@jbrowse/plugin-variants 2.2.0 → 2.2.2

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Files changed (18) hide show
  1. package/dist/LinearVariantDisplay/configSchema.d.ts +2 -2
  2. package/dist/LinearVariantDisplay/model.d.ts +2 -6
  3. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +1 -1
  4. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +2 -16
  5. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  6. package/esm/LinearVariantDisplay/configSchema.d.ts +2 -2
  7. package/esm/LinearVariantDisplay/model.d.ts +2 -6
  8. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +1 -1
  9. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +3 -14
  10. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  11. package/package.json +4 -4
  12. package/src/LinearVariantDisplay/configSchema.test.js +1 -1
  13. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +2 -25
  14. package/src/VariantFeatureWidget/VariantFeatureWidget.test.js +6 -4
  15. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap +1 -3
  16. package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap +79 -79
  17. package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap +79 -79
  18. package/src/__snapshots__/index.test.js.snap +5 -5
package/dist/LinearVariantDisplay/configSchema.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import { Instance } from 'mobx-state-tree';
2
2
  import PluginManager from '@jbrowse/core/PluginManager';
3
3
  export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
- export declare type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
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- export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
4
+ export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
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+ export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
package/dist/LinearVariantDisplay/model.d.ts CHANGED
@@ -61,12 +61,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
61
61
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
62
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  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
63
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  } & {
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- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
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- * #property
66
- */
67
- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
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- * #property
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- */
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+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
65
+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
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  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts CHANGED
@@ -11,7 +11,7 @@ interface ElidedRegion {
11
11
  elided: true;
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  regions: Region[];
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  }
14
- declare type AnyRegion = Region | ElidedRegion;
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+ type AnyRegion = Region | ElidedRegion;
15
15
  interface Block {
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  flipped: boolean;
17
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  bpPerRadian: number;
package/dist/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -22,25 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
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  __setModuleDefault(result, mod);
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  return result;
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  };
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
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  Object.defineProperty(exports, "__esModule", { value: true });
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  /* eslint-disable @typescript-eslint/no-explicit-any */
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  const react_1 = __importStar(require("react"));
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  const mobx_react_1 = require("mobx-react");
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  const material_1 = require("@mui/material");
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+ const ui_1 = require("@jbrowse/core/ui");
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  const mui_1 = require("tss-react/mui");
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- const Close_1 = __importDefault(require("@mui/icons-material/Close"));
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const util_1 = require("@jbrowse/core/util");
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  const useStyles = (0, mui_1.makeStyles)()(theme => ({
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- closeButton: {
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- position: 'absolute',
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- right: theme.spacing(1),
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- top: theme.spacing(1),
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- color: theme.palette.grey[500],
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- },
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  block: {
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  display: 'block',
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  },
@@ -49,12 +40,7 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
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  const { classes } = useStyles();
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  const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
51
42
  const [mirrorTracks, setMirrorTracks] = (0, react_1.useState)(true);
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- return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
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- react_1.default.createElement(material_1.DialogTitle, null,
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- "Breakpoint split view options",
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- handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
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- react_1.default.createElement(Close_1.default, null))) : null),
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- react_1.default.createElement(material_1.Divider, null),
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+ return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
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  react_1.default.createElement(material_1.DialogContent, null,
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  react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
60
46
  react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAC1C,qDAA6C;AAC7C,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAQ,IAAA,6BAAW,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;wBAChD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;wBACzC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY;4BACzC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE;4BAC9B,CAAC,CAAC,UAAU,CAAA;wBAEd,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,oBAAoB,CAAC,CAAA"}
package/esm/LinearVariantDisplay/configSchema.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import { Instance } from 'mobx-state-tree';
2
2
  import PluginManager from '@jbrowse/core/PluginManager';
3
3
  export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
4
- export declare type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
5
- export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
4
+ export type LinearVariantDisplayConfigModel = ReturnType<typeof configSchemaF>;
5
+ export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;
package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -61,12 +61,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
61
61
  userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
62
62
  userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
63
63
  } & {
64
- type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
65
- * #property
66
- */
67
- trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
68
- * #property
69
- */
64
+ type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
65
+ trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
70
66
  trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
71
67
  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
72
68
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts CHANGED
@@ -11,7 +11,7 @@ interface ElidedRegion {
11
11
  elided: true;
12
12
  regions: Region[];
13
13
  }
14
- declare type AnyRegion = Region | ElidedRegion;
14
+ type AnyRegion = Region | ElidedRegion;
15
15
  interface Block {
16
16
  flipped: boolean;
17
17
  bpPerRadian: number;
package/esm/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -1,18 +1,12 @@
1
1
  /* eslint-disable @typescript-eslint/no-explicit-any */
2
2
  import React, { useState } from 'react';
3
3
  import { observer } from 'mobx-react';
4
- import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, Divider, FormControlLabel, IconButton, } from '@mui/material';
4
+ import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, } from '@mui/material';
5
+ import { Dialog } from '@jbrowse/core/ui';
5
6
  import { makeStyles } from 'tss-react/mui';
6
- import CloseIcon from '@mui/icons-material/Close';
7
7
  import { getSnapshot } from 'mobx-state-tree';
8
8
  import { getSession } from '@jbrowse/core/util';
9
9
  const useStyles = makeStyles()(theme => ({
10
- closeButton: {
11
- position: 'absolute',
12
- right: theme.spacing(1),
13
- top: theme.spacing(1),
14
- color: theme.palette.grey[500],
15
- },
16
10
  block: {
17
11
  display: 'block',
18
12
  },
@@ -21,12 +15,7 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
21
15
  const { classes } = useStyles();
22
16
  const [copyTracks, setCopyTracks] = useState(true);
23
17
  const [mirrorTracks, setMirrorTracks] = useState(true);
24
- return (React.createElement(Dialog, { open: true, onClose: handleClose },
25
- React.createElement(DialogTitle, null,
26
- "Breakpoint split view options",
27
- handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
28
- React.createElement(CloseIcon, null))) : null),
29
- React.createElement(Divider, null),
18
+ return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
30
19
  React.createElement(DialogContent, null,
31
20
  React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
32
21
  React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAQ,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;wBAChD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;wBACzC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY;4BACzC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE;4BAC9B,CAAC,CAAC,UAAU,CAAA;wBAEd,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.2.0",
3
+ "version": "2.2.2",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -27,7 +27,7 @@
27
27
  "build": "npm-run-all build:*",
28
28
  "test": "cd ../..; jest plugins/variants",
29
29
  "prepublishOnly": "yarn test",
30
- "prepack": "yarn build; yarn useDist",
30
+ "prepack": "yarn build && yarn useDist",
31
31
  "postpack": "yarn useSrc",
32
32
  "useDist": "node ../../scripts/useDist.js",
33
33
  "useSrc": "node ../../scripts/useSrc.js",
@@ -40,7 +40,7 @@
40
40
  "@flatten-js/interval-tree": "^1.0.15",
41
41
  "@gmod/bgzf-filehandle": "^1.4.3",
42
42
  "@gmod/tabix": "^1.5.2",
43
- "@gmod/vcf": "^5.0.5",
43
+ "@gmod/vcf": "^5.0.9",
44
44
  "@mui/icons-material": "^5.0.2",
45
45
  "@mui/x-data-grid": "^5.0.1",
46
46
  "generic-filehandle": "^3.0.0"
@@ -65,5 +65,5 @@
65
65
  "distModule": "esm/index.js",
66
66
  "srcModule": "src/index.ts",
67
67
  "module": "esm/index.js",
68
- "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
68
+ "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
69
69
  }
package/src/LinearVariantDisplay/configSchema.test.js CHANGED
@@ -48,7 +48,7 @@ test('has a viewType attr', () => {
48
48
  )
49
49
  const config = configSchema.create({
50
50
  type: 'LinearVariantDisplay',
51
- displayId: 'diplayId0',
51
+ displayId: 'displayId0',
52
52
  name: 'Zonker Display',
53
53
  })
54
54
  expect(config.type).toEqual('LinearVariantDisplay')
package/src/VariantFeatureWidget/BreakendOptionDialog.tsx CHANGED
@@ -4,26 +4,16 @@ import { observer } from 'mobx-react'
4
4
  import {
5
5
  Button,
6
6
  Checkbox,
7
- Dialog,
8
7
  DialogActions,
9
8
  DialogContent,
10
- DialogTitle,
11
- Divider,
12
9
  FormControlLabel,
13
- IconButton,
14
10
  } from '@mui/material'
11
+ import { Dialog } from '@jbrowse/core/ui'
15
12
  import { makeStyles } from 'tss-react/mui'
16
- import CloseIcon from '@mui/icons-material/Close'
17
13
  import { getSnapshot } from 'mobx-state-tree'
18
14
  import { getSession, Feature } from '@jbrowse/core/util'
19
15
 
20
16
  const useStyles = makeStyles()(theme => ({
21
- closeButton: {
22
- position: 'absolute',
23
- right: theme.spacing(1),
24
- top: theme.spacing(1),
25
- color: theme.palette.grey[500],
26
- },
27
17
  block: {
28
18
  display: 'block',
29
19
  },
@@ -45,20 +35,7 @@ function BreakendOptionDialog({
45
35
  const [mirrorTracks, setMirrorTracks] = useState(true)
46
36
 
47
37
  return (
48
- <Dialog open onClose={handleClose}>
49
- <DialogTitle>
50
- Breakpoint split view options
51
- {handleClose ? (
52
- <IconButton
53
- className={classes.closeButton}
54
- onClick={() => handleClose()}
55
- >
56
- <CloseIcon />
57
- </IconButton>
58
- ) : null}
59
- </DialogTitle>
60
- <Divider />
61
-
38
+ <Dialog open onClose={handleClose} title="Breakpoint split view options">
62
39
  <DialogContent>
63
40
  <FormControlLabel
64
41
  className={classes.block}
package/src/VariantFeatureWidget/VariantFeatureWidget.test.js CHANGED
@@ -13,13 +13,15 @@ describe('VariantTrack widget', () => {
13
13
  const pluginManager = new PluginManager([])
14
14
  const Session = types.model({
15
15
  rpcManager: types.optional(types.frozen(), {}),
16
- pluginManager: types.optional(types.frozen(), {}),
17
16
  configuration: ConfigurationSchema('test', {}),
18
17
  widget: stateModelFactory(pluginManager),
19
18
  })
20
- const model = Session.create({
21
- widget: { type: 'VariantFeatureWidget' },
22
- })
19
+ const model = Session.create(
20
+ {
21
+ widget: { type: 'VariantFeatureWidget' },
22
+ },
23
+ { pluginManager },
24
+ )
23
25
  model.widget.setFeatureData({
24
26
  refName: 'ctgA',
25
27
  start: 176,
package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap CHANGED
@@ -73,9 +73,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
73
73
  <div
74
74
  class="css-1omt041-fieldValue"
75
75
  >
76
- <div>
77
- ctgA:177..177
78
- </div>
76
+ ctgA:177
79
77
  </div>
80
78
  </div>
81
79
  <div
package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap CHANGED
@@ -1,43 +1,43 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`adapter can fetch variants from volvox.vcf 1`] = `
4
- Array [
4
+ [
5
5
  "ctgA",
6
6
  ]
7
7
  `;
8
8
 
9
9
  exports[`adapter can fetch variants from volvox.vcf 2`] = `
10
- Array [
11
- Object {
12
- "ALT": Array [
10
+ [
11
+ {
12
+ "ALT": [
13
13
  "C",
14
14
  ],
15
15
  "CHROM": "ctgA",
16
16
  "FILTER": null,
17
17
  "ID": null,
18
- "INFO": Object {
19
- "AC1": Array [
18
+ "INFO": {
19
+ "AC1": [
20
20
  2,
21
21
  ],
22
- "AF1": Array [
22
+ "AF1": [
23
23
  1,
24
24
  ],
25
- "DP": Array [
25
+ "DP": [
26
26
  3,
27
27
  ],
28
- "DP4": Array [
28
+ "DP4": [
29
29
  0,
30
30
  0,
31
31
  3,
32
32
  0,
33
33
  ],
34
- "FQ": Array [
34
+ "FQ": [
35
35
  -36,
36
36
  ],
37
- "MQ": Array [
37
+ "MQ": [
38
38
  37,
39
39
  ],
40
- "VDB": Array [
40
+ "VDB": [
41
41
  0.0186,
42
42
  ],
43
43
  },
@@ -49,15 +49,15 @@ Array [
49
49
  "end": 277,
50
50
  "name": undefined,
51
51
  "refName": "ctgA",
52
- "samples": Object {
53
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
54
- "GQ": Array [
52
+ "samples": {
53
+ "sample_data/raw/volvox/volvox-sorted.bam": {
54
+ "GQ": [
55
55
  13,
56
56
  ],
57
- "GT": Array [
57
+ "GT": [
58
58
  "1/1",
59
59
  ],
60
- "PL": Array [
60
+ "PL": [
61
61
  42,
62
62
  9,
63
63
  0,
@@ -68,42 +68,42 @@ Array [
68
68
  "type": "SNV",
69
69
  "uniqueId": "test-0",
70
70
  },
71
- Object {
72
- "ALT": Array [
71
+ {
72
+ "ALT": [
73
73
  "C",
74
74
  ],
75
75
  "CHROM": "ctgA",
76
76
  "FILTER": null,
77
77
  "ID": null,
78
- "INFO": Object {
79
- "AC1": Array [
78
+ "INFO": {
79
+ "AC1": [
80
80
  2,
81
81
  ],
82
- "AF1": Array [
82
+ "AF1": [
83
83
  1,
84
84
  ],
85
- "DP": Array [
85
+ "DP": [
86
86
  23,
87
87
  ],
88
- "DP4": Array [
88
+ "DP4": [
89
89
  0,
90
90
  1,
91
91
  8,
92
92
  14,
93
93
  ],
94
- "FQ": Array [
94
+ "FQ": [
95
95
  -73,
96
96
  ],
97
- "MQ": Array [
97
+ "MQ": [
98
98
  37,
99
99
  ],
100
- "PV4": Array [
100
+ "PV4": [
101
101
  1,
102
102
  1,
103
103
  0.42,
104
104
  1,
105
105
  ],
106
- "VDB": Array [
106
+ "VDB": [
107
107
  0.0308,
108
108
  ],
109
109
  },
@@ -115,15 +115,15 @@ Array [
115
115
  "end": 1694,
116
116
  "name": undefined,
117
117
  "refName": "ctgA",
118
- "samples": Object {
119
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
120
- "GQ": Array [
118
+ "samples": {
119
+ "sample_data/raw/volvox/volvox-sorted.bam": {
120
+ "GQ": [
121
121
  89,
122
122
  ],
123
- "GT": Array [
123
+ "GT": [
124
124
  "1/1",
125
125
  ],
126
- "PL": Array [
126
+ "PL": [
127
127
  140,
128
128
  46,
129
129
  0,
@@ -134,42 +134,42 @@ Array [
134
134
  "type": "SNV",
135
135
  "uniqueId": "test-1",
136
136
  },
137
- Object {
138
- "ALT": Array [
137
+ {
138
+ "ALT": [
139
139
  "G",
140
140
  ],
141
141
  "CHROM": "ctgA",
142
142
  "FILTER": null,
143
143
  "ID": null,
144
- "INFO": Object {
145
- "AC1": Array [
144
+ "INFO": {
145
+ "AC1": [
146
146
  1,
147
147
  ],
148
- "AF1": Array [
148
+ "AF1": [
149
149
  0.5,
150
150
  ],
151
- "DP": Array [
151
+ "DP": [
152
152
  22,
153
153
  ],
154
- "DP4": Array [
154
+ "DP4": [
155
155
  6,
156
156
  5,
157
157
  3,
158
158
  8,
159
159
  ],
160
- "FQ": Array [
160
+ "FQ": [
161
161
  45.3,
162
162
  ],
163
- "MQ": Array [
163
+ "MQ": [
164
164
  37,
165
165
  ],
166
- "PV4": Array [
166
+ "PV4": [
167
167
  0.39,
168
168
  1,
169
169
  1,
170
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171
  ],
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- "VDB": Array [
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  ],
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  },
@@ -181,15 +181,15 @@ Array [
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181
  "end": 2644,
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  "name": undefined,
183
183
  "refName": "ctgA",
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- "samples": Object {
185
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
186
- "GQ": Array [
184
+ "samples": {
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+ "sample_data/raw/volvox/volvox-sorted.bam": {
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+ "GQ": [
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  75,
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  ],
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191
  ],
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- "PL": Array [
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+ "PL": [
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  74,
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  77,
@@ -200,36 +200,36 @@ Array [
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200
  "type": "SNV",
201
201
  "uniqueId": "test-2",
202
202
  },
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- Object {
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- "ALT": Array [
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+ {
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  "A",
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206
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207
  "CHROM": "ctgA",
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208
  "FILTER": null,
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- "MQ": Array [
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  36,
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- "VDB": Array [
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+ "VDB": [
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  ],
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@@ -241,15 +241,15 @@ Array [
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  "end": 3213,
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243
  "refName": "ctgA",
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- "samples": Object {
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- "sample_data/raw/volvox/volvox-sorted.bam": Object {
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+ "GT": [
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  ],
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+ "PL": [
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  157,
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@@ -260,37 +260,37 @@ Array [
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260
  "type": "SNV",
261
261
  "uniqueId": "test-3",
262
262
  },
263
- Object {
264
- "ALT": Array [
263
+ {
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+ "ALT": [
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265
  "ct",
266
266
  ],
267
267
  "CHROM": "ctgA",
268
268
  "FILTER": null,
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269
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  ],
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  "INDEL": true,
290
- "MQ": Array [
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  ],
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- "VDB": Array [
293
+ "VDB": [
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  0.0384,
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  ],
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  },
@@ -302,15 +302,15 @@ Array [
302
302
  "end": 3860,
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303
  "name": undefined,
304
304
  "refName": "ctgA",
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- "samples": Object {
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- "sample_data/raw/volvox/volvox-sorted.bam": Object {
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- "GQ": Array [
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+ "samples": {
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+ "sample_data/raw/volvox/volvox-sorted.bam": {
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  63,
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  ],
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+ "PL": [
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  201,
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package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap CHANGED
@@ -1,43 +1,43 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
3
  exports[`adapter can fetch variants from volvox.vcf.gz 1`] = `
4
- Array [
4
+ [
5
5
  "ctgA",
6
6
  ]
7
7
  `;
8
8
 
9
9
  exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
10
- Array [
11
- Object {
12
- "ALT": Array [
10
+ [
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+ {
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+ "ALT": [
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13
  "C",
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14
  ],
15
15
  "CHROM": "ctgA",
16
16
  "FILTER": null,
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17
  "ID": null,
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- "INFO": Object {
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  2,
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  ],
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- "AF1": Array [
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  1,
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- "DP": Array [
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- "DP4": Array [
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  0,
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- "FQ": Array [
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  37,
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  ],
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- "VDB": Array [
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+ "VDB": [
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  ],
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  },
@@ -49,15 +49,15 @@ Array [
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49
  "end": 277,
50
50
  "name": undefined,
51
51
  "refName": "ctgA",
52
- "samples": Object {
53
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
54
- "GQ": Array [
52
+ "samples": {
53
+ "sample_data/raw/volvox/volvox-sorted.bam": {
54
+ "GQ": [
55
55
  13,
56
56
  ],
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- "GT": Array [
57
+ "GT": [
58
58
  "1/1",
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  ],
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- "PL": Array [
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+ "PL": [
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  42,
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  9,
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  0,
@@ -68,42 +68,42 @@ Array [
68
68
  "type": "SNV",
69
69
  "uniqueId": "test-vcf-604452",
70
70
  },
71
- Object {
72
- "ALT": Array [
71
+ {
72
+ "ALT": [
73
73
  "C",
74
74
  ],
75
75
  "CHROM": "ctgA",
76
76
  "FILTER": null,
77
77
  "ID": null,
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- "INFO": Object {
79
- "AC1": Array [
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80
80
  2,
81
81
  ],
82
- "AF1": Array [
82
+ "AF1": [
83
83
  1,
84
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  ],
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- "DP": Array [
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87
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- "DP4": Array [
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+ "DP4": [
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89
  0,
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90
  1,
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91
  8,
92
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  14,
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  ],
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- "FQ": Array [
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+ "FQ": [
95
95
  -73,
96
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  ],
97
- "MQ": Array [
97
+ "MQ": [
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98
  37,
99
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  ],
100
- "PV4": Array [
100
+ "PV4": [
101
101
  1,
102
102
  1,
103
103
  0.42,
104
104
  1,
105
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  ],
106
- "VDB": Array [
106
+ "VDB": [
107
107
  0.0308,
108
108
  ],
109
109
  },
@@ -115,15 +115,15 @@ Array [
115
115
  "end": 1694,
116
116
  "name": undefined,
117
117
  "refName": "ctgA",
118
- "samples": Object {
119
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
120
- "GQ": Array [
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+ "samples": {
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+ "sample_data/raw/volvox/volvox-sorted.bam": {
120
+ "GQ": [
121
121
  89,
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  ],
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- "GT": Array [
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124
124
  "1/1",
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+ "PL": [
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  0,
@@ -134,42 +134,42 @@ Array [
134
134
  "type": "SNV",
135
135
  "uniqueId": "test-vcf-604550",
136
136
  },
137
- Object {
138
- "ALT": Array [
137
+ {
138
+ "ALT": [
139
139
  "G",
140
140
  ],
141
141
  "CHROM": "ctgA",
142
142
  "FILTER": null,
143
143
  "ID": null,
144
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145
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  1,
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  ],
148
- "AF1": Array [
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149
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152
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154
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161
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167
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168
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- "VDB": Array [
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  0.0253,
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  },
@@ -181,15 +181,15 @@ Array [
181
181
  "end": 2644,
182
182
  "name": undefined,
183
183
  "refName": "ctgA",
184
- "samples": Object {
185
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
186
- "GQ": Array [
184
+ "samples": {
185
+ "sample_data/raw/volvox/volvox-sorted.bam": {
186
+ "GQ": [
187
187
  75,
188
188
  ],
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- "GT": Array [
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+ "GT": [
190
190
  "0/1",
191
191
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192
- "PL": Array [
192
+ "PL": [
193
193
  74,
194
194
  0,
195
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  77,
@@ -200,36 +200,36 @@ Array [
200
200
  "type": "SNV",
201
201
  "uniqueId": "test-vcf-604667",
202
202
  },
203
- Object {
204
- "ALT": Array [
203
+ {
204
+ "ALT": [
205
205
  "A",
206
206
  ],
207
207
  "CHROM": "ctgA",
208
208
  "FILTER": null,
209
209
  "ID": null,
210
- "INFO": Object {
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- "AC1": Array [
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212
212
  2,
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214
- "AF1": Array [
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215
215
  1,
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- "FQ": Array [
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  -84,
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- "MQ": Array [
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+ "MQ": [
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  36,
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- "VDB": Array [
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+ "VDB": [
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233
  0.0384,
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  ],
235
235
  },
@@ -241,15 +241,15 @@ Array [
241
241
  "end": 3213,
242
242
  "name": undefined,
243
243
  "refName": "ctgA",
244
- "samples": Object {
245
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
246
- "GQ": Array [
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+ "samples": {
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247
247
  99,
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- "GT": Array [
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250
250
  "1/1",
251
251
  ],
252
- "PL": Array [
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253
  157,
254
254
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255
255
  0,
@@ -260,37 +260,37 @@ Array [
260
260
  "type": "SNV",
261
261
  "uniqueId": "test-vcf-604784",
262
262
  },
263
- Object {
264
- "ALT": Array [
263
+ {
264
+ "ALT": [
265
265
  "ct",
266
266
  ],
267
267
  "CHROM": "ctgA",
268
268
  "FILTER": null,
269
269
  "ID": null,
270
- "INFO": Object {
271
- "AC1": Array [
270
+ "INFO": {
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+ "AC1": [
272
272
  2,
273
273
  ],
274
- "AF1": Array [
274
+ "AF1": [
275
275
  1,
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277
- "DP": Array [
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278
  15,
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280
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281
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283
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285
  ],
286
- "FQ": Array [
286
+ "FQ": [
287
287
  -67.5,
288
288
  ],
289
289
  "INDEL": true,
290
- "MQ": Array [
290
+ "MQ": [
291
291
  37,
292
292
  ],
293
- "VDB": Array [
293
+ "VDB": [
294
294
  0.0384,
295
295
  ],
296
296
  },
@@ -302,15 +302,15 @@ Array [
302
302
  "end": 3860,
303
303
  "name": undefined,
304
304
  "refName": "ctgA",
305
- "samples": Object {
306
- "sample_data/raw/volvox/volvox-sorted.bam": Object {
307
- "GQ": Array [
305
+ "samples": {
306
+ "sample_data/raw/volvox/volvox-sorted.bam": {
307
+ "GQ": [
308
308
  63,
309
309
  ],
310
- "GT": Array [
310
+ "GT": [
311
311
  "1/1",
312
312
  ],
313
- "PL": Array [
313
+ "PL": [
314
314
  201,
315
315
  33,
316
316
  0,
package/src/__snapshots__/index.test.js.snap CHANGED
@@ -1,15 +1,15 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
2
2
 
3
- exports[`plugin in a stock JBrowse 1`] = `Object {}`;
3
+ exports[`plugin in a stock JBrowse 1`] = `{}`;
4
4
 
5
5
  exports[`plugin in a stock JBrowse 2`] = `
6
- Object {
7
- "displays": Array [
8
- Object {
6
+ {
7
+ "displays": [
8
+ {
9
9
  "displayId": "trackId0-LinearVariantDisplay",
10
10
  "type": "LinearVariantDisplay",
11
11
  },
12
- Object {
12
+ {
13
13
  "displayId": "trackId0-ChordVariantDisplay",
14
14
  "type": "ChordVariantDisplay",
15
15
  },