@jbrowse/plugin-variants 2.3.4 → 2.4.1

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Files changed (55) hide show
  1. package/dist/ChordVariantDisplay/index.js +1 -0
  2. package/dist/ChordVariantDisplay/index.js.map +1 -1
  3. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +9 -2
  4. package/dist/ChordVariantDisplay/models/stateModelFactory.js +1 -1
  5. package/dist/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
  6. package/dist/LinearVariantDisplay/model.d.ts +3 -1
  7. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  8. package/dist/StructuralVariantChordRenderer/ReactComponent.js +3 -5
  9. package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
  10. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
  11. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  12. package/dist/VariantFeatureWidget/VariantSampleGrid.js +11 -7
  13. package/dist/VariantFeatureWidget/VariantSampleGrid.js.map +1 -1
  14. package/dist/VcfAdapter/VcfAdapter.d.ts +3 -1
  15. package/dist/VcfAdapter/VcfAdapter.js +9 -10
  16. package/dist/VcfAdapter/VcfAdapter.js.map +1 -1
  17. package/dist/VcfFeature/index.js +1 -1
  18. package/dist/VcfFeature/index.js.map +1 -1
  19. package/dist/VcfFeature/util.js +4 -7
  20. package/dist/VcfFeature/util.js.map +1 -1
  21. package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  22. package/esm/ChordVariantDisplay/index.js +1 -0
  23. package/esm/ChordVariantDisplay/index.js.map +1 -1
  24. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +9 -2
  25. package/esm/ChordVariantDisplay/models/stateModelFactory.js +1 -1
  26. package/esm/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
  27. package/esm/LinearVariantDisplay/model.d.ts +3 -1
  28. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -3
  29. package/esm/StructuralVariantChordRenderer/ReactComponent.js +3 -5
  30. package/esm/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
  31. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
  32. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  33. package/esm/VariantFeatureWidget/VariantSampleGrid.js +11 -7
  34. package/esm/VariantFeatureWidget/VariantSampleGrid.js.map +1 -1
  35. package/esm/VcfAdapter/VcfAdapter.d.ts +3 -1
  36. package/esm/VcfAdapter/VcfAdapter.js +9 -10
  37. package/esm/VcfAdapter/VcfAdapter.js.map +1 -1
  38. package/esm/VcfFeature/index.js +1 -1
  39. package/esm/VcfFeature/index.js.map +1 -1
  40. package/esm/VcfFeature/util.js +4 -7
  41. package/esm/VcfFeature/util.js.map +1 -1
  42. package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
  43. package/package.json +3 -3
  44. package/src/ChordVariantDisplay/index.ts +2 -0
  45. package/src/ChordVariantDisplay/models/stateModelFactory.ts +2 -2
  46. package/src/StructuralVariantChordRenderer/ReactComponent.tsx +14 -15
  47. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +11 -5
  48. package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx +1 -1
  49. package/src/VariantFeatureWidget/VariantSampleGrid.tsx +48 -33
  50. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap +8 -8
  51. package/src/VcfAdapter/VcfAdapter.ts +15 -16
  52. package/src/VcfFeature/index.ts +1 -1
  53. package/src/VcfFeature/util.ts +4 -6
  54. package/src/VcfTabixAdapter/VcfTabixAdapter.ts +2 -2
  55. package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap +5 -5
package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
@@ -1 +1 @@
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1
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package/esm/VariantFeatureWidget/VariantSampleGrid.js CHANGED
@@ -4,12 +4,19 @@ import { DataGrid } from '@mui/x-data-grid';
4
4
  import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
5
5
  import { measureGridWidth } from '@jbrowse/core/util';
6
6
  import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
7
+ function SampleFilters({ columns, filter, setFilter, }) {
8
+ const [showFilters, setShowFilters] = useState(false);
9
+ return (React.createElement(React.Fragment, null,
10
+ React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
11
+ showFilters ? (React.createElement(React.Fragment, null,
12
+ React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
13
+ columns.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null));
14
+ }
7
15
  export default function VariantSamples(props) {
8
16
  var _a;
9
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  const { feature, descriptions = {} } = props;
10
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  const { ref, scrollLeft } = useResizeBar();
11
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  const [filter, setFilter] = useState({});
12
- const [showFilters, setShowFilters] = useState(false);
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  const samples = (feature.samples || {});
14
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  const preFilteredRows = Object.entries(samples);
15
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  let error;
@@ -40,7 +47,7 @@ export default function VariantSamples(props) {
40
47
  }
41
48
  const keys = ['sample', ...Object.keys(((_a = preFilteredRows[0]) === null || _a === void 0 ? void 0 : _a[1]) || {})];
42
49
  const [widths, setWidths] = useState(keys.map(e => measureGridWidth(rows.map(r => r[e]))));
43
- const infoFields = keys.map((field, index) => {
50
+ const columns = keys.map((field, index) => {
44
51
  var _a, _b;
45
52
  return ({
46
53
  field,
@@ -52,13 +59,10 @@ export default function VariantSamples(props) {
52
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  // https://github.com/mui-org/material-ui-x/issues/1197
53
60
  return !preFilteredRows.length ? null : (React.createElement(BaseCard, { ...props, title: "Samples" },
54
61
  error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
55
- React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: showFilters, onChange: () => setShowFilters(f => !f) }), label: "Show sample filters" }),
56
- showFilters ? (React.createElement(React.Fragment, null,
57
- React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
58
- infoFields.map(({ field }) => (React.createElement(TextField, { key: `filter-${field}`, placeholder: `Filter ${field}`, value: filter[field] || '', onChange: event => setFilter({ ...filter, [field]: event.target.value }) }))))) : null,
62
+ React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter }),
59
63
  React.createElement("div", { ref: ref },
60
64
  React.createElement(ResizeBar, { widths: widths, setWidths: setWidths, scrollLeft: scrollLeft }),
61
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  React.createElement("div", { ref: ref, style: { height: 600, width: '100%', overflow: 'auto' } },
62
- React.createElement(DataGrid, { rows: rows, columns: infoFields, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
66
+ React.createElement(DataGrid, { rows: rows, columns: columns, disableSelectionOnClick: true, rowHeight: 25, headerHeight: 35, disableColumnMenu: true })))));
63
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  }
64
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  //# sourceMappingURL=VariantSampleGrid.js.map
package/esm/VariantFeatureWidget/VariantSampleGrid.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/VcfAdapter/VcfAdapter.d.ts CHANGED
@@ -11,7 +11,9 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
11
11
  getMetadata(): Promise<any>;
12
12
  setupP(): Promise<{
13
13
  header: string;
14
- intervalTree: Record<string, IntervalTree<any>>;
14
+ intervalTree: {
15
+ [key: string]: IntervalTree<any>;
16
+ };
15
17
  }>;
16
18
  setup(): Promise<{
17
19
  header: string;
package/esm/VcfAdapter/VcfAdapter.js CHANGED
@@ -46,22 +46,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
46
46
  }
47
47
  const str = new TextDecoder().decode(buffer);
48
48
  const { header, lines } = readVcf(str);
49
- const intervalTree = lines
50
- .map((line, id) => {
49
+ const intervalTree = {};
50
+ for (const obj of lines.map((line, id) => {
51
51
  var _a;
52
52
  const [refName, startP, , ref, , , , info] = line.split('\t');
53
53
  const start = +startP - 1;
54
- const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
54
+ const def = start + ref.length;
55
+ const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
55
56
  return { line, refName, start, end, id };
56
- })
57
- .reduce((acc, obj) => {
57
+ })) {
58
58
  const key = obj.refName;
59
- if (!acc[key]) {
60
- acc[key] = new IntervalTree();
59
+ if (!intervalTree[key]) {
60
+ intervalTree[key] = new IntervalTree();
61
61
  }
62
- acc[key].insert([obj.start, obj.end], obj);
63
- return acc;
64
- }, {});
62
+ intervalTree[key].insert([obj.start, obj.end], obj);
63
+ }
65
64
  return { header, intervalTree };
66
65
  }
67
66
  async setup() {
package/esm/VcfAdapter/VcfAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
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+ {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
package/esm/VcfFeature/index.js CHANGED
@@ -32,7 +32,7 @@ export default class VCFFeature {
32
32
  const start = POS - 1;
33
33
  const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
34
34
  const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
35
- const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
35
+ const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
36
36
  return {
37
37
  refName: CHROM,
38
38
  start,
package/esm/VcfFeature/index.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/esm/VcfFeature/util.js CHANGED
@@ -70,7 +70,7 @@ export function getSOAndDescFromAltDefs(ref, alt, parser) {
70
70
  // try to look for a definition for a parent term if we can
71
71
  const modAlt = alt.split(':');
72
72
  if (modAlt.length > 1) {
73
- return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`, parser);
73
+ return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
74
74
  }
75
75
  // no parent
76
76
  return [];
@@ -102,12 +102,9 @@ export function getSOAndDescByExamination(ref, alt) {
102
102
  return ['sv', alt];
103
103
  }
104
104
  else if (ref.length === alt.length) {
105
- if (ref.split('').reverse().join('') === alt) {
106
- return ['inversion', makeDescriptionString('inversion', ref, alt)];
107
- }
108
- else {
109
- return ['substitution', makeDescriptionString('substitution', ref, alt)];
110
- }
105
+ return ref.split('').reverse().join('') === alt
106
+ ? ['inversion', makeDescriptionString('inversion', ref, alt)]
107
+ : ['substitution', makeDescriptionString('substitution', ref, alt)];
111
108
  }
112
109
  else if (ref.length <= alt.length) {
113
110
  return ['insertion', makeDescriptionString('insertion', ref, alt)];
package/esm/VcfFeature/util.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAMzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,YAAY,CAAC,aAAa,EAAE,EAAE,CAAC,CAAA;QAClD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,GAAG;YACH,MAAM,EAAE,IAAI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.3.4",
3
+ "version": "2.4.1",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -39,7 +39,7 @@
39
39
  "dependencies": {
40
40
  "@flatten-js/interval-tree": "^1.0.15",
41
41
  "@gmod/bgzf-filehandle": "^1.4.3",
42
- "@gmod/tabix": "^1.5.2",
42
+ "@gmod/tabix": "^1.5.6",
43
43
  "@gmod/vcf": "^5.0.9",
44
44
  "@mui/icons-material": "^5.0.2",
45
45
  "@mui/x-data-grid": "^5.0.1",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "98ae48be91ee2371e1b2768a907b4997995e9915"
67
+ "gitHead": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
68
68
  }
package/src/ChordVariantDisplay/index.ts CHANGED
@@ -1,6 +1,8 @@
1
1
  import PluginManager from '@jbrowse/core/PluginManager'
2
2
  import { BaseChordDisplayComponent } from '@jbrowse/plugin-circular-view'
3
3
  import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
4
+
5
+ // locals
4
6
  import configSchemaF from './models/configSchema'
5
7
  import stateModelF from './models/stateModelFactory'
6
8
 
package/src/ChordVariantDisplay/models/stateModelFactory.ts CHANGED
@@ -4,7 +4,7 @@ import {
4
4
  ConfigurationReference,
5
5
  } from '@jbrowse/core/configuration'
6
6
  import { types } from 'mobx-state-tree'
7
- import { getContainingView } from '@jbrowse/core/util'
7
+ import { Feature, getContainingView } from '@jbrowse/core/util'
8
8
  import { getParentRenderProps } from '@jbrowse/core/util/tracks'
9
9
 
10
10
  /**
@@ -48,7 +48,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
48
48
  radius: view.radiusPx,
49
49
  blockDefinitions: self.blockDefinitions,
50
50
  config: self.configuration.renderer,
51
- onChordClick: self.onChordClick,
51
+ onChordClick: (arg: Feature) => self.onChordClick(arg),
52
52
  }
53
53
  },
54
54
  }))
package/src/StructuralVariantChordRenderer/ReactComponent.tsx CHANGED
@@ -6,7 +6,16 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration'
6
6
  // locals
7
7
  import Chord, { Block, AnyRegion } from './Chord'
8
8
 
9
- function StructuralVariantChords(props: {
9
+ export default observer(function StructuralVariantChords({
10
+ features,
11
+ config,
12
+ displayModel,
13
+ blockDefinitions,
14
+ radius,
15
+ bezierRadius,
16
+ displayModel: { selectedFeatureId },
17
+ onChordClick,
18
+ }: {
10
19
  features: Map<string, Feature>
11
20
  radius: number
12
21
  config: AnyConfigurationModel
@@ -20,16 +29,6 @@ function StructuralVariantChords(props: {
20
29
  evt: unknown,
21
30
  ) => void
22
31
  }) {
23
- const {
24
- features,
25
- config,
26
- displayModel,
27
- blockDefinitions,
28
- radius,
29
- bezierRadius,
30
- displayModel: { selectedFeatureId },
31
- onChordClick,
32
- } = props
33
32
  // make a map of refName -> blockDefinition
34
33
  const blocksForRefsMemo = useMemo(() => {
35
34
  const blocksForRefs = {} as { [key: string]: Block }
@@ -57,7 +56,9 @@ function StructuralVariantChords(props: {
57
56
  />,
58
57
  )
59
58
  }
60
- const trackStyleId = `chords-${displayModel.id}`
59
+ const trackStyleId = `chords-${
60
+ typeof jest !== 'undefined' ? 'test' : displayModel.id
61
+ }`
61
62
  return (
62
63
  <g id={trackStyleId} data-testid="structuralVariantChordRenderer">
63
64
  <style
@@ -74,6 +75,4 @@ function StructuralVariantChords(props: {
74
75
  {chords}
75
76
  </g>
76
77
  )
77
- }
78
-
79
- export default observer(StructuralVariantChords)
78
+ })
package/src/VariantFeatureWidget/BreakendOptionDialog.tsx CHANGED
@@ -70,19 +70,25 @@ function BreakendOptionDialog({
70
70
  feature,
71
71
  view,
72
72
  )
73
- function remapIds(arr: any[]) {
74
- return arr.map((v: any) => ({
73
+
74
+ interface Track {
75
+ trackId: string
76
+ [key: string]: unknown
77
+ }
78
+ function remapIds(arr: Track[]) {
79
+ return arr.map(v => ({
75
80
  ...v,
76
- id: v.trackId + '-' + Math.random(),
81
+ id: `${v.trackId}-${Math.random()}`,
77
82
  }))
78
83
  }
79
84
  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
80
85
  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
81
86
  viewSnapshot.featureData = feature
82
- const viewTracks = getSnapshot(view.tracks) as any
87
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
88
+ const viewTracks = getSnapshot(view.tracks) as Track[]
83
89
  viewSnapshot.views[0].tracks = remapIds(viewTracks)
84
90
  viewSnapshot.views[1].tracks = remapIds(
85
- mirrorTracks ? viewTracks.slice().reverse() : viewTracks,
91
+ mirrorTracks ? [...viewTracks].reverse() : viewTracks,
86
92
  )
87
93
 
88
94
  session.addView('BreakpointSplitView', viewSnapshot)
package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx CHANGED
@@ -18,7 +18,7 @@ test('renders with just the required model elements', () => {
18
18
  const model = Session.create(
19
19
  {
20
20
  widget: {
21
- // @ts-ignore
21
+ // @ts-expect-error
22
22
  type: 'VariantFeatureWidget',
23
23
  },
24
24
  },
package/src/VariantFeatureWidget/VariantSampleGrid.tsx CHANGED
@@ -21,6 +21,51 @@ interface Entry {
21
21
  type InfoFields = Record<string, unknown>
22
22
  type Filters = Record<string, string>
23
23
 
24
+ function SampleFilters({
25
+ columns,
26
+ filter,
27
+ setFilter,
28
+ }: {
29
+ columns: { field: string }[]
30
+ filter: Filters
31
+ setFilter: (arg: Filters) => void
32
+ }) {
33
+ const [showFilters, setShowFilters] = useState(false)
34
+ return (
35
+ <>
36
+ <FormControlLabel
37
+ control={
38
+ <Checkbox
39
+ checked={showFilters}
40
+ onChange={() => setShowFilters(f => !f)}
41
+ />
42
+ }
43
+ label="Show sample filters"
44
+ />
45
+ {showFilters ? (
46
+ <>
47
+ <Typography>
48
+ These filters can use a plain text search or regex style query, e.g.
49
+ in the genotype field, entering 1 will query for all genotypes that
50
+ include the first alternate allele e.g. 0|1 or 1|1, entering
51
+ [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
52
+ </Typography>
53
+ {columns.map(({ field }) => (
54
+ <TextField
55
+ key={`filter-${field}`}
56
+ placeholder={`Filter ${field}`}
57
+ value={filter[field] || ''}
58
+ onChange={event =>
59
+ setFilter({ ...filter, [field]: event.target.value })
60
+ }
61
+ />
62
+ ))}
63
+ </>
64
+ ) : null}
65
+ </>
66
+ )
67
+ }
68
+
24
69
  export default function VariantSamples(props: {
25
70
  feature: SimpleFeatureSerialized
26
71
  // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -29,7 +74,6 @@ export default function VariantSamples(props: {
29
74
  const { feature, descriptions = {} } = props
30
75
  const { ref, scrollLeft } = useResizeBar()
31
76
  const [filter, setFilter] = useState<Filters>({})
32
- const [showFilters, setShowFilters] = useState(false)
33
77
  const samples = (feature.samples || {}) as Record<string, InfoFields>
34
78
  const preFilteredRows = Object.entries(samples)
35
79
 
@@ -69,7 +113,7 @@ export default function VariantSamples(props: {
69
113
  const [widths, setWidths] = useState(
70
114
  keys.map(e => measureGridWidth(rows.map(r => r[e]))),
71
115
  )
72
- const infoFields = keys.map((field, index) => ({
116
+ const columns = keys.map((field, index) => ({
73
117
  field,
74
118
  description: descriptions.FORMAT?.[field]?.Description,
75
119
  width: widths[index],
@@ -80,36 +124,7 @@ export default function VariantSamples(props: {
80
124
  return !preFilteredRows.length ? null : (
81
125
  <BaseCard {...props} title="Samples">
82
126
  {error ? <Typography color="error">{`${error}`}</Typography> : null}
83
-
84
- <FormControlLabel
85
- control={
86
- <Checkbox
87
- checked={showFilters}
88
- onChange={() => setShowFilters(f => !f)}
89
- />
90
- }
91
- label="Show sample filters"
92
- />
93
- {showFilters ? (
94
- <>
95
- <Typography>
96
- These filters can use a plain text search or regex style query, e.g.
97
- in the genotype field, entering 1 will query for all genotypes that
98
- include the first alternate allele e.g. 0|1 or 1|1, entering
99
- [1-9]\d* will find any non-zero allele e.g. 0|2 or 2/33
100
- </Typography>
101
- {infoFields.map(({ field }) => (
102
- <TextField
103
- key={`filter-${field}`}
104
- placeholder={`Filter ${field}`}
105
- value={filter[field] || ''}
106
- onChange={event =>
107
- setFilter({ ...filter, [field]: event.target.value })
108
- }
109
- />
110
- ))}
111
- </>
112
- ) : null}
127
+ <SampleFilters setFilter={setFilter} columns={columns} filter={filter} />
113
128
  <div ref={ref}>
114
129
  <ResizeBar
115
130
  widths={widths}
@@ -119,7 +134,7 @@ export default function VariantSamples(props: {
119
134
  <div ref={ref} style={{ height: 600, width: '100%', overflow: 'auto' }}>
120
135
  <DataGrid
121
136
  rows={rows}
122
- columns={infoFields}
137
+ columns={columns}
123
138
  disableSelectionOnClick
124
139
  rowHeight={25}
125
140
  headerHeight={35}
package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap CHANGED
@@ -29,7 +29,7 @@ exports[`renders with just the required model elements 1`] = `
29
29
  >
30
30
  <svg
31
31
  aria-hidden="true"
32
- class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
32
+ class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-ymsoo8-MuiSvgIcon-root-expandIcon"
33
33
  data-testid="ExpandMoreIcon"
34
34
  focusable="false"
35
35
  viewBox="0 0 24 24"
@@ -66,7 +66,7 @@ exports[`renders with just the required model elements 1`] = `
66
66
  class="css-1m8nxnb-field"
67
67
  >
68
68
  <div
69
- class="css-1y9c7n2-fieldName"
69
+ class="css-1q83rf3-fieldName"
70
70
  >
71
71
  Position
72
72
  </div>
@@ -80,7 +80,7 @@ exports[`renders with just the required model elements 1`] = `
80
80
  class="css-1m8nxnb-field"
81
81
  >
82
82
  <div
83
- class="css-1y9c7n2-fieldName"
83
+ class="css-1q83rf3-fieldName"
84
84
  >
85
85
  Name
86
86
  </div>
@@ -96,7 +96,7 @@ exports[`renders with just the required model elements 1`] = `
96
96
  class="css-1m8nxnb-field"
97
97
  >
98
98
  <div
99
- class="css-1y9c7n2-fieldName"
99
+ class="css-1q83rf3-fieldName"
100
100
  >
101
101
  Length
102
102
  </div>
@@ -121,7 +121,7 @@ exports[`renders with just the required model elements 1`] = `
121
121
  >
122
122
  <div
123
123
  aria-label="reference base(s): Each base must be one of A,C,G,T,N (case insensitive)."
124
- class="css-1qe2j6j-fieldDescription-fieldName"
124
+ class="css-18vnxxj-fieldDescription-fieldName"
125
125
  data-mui-internal-clone-element="true"
126
126
  >
127
127
  REF
@@ -139,7 +139,7 @@ exports[`renders with just the required model elements 1`] = `
139
139
  >
140
140
  <div
141
141
  aria-label="alternate base(s): Comma-separated list of alternate non-reference alleles"
142
- class="css-1qe2j6j-fieldDescription-fieldName"
142
+ class="css-18vnxxj-fieldDescription-fieldName"
143
143
  data-mui-internal-clone-element="true"
144
144
  >
145
145
  ALT
@@ -157,7 +157,7 @@ exports[`renders with just the required model elements 1`] = `
157
157
  >
158
158
  <div
159
159
  aria-label="quality: Phred-scaled quality score for the assertion made in ALT"
160
- class="css-1qe2j6j-fieldDescription-fieldName"
160
+ class="css-18vnxxj-fieldDescription-fieldName"
161
161
  data-mui-internal-clone-element="true"
162
162
  >
163
163
  QUAL
@@ -174,7 +174,7 @@ exports[`renders with just the required model elements 1`] = `
174
174
  class="css-1m8nxnb-field"
175
175
  >
176
176
  <div
177
- class="css-1y9c7n2-fieldName"
177
+ class="css-1q83rf3-fieldName"
178
178
  style="width: 62px;"
179
179
  >
180
180
  INFO.MQ
package/src/VcfAdapter/VcfAdapter.ts CHANGED
@@ -65,22 +65,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
65
65
 
66
66
  const str = new TextDecoder().decode(buffer)
67
67
  const { header, lines } = readVcf(str)
68
-
69
- const intervalTree = lines
70
- .map((line, id) => {
71
- const [refName, startP, , ref, , , , info] = line.split('\t')
72
- const start = +startP - 1
73
- const end = +(info.match(/END=(\d+)/)?.[1].trim() || start + ref.length)
74
- return { line, refName, start, end, id }
75
- })
76
- .reduce((acc, obj) => {
77
- const key = obj.refName
78
- if (!acc[key]) {
79
- acc[key] = new IntervalTree()
80
- }
81
- acc[key].insert([obj.start, obj.end], obj)
82
- return acc
83
- }, {} as Record<string, IntervalTree>)
68
+ const intervalTree = {} as { [key: string]: IntervalTree }
69
+
70
+ for (const obj of lines.map((line, id) => {
71
+ const [refName, startP, , ref, , , , info] = line.split('\t')
72
+ const start = +startP - 1
73
+ const def = start + ref.length
74
+ const end = +(info.match(/END=(\d+)/)?.[1].trim() || def)
75
+ return { line, refName, start, end, id }
76
+ })) {
77
+ const key = obj.refName
78
+ if (!intervalTree[key]) {
79
+ intervalTree[key] = new IntervalTree()
80
+ }
81
+ intervalTree[key].insert([obj.start, obj.end], obj)
82
+ }
84
83
 
85
84
  return { header, intervalTree }
86
85
  }
package/src/VcfFeature/index.ts CHANGED
@@ -79,7 +79,7 @@ export default class VCFFeature implements Feature {
79
79
  const start = POS - 1
80
80
  const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
81
81
  const isTRA = ALT?.some(f => f === '<TRA>')
82
- const isSymbolic = ALT?.some(f => f.indexOf('<') !== -1)
82
+ const isSymbolic = ALT?.some(f => f.includes('<'))
83
83
 
84
84
  return {
85
85
  refName: CHROM,