@jbrowse/plugin-alignments 1.7.9 → 2.0.0

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Files changed (294) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +192 -207
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
  3. package/dist/AlignmentsFeatureDetail/index.d.ts +28 -3
  4. package/dist/AlignmentsFeatureDetail/index.js +48 -55
  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.js +345 -585
  9. package/dist/BamAdapter/BamAdapter.js.map +1 -0
  10. package/dist/BamAdapter/BamSlightlyLazyFeature.js +143 -174
  11. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
  12. package/dist/BamAdapter/MismatchParser.js +340 -416
  13. package/dist/BamAdapter/MismatchParser.js.map +1 -0
  14. package/dist/BamAdapter/configSchema.js +33 -46
  15. package/dist/BamAdapter/configSchema.js.map +1 -0
  16. package/dist/BamAdapter/index.js +36 -32
  17. package/dist/BamAdapter/index.js.map +1 -0
  18. package/dist/CramAdapter/CramAdapter.js +376 -644
  19. package/dist/CramAdapter/CramAdapter.js.map +1 -0
  20. package/dist/CramAdapter/CramSlightlyLazyFeature.js +374 -439
  21. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
  22. package/dist/CramAdapter/CramTestAdapters.js +169 -227
  23. package/dist/CramAdapter/CramTestAdapters.js.map +1 -0
  24. package/dist/CramAdapter/configSchema.js +28 -38
  25. package/dist/CramAdapter/configSchema.js.map +1 -0
  26. package/dist/CramAdapter/index.js +37 -32
  27. package/dist/CramAdapter/index.js.map +1 -0
  28. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +91 -93
  29. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
  30. package/dist/HtsgetBamAdapter/configSchema.js +19 -29
  31. package/dist/HtsgetBamAdapter/configSchema.js.map +1 -0
  32. package/dist/HtsgetBamAdapter/index.js +44 -38
  33. package/dist/HtsgetBamAdapter/index.js.map +1 -0
  34. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +36 -65
  35. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
  36. package/dist/LinearAlignmentsDisplay/index.js +22 -28
  37. package/dist/LinearAlignmentsDisplay/index.js.map +1 -0
  38. package/dist/LinearAlignmentsDisplay/models/configSchema.js +12 -23
  39. package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
  40. package/dist/LinearAlignmentsDisplay/models/model.d.ts +10 -10
  41. package/dist/LinearAlignmentsDisplay/models/model.js +257 -245
  42. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -0
  43. package/dist/LinearPileupDisplay/components/ColorByModifications.js +98 -116
  44. package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
  45. package/dist/LinearPileupDisplay/components/ColorByTag.js +82 -91
  46. package/dist/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
  47. package/dist/LinearPileupDisplay/components/FilterByTag.js +156 -192
  48. package/dist/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
  49. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +15 -29
  50. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
  51. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +79 -93
  52. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
  53. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +78 -81
  54. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
  55. package/dist/LinearPileupDisplay/components/SortByTag.js +80 -88
  56. package/dist/LinearPileupDisplay/components/SortByTag.js.map +1 -0
  57. package/dist/LinearPileupDisplay/configSchema.js +40 -42
  58. package/dist/LinearPileupDisplay/configSchema.js.map +1 -0
  59. package/dist/LinearPileupDisplay/index.js +21 -27
  60. package/dist/LinearPileupDisplay/index.js.map +1 -0
  61. package/dist/LinearPileupDisplay/model.d.ts +33 -20
  62. package/dist/LinearPileupDisplay/model.js +702 -716
  63. package/dist/LinearPileupDisplay/model.js.map +1 -0
  64. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  65. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +105 -57
  66. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
  67. package/dist/LinearSNPCoverageDisplay/index.js +21 -27
  68. package/dist/LinearSNPCoverageDisplay/index.js.map +1 -0
  69. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +45 -55
  70. package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
  71. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +14 -12
  72. package/dist/LinearSNPCoverageDisplay/models/model.js +257 -230
  73. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -0
  74. package/dist/NestedFrequencyTable.js +104 -139
  75. package/dist/NestedFrequencyTable.js.map +1 -0
  76. package/dist/PileupRPC/rpcMethods.js +199 -278
  77. package/dist/PileupRPC/rpcMethods.js.map +1 -0
  78. package/dist/PileupRenderer/PileupLayoutSession.js +56 -76
  79. package/dist/PileupRenderer/PileupLayoutSession.js.map +1 -0
  80. package/dist/PileupRenderer/PileupRenderer.d.ts +56 -11
  81. package/dist/PileupRenderer/PileupRenderer.js +942 -1134
  82. package/dist/PileupRenderer/PileupRenderer.js.map +1 -0
  83. package/dist/PileupRenderer/components/PileupRendering.d.ts +1 -1
  84. package/dist/PileupRenderer/components/PileupRendering.js +173 -253
  85. package/dist/PileupRenderer/components/PileupRendering.js.map +1 -0
  86. package/dist/PileupRenderer/configSchema.js +65 -71
  87. package/dist/PileupRenderer/configSchema.js.map +1 -0
  88. package/dist/PileupRenderer/index.js +17 -22
  89. package/dist/PileupRenderer/index.js.map +1 -0
  90. package/dist/PileupRenderer/sortUtil.js +83 -107
  91. package/dist/PileupRenderer/sortUtil.js.map +1 -0
  92. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +2 -0
  93. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +436 -586
  94. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
  95. package/dist/SNPCoverageAdapter/configSchema.js +10 -20
  96. package/dist/SNPCoverageAdapter/configSchema.js.map +1 -0
  97. package/dist/SNPCoverageAdapter/index.js +46 -41
  98. package/dist/SNPCoverageAdapter/index.js.map +1 -0
  99. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +1 -1
  100. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +265 -290
  101. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
  102. package/dist/SNPCoverageRenderer/configSchema.js +30 -39
  103. package/dist/SNPCoverageRenderer/configSchema.js.map +1 -0
  104. package/dist/SNPCoverageRenderer/index.js +19 -30
  105. package/dist/SNPCoverageRenderer/index.js.map +1 -0
  106. package/dist/index.js +135 -152
  107. package/dist/index.js.map +1 -0
  108. package/dist/shared.js +84 -92
  109. package/dist/shared.js.map +1 -0
  110. package/dist/util.js +130 -121
  111. package/dist/util.js.map +1 -0
  112. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +6 -0
  113. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +145 -0
  114. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -0
  115. package/esm/AlignmentsFeatureDetail/index.d.ts +38 -0
  116. package/esm/AlignmentsFeatureDetail/index.js +23 -0
  117. package/esm/AlignmentsFeatureDetail/index.js.map +1 -0
  118. package/esm/AlignmentsTrack/index.d.ts +2 -0
  119. package/esm/AlignmentsTrack/index.js +23 -0
  120. package/esm/AlignmentsTrack/index.js.map +1 -0
  121. package/esm/BamAdapter/BamAdapter.d.ts +40 -0
  122. package/esm/BamAdapter/BamAdapter.js +173 -0
  123. package/esm/BamAdapter/BamAdapter.js.map +1 -0
  124. package/esm/BamAdapter/BamSlightlyLazyFeature.d.ts +33 -0
  125. package/esm/BamAdapter/BamSlightlyLazyFeature.js +107 -0
  126. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -0
  127. package/esm/BamAdapter/MismatchParser.d.ts +25 -0
  128. package/esm/BamAdapter/MismatchParser.js +294 -0
  129. package/esm/BamAdapter/MismatchParser.js.map +1 -0
  130. package/esm/BamAdapter/configSchema.d.ts +2 -0
  131. package/esm/BamAdapter/configSchema.js +31 -0
  132. package/esm/BamAdapter/configSchema.js.map +1 -0
  133. package/esm/BamAdapter/index.d.ts +3 -0
  134. package/esm/BamAdapter/index.js +10 -0
  135. package/esm/BamAdapter/index.js.map +1 -0
  136. package/esm/CramAdapter/CramAdapter.d.ts +53 -0
  137. package/esm/CramAdapter/CramAdapter.js +228 -0
  138. package/esm/CramAdapter/CramAdapter.js.map +1 -0
  139. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +49 -0
  140. package/esm/CramAdapter/CramSlightlyLazyFeature.js +349 -0
  141. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -0
  142. package/esm/CramAdapter/CramTestAdapters.d.ts +29 -0
  143. package/esm/CramAdapter/CramTestAdapters.js +70 -0
  144. package/esm/CramAdapter/CramTestAdapters.js.map +1 -0
  145. package/esm/CramAdapter/configSchema.d.ts +3 -0
  146. package/esm/CramAdapter/configSchema.js +26 -0
  147. package/esm/CramAdapter/configSchema.js.map +1 -0
  148. package/esm/CramAdapter/index.d.ts +3 -0
  149. package/esm/CramAdapter/index.js +11 -0
  150. package/esm/CramAdapter/index.js.map +1 -0
  151. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +9 -0
  152. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +27 -0
  153. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map +1 -0
  154. package/esm/HtsgetBamAdapter/configSchema.d.ts +2 -0
  155. package/esm/HtsgetBamAdapter/configSchema.js +17 -0
  156. package/esm/HtsgetBamAdapter/configSchema.js.map +1 -0
  157. package/esm/HtsgetBamAdapter/index.d.ts +3 -0
  158. package/esm/HtsgetBamAdapter/index.js +16 -0
  159. package/esm/HtsgetBamAdapter/index.js.map +1 -0
  160. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +7 -0
  161. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +34 -0
  162. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -0
  163. package/esm/LinearAlignmentsDisplay/index.d.ts +2 -0
  164. package/esm/LinearAlignmentsDisplay/index.js +19 -0
  165. package/esm/LinearAlignmentsDisplay/index.js.map +1 -0
  166. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +4 -0
  167. package/esm/LinearAlignmentsDisplay/models/configSchema.js +12 -0
  168. package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -0
  169. package/esm/LinearAlignmentsDisplay/models/model.d.ts +105 -0
  170. package/esm/LinearAlignmentsDisplay/models/model.js +181 -0
  171. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -0
  172. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +14 -0
  173. package/esm/LinearPileupDisplay/components/ColorByModifications.js +71 -0
  174. package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +1 -0
  175. package/esm/LinearPileupDisplay/components/ColorByTag.d.ts +9 -0
  176. package/esm/LinearPileupDisplay/components/ColorByTag.js +45 -0
  177. package/esm/LinearPileupDisplay/components/ColorByTag.js.map +1 -0
  178. package/esm/LinearPileupDisplay/components/FilterByTag.d.ts +18 -0
  179. package/esm/LinearPileupDisplay/components/FilterByTag.js +123 -0
  180. package/esm/LinearPileupDisplay/components/FilterByTag.js.map +1 -0
  181. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +13 -0
  182. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +13 -0
  183. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -0
  184. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +16 -0
  185. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +41 -0
  186. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +1 -0
  187. package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts +10 -0
  188. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +43 -0
  189. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +1 -0
  190. package/esm/LinearPileupDisplay/components/SortByTag.d.ts +9 -0
  191. package/esm/LinearPileupDisplay/components/SortByTag.js +43 -0
  192. package/esm/LinearPileupDisplay/components/SortByTag.js.map +1 -0
  193. package/esm/LinearPileupDisplay/configSchema.d.ts +6 -0
  194. package/esm/LinearPileupDisplay/configSchema.js +41 -0
  195. package/esm/LinearPileupDisplay/configSchema.js.map +1 -0
  196. package/esm/LinearPileupDisplay/index.d.ts +2 -0
  197. package/esm/LinearPileupDisplay/index.js +18 -0
  198. package/esm/LinearPileupDisplay/index.js.map +1 -0
  199. package/esm/LinearPileupDisplay/model.d.ts +332 -0
  200. package/esm/LinearPileupDisplay/model.js +576 -0
  201. package/esm/LinearPileupDisplay/model.js.map +1 -0
  202. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +10 -0
  203. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +57 -0
  204. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -0
  205. package/esm/LinearSNPCoverageDisplay/index.d.ts +2 -0
  206. package/esm/LinearSNPCoverageDisplay/index.js +18 -0
  207. package/esm/LinearSNPCoverageDisplay/index.js.map +1 -0
  208. package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +2 -0
  209. package/esm/LinearSNPCoverageDisplay/models/configSchema.js +44 -0
  210. package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map +1 -0
  211. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +348 -0
  212. package/esm/LinearSNPCoverageDisplay/models/model.js +185 -0
  213. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -0
  214. package/esm/NestedFrequencyTable.d.ts +14 -0
  215. package/esm/NestedFrequencyTable.js +101 -0
  216. package/esm/NestedFrequencyTable.js.map +1 -0
  217. package/esm/PileupRPC/rpcMethods.d.ts +34 -0
  218. package/esm/PileupRPC/rpcMethods.js +70 -0
  219. package/esm/PileupRPC/rpcMethods.js.map +1 -0
  220. package/esm/PileupRenderer/PileupLayoutSession.d.ts +32 -0
  221. package/esm/PileupRenderer/PileupLayoutSession.js +32 -0
  222. package/esm/PileupRenderer/PileupLayoutSession.js.map +1 -0
  223. package/esm/PileupRenderer/PileupRenderer.d.ts +182 -0
  224. package/esm/PileupRenderer/PileupRenderer.js +830 -0
  225. package/esm/PileupRenderer/PileupRenderer.js.map +1 -0
  226. package/esm/PileupRenderer/components/PileupRendering.d.ts +23 -0
  227. package/esm/PileupRenderer/components/PileupRendering.js +138 -0
  228. package/esm/PileupRenderer/components/PileupRendering.js.map +1 -0
  229. package/esm/PileupRenderer/configSchema.d.ts +2 -0
  230. package/esm/PileupRenderer/configSchema.js +64 -0
  231. package/esm/PileupRenderer/configSchema.js.map +1 -0
  232. package/esm/PileupRenderer/index.d.ts +2 -0
  233. package/esm/PileupRenderer/index.js +12 -0
  234. package/esm/PileupRenderer/index.js.map +1 -0
  235. package/esm/PileupRenderer/sortUtil.d.ts +8 -0
  236. package/esm/PileupRenderer/sortUtil.js +80 -0
  237. package/esm/PileupRenderer/sortUtil.js.map +1 -0
  238. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +67 -0
  239. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +259 -0
  240. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +1 -0
  241. package/esm/SNPCoverageAdapter/configSchema.d.ts +3 -0
  242. package/esm/SNPCoverageAdapter/configSchema.js +6 -0
  243. package/esm/SNPCoverageAdapter/configSchema.js.map +1 -0
  244. package/esm/SNPCoverageAdapter/index.d.ts +3 -0
  245. package/esm/SNPCoverageAdapter/index.js +18 -0
  246. package/esm/SNPCoverageAdapter/index.js.map +1 -0
  247. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +20 -0
  248. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +185 -0
  249. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -0
  250. package/esm/SNPCoverageRenderer/configSchema.d.ts +2 -0
  251. package/esm/SNPCoverageRenderer/configSchema.js +29 -0
  252. package/esm/SNPCoverageRenderer/configSchema.js.map +1 -0
  253. package/esm/SNPCoverageRenderer/index.d.ts +3 -0
  254. package/esm/SNPCoverageRenderer/index.js +14 -0
  255. package/esm/SNPCoverageRenderer/index.js.map +1 -0
  256. package/esm/index.d.ts +10 -0
  257. package/esm/index.js +91 -0
  258. package/esm/index.js.map +1 -0
  259. package/esm/shared.d.ts +25 -0
  260. package/esm/shared.js +28 -0
  261. package/esm/shared.js.map +1 -0
  262. package/esm/util.d.ts +19 -0
  263. package/esm/util.js +83 -0
  264. package/esm/util.js.map +1 -0
  265. package/package.json +19 -11
  266. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +16 -6
  267. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +321 -397
  268. package/src/AlignmentsFeatureDetail/index.ts +7 -17
  269. package/src/BamAdapter/MismatchParser.ts +1 -0
  270. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -3
  271. package/src/LinearPileupDisplay/components/ColorByModifications.tsx +7 -7
  272. package/src/LinearPileupDisplay/components/ColorByTag.tsx +5 -5
  273. package/src/LinearPileupDisplay/components/FilterByTag.tsx +5 -5
  274. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
  275. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +9 -9
  276. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +5 -5
  277. package/src/LinearPileupDisplay/components/SortByTag.tsx +5 -5
  278. package/src/LinearPileupDisplay/model.ts +90 -32
  279. package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +44 -30
  280. package/src/LinearSNPCoverageDisplay/models/model.ts +25 -25
  281. package/src/PileupRenderer/PileupRenderer.tsx +399 -198
  282. package/src/PileupRenderer/components/PileupRendering.tsx +11 -11
  283. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +5 -0
  284. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +7 -5
  285. package/dist/AlignmentsFeatureDetail/index.test.js +0 -60
  286. package/dist/BamAdapter/BamAdapter.test.js +0 -177
  287. package/dist/BamAdapter/MismatchParser.test.js +0 -251
  288. package/dist/CramAdapter/CramAdapter.test.js +0 -138
  289. package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +0 -83
  290. package/dist/LinearPileupDisplay/configSchema.test.js +0 -92
  291. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +0 -62
  292. package/dist/PileupRenderer/components/PileupRendering.test.js +0 -36
  293. package/dist/declare.d.js +0 -1
  294. package/dist/index.test.js +0 -26
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@@ -0,0 +1,23 @@
1
+ import React from 'react';
2
+ import { Region } from '@jbrowse/core/util/types';
3
+ import type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view';
4
+ declare function PileupRendering(props: {
5
+ blockKey: string;
6
+ displayModel: BaseLinearDisplayModel;
7
+ width: number;
8
+ height: number;
9
+ regions: Region[];
10
+ bpPerPx: number;
11
+ sortedBy?: {
12
+ type: string;
13
+ pos: number;
14
+ refName: string;
15
+ };
16
+ colorBy?: {
17
+ type: string;
18
+ tag?: string;
19
+ };
20
+ onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void;
21
+ }): JSX.Element;
22
+ declare const _default: typeof PileupRendering;
23
+ export default _default;
@@ -0,0 +1,138 @@
1
+ import React, { useRef, useState, useEffect } from 'react';
2
+ import { PrerenderedCanvas } from '@jbrowse/core/ui';
3
+ import { bpSpanPx } from '@jbrowse/core/util';
4
+ import { observer } from 'mobx-react';
5
+ // used so that user can click-away-from-feature below the laid out features
6
+ // (issue #1248)
7
+ const canvasPadding = 100;
8
+ function PileupRendering(props) {
9
+ const { onMouseMove, blockKey, displayModel, width, height, regions, bpPerPx, sortedBy, colorBy, } = props;
10
+ const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } = displayModel;
11
+ const [region] = regions;
12
+ const highlightOverlayCanvas = useRef(null);
13
+ const [mouseIsDown, setMouseIsDown] = useState(false);
14
+ const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] = useState(false);
15
+ useEffect(() => {
16
+ var _a, _b;
17
+ const canvas = highlightOverlayCanvas.current;
18
+ if (!canvas) {
19
+ return;
20
+ }
21
+ const ctx = canvas.getContext('2d');
22
+ if (!ctx) {
23
+ return;
24
+ }
25
+ ctx.clearRect(0, 0, canvas.width, canvas.height);
26
+ const selectedRect = selectedFeatureId
27
+ ? (_a = displayModel.getFeatureByID) === null || _a === void 0 ? void 0 : _a.call(displayModel, blockKey, selectedFeatureId)
28
+ : undefined;
29
+ if (selectedRect) {
30
+ const [leftBp, topPx, rightBp, bottomPx] = selectedRect;
31
+ const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx);
32
+ const rectTop = Math.round(topPx);
33
+ const rectHeight = Math.round(bottomPx - topPx);
34
+ ctx.shadowColor = '#222266';
35
+ ctx.shadowBlur = 10;
36
+ ctx.lineJoin = 'bevel';
37
+ ctx.lineWidth = 2;
38
+ ctx.strokeStyle = '#00b8ff';
39
+ ctx.strokeRect(leftPx - 2, rectTop - 2, rightPx - leftPx + 4, rectHeight + 4);
40
+ ctx.clearRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
41
+ }
42
+ const highlightedFeature = featureIdUnderMouse || (contextMenuFeature === null || contextMenuFeature === void 0 ? void 0 : contextMenuFeature.id());
43
+ const highlightedRect = highlightedFeature
44
+ ? (_b = displayModel.getFeatureByID) === null || _b === void 0 ? void 0 : _b.call(displayModel, blockKey, highlightedFeature)
45
+ : undefined;
46
+ if (highlightedRect) {
47
+ const [leftBp, topPx, rightBp, bottomPx] = highlightedRect;
48
+ const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx);
49
+ const rectTop = Math.round(topPx);
50
+ const rectHeight = Math.round(bottomPx - topPx);
51
+ ctx.fillStyle = '#0003';
52
+ ctx.fillRect(leftPx, rectTop, rightPx - leftPx, rectHeight);
53
+ }
54
+ }, [
55
+ bpPerPx,
56
+ region,
57
+ blockKey,
58
+ selectedFeatureId,
59
+ displayModel,
60
+ featureIdUnderMouse,
61
+ contextMenuFeature,
62
+ ]);
63
+ function onMouseDown(event) {
64
+ setMouseIsDown(true);
65
+ setMovedDuringLastMouseDown(false);
66
+ callMouseHandler('MouseDown', event);
67
+ }
68
+ function onMouseEnter(event) {
69
+ callMouseHandler('MouseEnter', event);
70
+ }
71
+ function onMouseOut(event) {
72
+ callMouseHandler('MouseOut', event);
73
+ callMouseHandler('MouseLeave', event);
74
+ }
75
+ function onMouseOver(event) {
76
+ callMouseHandler('MouseOver', event);
77
+ }
78
+ function onMouseUp(event) {
79
+ setMouseIsDown(false);
80
+ callMouseHandler('MouseUp', event);
81
+ }
82
+ function onClick(event) {
83
+ if (!movedDuringLastMouseDown) {
84
+ callMouseHandler('Click', event);
85
+ }
86
+ }
87
+ function onMouseLeave(event) {
88
+ callMouseHandler('MouseOut', event);
89
+ callMouseHandler('MouseLeave', event);
90
+ }
91
+ function onContextMenu(event) {
92
+ callMouseHandler('ContextMenu', event);
93
+ }
94
+ function mouseMove(event) {
95
+ if (mouseIsDown) {
96
+ setMovedDuringLastMouseDown(true);
97
+ }
98
+ let offsetX = 0;
99
+ let offsetY = 0;
100
+ const canvas = highlightOverlayCanvas.current;
101
+ if (canvas) {
102
+ const { left, top } = canvas.getBoundingClientRect();
103
+ offsetX = left;
104
+ offsetY = top;
105
+ }
106
+ offsetX = event.clientX - offsetX;
107
+ offsetY = event.clientY - offsetY;
108
+ const px = region.reversed ? width - offsetX : offsetX;
109
+ const clientBp = region.start + bpPerPx * px;
110
+ const featIdUnderMouse = displayModel.getFeatureOverlapping(blockKey, clientBp, offsetY);
111
+ if (onMouseMove) {
112
+ onMouseMove(event, featIdUnderMouse);
113
+ }
114
+ }
115
+ function callMouseHandler(handlerName, event) {
116
+ // @ts-ignore
117
+ // eslint-disable-next-line react/destructuring-assignment
118
+ const featureHandler = props[`onFeature${handlerName}`];
119
+ // @ts-ignore
120
+ // eslint-disable-next-line react/destructuring-assignment
121
+ const canvasHandler = props[`on${handlerName}`];
122
+ if (featureHandler && featureIdUnderMouse) {
123
+ featureHandler(event, featureIdUnderMouse);
124
+ }
125
+ else if (canvasHandler) {
126
+ canvasHandler(event, featureIdUnderMouse);
127
+ }
128
+ }
129
+ const canvasWidth = Math.ceil(width);
130
+ // need to call this in render so we get the right observer behavior
131
+ return (React.createElement("div", { className: "PileupRendering", "data-testid": `pileup-${sortedBy || colorBy
132
+ ? `${(sortedBy === null || sortedBy === void 0 ? void 0 : sortedBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || ''}${(colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) || ''}`
133
+ : 'normal'}`, style: { position: 'relative', width: canvasWidth, height } },
134
+ React.createElement(PrerenderedCanvas, { ...props, style: { position: 'absolute', left: 0, top: 0 } }),
135
+ React.createElement("canvas", { "data-testid": "pileup_overlay_canvas", width: canvasWidth, height: height + canvasPadding, style: { position: 'absolute', left: 0, top: 0 }, className: "highlightOverlayCanvas", ref: highlightOverlayCanvas, onMouseDown: event => onMouseDown(event), onMouseEnter: event => onMouseEnter(event), onMouseOut: event => onMouseOut(event), onMouseOver: event => onMouseOver(event), onMouseUp: event => onMouseUp(event), onMouseLeave: event => onMouseLeave(event), onMouseMove: event => mouseMove(event), onClick: event => onClick(event), onContextMenu: event => onContextMenu(event), onFocus: () => { }, onBlur: () => { } })));
136
+ }
137
+ export default observer(PileupRendering);
138
+ //# sourceMappingURL=PileupRendering.js.map
@@ -0,0 +1 @@
1
+ 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@@ -0,0 +1,2 @@
1
+ declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
2
+ export default _default;
@@ -0,0 +1,64 @@
1
+ import { ConfigurationSchema } from '@jbrowse/core/configuration';
2
+ import { types } from 'mobx-state-tree';
3
+ export default ConfigurationSchema('PileupRenderer', {
4
+ // default magenta here is used to detect the user has not customized this
5
+ color: {
6
+ type: 'color',
7
+ description: 'the color of each feature in a pileup alignment',
8
+ defaultValue: '#f0f',
9
+ contextVariable: ['feature'],
10
+ },
11
+ orientationType: {
12
+ type: 'stringEnum',
13
+ model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
14
+ defaultValue: 'fr',
15
+ description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
16
+ },
17
+ displayMode: {
18
+ type: 'stringEnum',
19
+ model: types.enumeration('displayMode', [
20
+ 'normal',
21
+ 'compact',
22
+ 'collapse',
23
+ ]),
24
+ description: 'Alternative display modes',
25
+ defaultValue: 'normal',
26
+ },
27
+ minSubfeatureWidth: {
28
+ type: 'number',
29
+ description: 'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
30
+ defaultValue: 0.7,
31
+ },
32
+ maxHeight: {
33
+ type: 'integer',
34
+ description: 'the maximum height to be used in a pileup rendering',
35
+ defaultValue: 1200,
36
+ },
37
+ maxClippingSize: {
38
+ type: 'integer',
39
+ description: 'the max clip size to be used in a pileup rendering',
40
+ defaultValue: 10000,
41
+ },
42
+ height: {
43
+ type: 'number',
44
+ description: 'the height of each feature in a pileup alignment',
45
+ defaultValue: 7,
46
+ contextVariable: ['feature'],
47
+ },
48
+ noSpacing: {
49
+ type: 'boolean',
50
+ description: 'remove spacing between features',
51
+ defaultValue: false,
52
+ },
53
+ largeInsertionIndicatorScale: {
54
+ type: 'number',
55
+ description: 'scale at which to draw the large insertion indicators (bp/pixel)',
56
+ defaultValue: 10,
57
+ },
58
+ mismatchAlpha: {
59
+ type: 'boolean',
60
+ defaultValue: false,
61
+ description: 'Fade low quality mismatches',
62
+ },
63
+ }, { explicitlyTyped: true });
64
+ //# sourceMappingURL=configSchema.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,eAAe,mBAAmB,CAChC,gBAAgB,EAChB;IACE,0EAA0E;IAC1E,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,mIAAmI;KACtI;IACD,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
@@ -0,0 +1,2 @@
1
+ import PluginManager from '@jbrowse/core/PluginManager';
2
+ export default function register(pluginManager: PluginManager): void;
@@ -0,0 +1,12 @@
1
+ import PileupRenderer from './PileupRenderer';
2
+ import ReactComponent from './components/PileupRendering';
3
+ import configSchema from './configSchema';
4
+ export default function register(pluginManager) {
5
+ pluginManager.addRendererType(() => new PileupRenderer({
6
+ name: 'PileupRenderer',
7
+ ReactComponent,
8
+ configSchema,
9
+ pluginManager,
10
+ }));
11
+ }
12
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,cAAc,MAAM,8BAA8B,CAAA;AACzD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,cAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}
@@ -0,0 +1,8 @@
1
+ import { Feature } from '@jbrowse/core/util/simpleFeature';
2
+ interface SortObject {
3
+ pos: number;
4
+ type: string;
5
+ tag?: string;
6
+ }
7
+ export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortObject) => Map<string, Feature>;
8
+ export {};
@@ -0,0 +1,80 @@
1
+ import { doesIntersect2 } from '@jbrowse/core/util/range';
2
+ export const sortFeature = (features, sortedBy) => {
3
+ const featureArray = Array.from(features.values());
4
+ const featuresInCenterLine = [];
5
+ const featuresOutsideCenter = [];
6
+ const { pos, type } = sortedBy;
7
+ // only sort on features that intersect center line, append those outside post-sort
8
+ featureArray.forEach(innerArray => {
9
+ const feature = innerArray;
10
+ const start = feature.get('start');
11
+ const end = feature.get('end');
12
+ if (doesIntersect2(pos - 1, pos, start, end)) {
13
+ featuresInCenterLine.push(innerArray);
14
+ }
15
+ else {
16
+ featuresOutsideCenter.push(innerArray);
17
+ }
18
+ });
19
+ const isCram = featureArray.length ? featureArray[0].get('tags') : false;
20
+ switch (type) {
21
+ case 'Start location': {
22
+ featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'));
23
+ break;
24
+ }
25
+ case 'tag': {
26
+ const tag = sortedBy.tag;
27
+ const getTag = (f, t) => {
28
+ return isCram ? f.get('tags')[t] : f.get(t);
29
+ };
30
+ const isString = featuresInCenterLine[0] &&
31
+ typeof getTag(featuresInCenterLine[0], tag) === 'string';
32
+ if (isString) {
33
+ featuresInCenterLine.sort((a, b) => getTag(b, tag).localeCompare(getTag(a, tag)));
34
+ }
35
+ else {
36
+ featuresInCenterLine.sort((a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0));
37
+ }
38
+ break;
39
+ }
40
+ // first sort all mismatches, then all reference bases at the end
41
+ case 'Base pair': {
42
+ const baseSortArray = [];
43
+ featuresInCenterLine.forEach(feature => {
44
+ const mismatches = feature.get('mismatches');
45
+ mismatches.forEach(mismatch => {
46
+ const start = feature.get('start');
47
+ const offset = start + mismatch.start + 1;
48
+ const consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
49
+ const len = consuming ? 0 : mismatch.length;
50
+ if (pos >= offset && pos < offset + len) {
51
+ baseSortArray.push([feature.id(), mismatch]);
52
+ }
53
+ });
54
+ });
55
+ const baseMap = new Map(baseSortArray);
56
+ featuresInCenterLine.sort((a, b) => {
57
+ const aMismatch = baseMap.get(a.id());
58
+ const bMismatch = baseMap.get(b.id());
59
+ const acode = bMismatch && bMismatch.base.toUpperCase();
60
+ const bcode = aMismatch && aMismatch.base.toUpperCase();
61
+ if (acode === bcode && acode === '*') {
62
+ // @ts-ignore
63
+ return aMismatch.length - bMismatch.length;
64
+ }
65
+ return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
66
+ });
67
+ break;
68
+ }
69
+ // sorts positive strands then negative strands
70
+ case 'Read strand': {
71
+ featuresInCenterLine.sort((a, b) => a.get('strand') <= b.get('strand') ? 1 : -1);
72
+ break;
73
+ }
74
+ }
75
+ const sortedMap = new Map(featuresInCenterLine
76
+ .concat(featuresOutsideCenter)
77
+ .map(feature => [feature.id(), feature]));
78
+ return sortedMap;
79
+ };
80
+ //# sourceMappingURL=sortUtil.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"sortUtil.js","sourceRoot":"","sources":["../../src/PileupRenderer/sortUtil.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAA;AAQzD,MAAM,CAAC,MAAM,WAAW,GAAG,CACzB,QAA8B,EAC9B,QAAoB,EACpB,EAAE;IACF,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAA;IAClD,MAAM,oBAAoB,GAAc,EAAE,CAAA;IAC1C,MAAM,qBAAqB,GAAc,EAAE,CAAA;IAC3C,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;IAE9B,mFAAmF;IACnF,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE;QAChC,MAAM,OAAO,GAAG,UAAU,CAAA;QAC1B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC9B,IAAI,cAAc,CAAC,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,CAAC,EAAE;YAC5C,oBAAoB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACtC;aAAM;YACL,qBAAqB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;SACvC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IACxE,QAAQ,IAAI,EAAE;QACZ,KAAK,gBAAgB,CAAC,CAAC;YACrB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YACpE,MAAK;SACN;QAED,KAAK,KAAK,CAAC,CAAC;YACV,MAAM,GAAG,GAAG,QAAQ,CAAC,GAAa,CAAA;YAClC,MAAM,MAAM,GAAG,CAAC,CAAU,EAAE,CAAS,EAAE,EAAE;gBACvC,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAC7C,CAAC,CAAA;YACD,MAAM,QAAQ,GACZ,oBAAoB,CAAC,CAAC,CAAC;gBACvB,OAAO,MAAM,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,QAAQ,CAAA;YAC1D,IAAI,QAAQ,EAAE;gBACZ,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAC7C,CAAA;aACF;iBAAM;gBACL,oBAAoB,CAAC,IAAI,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,CAAC,CAAC,CACxD,CAAA;aACF;YACD,MAAK;SACN;QAED,iEAAiE;QACjE,KAAK,WAAW,CAAC,CAAC;YAChB,MAAM,aAAa,GAAyB,EAAE,CAAA;YAC9C,oBAAoB,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;gBACrC,MAAM,UAAU,GAAe,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBACxD,UAAU,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE;oBAC5B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;oBAClC,MAAM,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAA;oBACzC,MAAM,SAAS,GACb,QAAQ,CAAC,IAAI,KAAK,WAAW,IAAI,QAAQ,CAAC,IAAI,KAAK,UAAU,CAAA;oBAC/D,MAAM,GAAG,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAA;oBAC3C,IAAI,GAAG,IAAI,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,GAAG,EAAE;wBACvC,aAAa,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,QAAQ,CAAC,CAAC,CAAA;qBAC7C;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YAEF,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;YACtC,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;gBACjC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;gBACrC,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,MAAM,KAAK,GAAG,SAAS,IAAI,SAAS,CAAC,IAAI,CAAC,WAAW,EAAE,CAAA;gBACvD,IAAI,KAAK,KAAK,KAAK,IAAI,KAAK,KAAK,GAAG,EAAE;oBACpC,aAAa;oBACb,OAAO,SAAS,CAAC,MAAM,GAAG,SAAS,CAAC,MAAM,CAAA;iBAC3C;gBACD,OAAO,CACL,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CACtE,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,MAAK;SACN;QAED,+CAA+C;QAC/C,KAAK,aAAa,CAAC,CAAC;YAClB,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACjC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC5C,CAAA;YACD,MAAK;SACN;KACF;IAED,MAAM,SAAS,GAAG,IAAI,GAAG,CACvB,oBAAoB;SACjB,MAAM,CAAC,qBAAqB,CAAC;SAC7B,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,OAAO,CAAC,CAAC,CAC3C,CAAA;IAED,OAAO,SAAS,CAAA;AAClB,CAAC,CAAA"}
@@ -0,0 +1,67 @@
1
+ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
2
+ import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
3
+ import { Feature } from '@jbrowse/core/util/simpleFeature';
4
+ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
5
+ protected configure(): Promise<{
6
+ subadapter: BaseFeatureDataAdapter;
7
+ sequenceAdapter: BaseFeatureDataAdapter | undefined;
8
+ }>;
9
+ fetchSequence(region: Region): Promise<any>;
10
+ getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
11
+ estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
12
+ getRefNames(opts?: BaseOptions): Promise<string[]>;
13
+ freeResources(): void;
14
+ generateCoverageBins(features: Feature[], region: Region, opts: {
15
+ bpPerPx?: number;
16
+ colorBy?: {
17
+ type: string;
18
+ tag?: string;
19
+ };
20
+ }): Promise<{
21
+ bins: {
22
+ refbase?: string | undefined;
23
+ total: number;
24
+ all: number;
25
+ ref: number;
26
+ '-1': 0;
27
+ '0': 0;
28
+ '1': 0;
29
+ lowqual: {
30
+ total: number;
31
+ strands: {
32
+ [key: string]: number;
33
+ };
34
+ };
35
+ cov: {
36
+ total: number;
37
+ strands: {
38
+ [key: string]: number;
39
+ };
40
+ };
41
+ delskips: {
42
+ total: number;
43
+ strands: {
44
+ [key: string]: number;
45
+ };
46
+ };
47
+ noncov: {
48
+ total: number;
49
+ strands: {
50
+ [key: string]: number;
51
+ };
52
+ };
53
+ }[];
54
+ skipmap: {
55
+ [key: string]: {
56
+ score: number;
57
+ feature: unknown;
58
+ start: number;
59
+ end: number;
60
+ strand: number;
61
+ xs: string;
62
+ };
63
+ };
64
+ }>;
65
+ }
66
+ declare const capabilities: string[];
67
+ export { capabilities };