@jbrowse/plugin-variants 2.5.0 → 2.6.2

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Files changed (190) hide show
  1. package/dist/ChordVariantDisplay/index.js +0 -1
  2. package/dist/ChordVariantDisplay/models/configSchema.js +0 -1
  3. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +11 -3
  4. package/dist/ChordVariantDisplay/models/stateModelFactory.js +0 -1
  5. package/dist/LinearVariantDisplay/configSchema.js +0 -1
  6. package/dist/LinearVariantDisplay/index.js +0 -1
  7. package/dist/LinearVariantDisplay/model.d.ts +52 -49
  8. package/dist/LinearVariantDisplay/model.js +0 -1
  9. package/dist/StructuralVariantChordRenderer/Chord.d.ts +2 -1
  10. package/dist/StructuralVariantChordRenderer/Chord.js +0 -1
  11. package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -1
  12. package/dist/StructuralVariantChordRenderer/ReactComponent.js +0 -1
  13. package/dist/StructuralVariantChordRenderer/configSchema.js +0 -1
  14. package/dist/StructuralVariantChordRenderer/index.js +0 -1
  15. package/dist/VariantFeatureWidget/AnnotGrid.d.ts +2 -1
  16. package/dist/VariantFeatureWidget/AnnotGrid.js +8 -14
  17. package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts +2 -1
  18. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +0 -1
  19. package/dist/VariantFeatureWidget/BreakendPanel.d.ts +2 -1
  20. package/dist/VariantFeatureWidget/BreakendPanel.js +0 -1
  21. package/dist/VariantFeatureWidget/VariantAnnotationTable.d.ts +6 -0
  22. package/dist/VariantFeatureWidget/VariantAnnotationTable.js +16 -0
  23. package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +8 -1
  24. package/dist/VariantFeatureWidget/VariantFeatureWidget.js +26 -15
  25. package/dist/VariantFeatureWidget/VariantSampleGrid.d.ts +9 -2
  26. package/dist/VariantFeatureWidget/VariantSampleGrid.js +0 -1
  27. package/dist/VariantFeatureWidget/index.js +0 -1
  28. package/dist/VariantTrack/configSchema.js +0 -1
  29. package/dist/VariantTrack/index.js +0 -1
  30. package/dist/VcfAdapter/VcfAdapter.js +0 -1
  31. package/dist/VcfAdapter/configSchema.js +0 -1
  32. package/dist/VcfAdapter/index.js +0 -1
  33. package/dist/VcfFeature/index.js +2 -2
  34. package/dist/VcfFeature/util.js +0 -1
  35. package/dist/VcfTabixAdapter/VcfTabixAdapter.js +0 -1
  36. package/dist/VcfTabixAdapter/configSchema.js +0 -1
  37. package/dist/VcfTabixAdapter/index.js +0 -1
  38. package/dist/extensionPoints.js +0 -1
  39. package/dist/index.js +0 -1
  40. package/esm/ChordVariantDisplay/index.js +0 -1
  41. package/esm/ChordVariantDisplay/models/configSchema.js +0 -1
  42. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +11 -3
  43. package/esm/ChordVariantDisplay/models/stateModelFactory.js +0 -1
  44. package/esm/LinearVariantDisplay/configSchema.js +0 -1
  45. package/esm/LinearVariantDisplay/index.js +0 -1
  46. package/esm/LinearVariantDisplay/model.d.ts +52 -49
  47. package/esm/LinearVariantDisplay/model.js +0 -1
  48. package/esm/StructuralVariantChordRenderer/Chord.d.ts +2 -1
  49. package/esm/StructuralVariantChordRenderer/Chord.js +0 -1
  50. package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +2 -1
  51. package/esm/StructuralVariantChordRenderer/ReactComponent.js +0 -1
  52. package/esm/StructuralVariantChordRenderer/configSchema.js +0 -1
  53. package/esm/StructuralVariantChordRenderer/index.js +0 -1
  54. package/esm/VariantFeatureWidget/AnnotGrid.d.ts +2 -1
  55. package/esm/VariantFeatureWidget/AnnotGrid.js +8 -14
  56. package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts +2 -1
  57. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +0 -1
  58. package/esm/VariantFeatureWidget/BreakendPanel.d.ts +2 -1
  59. package/esm/VariantFeatureWidget/BreakendPanel.js +0 -1
  60. package/esm/VariantFeatureWidget/VariantAnnotationTable.d.ts +6 -0
  61. package/esm/VariantFeatureWidget/VariantAnnotationTable.js +10 -0
  62. package/esm/VariantFeatureWidget/VariantFeatureWidget.d.ts +8 -1
  63. package/esm/VariantFeatureWidget/VariantFeatureWidget.js +26 -15
  64. package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts +9 -2
  65. package/esm/VariantFeatureWidget/VariantSampleGrid.js +0 -1
  66. package/esm/VariantFeatureWidget/index.js +0 -1
  67. package/esm/VariantTrack/configSchema.js +0 -1
  68. package/esm/VariantTrack/index.js +0 -1
  69. package/esm/VcfAdapter/VcfAdapter.js +0 -1
  70. package/esm/VcfAdapter/configSchema.js +0 -1
  71. package/esm/VcfAdapter/index.js +0 -1
  72. package/esm/VcfFeature/index.js +2 -2
  73. package/esm/VcfFeature/util.js +0 -1
  74. package/esm/VcfTabixAdapter/VcfTabixAdapter.js +0 -1
  75. package/esm/VcfTabixAdapter/configSchema.js +0 -1
  76. package/esm/VcfTabixAdapter/index.js +0 -1
  77. package/esm/extensionPoints.js +0 -1
  78. package/esm/index.js +0 -1
  79. package/package.json +3 -4
  80. package/dist/ChordVariantDisplay/index.js.map +0 -1
  81. package/dist/ChordVariantDisplay/models/configSchema.js.map +0 -1
  82. package/dist/ChordVariantDisplay/models/stateModelFactory.js.map +0 -1
  83. package/dist/LinearVariantDisplay/configSchema.js.map +0 -1
  84. package/dist/LinearVariantDisplay/index.js.map +0 -1
  85. package/dist/LinearVariantDisplay/model.js.map +0 -1
  86. package/dist/StructuralVariantChordRenderer/Chord.js.map +0 -1
  87. package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +0 -1
  88. package/dist/StructuralVariantChordRenderer/configSchema.js.map +0 -1
  89. package/dist/StructuralVariantChordRenderer/index.js.map +0 -1
  90. package/dist/VariantFeatureWidget/AnnotGrid.js.map +0 -1
  91. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +0 -1
  92. package/dist/VariantFeatureWidget/BreakendPanel.js.map +0 -1
  93. package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts +0 -4
  94. package/dist/VariantFeatureWidget/VariantAnnPanel.js +0 -25
  95. package/dist/VariantFeatureWidget/VariantAnnPanel.js.map +0 -1
  96. package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts +0 -4
  97. package/dist/VariantFeatureWidget/VariantCsqPanel.js +0 -25
  98. package/dist/VariantFeatureWidget/VariantCsqPanel.js.map +0 -1
  99. package/dist/VariantFeatureWidget/VariantFeatureWidget.js.map +0 -1
  100. package/dist/VariantFeatureWidget/VariantSampleGrid.js.map +0 -1
  101. package/dist/VariantFeatureWidget/index.js.map +0 -1
  102. package/dist/VariantTrack/configSchema.js.map +0 -1
  103. package/dist/VariantTrack/index.js.map +0 -1
  104. package/dist/VcfAdapter/VcfAdapter.js.map +0 -1
  105. package/dist/VcfAdapter/configSchema.js.map +0 -1
  106. package/dist/VcfAdapter/index.js.map +0 -1
  107. package/dist/VcfFeature/index.js.map +0 -1
  108. package/dist/VcfFeature/util.js.map +0 -1
  109. package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +0 -1
  110. package/dist/VcfTabixAdapter/configSchema.js.map +0 -1
  111. package/dist/VcfTabixAdapter/index.js.map +0 -1
  112. package/dist/extensionPoints.js.map +0 -1
  113. package/dist/index.js.map +0 -1
  114. package/esm/ChordVariantDisplay/index.js.map +0 -1
  115. package/esm/ChordVariantDisplay/models/configSchema.js.map +0 -1
  116. package/esm/ChordVariantDisplay/models/stateModelFactory.js.map +0 -1
  117. package/esm/LinearVariantDisplay/configSchema.js.map +0 -1
  118. package/esm/LinearVariantDisplay/index.js.map +0 -1
  119. package/esm/LinearVariantDisplay/model.js.map +0 -1
  120. package/esm/StructuralVariantChordRenderer/Chord.js.map +0 -1
  121. package/esm/StructuralVariantChordRenderer/ReactComponent.js.map +0 -1
  122. package/esm/StructuralVariantChordRenderer/configSchema.js.map +0 -1
  123. package/esm/StructuralVariantChordRenderer/index.js.map +0 -1
  124. package/esm/VariantFeatureWidget/AnnotGrid.js.map +0 -1
  125. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +0 -1
  126. package/esm/VariantFeatureWidget/BreakendPanel.js.map +0 -1
  127. package/esm/VariantFeatureWidget/VariantAnnPanel.d.ts +0 -4
  128. package/esm/VariantFeatureWidget/VariantAnnPanel.js +0 -19
  129. package/esm/VariantFeatureWidget/VariantAnnPanel.js.map +0 -1
  130. package/esm/VariantFeatureWidget/VariantCsqPanel.d.ts +0 -4
  131. package/esm/VariantFeatureWidget/VariantCsqPanel.js +0 -19
  132. package/esm/VariantFeatureWidget/VariantCsqPanel.js.map +0 -1
  133. package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map +0 -1
  134. package/esm/VariantFeatureWidget/VariantSampleGrid.js.map +0 -1
  135. package/esm/VariantFeatureWidget/index.js.map +0 -1
  136. package/esm/VariantTrack/configSchema.js.map +0 -1
  137. package/esm/VariantTrack/index.js.map +0 -1
  138. package/esm/VcfAdapter/VcfAdapter.js.map +0 -1
  139. package/esm/VcfAdapter/configSchema.js.map +0 -1
  140. package/esm/VcfAdapter/index.js.map +0 -1
  141. package/esm/VcfFeature/index.js.map +0 -1
  142. package/esm/VcfFeature/util.js.map +0 -1
  143. package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +0 -1
  144. package/esm/VcfTabixAdapter/configSchema.js.map +0 -1
  145. package/esm/VcfTabixAdapter/index.js.map +0 -1
  146. package/esm/extensionPoints.js.map +0 -1
  147. package/esm/index.js.map +0 -1
  148. package/src/ChordVariantDisplay/index.ts +0 -23
  149. package/src/ChordVariantDisplay/models/configSchema.ts +0 -33
  150. package/src/ChordVariantDisplay/models/stateModelFactory.ts +0 -63
  151. package/src/LinearVariantDisplay/configSchema.ts +0 -30
  152. package/src/LinearVariantDisplay/index.ts +0 -20
  153. package/src/LinearVariantDisplay/model.ts +0 -76
  154. package/src/StructuralVariantChordRenderer/Chord.tsx +0 -141
  155. package/src/StructuralVariantChordRenderer/ReactComponent.tsx +0 -78
  156. package/src/StructuralVariantChordRenderer/configSchema.ts +0 -42
  157. package/src/StructuralVariantChordRenderer/index.ts +0 -17
  158. package/src/VariantFeatureWidget/AnnotGrid.tsx +0 -52
  159. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +0 -117
  160. package/src/VariantFeatureWidget/BreakendPanel.tsx +0 -93
  161. package/src/VariantFeatureWidget/VariantAnnPanel.tsx +0 -31
  162. package/src/VariantFeatureWidget/VariantCsqPanel.tsx +0 -31
  163. package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx +0 -42
  164. package/src/VariantFeatureWidget/VariantFeatureWidget.tsx +0 -67
  165. package/src/VariantFeatureWidget/VariantSampleGrid.tsx +0 -152
  166. package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.tsx.snap +0 -244
  167. package/src/VariantFeatureWidget/index.ts +0 -32
  168. package/src/VariantTrack/configSchema.ts +0 -24
  169. package/src/VariantTrack/index.ts +0 -16
  170. package/src/VcfAdapter/VcfAdapter.test.ts +0 -28
  171. package/src/VcfAdapter/VcfAdapter.ts +0 -125
  172. package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap +0 -325
  173. package/src/VcfAdapter/configSchema.ts +0 -22
  174. package/src/VcfAdapter/index.ts +0 -15
  175. package/src/VcfAdapter/test_data/volvox.filtered.vcf +0 -73
  176. package/src/VcfFeature/index.test.ts +0 -132
  177. package/src/VcfFeature/index.ts +0 -104
  178. package/src/VcfFeature/util.ts +0 -138
  179. package/src/VcfTabixAdapter/VcfTabixAdapter.test.ts +0 -69
  180. package/src/VcfTabixAdapter/VcfTabixAdapter.ts +0 -90
  181. package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap +0 -325
  182. package/src/VcfTabixAdapter/configSchema.ts +0 -43
  183. package/src/VcfTabixAdapter/index.ts +0 -17
  184. package/src/VcfTabixAdapter/test_data/volvox.filtered.vcf.gz +0 -0
  185. package/src/VcfTabixAdapter/test_data/volvox.filtered.vcf.gz.csi +0 -0
  186. package/src/VcfTabixAdapter/test_data/volvox.filtered.vcf.gz.tbi +0 -0
  187. package/src/__snapshots__/index.test.ts.snap +0 -20
  188. package/src/extensionPoints.ts +0 -74
  189. package/src/index.test.ts +0 -32
  190. package/src/index.ts +0 -27
package/esm/extensionPoints.js CHANGED
@@ -46,4 +46,3 @@ export default (pluginManager) => {
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  };
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  });
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  };
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- //# sourceMappingURL=extensionPoints.js.map
package/esm/index.js CHANGED
@@ -24,4 +24,3 @@ export default class VariantsPlugin extends Plugin {
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  }
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  }
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  export { default as VcfFeature } from './VcfFeature';
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- //# sourceMappingURL=index.js.map
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-variants",
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- "version": "2.5.0",
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+ "version": "2.6.2",
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  "description": "JBrowse 2 variant adapters, tracks, etc.",
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  "keywords": [
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  "jbrowse",
@@ -20,7 +20,6 @@
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  "main": "dist/index.js",
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  "files": [
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  "dist",
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- "src",
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  "esm"
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  ],
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  "scripts": {
@@ -33,7 +32,7 @@
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  "useSrc": "node ../../scripts/useSrc.js",
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  "prebuild": "npm run clean",
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  "build:esm": "tsc --build tsconfig.build.esm.json",
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- "build:es5": "tsc --build tsconfig.build.es5.json",
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+ "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
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  "clean": "rimraf dist esm *.tsbuildinfo"
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  },
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  "dependencies": {
@@ -64,5 +63,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
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+ "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
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  }
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package/dist/VariantFeatureWidget/VariantAnnPanel.d.ts DELETED
@@ -1,4 +0,0 @@
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- export default function VariantAnnPanel({ feature, descriptions, }: {
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- feature: any;
3
- descriptions: any;
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- }): JSX.Element | null;
package/dist/VariantFeatureWidget/VariantAnnPanel.js DELETED
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- "use strict";
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
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- Object.defineProperty(exports, "__esModule", { value: true });
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- /* eslint-disable @typescript-eslint/no-explicit-any */
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- const react_1 = __importDefault(require("react"));
8
- const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
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- const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
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- function VariantAnnPanel({ feature, descriptions, }) {
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- var _a, _b, _c, _d;
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- const annFields = (((_d = (_c = (_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) === null || _c === void 0 ? void 0 : _c.match(/.*Functional annotations:'(.*)'$/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
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- const ann = (feature.INFO.ANN || []);
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- const rows = ann.map((elt, id) => ({
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- id,
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- ...Object.fromEntries(elt.split('|').map((e, i) => [annFields[i], e])),
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- })) || [];
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- const columns = annFields.map(c => ({
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- field: c,
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- }));
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- return ann.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "ANN table" },
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- react_1.default.createElement(AnnotGrid_1.default, { rows: rows, columns: columns }))) : null;
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- }
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- exports.default = VariantAnnPanel;
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- //# sourceMappingURL=VariantAnnPanel.js.map
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package/dist/VariantFeatureWidget/VariantCsqPanel.d.ts DELETED
@@ -1,4 +0,0 @@
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- export default function VariantCsqPanel({ feature, descriptions, }: {
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- feature: any;
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- descriptions: any;
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- }): JSX.Element | null;
package/dist/VariantFeatureWidget/VariantCsqPanel.js DELETED
@@ -1,25 +0,0 @@
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- "use strict";
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- const AnnotGrid_1 = __importDefault(require("./AnnotGrid"));
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- function VariantCsqPanel({ feature, descriptions, }) {
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- var _a, _b, _c, _d;
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- const csqFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Format: (.*)/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
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- const csq = (feature.INFO.CSQ || []);
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- const rows = csq.map((elt, id) => ({
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- id,
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- ...Object.fromEntries(elt.split('|').map((e, i) => [csqFields[i], e])),
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- })) || [];
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- const columns = csqFields.map(c => ({
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- field: c,
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- }));
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- return csq.length ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "CSQ table" },
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- react_1.default.createElement(AnnotGrid_1.default, { rows: rows, columns: columns }))) : null;
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- exports.default = VariantCsqPanel;
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- //# sourceMappingURL=VariantCsqPanel.js.map
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package/dist/VariantFeatureWidget/index.js.map DELETED
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package/esm/VariantFeatureWidget/VariantAnnPanel.d.ts DELETED
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- export default function VariantAnnPanel({ feature, descriptions, }: {
2
- feature: any;
3
- descriptions: any;
4
- }): JSX.Element | null;
package/esm/VariantFeatureWidget/VariantAnnPanel.js DELETED
@@ -1,19 +0,0 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
- import React from 'react';
3
- import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
4
- import AnnotGrid from './AnnotGrid';
5
- export default function VariantAnnPanel({ feature, descriptions, }) {
6
- var _a, _b, _c, _d;
7
- const annFields = (((_d = (_c = (_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) === null || _c === void 0 ? void 0 : _c.match(/.*Functional annotations:'(.*)'$/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
8
- const ann = (feature.INFO.ANN || []);
9
- const rows = ann.map((elt, id) => ({
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- ...Object.fromEntries(elt.split('|').map((e, i) => [annFields[i], e])),
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- const columns = annFields.map(c => ({
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- }));
16
- return ann.length ? (React.createElement(BaseCard, { title: "ANN table" },
17
- React.createElement(AnnotGrid, { rows: rows, columns: columns }))) : null;
18
- }
19
- //# sourceMappingURL=VariantAnnPanel.js.map
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package/esm/VariantFeatureWidget/VariantCsqPanel.d.ts DELETED
@@ -1,4 +0,0 @@
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- export default function VariantCsqPanel({ feature, descriptions, }: {
2
- feature: any;
3
- descriptions: any;
4
- }): JSX.Element | null;
package/esm/VariantFeatureWidget/VariantCsqPanel.js DELETED
@@ -1,19 +0,0 @@
1
- /* eslint-disable @typescript-eslint/no-explicit-any */
2
- import React from 'react';
3
- import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
4
- import AnnotGrid from './AnnotGrid';
5
- export default function VariantCsqPanel({ feature, descriptions, }) {
6
- var _a, _b, _c, _d;
7
- const csqFields = (((_d = (_c = (_b = (_a = descriptions === null || descriptions === void 0 ? void 0 : descriptions.INFO) === null || _a === void 0 ? void 0 : _a.CSQ) === null || _b === void 0 ? void 0 : _b.Description) === null || _c === void 0 ? void 0 : _c.match(/.*Format: (.*)/)) === null || _d === void 0 ? void 0 : _d[1].split('|')) || []);
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- const columns = csqFields.map(c => ({
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15
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- return csq.length ? (React.createElement(BaseCard, { title: "CSQ table" },
17
- React.createElement(AnnotGrid, { rows: rows, columns: columns }))) : null;
18
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19
- //# sourceMappingURL=VariantCsqPanel.js.map
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package/esm/VariantFeatureWidget/VariantFeatureWidget.js.map DELETED
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