyLazyFeature';
|
|
8
9
|
export default class CramAdapter extends BaseFeatureDataAdapter {
|
|
9
10
|
constructor() {
|
|
@@ -59,15 +60,14 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
|
|
|
59
60
|
if (!refName) {
|
|
60
61
|
throw new Error('unknown');
|
|
61
62
|
}
|
|
62
|
-
const seqChunks = await sequenceAdapter
|
|
63
|
+
const seqChunks = await firstValueFrom(sequenceAdapter
|
|
63
64
|
.getFeatures({
|
|
64
65
|
refName,
|
|
65
66
|
start,
|
|
66
67
|
end,
|
|
67
68
|
assemblyName: '',
|
|
68
69
|
})
|
|
69
|
-
.pipe(toArray())
|
|
70
|
-
.toPromise();
|
|
70
|
+
.pipe(toArray()));
|
|
71
71
|
const sequence = seqChunks
|
|
72
72
|
.sort((a, b) => a.get('start') - b.get('start'))
|
|
73
73
|
.map(chunk => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,eAAe,EAAc,MAAM,YAAY,CAAA;AACnE,OAAO,EACL,sBAAsB,GAGvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAmB,MAAM,oBAAoB,CAAA;AACtE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAe/D,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,sBAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;
|
|
1
|
+
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@@ -22,6 +22,14 @@ function configSchemaF(pluginManager) {
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22
22
|
description: 'set arc line width',
|
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23
23
|
defaultValue: 1,
|
|
24
24
|
},
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|
25
|
+
/**
|
|
26
|
+
* #slot
|
|
27
|
+
*/
|
|
28
|
+
jitter: {
|
|
29
|
+
type: 'number',
|
|
30
|
+
description: 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
|
|
31
|
+
defaultValue: 0,
|
|
32
|
+
},
|
|
25
33
|
/**
|
|
26
34
|
* #slot
|
|
27
35
|
*/
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|