@jbrowse/plugin-variants 2.10.0 → 2.10.2

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Files changed (39) hide show
  1. package/dist/StructuralVariantChordRenderer/Chord.d.ts +1 -1
  2. package/dist/StructuralVariantChordRenderer/Chord.js +1 -1
  3. package/dist/StructuralVariantChordRenderer/ReactComponent.js +5 -17
  4. package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts +4 -2
  5. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +30 -18
  6. package/dist/VariantFeatureWidget/BreakendPanel.d.ts +3 -2
  7. package/dist/VariantFeatureWidget/BreakendPanel.js +35 -31
  8. package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +2 -5
  9. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +2 -13
  10. package/dist/VariantFeatureWidget/configSchema.d.ts +1 -0
  11. package/dist/VariantFeatureWidget/configSchema.js +5 -0
  12. package/dist/VariantFeatureWidget/index.d.ts +0 -49
  13. package/dist/VariantFeatureWidget/index.js +4 -15
  14. package/dist/VariantFeatureWidget/stateModelFactory.d.ts +52 -0
  15. package/dist/VariantFeatureWidget/stateModelFactory.js +13 -0
  16. package/dist/VariantFeatureWidget/variantFieldDescriptions.d.ts +9 -0
  17. package/dist/VariantFeatureWidget/variantFieldDescriptions.js +12 -0
  18. package/dist/VcfAdapter/VcfAdapter.d.ts +4 -3
  19. package/dist/VcfAdapter/VcfAdapter.js +14 -17
  20. package/esm/StructuralVariantChordRenderer/Chord.d.ts +1 -1
  21. package/esm/StructuralVariantChordRenderer/Chord.js +1 -1
  22. package/esm/StructuralVariantChordRenderer/ReactComponent.js +5 -17
  23. package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts +4 -2
  24. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +30 -18
  25. package/esm/VariantFeatureWidget/BreakendPanel.d.ts +3 -2
  26. package/esm/VariantFeatureWidget/BreakendPanel.js +37 -30
  27. package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +2 -5
  28. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +3 -14
  29. package/esm/VariantFeatureWidget/configSchema.d.ts +1 -0
  30. package/esm/VariantFeatureWidget/configSchema.js +2 -0
  31. package/esm/VariantFeatureWidget/index.d.ts +0 -49
  32. package/esm/VariantFeatureWidget/index.js +3 -12
  33. package/esm/VariantFeatureWidget/stateModelFactory.d.ts +52 -0
  34. package/esm/VariantFeatureWidget/stateModelFactory.js +9 -0
  35. package/esm/VariantFeatureWidget/variantFieldDescriptions.d.ts +9 -0
  36. package/esm/VariantFeatureWidget/variantFieldDescriptions.js +9 -0
  37. package/esm/VcfAdapter/VcfAdapter.d.ts +4 -3
  38. package/esm/VcfAdapter/VcfAdapter.js +14 -17
  39. package/package.json +2 -2
package/dist/StructuralVariantChordRenderer/Chord.d.ts CHANGED
@@ -25,6 +25,6 @@ declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, se
25
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  config: AnyConfigurationModel;
26
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  bezierRadius: number;
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  selected: boolean;
28
- onClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
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+ onClick: (feat: Feature, reg: AnyRegion, end: AnyRegion, evt: unknown) => void;
29
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  }) => React.JSX.Element | null;
30
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  export default Chord;
package/dist/StructuralVariantChordRenderer/Chord.js CHANGED
@@ -87,7 +87,7 @@ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs
87
87
  const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
88
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  feature,
89
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  });
90
- return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
90
+ return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
91
91
  if (endBlock && startBlock) {
92
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  onClick(feature, startBlock.region, endBlock.region, evt);
93
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  }
package/dist/StructuralVariantChordRenderer/ReactComponent.js CHANGED
@@ -44,22 +44,10 @@ const StructuralVariantChordsReactComponent = (0, mobx_react_1.observer)(functio
44
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  }
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  return blocksForRefs;
46
46
  }, [blockDefinitions]);
47
- const trackStyleId = `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`;
48
- return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
49
- react_1.default.createElement("style", {
50
- // eslint-disable-next-line react/no-danger
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- dangerouslySetInnerHTML: {
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- __html: `
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- #${trackStyleId} > path {
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- cursor: crosshair;
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- fill: none;
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- }
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- `,
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- } }),
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- [...features.values()].map(feature => {
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- const id = feature.id();
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- const selected = String(selectedFeatureId) === String(id);
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- return (react_1.default.createElement(Chord_1.default, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
63
- })));
47
+ return (react_1.default.createElement("g", { id: `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`, "data-testid": "structuralVariantChordRenderer" }, [...features.values()].map(feature => {
48
+ const id = feature.id();
49
+ const selected = String(selectedFeatureId) === String(id);
50
+ return (react_1.default.createElement(Chord_1.default, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
51
+ })));
64
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  });
65
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  exports.default = StructuralVariantChordsReactComponent;
package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts CHANGED
@@ -1,9 +1,11 @@
1
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  import React from 'react';
2
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  import { Feature } from '@jbrowse/core/util';
3
+ import { ViewType } from '@jbrowse/core/pluggableElementTypes';
4
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
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  declare const BreakendOptionDialog: ({ model, handleClose, feature, viewType, }: {
4
- model: any;
6
+ model: VariantFeatureWidgetModel;
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7
  handleClose: () => void;
6
8
  feature: Feature;
7
- viewType: any;
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+ viewType: ViewType;
8
10
  }) => React.JSX.Element;
9
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  export default BreakendOptionDialog;
package/dist/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -23,13 +23,11 @@ var __importStar = (this && this.__importStar) || function (mod) {
23
23
  return result;
24
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  };
25
25
  Object.defineProperty(exports, "__esModule", { value: true });
26
- /* eslint-disable @typescript-eslint/no-explicit-any */
27
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  const react_1 = __importStar(require("react"));
28
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  const mobx_react_1 = require("mobx-react");
29
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  const material_1 = require("@mui/material");
30
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  const mui_1 = require("tss-react/mui");
31
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  const mobx_state_tree_1 = require("mobx-state-tree");
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- // jbrowse
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  const ui_1 = require("@jbrowse/core/ui");
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  const util_1 = require("@jbrowse/core/util");
35
33
  const useStyles = (0, mui_1.makeStyles)()({
@@ -37,34 +35,48 @@ const useStyles = (0, mui_1.makeStyles)()({
37
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  display: 'block',
38
36
  },
39
37
  });
40
- const BreakendOptionDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, feature, viewType, }) {
38
+ function stripIds(arr) {
39
+ return arr.map(({ id, displays, ...rest }) => ({
40
+ ...rest,
41
+ displays: displays.map(({ id, ...rest }) => rest),
42
+ }));
43
+ }
44
+ function Checkbox2({ checked, label, onChange, }) {
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  const { classes } = useStyles();
46
+ return (react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: onChange }), label: label }));
47
+ }
48
+ const BreakendOptionDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, feature, viewType, }) {
42
49
  const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
43
- const [mirrorTracks, setMirrorTracks] = (0, react_1.useState)(true);
50
+ const [mirror, setMirror] = (0, react_1.useState)(true);
44
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  return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
45
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  react_1.default.createElement(material_1.DialogContent, null,
46
- react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked) }), label: "Copy tracks into the new view" }),
47
- react_1.default.createElement(material_1.FormControlLabel, { className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: mirrorTracks, onChange: event => setMirrorTracks(event.target.checked) }), label: "Mirror tracks vertically in vertically stacked view" })),
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+ react_1.default.createElement(Checkbox2, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked), label: "Copy tracks into the new view" }),
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+ react_1.default.createElement(Checkbox2, { checked: mirror, onChange: event => setMirror(event.target.checked), label: "Mirror tracks vertically in vertically stacked view" })),
48
55
  react_1.default.createElement(material_1.DialogActions, null,
49
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  react_1.default.createElement(material_1.Button, { onClick: () => {
50
57
  const { view } = model;
51
58
  const session = (0, util_1.getSession)(model);
52
59
  try {
60
+ // @ts-expect-error
53
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  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
54
- function remapIds(arr) {
55
- return arr.map(v => ({
56
- ...v,
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- id: `${v.trackId}-${Math.random()}`,
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- }));
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- }
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- viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
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- viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
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- viewSnapshot.featureData = feature;
62
+ const [view1, view2] = viewSnapshot.views;
63
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  // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
64
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  const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
65
- viewSnapshot.views[0].tracks = remapIds(viewTracks);
66
- viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
67
- session.addView('BreakpointSplitView', viewSnapshot);
65
+ session.addView('BreakpointSplitView', {
66
+ ...viewSnapshot,
67
+ views: [
68
+ {
69
+ ...view1,
70
+ tracks: stripIds(viewTracks),
71
+ offsetPx: view1.offsetPx - view.width / 2 + 100,
72
+ },
73
+ {
74
+ ...view2,
75
+ tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
76
+ offsetPx: view2.offsetPx - view.width / 2 + 100,
77
+ },
78
+ ],
79
+ });
68
80
  }
69
81
  catch (e) {
70
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  console.error(e);
package/dist/VariantFeatureWidget/BreakendPanel.d.ts CHANGED
@@ -1,7 +1,8 @@
1
1
  import React from 'react';
2
- import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
2
+ import { SimpleFeatureSerialized } from '@jbrowse/core/util';
3
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
4
  export default function BreakendPanel(props: {
4
5
  locStrings: string[];
5
- model: any;
6
+ model: VariantFeatureWidgetModel;
6
7
  feature: SimpleFeatureSerialized;
7
8
  }): React.JSX.Element;
package/dist/VariantFeatureWidget/BreakendPanel.js CHANGED
@@ -22,33 +22,18 @@ var __importStar = (this && this.__importStar) || function (mod) {
22
22
  __setModuleDefault(result, mod);
23
23
  return result;
24
24
  };
25
- var __importDefault = (this && this.__importDefault) || function (mod) {
26
- return (mod && mod.__esModule) ? mod : { "default": mod };
27
- };
28
25
  Object.defineProperty(exports, "__esModule", { value: true });
29
- /* eslint-disable @typescript-eslint/no-explicit-any */
30
26
  const react_1 = __importStar(require("react"));
31
27
  const material_1 = require("@mui/material");
32
- const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
33
28
  const util_1 = require("@jbrowse/core/util");
34
29
  const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
35
- const BreakendOptionDialog_1 = __importDefault(require("./BreakendOptionDialog"));
36
- function BreakendPanel(props) {
37
- const { model, locStrings, feature } = props;
30
+ // lazies
31
+ const BreakendOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendOptionDialog'))));
32
+ function LocStringList({ locStrings, model, }) {
38
33
  const session = (0, util_1.getSession)(model);
39
- const { pluginManager } = (0, util_1.getEnv)(session);
40
- const [breakpointDialog, setBreakpointDialog] = (0, react_1.useState)(false);
41
- let viewType;
42
- try {
43
- viewType = pluginManager.getViewType('BreakpointSplitView');
44
- }
45
- catch (e) {
46
- // ignore
47
- }
48
- const simpleFeature = new simpleFeature_1.default(feature);
49
- return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Breakends" },
34
+ return (react_1.default.createElement("div", null,
50
35
  react_1.default.createElement(material_1.Typography, null, "Link to linear view of breakend endpoints"),
51
- react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: `${JSON.stringify(locString)}` },
36
+ react_1.default.createElement("ul", null, locStrings.map((locString, index) => (react_1.default.createElement("li", { key: `${locString}-${index}` },
52
37
  react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
53
38
  var _a;
54
39
  event.preventDefault();
@@ -65,16 +50,35 @@ function BreakendPanel(props) {
65
50
  console.error(e);
66
51
  session.notify(`${e}`);
67
52
  }
68
- } }, `LGV - ${locString}`))))),
69
- viewType ? (react_1.default.createElement("div", null,
70
- react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
71
- react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: `${JSON.stringify(locString)}` },
72
- react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
73
- event.preventDefault();
74
- setBreakpointDialog(true);
75
- } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
76
- breakpointDialog ? (react_1.default.createElement(BreakendOptionDialog_1.default, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
77
- setBreakpointDialog(false);
78
- } })) : null)) : null));
53
+ } }, `LGV - ${locString}`)))))));
54
+ }
55
+ function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType, }) {
56
+ const session = (0, util_1.getSession)(model);
57
+ const simpleFeature = new util_1.SimpleFeature(feature);
58
+ return (react_1.default.createElement("div", null,
59
+ react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
60
+ react_1.default.createElement("ul", null, locStrings.map(locString => (react_1.default.createElement("li", { key: `${JSON.stringify(locString)}` },
61
+ react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
62
+ event.preventDefault();
63
+ session.queueDialog(handleClose => [
64
+ BreakendOptionDialog,
65
+ { handleClose, model, feature: simpleFeature, viewType },
66
+ ]);
67
+ } }, `${feature.refName}:${feature.start} // ${locString} (split view)`)))))));
68
+ }
69
+ function BreakendPanel(props) {
70
+ const { model, locStrings, feature } = props;
71
+ const session = (0, util_1.getSession)(model);
72
+ const { pluginManager } = (0, util_1.getEnv)(session);
73
+ let viewType;
74
+ try {
75
+ viewType = pluginManager.getViewType('BreakpointSplitView');
76
+ }
77
+ catch (e) {
78
+ // ignore
79
+ }
80
+ return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Breakends" },
81
+ react_1.default.createElement(LocStringList, { model: model, locStrings: locStrings }),
82
+ viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, locStrings: locStrings, feature: feature })) : null));
79
83
  }
80
84
  exports.default = BreakendPanel;
package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts CHANGED
@@ -1,9 +1,6 @@
1
1
  import React from 'react';
2
- import { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
3
  declare const VariantFeatureWidget: (props: {
4
- model: {
5
- featureData: SimpleFeatureSerialized;
6
- descriptions: Record<string, string>;
7
- };
4
+ model: VariantFeatureWidgetModel;
8
5
  }) => React.JSX.Element;
9
6
  export default VariantFeatureWidget;
package/dist/VariantFeatureWidget/VariantFeatureWidget.js CHANGED
@@ -12,15 +12,7 @@ const vcf_1 = require("@gmod/vcf");
12
12
  const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
13
13
  const BreakendPanel_1 = __importDefault(require("./BreakendPanel"));
14
14
  const VariantAnnotationTable_1 = __importDefault(require("./VariantAnnotationTable"));
15
- const basicDescriptions = {
16
- CHROM: 'chromosome: An identifier from the reference genome',
17
- POS: 'position: The reference position, with the 1st base having position 1',
18
- ID: 'identifier: Semi-colon separated list of unique identifiers where available',
19
- REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
20
- ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
21
- QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
22
- FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
23
- };
15
+ const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
24
16
  function AnnPanel({ descriptions, feature, }) {
25
17
  var _a, _b, _c, _d;
26
18
  const annDesc = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description;
@@ -41,12 +33,9 @@ const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
41
33
  const feat = JSON.parse(JSON.stringify(featureData));
42
34
  const { samples, ...rest } = feat;
43
35
  return (react_1.default.createElement(material_1.Paper, { "data-testid": "variant-side-drawer" },
44
- react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
45
- react_1.default.createElement(material_1.Divider, null),
36
+ react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { feature: rest, descriptions: { ...variantFieldDescriptions_1.variantFieldDescriptions, ...descriptions }, ...props }),
46
37
  react_1.default.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
47
- react_1.default.createElement(material_1.Divider, null),
48
38
  react_1.default.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
49
- react_1.default.createElement(material_1.Divider, null),
50
39
  feat.type === 'breakend' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = (0, vcf_1.parseBreakend)(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
51
40
  feat.type === 'translocation' ? (react_1.default.createElement(BreakendPanel_1.default, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
52
41
  react_1.default.createElement(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })));
package/dist/VariantFeatureWidget/configSchema.d.ts ADDED
@@ -0,0 +1 @@
1
+ export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
package/dist/VariantFeatureWidget/configSchema.js ADDED
@@ -0,0 +1,5 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.configSchema = void 0;
4
+ const configuration_1 = require("@jbrowse/core/configuration");
5
+ exports.configSchema = (0, configuration_1.ConfigurationSchema)('VariantFeatureWidget', {});
package/dist/VariantFeatureWidget/index.d.ts CHANGED
@@ -1,52 +1,3 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3
- export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
6
- featureData: import("mobx-state-tree").IType<any, any, any>;
7
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
8
- unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
13
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
14
- } & {
15
- type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
16
- descriptions: import("mobx-state-tree").IType<any, any, any>;
17
- }, {
18
- error: unknown;
19
- } & {
20
- setFeatureData(featureData: Record<string, unknown>): void;
21
- clearFeatureData(): void;
22
- setFormattedData(feat: Record<string, unknown>): void;
23
- setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
24
- setError(e: unknown): void;
25
- } & {
26
- afterCreate(): void;
27
- }, {
28
- type: "BaseFeatureWidget";
29
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
30
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
31
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
32
- featureData: import("mobx-state-tree").IType<any, any, any>;
33
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
34
- unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
35
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
36
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
37
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
39
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
40
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
41
- type: "BaseFeatureWidget";
42
- id: string;
43
- track: import("mobx-state-tree").ReferenceIdentifier | undefined;
44
- view: import("mobx-state-tree").ReferenceIdentifier | undefined;
45
- trackId: string | undefined;
46
- trackType: string | undefined;
47
- maxDepth: number | undefined;
48
- formattedFields: any;
49
- finalizedFeatureData: any;
50
- } & import("mobx-state-tree")._NotCustomized>;
51
2
  declare const _default: (pluginManager: PluginManager) => void;
52
3
  export default _default;
package/dist/VariantFeatureWidget/index.js CHANGED
@@ -26,27 +26,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
26
26
  return (mod && mod.__esModule) ? mod : { "default": mod };
27
27
  };
28
28
  Object.defineProperty(exports, "__esModule", { value: true });
29
- exports.stateModelFactory = exports.configSchema = void 0;
30
29
  const react_1 = require("react");
31
- const configuration_1 = require("@jbrowse/core/configuration");
32
30
  const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
33
- const mobx_state_tree_1 = require("mobx-state-tree");
34
- const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
35
- exports.configSchema = (0, configuration_1.ConfigurationSchema)('VariantFeatureWidget', {});
36
- function stateModelFactory(pluginManager) {
37
- const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
38
- return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('VariantFeatureWidget', {
39
- type: mobx_state_tree_1.types.literal('VariantFeatureWidget'),
40
- descriptions: mobx_state_tree_1.types.frozen(),
41
- }));
42
- }
43
- exports.stateModelFactory = stateModelFactory;
31
+ const stateModelFactory_1 = require("./stateModelFactory");
32
+ const configSchema_1 = require("./configSchema");
44
33
  exports.default = (pluginManager) => {
45
34
  pluginManager.addWidgetType(() => new WidgetType_1.default({
46
35
  name: 'VariantFeatureWidget',
47
36
  heading: 'Feature details',
48
- configSchema: exports.configSchema,
49
- stateModel: stateModelFactory(pluginManager),
37
+ configSchema: configSchema_1.configSchema,
38
+ stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
50
39
  ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
51
40
  }));
52
41
  };
package/dist/VariantFeatureWidget/stateModelFactory.d.ts ADDED
@@ -0,0 +1,52 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ import { Instance } from 'mobx-state-tree';
3
+ export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
+ type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
6
+ featureData: import("mobx-state-tree").IType<any, any, any>;
7
+ formattedFields: import("mobx-state-tree").IType<any, any, any>;
8
+ unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
+ view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
+ track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
13
+ maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
14
+ } & {
15
+ type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
16
+ descriptions: import("mobx-state-tree").IType<any, any, any>;
17
+ }, {
18
+ error: unknown;
19
+ } & {
20
+ setFeatureData(featureData: Record<string, unknown>): void;
21
+ clearFeatureData(): void;
22
+ setFormattedData(feat: Record<string, unknown>): void;
23
+ setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
24
+ setError(e: unknown): void;
25
+ } & {
26
+ afterCreate(): void;
27
+ }, {
28
+ type: "BaseFeatureWidget";
29
+ } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
30
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
31
+ type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
32
+ featureData: import("mobx-state-tree").IType<any, any, any>;
33
+ formattedFields: import("mobx-state-tree").IType<any, any, any>;
34
+ unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
35
+ view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
36
+ track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
37
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
39
+ maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
40
+ }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
41
+ type: "BaseFeatureWidget";
42
+ id: string;
43
+ track: import("mobx-state-tree").ReferenceIdentifier | undefined;
44
+ view: import("mobx-state-tree").ReferenceIdentifier | undefined;
45
+ trackId: string | undefined;
46
+ trackType: string | undefined;
47
+ maxDepth: number | undefined;
48
+ formattedFields: any;
49
+ finalizedFeatureData: any;
50
+ } & import("mobx-state-tree")._NotCustomized>;
51
+ export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
52
+ export type VariantFeatureWidgetModel = Instance<VariantFeatureWidgetStateModel>;
package/dist/VariantFeatureWidget/stateModelFactory.js ADDED
@@ -0,0 +1,13 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.stateModelFactory = void 0;
4
+ const mobx_state_tree_1 = require("mobx-state-tree");
5
+ const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
6
+ function stateModelFactory(pluginManager) {
7
+ const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
8
+ return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('VariantFeatureWidget', {
9
+ type: mobx_state_tree_1.types.literal('VariantFeatureWidget'),
10
+ descriptions: mobx_state_tree_1.types.frozen(),
11
+ }));
12
+ }
13
+ exports.stateModelFactory = stateModelFactory;
package/dist/VariantFeatureWidget/variantFieldDescriptions.d.ts ADDED
@@ -0,0 +1,9 @@
1
+ export declare const variantFieldDescriptions: {
2
+ CHROM: string;
3
+ POS: string;
4
+ ID: string;
5
+ REF: string;
6
+ ALT: string;
7
+ QUAL: string;
8
+ FILTER: string;
9
+ };
package/dist/VariantFeatureWidget/variantFieldDescriptions.js ADDED
@@ -0,0 +1,12 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.variantFieldDescriptions = void 0;
4
+ exports.variantFieldDescriptions = {
5
+ CHROM: 'chromosome: An identifier from the reference genome',
6
+ POS: 'position: The reference position, with the 1st base having position 1',
7
+ ID: 'identifier: Semi-colon separated list of unique identifiers where available',
8
+ REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
9
+ ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
10
+ QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
11
+ FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
12
+ };
package/dist/VcfAdapter/VcfAdapter.d.ts CHANGED
@@ -1,21 +1,22 @@
1
1
  import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  import { Region, Feature } from '@jbrowse/core/util';
3
3
  import IntervalTree from '@flatten-js/interval-tree';
4
+ import VcfFeature from '../VcfFeature';
4
5
  export default class VcfAdapter extends BaseFeatureDataAdapter {
5
6
  static capabilities: string[];
6
7
  protected vcfFeatures?: Promise<{
7
8
  header: string;
8
- intervalTree: Record<string, IntervalTree>;
9
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
9
10
  }>;
10
11
  getHeader(): Promise<string>;
11
12
  getMetadata(): Promise<any>;
12
13
  setupP(): Promise<{
13
14
  header: string;
14
- intervalTree: Record<string, IntervalTree<any>>;
15
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
15
16
  }>;
16
17
  setup(): Promise<{
17
18
  header: string;
18
- intervalTree: Record<string, IntervalTree<any>>;
19
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
19
20
  }>;
20
21
  getRefNames(_?: BaseOptions): Promise<string[]>;
21
22
  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/dist/VcfAdapter/VcfAdapter.js CHANGED
@@ -52,19 +52,19 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
52
52
  const str = new TextDecoder().decode(buffer);
53
53
  const { header, lines } = readVcf(str);
54
54
  const intervalTree = {};
55
- for (const obj of lines.map((line, id) => {
56
- var _a;
57
- const [refName, startP, , ref, , , , info] = line.split('\t');
58
- const start = +startP - 1;
59
- const def = start + ref.length;
60
- const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
61
- return { line, refName, start, end, id };
62
- })) {
63
- const key = obj.refName;
55
+ const parser = new vcf_1.default({ header });
56
+ let idx = 0;
57
+ for (const line of lines) {
58
+ const f = new VcfFeature_1.default({
59
+ variant: parser.parseLine(line),
60
+ parser,
61
+ id: `${this.id}-${idx++}`,
62
+ });
63
+ const key = f.get('refName');
64
64
  if (!intervalTree[key]) {
65
65
  intervalTree[key] = new interval_tree_1.default();
66
66
  }
67
- intervalTree[key].insert([obj.start, obj.end], obj);
67
+ intervalTree[key].insert([f.get('start'), f.get('end')], f);
68
68
  }
69
69
  return { header, intervalTree };
70
70
  }
@@ -86,13 +86,10 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
86
86
  var _a;
87
87
  try {
88
88
  const { start, end, refName } = region;
89
- const { header, intervalTree } = await this.setup();
90
- const parser = new vcf_1.default({ header });
91
- (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature_1.default({
92
- variant: parser.parseLine(f.line),
93
- parser,
94
- id: `${this.id}-${f.id}`,
95
- })));
89
+ const { intervalTree } = await this.setup();
90
+ (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach((f) => {
91
+ observer.next(f);
92
+ });
96
93
  observer.complete();
97
94
  }
98
95
  catch (e) {
package/esm/StructuralVariantChordRenderer/Chord.d.ts CHANGED
@@ -25,6 +25,6 @@ declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, se
25
25
  config: AnyConfigurationModel;
26
26
  bezierRadius: number;
27
27
  selected: boolean;
28
- onClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
28
+ onClick: (feat: Feature, reg: AnyRegion, end: AnyRegion, evt: unknown) => void;
29
29
  }) => React.JSX.Element | null;
30
30
  export default Chord;
package/esm/StructuralVariantChordRenderer/Chord.js CHANGED
@@ -62,7 +62,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
62
62
  const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
63
63
  feature,
64
64
  });
65
- return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
65
+ return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
66
66
  if (endBlock && startBlock) {
67
67
  onClick(feature, startBlock.region, endBlock.region, evt);
68
68
  }
package/esm/StructuralVariantChordRenderer/ReactComponent.js CHANGED
@@ -16,22 +16,10 @@ const StructuralVariantChordsReactComponent = observer(function ({ features, con
16
16
  }
17
17
  return blocksForRefs;
18
18
  }, [blockDefinitions]);
19
- const trackStyleId = `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`;
20
- return (React.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
21
- React.createElement("style", {
22
- // eslint-disable-next-line react/no-danger
23
- dangerouslySetInnerHTML: {
24
- __html: `
25
- #${trackStyleId} > path {
26
- cursor: crosshair;
27
- fill: none;
28
- }
29
- `,
30
- } }),
31
- [...features.values()].map(feature => {
32
- const id = feature.id();
33
- const selected = String(selectedFeatureId) === String(id);
34
- return (React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
35
- })));
19
+ return (React.createElement("g", { id: `chords-${typeof jest !== 'undefined' ? 'test' : displayModel.id}`, "data-testid": "structuralVariantChordRenderer" }, [...features.values()].map(feature => {
20
+ const id = feature.id();
21
+ const selected = String(selectedFeatureId) === String(id);
22
+ return (React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
23
+ })));
36
24
  });
37
25
  export default StructuralVariantChordsReactComponent;
package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts CHANGED
@@ -1,9 +1,11 @@
1
1
  import React from 'react';
2
2
  import { Feature } from '@jbrowse/core/util';
3
+ import { ViewType } from '@jbrowse/core/pluggableElementTypes';
4
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
5
  declare const BreakendOptionDialog: ({ model, handleClose, feature, viewType, }: {
4
- model: any;
6
+ model: VariantFeatureWidgetModel;
5
7
  handleClose: () => void;
6
8
  feature: Feature;
7
- viewType: any;
9
+ viewType: ViewType;
8
10
  }) => React.JSX.Element;
9
11
  export default BreakendOptionDialog;
package/esm/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -1,10 +1,8 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
1
  import React, { useState } from 'react';
3
2
  import { observer } from 'mobx-react';
4
3
  import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, } from '@mui/material';
5
4
  import { makeStyles } from 'tss-react/mui';
6
5
  import { getSnapshot } from 'mobx-state-tree';
7
- // jbrowse
8
6
  import { Dialog } from '@jbrowse/core/ui';
9
7
  import { getSession } from '@jbrowse/core/util';
10
8
  const useStyles = makeStyles()({
@@ -12,34 +10,48 @@ const useStyles = makeStyles()({
12
10
  display: 'block',
13
11
  },
14
12
  });
15
- const BreakendOptionDialog = observer(function ({ model, handleClose, feature, viewType, }) {
13
+ function stripIds(arr) {
14
+ return arr.map(({ id, displays, ...rest }) => ({
15
+ ...rest,
16
+ displays: displays.map(({ id, ...rest }) => rest),
17
+ }));
18
+ }
19
+ function Checkbox2({ checked, label, onChange, }) {
16
20
  const { classes } = useStyles();
21
+ return (React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: checked, onChange: onChange }), label: label }));
22
+ }
23
+ const BreakendOptionDialog = observer(function ({ model, handleClose, feature, viewType, }) {
17
24
  const [copyTracks, setCopyTracks] = useState(true);
18
- const [mirrorTracks, setMirrorTracks] = useState(true);
25
+ const [mirror, setMirror] = useState(true);
19
26
  return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
20
27
  React.createElement(DialogContent, null,
21
- React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked) }), label: "Copy tracks into the new view" }),
22
- React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: event => setMirrorTracks(event.target.checked) }), label: "Mirror tracks vertically in vertically stacked view" })),
28
+ React.createElement(Checkbox2, { checked: copyTracks, onChange: event => setCopyTracks(event.target.checked), label: "Copy tracks into the new view" }),
29
+ React.createElement(Checkbox2, { checked: mirror, onChange: event => setMirror(event.target.checked), label: "Mirror tracks vertically in vertically stacked view" })),
23
30
  React.createElement(DialogActions, null,
24
31
  React.createElement(Button, { onClick: () => {
25
32
  const { view } = model;
26
33
  const session = getSession(model);
27
34
  try {
35
+ // @ts-expect-error
28
36
  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
29
- function remapIds(arr) {
30
- return arr.map(v => ({
31
- ...v,
32
- id: `${v.trackId}-${Math.random()}`,
33
- }));
34
- }
35
- viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
36
- viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
37
- viewSnapshot.featureData = feature;
37
+ const [view1, view2] = viewSnapshot.views;
38
38
  // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
39
39
  const viewTracks = getSnapshot(view.tracks);
40
- viewSnapshot.views[0].tracks = remapIds(viewTracks);
41
- viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
42
- session.addView('BreakpointSplitView', viewSnapshot);
40
+ session.addView('BreakpointSplitView', {
41
+ ...viewSnapshot,
42
+ views: [
43
+ {
44
+ ...view1,
45
+ tracks: stripIds(viewTracks),
46
+ offsetPx: view1.offsetPx - view.width / 2 + 100,
47
+ },
48
+ {
49
+ ...view2,
50
+ tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
51
+ offsetPx: view2.offsetPx - view.width / 2 + 100,
52
+ },
53
+ ],
54
+ });
43
55
  }
44
56
  catch (e) {
45
57
  console.error(e);
package/esm/VariantFeatureWidget/BreakendPanel.d.ts CHANGED
@@ -1,7 +1,8 @@
1
1
  import React from 'react';
2
- import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
2
+ import { SimpleFeatureSerialized } from '@jbrowse/core/util';
3
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
4
  export default function BreakendPanel(props: {
4
5
  locStrings: string[];
5
- model: any;
6
+ model: VariantFeatureWidgetModel;
6
7
  feature: SimpleFeatureSerialized;
7
8
  }): React.JSX.Element;
package/esm/VariantFeatureWidget/BreakendPanel.js CHANGED
@@ -1,26 +1,14 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
- import React, { useState } from 'react';
1
+ import React, { lazy } from 'react';
3
2
  import { Link, Typography } from '@mui/material';
4
- import SimpleFeature from '@jbrowse/core/util/simpleFeature';
5
- import { getEnv, getSession } from '@jbrowse/core/util';
3
+ import { getEnv, getSession, SimpleFeature, } from '@jbrowse/core/util';
6
4
  import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
7
- import BreakendOptionDialog from './BreakendOptionDialog';
8
- export default function BreakendPanel(props) {
9
- const { model, locStrings, feature } = props;
5
+ // lazies
6
+ const BreakendOptionDialog = lazy(() => import('./BreakendOptionDialog'));
7
+ function LocStringList({ locStrings, model, }) {
10
8
  const session = getSession(model);
11
- const { pluginManager } = getEnv(session);
12
- const [breakpointDialog, setBreakpointDialog] = useState(false);
13
- let viewType;
14
- try {
15
- viewType = pluginManager.getViewType('BreakpointSplitView');
16
- }
17
- catch (e) {
18
- // ignore
19
- }
20
- const simpleFeature = new SimpleFeature(feature);
21
- return (React.createElement(BaseCard, { ...props, title: "Breakends" },
9
+ return (React.createElement("div", null,
22
10
  React.createElement(Typography, null, "Link to linear view of breakend endpoints"),
23
- React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
11
+ React.createElement("ul", null, locStrings.map((locString, index) => (React.createElement("li", { key: `${locString}-${index}` },
24
12
  React.createElement(Link, { href: "#", onClick: event => {
25
13
  var _a;
26
14
  event.preventDefault();
@@ -37,15 +25,34 @@ export default function BreakendPanel(props) {
37
25
  console.error(e);
38
26
  session.notify(`${e}`);
39
27
  }
40
- } }, `LGV - ${locString}`))))),
41
- viewType ? (React.createElement("div", null,
42
- React.createElement(Typography, null, "Launch split views with breakend source and target"),
43
- React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
44
- React.createElement(Link, { href: "#", onClick: event => {
45
- event.preventDefault();
46
- setBreakpointDialog(true);
47
- } }, `${feature.refName}:${feature.start} // ${locString} (split view)`))))),
48
- breakpointDialog ? (React.createElement(BreakendOptionDialog, { model: model, feature: simpleFeature, viewType: viewType, handleClose: () => {
49
- setBreakpointDialog(false);
50
- } })) : null)) : null));
28
+ } }, `LGV - ${locString}`)))))));
29
+ }
30
+ function LaunchBreakpointSplitViewPanel({ locStrings, model, feature, viewType, }) {
31
+ const session = getSession(model);
32
+ const simpleFeature = new SimpleFeature(feature);
33
+ return (React.createElement("div", null,
34
+ React.createElement(Typography, null, "Launch split views with breakend source and target"),
35
+ React.createElement("ul", null, locStrings.map(locString => (React.createElement("li", { key: `${JSON.stringify(locString)}` },
36
+ React.createElement(Link, { href: "#", onClick: event => {
37
+ event.preventDefault();
38
+ session.queueDialog(handleClose => [
39
+ BreakendOptionDialog,
40
+ { handleClose, model, feature: simpleFeature, viewType },
41
+ ]);
42
+ } }, `${feature.refName}:${feature.start} // ${locString} (split view)`)))))));
43
+ }
44
+ export default function BreakendPanel(props) {
45
+ const { model, locStrings, feature } = props;
46
+ const session = getSession(model);
47
+ const { pluginManager } = getEnv(session);
48
+ let viewType;
49
+ try {
50
+ viewType = pluginManager.getViewType('BreakpointSplitView');
51
+ }
52
+ catch (e) {
53
+ // ignore
54
+ }
55
+ return (React.createElement(BaseCard, { ...props, title: "Breakends" },
56
+ React.createElement(LocStringList, { model: model, locStrings: locStrings }),
57
+ viewType ? (React.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, locStrings: locStrings, feature: feature })) : null));
51
58
  }
package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts CHANGED
@@ -1,9 +1,6 @@
1
1
  import React from 'react';
2
- import { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
+ import { VariantFeatureWidgetModel } from './stateModelFactory';
3
3
  declare const VariantFeatureWidget: (props: {
4
- model: {
5
- featureData: SimpleFeatureSerialized;
6
- descriptions: Record<string, string>;
7
- };
4
+ model: VariantFeatureWidgetModel;
8
5
  }) => React.JSX.Element;
9
6
  export default VariantFeatureWidget;
package/esm/VariantFeatureWidget/VariantFeatureWidget.js CHANGED
@@ -1,21 +1,13 @@
1
1
  import React from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import { Divider, Paper } from '@mui/material';
3
+ import { Paper } from '@mui/material';
4
4
  import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
5
5
  import { parseBreakend } from '@gmod/vcf';
6
6
  // locals
7
7
  import VariantSampleGrid from './VariantSampleGrid';
8
8
  import BreakendPanel from './BreakendPanel';
9
9
  import VariantAnnotationTable from './VariantAnnotationTable';
10
- const basicDescriptions = {
11
- CHROM: 'chromosome: An identifier from the reference genome',
12
- POS: 'position: The reference position, with the 1st base having position 1',
13
- ID: 'identifier: Semi-colon separated list of unique identifiers where available',
14
- REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
15
- ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
16
- QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
17
- FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
18
- };
10
+ import { variantFieldDescriptions } from './variantFieldDescriptions';
19
11
  function AnnPanel({ descriptions, feature, }) {
20
12
  var _a, _b, _c, _d;
21
13
  const annDesc = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.ANN) === null || _b === void 0 ? void 0 : _b.Description;
@@ -36,12 +28,9 @@ const VariantFeatureWidget = observer(function (props) {
36
28
  const feat = JSON.parse(JSON.stringify(featureData));
37
29
  const { samples, ...rest } = feat;
38
30
  return (React.createElement(Paper, { "data-testid": "variant-side-drawer" },
39
- React.createElement(FeatureDetails, { feature: rest, descriptions: { ...basicDescriptions, ...descriptions }, ...props }),
40
- React.createElement(Divider, null),
31
+ React.createElement(FeatureDetails, { feature: rest, descriptions: { ...variantFieldDescriptions, ...descriptions }, ...props }),
41
32
  React.createElement(CsqPanel, { feature: rest, descriptions: descriptions }),
42
- React.createElement(Divider, null),
43
33
  React.createElement(AnnPanel, { feature: rest, descriptions: descriptions }),
44
- React.createElement(Divider, null),
45
34
  feat.type === 'breakend' ? (React.createElement(BreakendPanel, { feature: feat, locStrings: feat.ALT.map((alt) => { var _a; return ((_a = parseBreakend(alt)) === null || _a === void 0 ? void 0 : _a.MatePosition) || ''; }), model: model })) : null,
46
35
  feat.type === 'translocation' ? (React.createElement(BreakendPanel, { feature: feat, model: model, locStrings: [`${feat.INFO.CHR2[0]}:${feat.INFO.END}`] })) : null,
47
36
  React.createElement(VariantSampleGrid, { feature: feat, ...props, descriptions: descriptions })));
package/esm/VariantFeatureWidget/configSchema.d.ts ADDED
@@ -0,0 +1 @@
1
+ export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
package/esm/VariantFeatureWidget/configSchema.js ADDED
@@ -0,0 +1,2 @@
1
+ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
+ export const configSchema = ConfigurationSchema('VariantFeatureWidget', {});
package/esm/VariantFeatureWidget/index.d.ts CHANGED
@@ -1,52 +1,3 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager';
2
- export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
3
- export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
6
- featureData: import("mobx-state-tree").IType<any, any, any>;
7
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
8
- unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
13
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
14
- } & {
15
- type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
16
- descriptions: import("mobx-state-tree").IType<any, any, any>;
17
- }, {
18
- error: unknown;
19
- } & {
20
- setFeatureData(featureData: Record<string, unknown>): void;
21
- clearFeatureData(): void;
22
- setFormattedData(feat: Record<string, unknown>): void;
23
- setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
24
- setError(e: unknown): void;
25
- } & {
26
- afterCreate(): void;
27
- }, {
28
- type: "BaseFeatureWidget";
29
- } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
30
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
31
- type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
32
- featureData: import("mobx-state-tree").IType<any, any, any>;
33
- formattedFields: import("mobx-state-tree").IType<any, any, any>;
34
- unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
35
- view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
36
- track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
37
- trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
- trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
39
- maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
40
- }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
41
- type: "BaseFeatureWidget";
42
- id: string;
43
- track: import("mobx-state-tree").ReferenceIdentifier | undefined;
44
- view: import("mobx-state-tree").ReferenceIdentifier | undefined;
45
- trackId: string | undefined;
46
- trackType: string | undefined;
47
- maxDepth: number | undefined;
48
- formattedFields: any;
49
- finalizedFeatureData: any;
50
- } & import("mobx-state-tree")._NotCustomized>;
51
2
  declare const _default: (pluginManager: PluginManager) => void;
52
3
  export default _default;
package/esm/VariantFeatureWidget/index.js CHANGED
@@ -1,21 +1,12 @@
1
1
  import { lazy } from 'react';
2
- import { ConfigurationSchema } from '@jbrowse/core/configuration';
3
2
  import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
4
- import { types } from 'mobx-state-tree';
5
- import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
6
- export const configSchema = ConfigurationSchema('VariantFeatureWidget', {});
7
- export function stateModelFactory(pluginManager) {
8
- const baseModel = baseModelFactory(pluginManager);
9
- return types.compose(baseModel, types.model('VariantFeatureWidget', {
10
- type: types.literal('VariantFeatureWidget'),
11
- descriptions: types.frozen(),
12
- }));
13
- }
3
+ import { stateModelFactory } from './stateModelFactory';
4
+ import { configSchema } from './configSchema';
14
5
  export default (pluginManager) => {
15
6
  pluginManager.addWidgetType(() => new WidgetType({
16
7
  name: 'VariantFeatureWidget',
17
8
  heading: 'Feature details',
18
- configSchema,
9
+ configSchema: configSchema,
19
10
  stateModel: stateModelFactory(pluginManager),
20
11
  ReactComponent: lazy(() => import('./VariantFeatureWidget')),
21
12
  }));
package/esm/VariantFeatureWidget/stateModelFactory.d.ts ADDED
@@ -0,0 +1,52 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ import { Instance } from 'mobx-state-tree';
3
+ export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
4
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
5
+ type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
6
+ featureData: import("mobx-state-tree").IType<any, any, any>;
7
+ formattedFields: import("mobx-state-tree").IType<any, any, any>;
8
+ unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
+ view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
+ track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
13
+ maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
14
+ } & {
15
+ type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
16
+ descriptions: import("mobx-state-tree").IType<any, any, any>;
17
+ }, {
18
+ error: unknown;
19
+ } & {
20
+ setFeatureData(featureData: Record<string, unknown>): void;
21
+ clearFeatureData(): void;
22
+ setFormattedData(feat: Record<string, unknown>): void;
23
+ setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
24
+ setError(e: unknown): void;
25
+ } & {
26
+ afterCreate(): void;
27
+ }, {
28
+ type: "BaseFeatureWidget";
29
+ } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
30
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
31
+ type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
32
+ featureData: import("mobx-state-tree").IType<any, any, any>;
33
+ formattedFields: import("mobx-state-tree").IType<any, any, any>;
34
+ unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
35
+ view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
36
+ track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
37
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
39
+ maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
40
+ }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
41
+ type: "BaseFeatureWidget";
42
+ id: string;
43
+ track: import("mobx-state-tree").ReferenceIdentifier | undefined;
44
+ view: import("mobx-state-tree").ReferenceIdentifier | undefined;
45
+ trackId: string | undefined;
46
+ trackType: string | undefined;
47
+ maxDepth: number | undefined;
48
+ formattedFields: any;
49
+ finalizedFeatureData: any;
50
+ } & import("mobx-state-tree")._NotCustomized>;
51
+ export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
52
+ export type VariantFeatureWidgetModel = Instance<VariantFeatureWidgetStateModel>;
package/esm/VariantFeatureWidget/stateModelFactory.js ADDED
@@ -0,0 +1,9 @@
1
+ import { types } from 'mobx-state-tree';
2
+ import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
3
+ export function stateModelFactory(pluginManager) {
4
+ const baseModel = baseModelFactory(pluginManager);
5
+ return types.compose(baseModel, types.model('VariantFeatureWidget', {
6
+ type: types.literal('VariantFeatureWidget'),
7
+ descriptions: types.frozen(),
8
+ }));
9
+ }
package/esm/VariantFeatureWidget/variantFieldDescriptions.d.ts ADDED
@@ -0,0 +1,9 @@
1
+ export declare const variantFieldDescriptions: {
2
+ CHROM: string;
3
+ POS: string;
4
+ ID: string;
5
+ REF: string;
6
+ ALT: string;
7
+ QUAL: string;
8
+ FILTER: string;
9
+ };
package/esm/VariantFeatureWidget/variantFieldDescriptions.js ADDED
@@ -0,0 +1,9 @@
1
+ export const variantFieldDescriptions = {
2
+ CHROM: 'chromosome: An identifier from the reference genome',
3
+ POS: 'position: The reference position, with the 1st base having position 1',
4
+ ID: 'identifier: Semi-colon separated list of unique identifiers where available',
5
+ REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
6
+ ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
7
+ QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
8
+ FILTER: 'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',
9
+ };
package/esm/VcfAdapter/VcfAdapter.d.ts CHANGED
@@ -1,21 +1,22 @@
1
1
  import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
2
2
  import { Region, Feature } from '@jbrowse/core/util';
3
3
  import IntervalTree from '@flatten-js/interval-tree';
4
+ import VcfFeature from '../VcfFeature';
4
5
  export default class VcfAdapter extends BaseFeatureDataAdapter {
5
6
  static capabilities: string[];
6
7
  protected vcfFeatures?: Promise<{
7
8
  header: string;
8
- intervalTree: Record<string, IntervalTree>;
9
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
9
10
  }>;
10
11
  getHeader(): Promise<string>;
11
12
  getMetadata(): Promise<any>;
12
13
  setupP(): Promise<{
13
14
  header: string;
14
- intervalTree: Record<string, IntervalTree<any>>;
15
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
15
16
  }>;
16
17
  setup(): Promise<{
17
18
  header: string;
18
- intervalTree: Record<string, IntervalTree<any>>;
19
+ intervalTree: Record<string, IntervalTree<VcfFeature>>;
19
20
  }>;
20
21
  getRefNames(_?: BaseOptions): Promise<string[]>;
21
22
  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/esm/VcfAdapter/VcfAdapter.js CHANGED
@@ -47,19 +47,19 @@ class VcfAdapter extends BaseFeatureDataAdapter {
47
47
  const str = new TextDecoder().decode(buffer);
48
48
  const { header, lines } = readVcf(str);
49
49
  const intervalTree = {};
50
- for (const obj of lines.map((line, id) => {
51
- var _a;
52
- const [refName, startP, , ref, , , , info] = line.split('\t');
53
- const start = +startP - 1;
54
- const def = start + ref.length;
55
- const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
56
- return { line, refName, start, end, id };
57
- })) {
58
- const key = obj.refName;
50
+ const parser = new VCF({ header });
51
+ let idx = 0;
52
+ for (const line of lines) {
53
+ const f = new VcfFeature({
54
+ variant: parser.parseLine(line),
55
+ parser,
56
+ id: `${this.id}-${idx++}`,
57
+ });
58
+ const key = f.get('refName');
59
59
  if (!intervalTree[key]) {
60
60
  intervalTree[key] = new IntervalTree();
61
61
  }
62
- intervalTree[key].insert([obj.start, obj.end], obj);
62
+ intervalTree[key].insert([f.get('start'), f.get('end')], f);
63
63
  }
64
64
  return { header, intervalTree };
65
65
  }
@@ -81,13 +81,10 @@ class VcfAdapter extends BaseFeatureDataAdapter {
81
81
  var _a;
82
82
  try {
83
83
  const { start, end, refName } = region;
84
- const { header, intervalTree } = await this.setup();
85
- const parser = new VCF({ header });
86
- (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(f => observer.next(new VcfFeature({
87
- variant: parser.parseLine(f.line),
88
- parser,
89
- id: `${this.id}-${f.id}`,
90
- })));
84
+ const { intervalTree } = await this.setup();
85
+ (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach((f) => {
86
+ observer.next(f);
87
+ });
91
88
  observer.complete();
92
89
  }
93
90
  catch (e) {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.10.0",
3
+ "version": "2.10.2",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
66
+ "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
67
67
  }