@jbrowse/plugin-alignments 1.7.11 → 2.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (295) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +192 -216
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
  3. package/dist/AlignmentsFeatureDetail/index.d.ts +3 -3
  4. package/dist/AlignmentsFeatureDetail/index.js +48 -44
  5. package/dist/AlignmentsFeatureDetail/index.js.map +1 -0
  6. package/dist/AlignmentsTrack/index.js +24 -32
  7. package/dist/AlignmentsTrack/index.js.map +1 -0
  8. package/dist/BamAdapter/BamAdapter.d.ts +6 -1
  9. package/dist/BamAdapter/BamAdapter.js +345 -585
  10. package/dist/BamAdapter/BamAdapter.js.map +1 -0
  11. package/dist/BamAdapter/BamSlightlyLazyFeature.js +143 -174
  12. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
  13. package/dist/BamAdapter/MismatchParser.d.ts +1 -1
  14. package/dist/BamAdapter/MismatchParser.js +341 -417
  15. package/dist/BamAdapter/MismatchParser.js.map +1 -0
  16. package/dist/BamAdapter/configSchema.js +33 -46
  17. package/dist/BamAdapter/configSchema.js.map +1 -0
  18. package/dist/BamAdapter/index.js +36 -32
  19. package/dist/BamAdapter/index.js.map +1 -0
  20. package/dist/CramAdapter/CramAdapter.js +376 -644
  21. package/dist/CramAdapter/CramAdapter.js.map +1 -0
  22. package/dist/CramAdapter/CramSlightlyLazyFeature.js +374 -439
  23. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
  24. package/dist/CramAdapter/CramTestAdapters.js +169 -227
  25. package/dist/CramAdapter/CramTestAdapters.js.map +1 -0
  26. package/dist/CramAdapter/configSchema.js +28 -38
  27. package/dist/CramAdapter/configSchema.js.map +1 -0
  28. package/dist/CramAdapter/index.js +37 -32
  29. package/dist/CramAdapter/index.js.map +1 -0
  30. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +91 -93
  31. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
  32. package/dist/HtsgetBamAdapter/configSchema.js +19 -29
  33. package/dist/HtsgetBamAdapter/configSchema.js.map +1 -0
  34. package/dist/HtsgetBamAdapter/index.js +44 -38
  35. package/dist/HtsgetBamAdapter/index.js.map +1 -0
  36. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +36 -65
  37. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
  38. package/dist/LinearAlignmentsDisplay/index.js +22 -28
  39. package/dist/LinearAlignmentsDisplay/index.js.map +1 -0
  40. package/dist/LinearAlignmentsDisplay/models/configSchema.js +12 -23
  41. package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
  42. package/dist/LinearAlignmentsDisplay/models/model.d.ts +10 -10
  43. package/dist/LinearAlignmentsDisplay/models/model.js +257 -245
  44. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -0
  45. package/dist/LinearPileupDisplay/components/ColorByModifications.js +98 -116
  46. package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
  47. package/dist/LinearPileupDisplay/components/ColorByTag.js +82 -91
  48. package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
  49. package/dist/LinearPileupDisplay/components/FilterByTag.js +156 -192
  50. package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
  51. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +15 -29
  52. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
  53. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +79 -93
  54. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
  55. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +78 -81
  56. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
  57. package/dist/LinearPileupDisplay/components/SortByTag.js +80 -88
  58. package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -0
  59. package/dist/LinearPileupDisplay/configSchema.js +40 -42
  60. package/dist/LinearPileupDisplay/configSchema.js.map +1 -0
  61. package/dist/LinearPileupDisplay/index.js +21 -27
  62. package/dist/LinearPileupDisplay/index.js.map +1 -0
  63. package/dist/LinearPileupDisplay/model.d.ts +27 -17
  64. package/dist/LinearPileupDisplay/model.js +701 -797
  65. package/dist/LinearPileupDisplay/model.js.map +1 -0
  66. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +5 -2
  67. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +103 -77
  68. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
  69. package/dist/LinearSNPCoverageDisplay/index.js +21 -27
  70. package/dist/LinearSNPCoverageDisplay/index.js.map +1 -0
  71. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +45 -55
  72. package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
  73. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +41 -17
  74. package/dist/LinearSNPCoverageDisplay/models/model.js +258 -230
  75. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -0
  76. package/dist/NestedFrequencyTable.js +104 -139
  77. package/dist/NestedFrequencyTable.js.map +1 -0
  78. package/dist/PileupRPC/rpcMethods.js +199 -278
  79. package/dist/PileupRPC/rpcMethods.js.map +1 -0
  80. package/dist/PileupRenderer/PileupLayoutSession.js +56 -76
  81. package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -0
  82. package/dist/PileupRenderer/PileupRenderer.d.ts +4 -8
  83. package/dist/PileupRenderer/PileupRenderer.js +938 -1205
  84. package/dist/PileupRenderer/PileupRenderer.js.map +1 -0
  85. package/dist/PileupRenderer/components/PileupRendering.d.ts +1 -1
  86. package/dist/PileupRenderer/components/PileupRendering.js +173 -253
  87. package/dist/PileupRenderer/components/PileupRendering.js.map +1 -0
  88. package/dist/PileupRenderer/configSchema.js +65 -71
  89. package/dist/PileupRenderer/configSchema.js.map +1 -0
  90. package/dist/PileupRenderer/index.js +17 -22
  91. package/dist/PileupRenderer/index.js.map +1 -0
  92. package/dist/PileupRenderer/sortUtil.js +83 -107
  93. package/dist/PileupRenderer/sortUtil.js.map +1 -0
  94. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +437 -589
  95. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
  96. package/dist/SNPCoverageAdapter/configSchema.js +10 -20
  97. package/dist/SNPCoverageAdapter/configSchema.js.map +1 -0
  98. package/dist/SNPCoverageAdapter/index.js +46 -41
  99. package/dist/SNPCoverageAdapter/index.js.map +1 -0
  100. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -2
  101. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +265 -290
  102. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
  103. package/dist/SNPCoverageRenderer/configSchema.js +30 -39
  104. package/dist/SNPCoverageRenderer/configSchema.js.map +1 -0
  105. package/dist/SNPCoverageRenderer/index.js +19 -30
  106. package/dist/SNPCoverageRenderer/index.js.map +1 -0
  107. package/dist/index.js +135 -152
  108. package/dist/index.js.map +1 -0
  109. package/dist/shared.js +84 -92
  110. package/dist/shared.js.map +1 -0
  111. package/dist/util.js +130 -121
  112. package/dist/util.js.map +1 -0
  113. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +6 -0
  114. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +145 -0
  115. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
  116. package/esm/AlignmentsFeatureDetail/index.d.ts +38 -0
  117. package/esm/AlignmentsFeatureDetail/index.js +23 -0
  118. package/esm/AlignmentsFeatureDetail/index.js.map +1 -0
  119. package/esm/AlignmentsTrack/index.d.ts +2 -0
  120. package/esm/AlignmentsTrack/index.js +23 -0
  121. package/esm/AlignmentsTrack/index.js.map +1 -0
  122. package/esm/BamAdapter/BamAdapter.d.ts +45 -0
  123. package/esm/BamAdapter/BamAdapter.js +173 -0
  124. package/esm/BamAdapter/BamAdapter.js.map +1 -0
  125. package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +33 -0
  126. package/esm/BamAdapter/BamSlightlyLazyFeature.js +107 -0
  127. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
  128. package/esm/BamAdapter/MismatchParser.d.ts +25 -0
  129. package/esm/BamAdapter/MismatchParser.js +294 -0
  130. package/esm/BamAdapter/MismatchParser.js.map +1 -0
  131. package/esm/BamAdapter/configSchema.d.ts +2 -0
  132. package/esm/BamAdapter/configSchema.js +31 -0
  133. package/esm/BamAdapter/configSchema.js.map +1 -0
  134. package/esm/BamAdapter/index.d.ts +3 -0
  135. package/esm/BamAdapter/index.js +10 -0
  136. package/esm/BamAdapter/index.js.map +1 -0
  137. package/esm/CramAdapter/CramAdapter.d.ts +53 -0
  138. package/esm/CramAdapter/CramAdapter.js +228 -0
  139. package/esm/CramAdapter/CramAdapter.js.map +1 -0
  140. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +49 -0
  141. package/esm/CramAdapter/CramSlightlyLazyFeature.js +349 -0
  142. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
  143. package/esm/CramAdapter/CramTestAdapters.d.ts +29 -0
  144. package/esm/CramAdapter/CramTestAdapters.js +70 -0
  145. package/esm/CramAdapter/CramTestAdapters.js.map +1 -0
  146. package/esm/CramAdapter/configSchema.d.ts +3 -0
  147. package/esm/CramAdapter/configSchema.js +26 -0
  148. package/esm/CramAdapter/configSchema.js.map +1 -0
  149. package/esm/CramAdapter/index.d.ts +3 -0
  150. package/esm/CramAdapter/index.js +11 -0
  151. package/esm/CramAdapter/index.js.map +1 -0
  152. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +9 -0
  153. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +27 -0
  154. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
  155. package/esm/HtsgetBamAdapter/configSchema.d.ts +2 -0
  156. package/esm/HtsgetBamAdapter/configSchema.js +17 -0
  157. package/esm/HtsgetBamAdapter/configSchema.js.map +1 -0
  158. package/esm/HtsgetBamAdapter/index.d.ts +3 -0
  159. package/esm/HtsgetBamAdapter/index.js +16 -0
  160. package/esm/HtsgetBamAdapter/index.js.map +1 -0
  161. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +7 -0
  162. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +34 -0
  163. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
  164. package/esm/LinearAlignmentsDisplay/index.d.ts +2 -0
  165. package/esm/LinearAlignmentsDisplay/index.js +19 -0
  166. package/esm/LinearAlignmentsDisplay/index.js.map +1 -0
  167. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +4 -0
  168. package/esm/LinearAlignmentsDisplay/models/configSchema.js +12 -0
  169. package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
  170. package/esm/LinearAlignmentsDisplay/models/model.d.ts +105 -0
  171. package/esm/LinearAlignmentsDisplay/models/model.js +181 -0
  172. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -0
  173. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +14 -0
  174. package/esm/LinearPileupDisplay/components/ColorByModifications.js +71 -0
  175. package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
  176. package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +9 -0
  177. package/esm/LinearPileupDisplay/components/ColorByTag.js +45 -0
  178. package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
  179. package/esm/LinearPileupDisplay/components/FilterByTag.d.ts +18 -0
  180. package/esm/LinearPileupDisplay/components/FilterByTag.js +123 -0
  181. package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
  182. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +13 -0
  183. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +13 -0
  184. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
  185. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +16 -0
  186. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +41 -0
  187. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
  188. package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +10 -0
  189. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +43 -0
  190. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
  191. package/esm/LinearPileupDisplay/components/SortByTag.d.ts +9 -0
  192. package/esm/LinearPileupDisplay/components/SortByTag.js +43 -0
  193. package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -0
  194. package/esm/LinearPileupDisplay/configSchema.d.ts +6 -0
  195. package/esm/LinearPileupDisplay/configSchema.js +41 -0
  196. package/esm/LinearPileupDisplay/configSchema.js.map +1 -0
  197. package/esm/LinearPileupDisplay/index.d.ts +2 -0
  198. package/esm/LinearPileupDisplay/index.js +18 -0
  199. package/esm/LinearPileupDisplay/index.js.map +1 -0
  200. package/esm/LinearPileupDisplay/model.d.ts +332 -0
  201. package/esm/LinearPileupDisplay/model.js +575 -0
  202. package/esm/LinearPileupDisplay/model.js.map +1 -0
  203. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +13 -0
  204. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +56 -0
  205. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
  206. package/esm/LinearSNPCoverageDisplay/index.d.ts +2 -0
  207. package/esm/LinearSNPCoverageDisplay/index.js +18 -0
  208. package/esm/LinearSNPCoverageDisplay/index.js.map +1 -0
  209. package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +2 -0
  210. package/esm/LinearSNPCoverageDisplay/models/configSchema.js +44 -0
  211. package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
  212. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +370 -0
  213. package/esm/LinearSNPCoverageDisplay/models/model.js +186 -0
  214. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -0
  215. package/esm/NestedFrequencyTable.d.ts +14 -0
  216. package/esm/NestedFrequencyTable.js +101 -0
  217. package/esm/NestedFrequencyTable.js.map +1 -0
  218. package/esm/PileupRPC/rpcMethods.d.ts +34 -0
  219. package/esm/PileupRPC/rpcMethods.js +70 -0
  220. package/esm/PileupRPC/rpcMethods.js.map +1 -0
  221. package/esm/PileupRenderer/PileupLayoutSession.d.ts +32 -0
  222. package/esm/PileupRenderer/PileupLayoutSession.js +32 -0
  223. package/esm/PileupRenderer/PileupLayoutSession.js.map +1 -0
  224. package/esm/PileupRenderer/PileupRenderer.d.ts +178 -0
  225. package/esm/PileupRenderer/PileupRenderer.js +830 -0
  226. package/esm/PileupRenderer/PileupRenderer.js.map +1 -0
  227. package/esm/PileupRenderer/components/PileupRendering.d.ts +23 -0
  228. package/esm/PileupRenderer/components/PileupRendering.js +138 -0
  229. package/esm/PileupRenderer/components/PileupRendering.js.map +1 -0
  230. package/esm/PileupRenderer/configSchema.d.ts +2 -0
  231. package/esm/PileupRenderer/configSchema.js +64 -0
  232. package/esm/PileupRenderer/configSchema.js.map +1 -0
  233. package/esm/PileupRenderer/index.d.ts +2 -0
  234. package/esm/PileupRenderer/index.js +12 -0
  235. package/esm/PileupRenderer/index.js.map +1 -0
  236. package/esm/PileupRenderer/sortUtil.d.ts +8 -0
  237. package/esm/PileupRenderer/sortUtil.js +80 -0
  238. package/esm/PileupRenderer/sortUtil.js.map +1 -0
  239. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +67 -0
  240. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +260 -0
  241. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
  242. package/esm/SNPCoverageAdapter/configSchema.d.ts +3 -0
  243. package/esm/SNPCoverageAdapter/configSchema.js +6 -0
  244. package/esm/SNPCoverageAdapter/configSchema.js.map +1 -0
  245. package/esm/SNPCoverageAdapter/index.d.ts +3 -0
  246. package/esm/SNPCoverageAdapter/index.js +18 -0
  247. package/esm/SNPCoverageAdapter/index.js.map +1 -0
  248. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +20 -0
  249. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +185 -0
  250. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
  251. package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -0
  252. package/esm/SNPCoverageRenderer/configSchema.js +29 -0
  253. package/esm/SNPCoverageRenderer/configSchema.js.map +1 -0
  254. package/esm/SNPCoverageRenderer/index.d.ts +3 -0
  255. package/esm/SNPCoverageRenderer/index.js +14 -0
  256. package/esm/SNPCoverageRenderer/index.js.map +1 -0
  257. package/esm/index.d.ts +10 -0
  258. package/esm/index.js +91 -0
  259. package/esm/index.js.map +1 -0
  260. package/esm/shared.d.ts +25 -0
  261. package/esm/shared.js +28 -0
  262. package/esm/shared.js.map +1 -0
  263. package/esm/util.d.ts +19 -0
  264. package/esm/util.js +83 -0
  265. package/esm/util.js.map +1 -0
  266. package/package.json +23 -15
  267. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +4 -4
  268. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +321 -397
  269. package/src/BamAdapter/BamAdapter.ts +1 -1
  270. package/src/BamAdapter/MismatchParser.ts +2 -2
  271. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -3
  272. package/src/LinearPileupDisplay/components/ColorByModifications.tsx +7 -7
  273. package/src/LinearPileupDisplay/components/ColorByTag.tsx +5 -5
  274. package/src/LinearPileupDisplay/components/FilterByTag.tsx +5 -5
  275. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
  276. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +9 -9
  277. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +5 -5
  278. package/src/LinearPileupDisplay/components/SortByTag.tsx +5 -5
  279. package/src/LinearPileupDisplay/model.ts +18 -12
  280. package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +3 -4
  281. package/src/LinearSNPCoverageDisplay/models/model.ts +28 -26
  282. package/src/PileupRenderer/PileupRenderer.tsx +66 -56
  283. package/src/PileupRenderer/components/PileupRendering.tsx +11 -11
  284. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +4 -3
  285. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +8 -7
  286. package/dist/AlignmentsFeatureDetail/index.test.js +0 -60
  287. package/dist/BamAdapter/BamAdapter.test.js +0 -177
  288. package/dist/BamAdapter/MismatchParser.test.js +0 -251
  289. package/dist/CramAdapter/CramAdapter.test.js +0 -138
  290. package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +0 -83
  291. package/dist/LinearPileupDisplay/configSchema.test.js +0 -92
  292. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +0 -62
  293. package/dist/PileupRenderer/components/PileupRendering.test.js +0 -36
  294. package/dist/declare.d.js +0 -1
  295. package/dist/index.test.js +0 -26
@@ -1,34 +1,23 @@
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  "use strict";
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-
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- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
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-
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- Object.defineProperty(exports, "__esModule", {
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- value: true
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- });
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+ var __importDefault = (this && this.__importDefault) || function (mod) {
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+ return (mod && mod.__esModule) ? mod : { "default": mod };
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+ };
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+ Object.defineProperty(exports, "__esModule", { value: true });
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  exports.configSchema = void 0;
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- exports.default = register;
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-
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- var _configuration = require("@jbrowse/core/configuration");
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-
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- var _configSchema = _interopRequireDefault(require("./configSchema"));
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-
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- var _SNPCoverageRenderer = _interopRequireDefault(require("./SNPCoverageRenderer"));
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-
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- var _pluginWiggle = require("@jbrowse/plugin-wiggle");
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-
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- var configSchema = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {}, {
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- baseConfiguration: _configSchema.default,
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- explicitlyTyped: true
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- });
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- exports.configSchema = configSchema;
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-
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+ var configuration_1 = require("@jbrowse/core/configuration");
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+ var configSchema_1 = __importDefault(require("./configSchema"));
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+ var SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
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+ var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
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+ exports.configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageRenderer', {}, { baseConfiguration: configSchema_1.default, explicitlyTyped: true });
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  function register(pluginManager) {
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- pluginManager.addRendererType(function () {
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- return new _SNPCoverageRenderer.default({
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- name: 'SNPCoverageRenderer',
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- ReactComponent: _pluginWiggle.WiggleRendering,
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- configSchema: configSchema,
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- pluginManager: pluginManager
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+ pluginManager.addRendererType(function () {
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+ return new SNPCoverageRenderer_1.default({
15
+ name: 'SNPCoverageRenderer',
16
+ ReactComponent: plugin_wiggle_1.WiggleRendering,
17
+ configSchema: exports.configSchema,
18
+ pluginManager: pluginManager,
19
+ });
32
20
  });
33
- });
34
- }
21
+ }
22
+ exports.default = register;
23
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageRenderer/index.ts"],"names":[],"mappings":";;;;;;AAAA,6DAAiE;AACjE,gEAAyC;AAEzC,8EAAuD;AAEvD,wDAAwD;AAE3C,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,qBAAqB,EACrB,EAAE,EACF,EAAE,iBAAiB,EAAE,sBAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AAED,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B;QACE,OAAA,IAAI,6BAAmB,CAAC;YACtB,IAAI,EAAE,qBAAqB;YAC3B,cAAc,EAAE,+BAAe;YAC/B,YAAY,sBAAA;YACZ,aAAa,eAAA;SACd,CAAC;IALF,CAKE,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}
package/dist/index.js CHANGED
@@ -1,156 +1,139 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- var _typeof = require("@babel/runtime/helpers/typeof");
6
-
7
- Object.defineProperty(exports, "__esModule", {
8
- value: true
2
+ var __extends = (this && this.__extends) || (function () {
3
+ var extendStatics = function (d, b) {
4
+ extendStatics = Object.setPrototypeOf ||
5
+ ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
6
+ function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
7
+ return extendStatics(d, b);
8
+ };
9
+ return function (d, b) {
10
+ if (typeof b !== "function" && b !== null)
11
+ throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
12
+ extendStatics(d, b);
13
+ function __() { this.constructor = d; }
14
+ d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
15
+ };
16
+ })();
17
+ var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
18
+ if (k2 === undefined) k2 = k;
19
+ var desc = Object.getOwnPropertyDescriptor(m, k);
20
+ if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
21
+ desc = { enumerable: true, get: function() { return m[k]; } };
22
+ }
23
+ Object.defineProperty(o, k2, desc);
24
+ }) : (function(o, m, k, k2) {
25
+ if (k2 === undefined) k2 = k;
26
+ o[k2] = m[k];
27
+ }));
28
+ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
29
+ Object.defineProperty(o, "default", { enumerable: true, value: v });
30
+ }) : function(o, v) {
31
+ o["default"] = v;
9
32
  });
10
- exports.default = exports.MismatchParser = void 0;
11
-
12
- var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
13
-
14
- var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
15
-
16
- var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
17
-
18
- var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
19
-
20
- var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
21
-
22
- var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
23
-
24
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
25
-
26
- var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
27
-
28
- var MismatchParser = _interopRequireWildcard(require("./BamAdapter/MismatchParser"));
29
-
33
+ var __importStar = (this && this.__importStar) || function (mod) {
34
+ if (mod && mod.__esModule) return mod;
35
+ var result = {};
36
+ if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
37
+ __setModuleDefault(result, mod);
38
+ return result;
39
+ };
40
+ var __importDefault = (this && this.__importDefault) || function (mod) {
41
+ return (mod && mod.__esModule) ? mod : { "default": mod };
42
+ };
43
+ Object.defineProperty(exports, "__esModule", { value: true });
44
+ exports.MismatchParser = void 0;
45
+ var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
46
+ var MismatchParser = __importStar(require("./BamAdapter/MismatchParser"));
30
47
  exports.MismatchParser = MismatchParser;
31
-
32
- var _CramAdapter = _interopRequireDefault(require("./CramAdapter"));
33
-
34
- var _BamAdapter = _interopRequireDefault(require("./BamAdapter"));
35
-
36
- var _HtsgetBamAdapter = _interopRequireDefault(require("./HtsgetBamAdapter"));
37
-
38
- var _SNPCoverageAdapter = _interopRequireDefault(require("./SNPCoverageAdapter"));
39
-
40
- var _SNPCoverageRenderer = _interopRequireDefault(require("./SNPCoverageRenderer"));
41
-
42
- var _PileupRenderer = _interopRequireDefault(require("./PileupRenderer"));
43
-
44
- var _LinearAlignmentsDisplay = _interopRequireDefault(require("./LinearAlignmentsDisplay"));
45
-
46
- var _LinearSNPCoverageDisplay = _interopRequireDefault(require("./LinearSNPCoverageDisplay"));
47
-
48
- var _LinearPileupDisplay = _interopRequireDefault(require("./LinearPileupDisplay"));
49
-
50
- var _AlignmentsTrack = _interopRequireDefault(require("./AlignmentsTrack"));
51
-
52
- var _AlignmentsFeatureDetail = _interopRequireDefault(require("./AlignmentsFeatureDetail"));
53
-
54
- var _rpcMethods = require("./PileupRPC/rpcMethods");
55
-
56
- var _tracks = require("@jbrowse/core/util/tracks");
57
-
58
- function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
59
-
60
- function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
61
-
62
- function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
63
-
64
- function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
65
-
66
- var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
67
- (0, _inherits2.default)(AlignmentsPlugin, _Plugin);
68
-
69
- var _super = _createSuper(AlignmentsPlugin);
70
-
71
- function AlignmentsPlugin() {
72
- var _this;
73
-
74
- (0, _classCallCheck2.default)(this, AlignmentsPlugin);
75
-
76
- for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
77
- args[_key] = arguments[_key];
78
- }
79
-
80
- _this = _super.call.apply(_super, [this].concat(args));
81
- (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'AlignmentsPlugin');
82
- return _this;
83
- }
84
-
85
- (0, _createClass2.default)(AlignmentsPlugin, [{
86
- key: "install",
87
- value: function install(pluginManager) {
88
- ;
89
- [_BamAdapter.default, _CramAdapter.default, _LinearPileupDisplay.default, _LinearSNPCoverageDisplay.default, _AlignmentsTrack.default, _SNPCoverageAdapter.default, _HtsgetBamAdapter.default, _PileupRenderer.default, _SNPCoverageRenderer.default, _LinearAlignmentsDisplay.default, _AlignmentsFeatureDetail.default].map(function (f) {
90
- return f(pluginManager);
91
- });
92
- pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
93
- return function (file, index, adapterHint) {
94
- var regexGuess = /\.cram$/i;
95
- var adapterName = 'CramAdapter';
96
- var fileName = (0, _tracks.getFileName)(file);
97
- var obj = {
98
- type: adapterName,
99
- cramLocation: file,
100
- craiLocation: index || (0, _tracks.makeIndex)(file, '.crai')
101
- };
102
-
103
- if (regexGuess.test(fileName) && !adapterHint) {
104
- return obj;
105
- } else if (adapterHint === adapterName) {
106
- return obj;
107
- }
108
-
109
- return adapterGuesser(file, index, adapterHint);
110
- };
111
- });
112
- pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
113
- return function (file, index, adapterHint) {
114
- var regexGuess = /\.bam$/i;
115
- var adapterName = 'BamAdapter';
116
- var fileName = (0, _tracks.getFileName)(file);
117
- var indexName = index && (0, _tracks.getFileName)(index);
118
- var obj = {
119
- type: adapterName,
120
- bamLocation: file,
121
- index: {
122
- location: index || (0, _tracks.makeIndex)(file, '.bai'),
123
- indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'BAI')
124
- }
125
- };
126
-
127
- if (regexGuess.test(fileName) && !adapterHint) {
128
- return obj;
129
- } else if (adapterHint === adapterName) {
130
- return obj;
131
- }
132
-
133
- return adapterGuesser(file, index, adapterHint);
134
- };
135
- });
136
- pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
137
- return function (adapterName) {
138
- if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
139
- return 'AlignmentsTrack';
140
- }
141
-
142
- return trackTypeGuesser(adapterName);
143
- };
144
- });
145
- pluginManager.addRpcMethod(function () {
146
- return new _rpcMethods.PileupGetGlobalValueForTag(pluginManager);
147
- });
148
- pluginManager.addRpcMethod(function () {
149
- return new _rpcMethods.PileupGetVisibleModifications(pluginManager);
150
- });
48
+ var CramAdapter_1 = __importDefault(require("./CramAdapter"));
49
+ var BamAdapter_1 = __importDefault(require("./BamAdapter"));
50
+ var HtsgetBamAdapter_1 = __importDefault(require("./HtsgetBamAdapter"));
51
+ var SNPCoverageAdapter_1 = __importDefault(require("./SNPCoverageAdapter"));
52
+ var SNPCoverageRenderer_1 = __importDefault(require("./SNPCoverageRenderer"));
53
+ var PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
54
+ var LinearAlignmentsDisplay_1 = __importDefault(require("./LinearAlignmentsDisplay"));
55
+ var LinearSNPCoverageDisplay_1 = __importDefault(require("./LinearSNPCoverageDisplay"));
56
+ var LinearPileupDisplay_1 = __importDefault(require("./LinearPileupDisplay"));
57
+ var AlignmentsTrack_1 = __importDefault(require("./AlignmentsTrack"));
58
+ var AlignmentsFeatureDetail_1 = __importDefault(require("./AlignmentsFeatureDetail"));
59
+ var rpcMethods_1 = require("./PileupRPC/rpcMethods");
60
+ var tracks_1 = require("@jbrowse/core/util/tracks");
61
+ var AlignmentsPlugin = /** @class */ (function (_super) {
62
+ __extends(AlignmentsPlugin, _super);
63
+ function AlignmentsPlugin() {
64
+ var _this = _super !== null && _super.apply(this, arguments) || this;
65
+ _this.name = 'AlignmentsPlugin';
66
+ return _this;
151
67
  }
152
- }]);
153
- return AlignmentsPlugin;
154
- }(_Plugin2.default);
155
-
156
- exports.default = AlignmentsPlugin;
68
+ AlignmentsPlugin.prototype.install = function (pluginManager) {
69
+ ;
70
+ [
71
+ BamAdapter_1.default,
72
+ CramAdapter_1.default,
73
+ LinearPileupDisplay_1.default,
74
+ LinearSNPCoverageDisplay_1.default,
75
+ AlignmentsTrack_1.default,
76
+ SNPCoverageAdapter_1.default,
77
+ HtsgetBamAdapter_1.default,
78
+ PileupRenderer_1.default,
79
+ SNPCoverageRenderer_1.default,
80
+ LinearAlignmentsDisplay_1.default,
81
+ AlignmentsFeatureDetail_1.default,
82
+ ].map(function (f) { return f(pluginManager); });
83
+ pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
84
+ return function (file, index, adapterHint) {
85
+ var regexGuess = /\.cram$/i;
86
+ var adapterName = 'CramAdapter';
87
+ var fileName = (0, tracks_1.getFileName)(file);
88
+ var obj = {
89
+ type: adapterName,
90
+ cramLocation: file,
91
+ craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
92
+ };
93
+ if (regexGuess.test(fileName) && !adapterHint) {
94
+ return obj;
95
+ }
96
+ else if (adapterHint === adapterName) {
97
+ return obj;
98
+ }
99
+ return adapterGuesser(file, index, adapterHint);
100
+ };
101
+ });
102
+ pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
103
+ return function (file, index, adapterHint) {
104
+ var regexGuess = /\.bam$/i;
105
+ var adapterName = 'BamAdapter';
106
+ var fileName = (0, tracks_1.getFileName)(file);
107
+ var indexName = index && (0, tracks_1.getFileName)(index);
108
+ var obj = {
109
+ type: adapterName,
110
+ bamLocation: file,
111
+ index: {
112
+ location: index || (0, tracks_1.makeIndex)(file, '.bai'),
113
+ indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
114
+ },
115
+ };
116
+ if (regexGuess.test(fileName) && !adapterHint) {
117
+ return obj;
118
+ }
119
+ else if (adapterHint === adapterName) {
120
+ return obj;
121
+ }
122
+ return adapterGuesser(file, index, adapterHint);
123
+ };
124
+ });
125
+ pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
126
+ return function (adapterName) {
127
+ if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
128
+ return 'AlignmentsTrack';
129
+ }
130
+ return trackTypeGuesser(adapterName);
131
+ };
132
+ });
133
+ pluginManager.addRpcMethod(function () { return new rpcMethods_1.PileupGetGlobalValueForTag(pluginManager); });
134
+ pluginManager.addRpcMethod(function () { return new rpcMethods_1.PileupGetVisibleModifications(pluginManager); });
135
+ };
136
+ return AlignmentsPlugin;
137
+ }(Plugin_1.default));
138
+ exports.default = AlignmentsPlugin;
139
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
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package/dist/shared.js CHANGED
@@ -1,96 +1,88 @@
1
1
  "use strict";
2
-
3
- var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
4
-
5
- Object.defineProperty(exports, "__esModule", {
6
- value: true
7
- });
8
- exports.getUniqueModificationValues = getUniqueModificationValues;
9
- exports.getUniqueTagValues = getUniqueTagValues;
10
-
11
- var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
12
-
13
- var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
14
-
15
- var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
16
-
17
- var _util = require("@jbrowse/core/util");
18
-
19
- var _tracks = require("@jbrowse/core/util/tracks");
20
-
21
- function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
22
-
23
- function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
24
-
25
- function getUniqueTagValues(_x, _x2, _x3, _x4) {
26
- return _getUniqueTagValues.apply(this, arguments);
27
- }
28
-
29
- function _getUniqueTagValues() {
30
- _getUniqueTagValues = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(self, colorScheme, blocks, opts) {
31
- var _getSession, rpcManager, adapterConfig, sessionId, values;
32
-
33
- return _regenerator.default.wrap(function _callee$(_context) {
34
- while (1) {
35
- switch (_context.prev = _context.next) {
36
- case 0:
37
- _getSession = (0, _util.getSession)(self), rpcManager = _getSession.rpcManager;
38
- adapterConfig = self.adapterConfig;
39
- sessionId = (0, _tracks.getRpcSessionId)(self);
40
- _context.next = 5;
41
- return rpcManager.call((0, _tracks.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', _objectSpread({
42
- adapterConfig: adapterConfig,
43
- tag: colorScheme.tag,
44
- sessionId: sessionId,
45
- regions: blocks.contentBlocks
46
- }, opts));
47
-
48
- case 5:
49
- values = _context.sent;
50
- return _context.abrupt("return", values);
51
-
52
- case 7:
53
- case "end":
54
- return _context.stop();
2
+ var __assign = (this && this.__assign) || function () {
3
+ __assign = Object.assign || function(t) {
4
+ for (var s, i = 1, n = arguments.length; i < n; i++) {
5
+ s = arguments[i];
6
+ for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
7
+ t[p] = s[p];
55
8
  }
56
- }
57
- }, _callee);
58
- }));
59
- return _getUniqueTagValues.apply(this, arguments);
9
+ return t;
10
+ };
11
+ return __assign.apply(this, arguments);
12
+ };
13
+ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
14
+ function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
15
+ return new (P || (P = Promise))(function (resolve, reject) {
16
+ function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
17
+ function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
18
+ function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
19
+ step((generator = generator.apply(thisArg, _arguments || [])).next());
20
+ });
21
+ };
22
+ var __generator = (this && this.__generator) || function (thisArg, body) {
23
+ var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
24
+ return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
25
+ function verb(n) { return function (v) { return step([n, v]); }; }
26
+ function step(op) {
27
+ if (f) throw new TypeError("Generator is already executing.");
28
+ while (_) try {
29
+ if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
30
+ if (y = 0, t) op = [op[0] & 2, t.value];
31
+ switch (op[0]) {
32
+ case 0: case 1: t = op; break;
33
+ case 4: _.label++; return { value: op[1], done: false };
34
+ case 5: _.label++; y = op[1]; op = [0]; continue;
35
+ case 7: op = _.ops.pop(); _.trys.pop(); continue;
36
+ default:
37
+ if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
38
+ if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
39
+ if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
40
+ if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
41
+ if (t[2]) _.ops.pop();
42
+ _.trys.pop(); continue;
43
+ }
44
+ op = body.call(thisArg, _);
45
+ } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
46
+ if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
47
+ }
48
+ };
49
+ Object.defineProperty(exports, "__esModule", { value: true });
50
+ exports.getUniqueModificationValues = exports.getUniqueTagValues = void 0;
51
+ var util_1 = require("@jbrowse/core/util");
52
+ var tracks_1 = require("@jbrowse/core/util/tracks");
53
+ function getUniqueTagValues(self, colorScheme, blocks, opts) {
54
+ return __awaiter(this, void 0, void 0, function () {
55
+ var rpcManager, adapterConfig, sessionId, values;
56
+ return __generator(this, function (_a) {
57
+ switch (_a.label) {
58
+ case 0:
59
+ rpcManager = (0, util_1.getSession)(self).rpcManager;
60
+ adapterConfig = self.adapterConfig;
61
+ sessionId = (0, tracks_1.getRpcSessionId)(self);
62
+ return [4 /*yield*/, rpcManager.call((0, tracks_1.getRpcSessionId)(self), 'PileupGetGlobalValueForTag', __assign({ adapterConfig: adapterConfig, tag: colorScheme.tag, sessionId: sessionId, regions: blocks.contentBlocks }, opts))];
63
+ case 1:
64
+ values = _a.sent();
65
+ return [2 /*return*/, values];
66
+ }
67
+ });
68
+ });
60
69
  }
61
-
62
- function getUniqueModificationValues(_x5, _x6, _x7, _x8, _x9) {
63
- return _getUniqueModificationValues.apply(this, arguments);
70
+ exports.getUniqueTagValues = getUniqueTagValues;
71
+ function getUniqueModificationValues(self, adapterConfig, colorScheme, blocks, opts) {
72
+ return __awaiter(this, void 0, void 0, function () {
73
+ var rpcManager, sessionId, values;
74
+ return __generator(this, function (_a) {
75
+ switch (_a.label) {
76
+ case 0:
77
+ rpcManager = (0, util_1.getSession)(self).rpcManager;
78
+ sessionId = (0, tracks_1.getRpcSessionId)(self);
79
+ return [4 /*yield*/, rpcManager.call(sessionId, 'PileupGetVisibleModifications', __assign({ adapterConfig: adapterConfig, tag: colorScheme.tag, sessionId: sessionId, regions: blocks.contentBlocks }, opts))];
80
+ case 1:
81
+ values = _a.sent();
82
+ return [2 /*return*/, values];
83
+ }
84
+ });
85
+ });
64
86
  }
65
-
66
- function _getUniqueModificationValues() {
67
- _getUniqueModificationValues = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(self, adapterConfig, colorScheme, blocks, opts) {
68
- var _getSession2, rpcManager, sessionId, values;
69
-
70
- return _regenerator.default.wrap(function _callee2$(_context2) {
71
- while (1) {
72
- switch (_context2.prev = _context2.next) {
73
- case 0:
74
- _getSession2 = (0, _util.getSession)(self), rpcManager = _getSession2.rpcManager;
75
- sessionId = (0, _tracks.getRpcSessionId)(self);
76
- _context2.next = 4;
77
- return rpcManager.call(sessionId, 'PileupGetVisibleModifications', _objectSpread({
78
- adapterConfig: adapterConfig,
79
- tag: colorScheme.tag,
80
- sessionId: sessionId,
81
- regions: blocks.contentBlocks
82
- }, opts));
83
-
84
- case 4:
85
- values = _context2.sent;
86
- return _context2.abrupt("return", values);
87
-
88
- case 6:
89
- case "end":
90
- return _context2.stop();
91
- }
92
- }
93
- }, _callee2);
94
- }));
95
- return _getUniqueModificationValues.apply(this, arguments);
96
- }
87
+ exports.getUniqueModificationValues = getUniqueModificationValues;
88
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