@jbrowse/plugin-alignments 2.6.1 → 2.6.3

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Files changed (534) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +0 -1
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +0 -1
  3. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +0 -1
  4. package/dist/AlignmentsFeatureDetail/index.js +0 -1
  5. package/dist/AlignmentsFeatureDetail/util.js +0 -1
  6. package/dist/AlignmentsTrack/configSchemaF.js +0 -1
  7. package/dist/AlignmentsTrack/index.js +0 -1
  8. package/dist/BamAdapter/BamAdapter.js +0 -1
  9. package/dist/BamAdapter/BamSlightlyLazyFeature.js +0 -1
  10. package/dist/BamAdapter/configSchema.js +0 -1
  11. package/dist/BamAdapter/index.js +0 -1
  12. package/dist/CramAdapter/CramAdapter.js +0 -1
  13. package/dist/CramAdapter/CramSlightlyLazyFeature.js +0 -1
  14. package/dist/CramAdapter/CramTestAdapters.js +0 -1
  15. package/dist/CramAdapter/configSchema.js +0 -1
  16. package/dist/CramAdapter/index.js +0 -1
  17. package/dist/CramAdapter/util.js +0 -1
  18. package/dist/GuessAlignmentsTypes/index.js +0 -1
  19. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +0 -1
  20. package/dist/HtsgetBamAdapter/configSchema.js +0 -1
  21. package/dist/HtsgetBamAdapter/index.js +0 -1
  22. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +1 -1
  23. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +5 -2
  24. package/dist/LinearAlignmentsDisplay/index.js +0 -1
  25. package/dist/LinearAlignmentsDisplay/models/configSchema.js +0 -1
  26. package/dist/LinearAlignmentsDisplay/models/model.js +5 -2
  27. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +492 -0
  28. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +529 -0
  29. package/dist/LinearPileupDisplay/components/ColorByModifications.js +0 -1
  30. package/dist/LinearPileupDisplay/components/ColorByTag.js +0 -1
  31. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +0 -1
  32. package/dist/LinearPileupDisplay/components/ModificationsTable.js +0 -1
  33. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +0 -1
  34. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +0 -1
  35. package/dist/LinearPileupDisplay/components/SortByTag.js +0 -1
  36. package/dist/LinearPileupDisplay/configSchema.js +0 -1
  37. package/dist/LinearPileupDisplay/index.d.ts +1 -0
  38. package/dist/LinearPileupDisplay/index.js +3 -2
  39. package/dist/LinearPileupDisplay/model.d.ts +110 -231
  40. package/dist/LinearPileupDisplay/model.js +47 -445
  41. package/dist/LinearReadArcsDisplay/components/ReactComponent.js +0 -1
  42. package/dist/LinearReadArcsDisplay/configSchema.js +0 -1
  43. package/dist/LinearReadArcsDisplay/drawFeats.js +0 -1
  44. package/dist/LinearReadArcsDisplay/index.js +0 -1
  45. package/dist/LinearReadArcsDisplay/model.js +0 -1
  46. package/dist/LinearReadArcsDisplay/util.js +0 -1
  47. package/dist/LinearReadCloudDisplay/components/ReactComponent.js +0 -1
  48. package/dist/LinearReadCloudDisplay/configSchema.d.ts +4 -4
  49. package/dist/LinearReadCloudDisplay/configSchema.js +0 -1
  50. package/dist/LinearReadCloudDisplay/drawFeats.js +0 -1
  51. package/dist/LinearReadCloudDisplay/drawLongReadChains.js +0 -1
  52. package/dist/LinearReadCloudDisplay/drawPairChains.js +0 -1
  53. package/dist/LinearReadCloudDisplay/index.js +0 -1
  54. package/dist/LinearReadCloudDisplay/model.d.ts +1 -3
  55. package/dist/LinearReadCloudDisplay/model.js +0 -1
  56. package/dist/LinearReadCloudDisplay/util.js +0 -1
  57. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +0 -1
  58. package/dist/LinearSNPCoverageDisplay/index.js +0 -1
  59. package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts +3 -0
  60. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +0 -1
  61. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +31 -15
  62. package/dist/LinearSNPCoverageDisplay/models/model.js +0 -1
  63. package/dist/MismatchParser/index.js +0 -1
  64. package/dist/PileupRPC/base.js +0 -1
  65. package/dist/PileupRPC/index.js +0 -1
  66. package/dist/PileupRPC/methods/GetGlobalValueForTag.js +0 -1
  67. package/dist/PileupRPC/methods/GetReducedFeatures.js +0 -1
  68. package/dist/PileupRPC/methods/GetVisibleModifications.js +0 -1
  69. package/dist/PileupRPC/rpcMethods.js +0 -1
  70. package/dist/PileupRPC/util.js +0 -1
  71. package/dist/PileupRenderer/PileupLayoutSession.js +0 -1
  72. package/dist/PileupRenderer/PileupRenderer.js +0 -1
  73. package/dist/PileupRenderer/colorBy.js +8 -7
  74. package/dist/PileupRenderer/components/PileupRendering.js +0 -1
  75. package/dist/PileupRenderer/configSchema.js +0 -1
  76. package/dist/PileupRenderer/getAlignmentShapeColor.js +0 -1
  77. package/dist/PileupRenderer/index.js +0 -1
  78. package/dist/PileupRenderer/layoutFeature.js +0 -1
  79. package/dist/PileupRenderer/layoutFeatures.js +0 -1
  80. package/dist/PileupRenderer/makeImageData.js +0 -1
  81. package/dist/PileupRenderer/renderAlignment.js +0 -1
  82. package/dist/PileupRenderer/renderAlignmentShape.js +1 -2
  83. package/dist/PileupRenderer/renderMethylation.js +0 -1
  84. package/dist/PileupRenderer/renderMismatches.js +0 -1
  85. package/dist/PileupRenderer/renderModifications.js +0 -1
  86. package/dist/PileupRenderer/renderPerBaseLettering.js +0 -1
  87. package/dist/PileupRenderer/renderPerBaseQuality.js +0 -1
  88. package/dist/PileupRenderer/renderSoftClipping.js +0 -1
  89. package/dist/PileupRenderer/sortUtil.js +0 -1
  90. package/dist/PileupRenderer/util.js +0 -1
  91. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +0 -1
  92. package/dist/SNPCoverageAdapter/configSchema.js +0 -1
  93. package/dist/SNPCoverageAdapter/generateCoverageBins.js +0 -1
  94. package/dist/SNPCoverageAdapter/index.js +0 -1
  95. package/dist/SNPCoverageAdapter/util.js +0 -1
  96. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +0 -1
  97. package/dist/SNPCoverageRenderer/configSchema.js +0 -1
  98. package/dist/SNPCoverageRenderer/index.js +0 -1
  99. package/dist/index.d.ts +1 -1
  100. package/dist/index.js +2 -2
  101. package/dist/shared/BaseDisplayComponent.js +0 -1
  102. package/dist/shared/FilterByTag.js +0 -1
  103. package/dist/shared/afterAttach.js +0 -1
  104. package/dist/shared/color.d.ts +10 -0
  105. package/dist/shared/color.js +7 -2
  106. package/dist/shared/fetchChains.js +0 -1
  107. package/dist/shared/index.js +0 -1
  108. package/dist/shared/renderSvg.js +0 -1
  109. package/dist/shared/util.js +0 -1
  110. package/dist/util.js +0 -1
  111. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +0 -1
  112. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js +0 -1
  113. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js +0 -1
  114. package/esm/AlignmentsFeatureDetail/index.js +0 -1
  115. package/esm/AlignmentsFeatureDetail/util.js +0 -1
  116. package/esm/AlignmentsTrack/configSchemaF.js +0 -1
  117. package/esm/AlignmentsTrack/index.js +0 -1
  118. package/esm/BamAdapter/BamAdapter.js +0 -1
  119. package/esm/BamAdapter/BamSlightlyLazyFeature.js +0 -1
  120. package/esm/BamAdapter/configSchema.js +0 -1
  121. package/esm/BamAdapter/index.js +0 -1
  122. package/esm/CramAdapter/CramAdapter.js +0 -1
  123. package/esm/CramAdapter/CramSlightlyLazyFeature.js +0 -1
  124. package/esm/CramAdapter/CramTestAdapters.js +0 -1
  125. package/esm/CramAdapter/configSchema.js +0 -1
  126. package/esm/CramAdapter/index.js +0 -1
  127. package/esm/CramAdapter/util.js +0 -1
  128. package/esm/GuessAlignmentsTypes/index.js +0 -1
  129. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js +0 -1
  130. package/esm/HtsgetBamAdapter/configSchema.js +0 -1
  131. package/esm/HtsgetBamAdapter/index.js +0 -1
  132. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +1 -1
  133. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +5 -2
  134. package/esm/LinearAlignmentsDisplay/index.js +0 -1
  135. package/esm/LinearAlignmentsDisplay/models/configSchema.js +0 -1
  136. package/esm/LinearAlignmentsDisplay/models/model.js +5 -2
  137. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +492 -0
  138. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +499 -0
  139. package/esm/LinearPileupDisplay/components/ColorByModifications.js +0 -1
  140. package/esm/LinearPileupDisplay/components/ColorByTag.js +0 -1
  141. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +0 -1
  142. package/esm/LinearPileupDisplay/components/ModificationsTable.js +0 -1
  143. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js +0 -1
  144. package/esm/LinearPileupDisplay/components/SetMaxHeight.js +0 -1
  145. package/esm/LinearPileupDisplay/components/SortByTag.js +0 -1
  146. package/esm/LinearPileupDisplay/configSchema.js +0 -1
  147. package/esm/LinearPileupDisplay/index.d.ts +1 -0
  148. package/esm/LinearPileupDisplay/index.js +1 -1
  149. package/esm/LinearPileupDisplay/model.d.ts +110 -231
  150. package/esm/LinearPileupDisplay/model.js +48 -446
  151. package/esm/LinearReadArcsDisplay/components/ReactComponent.js +0 -1
  152. package/esm/LinearReadArcsDisplay/configSchema.js +0 -1
  153. package/esm/LinearReadArcsDisplay/drawFeats.js +0 -1
  154. package/esm/LinearReadArcsDisplay/index.js +0 -1
  155. package/esm/LinearReadArcsDisplay/model.js +0 -1
  156. package/esm/LinearReadArcsDisplay/util.js +0 -1
  157. package/esm/LinearReadCloudDisplay/components/ReactComponent.js +0 -1
  158. package/esm/LinearReadCloudDisplay/configSchema.d.ts +4 -4
  159. package/esm/LinearReadCloudDisplay/configSchema.js +0 -1
  160. package/esm/LinearReadCloudDisplay/drawFeats.js +0 -1
  161. package/esm/LinearReadCloudDisplay/drawLongReadChains.js +0 -1
  162. package/esm/LinearReadCloudDisplay/drawPairChains.js +0 -1
  163. package/esm/LinearReadCloudDisplay/index.js +0 -1
  164. package/esm/LinearReadCloudDisplay/model.d.ts +1 -3
  165. package/esm/LinearReadCloudDisplay/model.js +0 -1
  166. package/esm/LinearReadCloudDisplay/util.js +0 -1
  167. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +0 -1
  168. package/esm/LinearSNPCoverageDisplay/index.js +0 -1
  169. package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts +3 -0
  170. package/esm/LinearSNPCoverageDisplay/models/configSchema.js +0 -1
  171. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +31 -15
  172. package/esm/LinearSNPCoverageDisplay/models/model.js +0 -1
  173. package/esm/MismatchParser/index.js +0 -1
  174. package/esm/PileupRPC/base.js +0 -1
  175. package/esm/PileupRPC/index.js +0 -1
  176. package/esm/PileupRPC/methods/GetGlobalValueForTag.js +0 -1
  177. package/esm/PileupRPC/methods/GetReducedFeatures.js +0 -1
  178. package/esm/PileupRPC/methods/GetVisibleModifications.js +0 -1
  179. package/esm/PileupRPC/rpcMethods.js +0 -1
  180. package/esm/PileupRPC/util.js +0 -1
  181. package/esm/PileupRenderer/PileupLayoutSession.js +0 -1
  182. package/esm/PileupRenderer/PileupRenderer.js +0 -1
  183. package/esm/PileupRenderer/colorBy.js +8 -7
  184. package/esm/PileupRenderer/components/PileupRendering.js +0 -1
  185. package/esm/PileupRenderer/configSchema.js +0 -1
  186. package/esm/PileupRenderer/getAlignmentShapeColor.js +0 -1
  187. package/esm/PileupRenderer/index.js +0 -1
  188. package/esm/PileupRenderer/layoutFeature.js +0 -1
  189. package/esm/PileupRenderer/layoutFeatures.js +0 -1
  190. package/esm/PileupRenderer/makeImageData.js +0 -1
  191. package/esm/PileupRenderer/renderAlignment.js +0 -1
  192. package/esm/PileupRenderer/renderAlignmentShape.js +1 -2
  193. package/esm/PileupRenderer/renderMethylation.js +0 -1
  194. package/esm/PileupRenderer/renderMismatches.js +0 -1
  195. package/esm/PileupRenderer/renderModifications.js +0 -1
  196. package/esm/PileupRenderer/renderPerBaseLettering.js +0 -1
  197. package/esm/PileupRenderer/renderPerBaseQuality.js +0 -1
  198. package/esm/PileupRenderer/renderSoftClipping.js +0 -1
  199. package/esm/PileupRenderer/sortUtil.js +0 -1
  200. package/esm/PileupRenderer/util.js +0 -1
  201. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js +0 -1
  202. package/esm/SNPCoverageAdapter/configSchema.js +0 -1
  203. package/esm/SNPCoverageAdapter/generateCoverageBins.js +0 -1
  204. package/esm/SNPCoverageAdapter/index.js +0 -1
  205. package/esm/SNPCoverageAdapter/util.js +0 -1
  206. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +0 -1
  207. package/esm/SNPCoverageRenderer/configSchema.js +0 -1
  208. package/esm/SNPCoverageRenderer/index.js +0 -1
  209. package/esm/index.d.ts +1 -1
  210. package/esm/index.js +1 -2
  211. package/esm/shared/BaseDisplayComponent.js +0 -1
  212. package/esm/shared/FilterByTag.js +0 -1
  213. package/esm/shared/afterAttach.js +0 -1
  214. package/esm/shared/color.d.ts +10 -0
  215. package/esm/shared/color.js +6 -1
  216. package/esm/shared/fetchChains.js +0 -1
  217. package/esm/shared/index.js +0 -1
  218. package/esm/shared/renderSvg.js +0 -1
  219. package/esm/shared/util.js +0 -1
  220. package/esm/util.js +0 -1
  221. package/package.json +4 -5
  222. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +0 -1
  223. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +0 -1
  224. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +0 -1
  225. package/dist/AlignmentsFeatureDetail/index.js.map +0 -1
  226. package/dist/AlignmentsFeatureDetail/util.js.map +0 -1
  227. package/dist/AlignmentsTrack/configSchemaF.js.map +0 -1
  228. package/dist/AlignmentsTrack/index.js.map +0 -1
  229. package/dist/BamAdapter/BamAdapter.js.map +0 -1
  230. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +0 -1
  231. package/dist/BamAdapter/configSchema.js.map +0 -1
  232. package/dist/BamAdapter/index.js.map +0 -1
  233. package/dist/CramAdapter/CramAdapter.js.map +0 -1
  234. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +0 -1
  235. package/dist/CramAdapter/CramTestAdapters.js.map +0 -1
  236. package/dist/CramAdapter/configSchema.js.map +0 -1
  237. package/dist/CramAdapter/index.js.map +0 -1
  238. package/dist/CramAdapter/util.js.map +0 -1
  239. package/dist/GuessAlignmentsTypes/index.js.map +0 -1
  240. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map +0 -1
  241. package/dist/HtsgetBamAdapter/configSchema.js.map +0 -1
  242. package/dist/HtsgetBamAdapter/index.js.map +0 -1
  243. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +0 -1
  244. package/dist/LinearAlignmentsDisplay/index.js.map +0 -1
  245. package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +0 -1
  246. package/dist/LinearAlignmentsDisplay/models/model.js.map +0 -1
  247. package/dist/LinearPileupDisplay/components/ColorByModifications.js.map +0 -1
  248. package/dist/LinearPileupDisplay/components/ColorByTag.js.map +0 -1
  249. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +0 -1
  250. package/dist/LinearPileupDisplay/components/ModificationsTable.js.map +0 -1
  251. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js.map +0 -1
  252. package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map +0 -1
  253. package/dist/LinearPileupDisplay/components/SortByTag.js.map +0 -1
  254. package/dist/LinearPileupDisplay/configSchema.js.map +0 -1
  255. package/dist/LinearPileupDisplay/index.js.map +0 -1
  256. package/dist/LinearPileupDisplay/model.js.map +0 -1
  257. package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map +0 -1
  258. package/dist/LinearReadArcsDisplay/configSchema.js.map +0 -1
  259. package/dist/LinearReadArcsDisplay/drawFeats.js.map +0 -1
  260. package/dist/LinearReadArcsDisplay/index.js.map +0 -1
  261. package/dist/LinearReadArcsDisplay/model.js.map +0 -1
  262. package/dist/LinearReadArcsDisplay/util.js.map +0 -1
  263. package/dist/LinearReadCloudDisplay/components/ReactComponent.js.map +0 -1
  264. package/dist/LinearReadCloudDisplay/configSchema.js.map +0 -1
  265. package/dist/LinearReadCloudDisplay/drawFeats.js.map +0 -1
  266. package/dist/LinearReadCloudDisplay/drawLongReadChains.js.map +0 -1
  267. package/dist/LinearReadCloudDisplay/drawPairChains.js.map +0 -1
  268. package/dist/LinearReadCloudDisplay/index.js.map +0 -1
  269. package/dist/LinearReadCloudDisplay/model.js.map +0 -1
  270. package/dist/LinearReadCloudDisplay/util.js.map +0 -1
  271. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +0 -1
  272. package/dist/LinearSNPCoverageDisplay/index.js.map +0 -1
  273. package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map +0 -1
  274. package/dist/LinearSNPCoverageDisplay/models/model.js.map +0 -1
  275. package/dist/MismatchParser/index.js.map +0 -1
  276. package/dist/PileupRPC/base.js.map +0 -1
  277. package/dist/PileupRPC/index.js.map +0 -1
  278. package/dist/PileupRPC/methods/GetGlobalValueForTag.js.map +0 -1
  279. package/dist/PileupRPC/methods/GetReducedFeatures.js.map +0 -1
  280. package/dist/PileupRPC/methods/GetVisibleModifications.js.map +0 -1
  281. package/dist/PileupRPC/rpcMethods.js.map +0 -1
  282. package/dist/PileupRPC/util.js.map +0 -1
  283. package/dist/PileupRenderer/PileupLayoutSession.js.map +0 -1
  284. package/dist/PileupRenderer/PileupRenderer.js.map +0 -1
  285. package/dist/PileupRenderer/colorBy.js.map +0 -1
  286. package/dist/PileupRenderer/components/PileupRendering.js.map +0 -1
  287. package/dist/PileupRenderer/configSchema.js.map +0 -1
  288. package/dist/PileupRenderer/getAlignmentShapeColor.js.map +0 -1
  289. package/dist/PileupRenderer/index.js.map +0 -1
  290. package/dist/PileupRenderer/layoutFeature.js.map +0 -1
  291. package/dist/PileupRenderer/layoutFeatures.js.map +0 -1
  292. package/dist/PileupRenderer/makeImageData.js.map +0 -1
  293. package/dist/PileupRenderer/renderAlignment.js.map +0 -1
  294. package/dist/PileupRenderer/renderAlignmentShape.js.map +0 -1
  295. package/dist/PileupRenderer/renderMethylation.js.map +0 -1
  296. package/dist/PileupRenderer/renderMismatches.js.map +0 -1
  297. package/dist/PileupRenderer/renderModifications.js.map +0 -1
  298. package/dist/PileupRenderer/renderPerBaseLettering.js.map +0 -1
  299. package/dist/PileupRenderer/renderPerBaseQuality.js.map +0 -1
  300. package/dist/PileupRenderer/renderSoftClipping.js.map +0 -1
  301. package/dist/PileupRenderer/sortUtil.js.map +0 -1
  302. package/dist/PileupRenderer/util.js.map +0 -1
  303. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js.map +0 -1
  304. package/dist/SNPCoverageAdapter/configSchema.js.map +0 -1
  305. package/dist/SNPCoverageAdapter/generateCoverageBins.js.map +0 -1
  306. package/dist/SNPCoverageAdapter/index.js.map +0 -1
  307. package/dist/SNPCoverageAdapter/util.js.map +0 -1
  308. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +0 -1
  309. package/dist/SNPCoverageRenderer/configSchema.js.map +0 -1
  310. package/dist/SNPCoverageRenderer/index.js.map +0 -1
  311. package/dist/index.js.map +0 -1
  312. package/dist/shared/BaseDisplayComponent.js.map +0 -1
  313. package/dist/shared/FilterByTag.js.map +0 -1
  314. package/dist/shared/afterAttach.js.map +0 -1
  315. package/dist/shared/color.js.map +0 -1
  316. package/dist/shared/fetchChains.js.map +0 -1
  317. package/dist/shared/index.js.map +0 -1
  318. package/dist/shared/renderSvg.js.map +0 -1
  319. package/dist/shared/util.js.map +0 -1
  320. package/dist/util.js.map +0 -1
  321. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +0 -1
  322. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.js.map +0 -1
  323. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.js.map +0 -1
  324. package/esm/AlignmentsFeatureDetail/index.js.map +0 -1
  325. package/esm/AlignmentsFeatureDetail/util.js.map +0 -1
  326. package/esm/AlignmentsTrack/configSchemaF.js.map +0 -1
  327. package/esm/AlignmentsTrack/index.js.map +0 -1
  328. package/esm/BamAdapter/BamAdapter.js.map +0 -1
  329. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +0 -1
  330. package/esm/BamAdapter/configSchema.js.map +0 -1
  331. package/esm/BamAdapter/index.js.map +0 -1
  332. package/esm/CramAdapter/CramAdapter.js.map +0 -1
  333. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +0 -1
  334. package/esm/CramAdapter/CramTestAdapters.js.map +0 -1
  335. package/esm/CramAdapter/configSchema.js.map +0 -1
  336. package/esm/CramAdapter/index.js.map +0 -1
  337. package/esm/CramAdapter/util.js.map +0 -1
  338. package/esm/GuessAlignmentsTypes/index.js.map +0 -1
  339. package/esm/HtsgetBamAdapter/HtsgetBamAdapter.js.map +0 -1
  340. package/esm/HtsgetBamAdapter/configSchema.js.map +0 -1
  341. package/esm/HtsgetBamAdapter/index.js.map +0 -1
  342. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +0 -1
  343. package/esm/LinearAlignmentsDisplay/index.js.map +0 -1
  344. package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +0 -1
  345. package/esm/LinearAlignmentsDisplay/models/model.js.map +0 -1
  346. package/esm/LinearPileupDisplay/components/ColorByModifications.js.map +0 -1
  347. package/esm/LinearPileupDisplay/components/ColorByTag.js.map +0 -1
  348. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +0 -1
  349. package/esm/LinearPileupDisplay/components/ModificationsTable.js.map +0 -1
  350. package/esm/LinearPileupDisplay/components/SetFeatureHeight.js.map +0 -1
  351. package/esm/LinearPileupDisplay/components/SetMaxHeight.js.map +0 -1
  352. package/esm/LinearPileupDisplay/components/SortByTag.js.map +0 -1
  353. package/esm/LinearPileupDisplay/configSchema.js.map +0 -1
  354. package/esm/LinearPileupDisplay/index.js.map +0 -1
  355. package/esm/LinearPileupDisplay/model.js.map +0 -1
  356. package/esm/LinearReadArcsDisplay/components/ReactComponent.js.map +0 -1
  357. package/esm/LinearReadArcsDisplay/configSchema.js.map +0 -1
  358. package/esm/LinearReadArcsDisplay/drawFeats.js.map +0 -1
  359. package/esm/LinearReadArcsDisplay/index.js.map +0 -1
  360. package/esm/LinearReadArcsDisplay/model.js.map +0 -1
  361. package/esm/LinearReadArcsDisplay/util.js.map +0 -1
  362. package/esm/LinearReadCloudDisplay/components/ReactComponent.js.map +0 -1
  363. package/esm/LinearReadCloudDisplay/configSchema.js.map +0 -1
  364. package/esm/LinearReadCloudDisplay/drawFeats.js.map +0 -1
  365. package/esm/LinearReadCloudDisplay/drawLongReadChains.js.map +0 -1
  366. package/esm/LinearReadCloudDisplay/drawPairChains.js.map +0 -1
  367. package/esm/LinearReadCloudDisplay/index.js.map +0 -1
  368. package/esm/LinearReadCloudDisplay/model.js.map +0 -1
  369. package/esm/LinearReadCloudDisplay/util.js.map +0 -1
  370. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +0 -1
  371. package/esm/LinearSNPCoverageDisplay/index.js.map +0 -1
  372. package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map +0 -1
  373. package/esm/LinearSNPCoverageDisplay/models/model.js.map +0 -1
  374. package/esm/MismatchParser/index.js.map +0 -1
  375. package/esm/PileupRPC/base.js.map +0 -1
  376. package/esm/PileupRPC/index.js.map +0 -1
  377. package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map +0 -1
  378. package/esm/PileupRPC/methods/GetReducedFeatures.js.map +0 -1
  379. package/esm/PileupRPC/methods/GetVisibleModifications.js.map +0 -1
  380. package/esm/PileupRPC/rpcMethods.js.map +0 -1
  381. package/esm/PileupRPC/util.js.map +0 -1
  382. package/esm/PileupRenderer/PileupLayoutSession.js.map +0 -1
  383. package/esm/PileupRenderer/PileupRenderer.js.map +0 -1
  384. package/esm/PileupRenderer/colorBy.js.map +0 -1
  385. package/esm/PileupRenderer/components/PileupRendering.js.map +0 -1
  386. package/esm/PileupRenderer/configSchema.js.map +0 -1
  387. package/esm/PileupRenderer/getAlignmentShapeColor.js.map +0 -1
  388. package/esm/PileupRenderer/index.js.map +0 -1
  389. package/esm/PileupRenderer/layoutFeature.js.map +0 -1
  390. package/esm/PileupRenderer/layoutFeatures.js.map +0 -1
  391. package/esm/PileupRenderer/makeImageData.js.map +0 -1
  392. package/esm/PileupRenderer/renderAlignment.js.map +0 -1
  393. package/esm/PileupRenderer/renderAlignmentShape.js.map +0 -1
  394. package/esm/PileupRenderer/renderMethylation.js.map +0 -1
  395. package/esm/PileupRenderer/renderMismatches.js.map +0 -1
  396. package/esm/PileupRenderer/renderModifications.js.map +0 -1
  397. package/esm/PileupRenderer/renderPerBaseLettering.js.map +0 -1
  398. package/esm/PileupRenderer/renderPerBaseQuality.js.map +0 -1
  399. package/esm/PileupRenderer/renderSoftClipping.js.map +0 -1
  400. package/esm/PileupRenderer/sortUtil.js.map +0 -1
  401. package/esm/PileupRenderer/util.js.map +0 -1
  402. package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map +0 -1
  403. package/esm/SNPCoverageAdapter/configSchema.js.map +0 -1
  404. package/esm/SNPCoverageAdapter/generateCoverageBins.js.map +0 -1
  405. package/esm/SNPCoverageAdapter/index.js.map +0 -1
  406. package/esm/SNPCoverageAdapter/util.js.map +0 -1
  407. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +0 -1
  408. package/esm/SNPCoverageRenderer/configSchema.js.map +0 -1
  409. package/esm/SNPCoverageRenderer/index.js.map +0 -1
  410. package/esm/index.js.map +0 -1
  411. package/esm/shared/BaseDisplayComponent.js.map +0 -1
  412. package/esm/shared/FilterByTag.js.map +0 -1
  413. package/esm/shared/afterAttach.js.map +0 -1
  414. package/esm/shared/color.js.map +0 -1
  415. package/esm/shared/fetchChains.js.map +0 -1
  416. package/esm/shared/index.js.map +0 -1
  417. package/esm/shared/renderSvg.js.map +0 -1
  418. package/esm/shared/util.js.map +0 -1
  419. package/esm/util.js.map +0 -1
  420. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +0 -155
  421. package/src/AlignmentsFeatureDetail/AlignmentsFeatureFlags.tsx +0 -60
  422. package/src/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.tsx +0 -51
  423. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +0 -327
  424. package/src/AlignmentsFeatureDetail/index.test.tsx +0 -47
  425. package/src/AlignmentsFeatureDetail/index.ts +0 -33
  426. package/src/AlignmentsFeatureDetail/util.ts +0 -27
  427. package/src/AlignmentsTrack/configSchemaF.ts +0 -22
  428. package/src/AlignmentsTrack/index.ts +0 -22
  429. package/src/BamAdapter/BamAdapter.test.ts +0 -124
  430. package/src/BamAdapter/BamAdapter.ts +0 -251
  431. package/src/BamAdapter/BamSlightlyLazyFeature.ts +0 -149
  432. package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +0 -1105
  433. package/src/BamAdapter/configSchema.ts +0 -65
  434. package/src/BamAdapter/index.ts +0 -14
  435. package/src/CombinationTest.test.ts +0 -108
  436. package/src/CramAdapter/CramAdapter.test.ts +0 -85
  437. package/src/CramAdapter/CramAdapter.ts +0 -323
  438. package/src/CramAdapter/CramSlightlyLazyFeature.ts +0 -185
  439. package/src/CramAdapter/CramTestAdapters.ts +0 -98
  440. package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +0 -256
  441. package/src/CramAdapter/__snapshots__/util.test.ts.snap +0 -14
  442. package/src/CramAdapter/configSchema.ts +0 -57
  443. package/src/CramAdapter/index.ts +0 -16
  444. package/src/CramAdapter/util.test.ts +0 -26
  445. package/src/CramAdapter/util.ts +0 -251
  446. package/src/GuessAlignmentsTypes/index.ts +0 -79
  447. package/src/HtsgetBamAdapter/HtsgetBamAdapter.ts +0 -24
  448. package/src/HtsgetBamAdapter/configSchema.ts +0 -40
  449. package/src/HtsgetBamAdapter/index.ts +0 -17
  450. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +0 -52
  451. package/src/LinearAlignmentsDisplay/index.ts +0 -21
  452. package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +0 -60
  453. package/src/LinearAlignmentsDisplay/models/configSchema.ts +0 -41
  454. package/src/LinearAlignmentsDisplay/models/model.tsx +0 -403
  455. package/src/LinearPileupDisplay/components/ColorByModifications.tsx +0 -102
  456. package/src/LinearPileupDisplay/components/ColorByTag.tsx +0 -61
  457. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +0 -32
  458. package/src/LinearPileupDisplay/components/ModificationsTable.tsx +0 -38
  459. package/src/LinearPileupDisplay/components/SetFeatureHeight.tsx +0 -82
  460. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +0 -71
  461. package/src/LinearPileupDisplay/components/SortByTag.tsx +0 -64
  462. package/src/LinearPileupDisplay/configSchema.test.js +0 -55
  463. package/src/LinearPileupDisplay/configSchema.ts +0 -67
  464. package/src/LinearPileupDisplay/index.ts +0 -24
  465. package/src/LinearPileupDisplay/model.ts +0 -884
  466. package/src/LinearReadArcsDisplay/components/ReactComponent.tsx +0 -50
  467. package/src/LinearReadArcsDisplay/configSchema.ts +0 -68
  468. package/src/LinearReadArcsDisplay/declare.d.ts +0 -1
  469. package/src/LinearReadArcsDisplay/drawFeats.ts +0 -210
  470. package/src/LinearReadArcsDisplay/index.ts +0 -23
  471. package/src/LinearReadArcsDisplay/model.tsx +0 -355
  472. package/src/LinearReadArcsDisplay/util.ts +0 -10
  473. package/src/LinearReadCloudDisplay/components/ReactComponent.tsx +0 -48
  474. package/src/LinearReadCloudDisplay/configSchema.ts +0 -57
  475. package/src/LinearReadCloudDisplay/drawFeats.ts +0 -35
  476. package/src/LinearReadCloudDisplay/drawLongReadChains.ts +0 -85
  477. package/src/LinearReadCloudDisplay/drawPairChains.ts +0 -139
  478. package/src/LinearReadCloudDisplay/index.ts +0 -23
  479. package/src/LinearReadCloudDisplay/model.tsx +0 -246
  480. package/src/LinearReadCloudDisplay/util.ts +0 -47
  481. package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +0 -128
  482. package/src/LinearSNPCoverageDisplay/index.ts +0 -20
  483. package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +0 -35
  484. package/src/LinearSNPCoverageDisplay/models/configSchema.ts +0 -82
  485. package/src/LinearSNPCoverageDisplay/models/model.ts +0 -336
  486. package/src/MismatchParser/index.test.ts +0 -283
  487. package/src/MismatchParser/index.ts +0 -508
  488. package/src/PileupRPC/base.ts +0 -24
  489. package/src/PileupRPC/index.ts +0 -12
  490. package/src/PileupRPC/methods/GetGlobalValueForTag.ts +0 -44
  491. package/src/PileupRPC/methods/GetReducedFeatures.ts +0 -67
  492. package/src/PileupRPC/methods/GetVisibleModifications.ts +0 -45
  493. package/src/PileupRPC/rpcMethods.ts +0 -3
  494. package/src/PileupRPC/util.ts +0 -19
  495. package/src/PileupRenderer/PileupLayoutSession.ts +0 -64
  496. package/src/PileupRenderer/PileupRenderer.ts +0 -142
  497. package/src/PileupRenderer/colorBy.ts +0 -74
  498. package/src/PileupRenderer/components/PileupRendering.tsx +0 -209
  499. package/src/PileupRenderer/configSchema.ts +0 -108
  500. package/src/PileupRenderer/getAlignmentShapeColor.ts +0 -87
  501. package/src/PileupRenderer/index.ts +0 -16
  502. package/src/PileupRenderer/layoutFeature.ts +0 -83
  503. package/src/PileupRenderer/layoutFeatures.ts +0 -44
  504. package/src/PileupRenderer/makeImageData.ts +0 -93
  505. package/src/PileupRenderer/renderAlignment.ts +0 -97
  506. package/src/PileupRenderer/renderAlignmentShape.ts +0 -45
  507. package/src/PileupRenderer/renderMethylation.ts +0 -75
  508. package/src/PileupRenderer/renderMismatches.ts +0 -206
  509. package/src/PileupRenderer/renderModifications.ts +0 -74
  510. package/src/PileupRenderer/renderPerBaseLettering.ts +0 -67
  511. package/src/PileupRenderer/renderPerBaseQuality.ts +0 -46
  512. package/src/PileupRenderer/renderSoftClipping.ts +0 -78
  513. package/src/PileupRenderer/sortUtil.ts +0 -107
  514. package/src/PileupRenderer/util.ts +0 -63
  515. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +0 -111
  516. package/src/SNPCoverageAdapter/configSchema.ts +0 -23
  517. package/src/SNPCoverageAdapter/generateCoverageBins.ts +0 -259
  518. package/src/SNPCoverageAdapter/index.ts +0 -18
  519. package/src/SNPCoverageAdapter/util.ts +0 -33
  520. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +0 -270
  521. package/src/SNPCoverageRenderer/configSchema.ts +0 -64
  522. package/src/SNPCoverageRenderer/index.ts +0 -17
  523. package/src/__snapshots__/index.test.ts.snap +0 -3
  524. package/src/index.test.ts +0 -17
  525. package/src/index.ts +0 -48
  526. package/src/shared/BaseDisplayComponent.tsx +0 -83
  527. package/src/shared/FilterByTag.tsx +0 -187
  528. package/src/shared/afterAttach.tsx +0 -66
  529. package/src/shared/color.ts +0 -86
  530. package/src/shared/fetchChains.ts +0 -62
  531. package/src/shared/index.ts +0 -75
  532. package/src/shared/renderSvg.tsx +0 -64
  533. package/src/shared/util.ts +0 -10
  534. package/src/util.ts +0 -154
package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap DELETED
@@ -1,1105 +0,0 @@
1
- // Jest Snapshot v1, https://goo.gl/fbAQLP
2
-
3
- exports[`adapter can fetch features from volvox.bam 1`] = `
4
- [
5
- {
6
- "CIGAR": "100M",
7
- "MD": "22A32C15T12A15",
8
- "MQ": 37,
9
- "NM": 4,
10
- "X0": 1,
11
- "X1": 0,
12
- "XG": 0,
13
- "XM": 4,
14
- "XO": 0,
15
- "XT": "U",
16
- "clipPos": 0,
17
- "end": 5540,
18
- "flags": 16,
19
- "length_on_ref": 100,
20
- "name": "ctgA_5060_5540_1:0:0_3:1:0_15a3",
21
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
22
- "refName": "ctgA",
23
- "score": 37,
24
- "seq": "TACACTGGTTCGGAGACGGTTCGTGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGACCGGCGGCACGACTAATATAGTGCAAGA",
25
- "seq_length": 100,
26
- "start": 5440,
27
- "strand": -1,
28
- "template_length": 0,
29
- "type": "match",
30
- "uniqueId": "test-10158054",
31
- },
32
- {
33
- "CIGAR": "100M",
34
- "MD": "66G33",
35
- "MQ": 37,
36
- "NM": 1,
37
- "X0": 1,
38
- "X1": 0,
39
- "XG": 0,
40
- "XM": 1,
41
- "XO": 0,
42
- "XT": "U",
43
- "clipPos": 0,
44
- "end": 5541,
45
- "flags": 16,
46
- "length_on_ref": 100,
47
- "name": "ctgA_4973_5541_1:0:0_1:0:0_1569",
48
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
49
- "refName": "ctgA",
50
- "score": 37,
51
- "seq": "ACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCCCTGTCCGGCGGCACGAATAATATAGTGCAAGAA",
52
- "seq_length": 100,
53
- "start": 5441,
54
- "strand": -1,
55
- "template_length": 0,
56
- "type": "match",
57
- "uniqueId": "test-10158322",
58
- },
59
- {
60
- "CIGAR": "100M",
61
- "MD": "25G23C1C24A23",
62
- "MQ": 37,
63
- "NM": 4,
64
- "X0": 1,
65
- "X1": 0,
66
- "XG": 0,
67
- "XM": 4,
68
- "XO": 0,
69
- "XT": "U",
70
- "clipPos": 0,
71
- "end": 5544,
72
- "flags": 0,
73
- "length_on_ref": 100,
74
- "name": "ctgA_5445_5947_3:1:0_2:0:0_2b9",
75
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
76
- "refName": "ctgA",
77
- "score": 37,
78
- "seq": "CTGGTTCGGAGACGGTTCATGACGACCGCGCTATATGTCGGCATCTGCGTCGCATGAGCGGCCGCTGTCCGGCGGCTCGAATAATATAGTGCAAGAAAAA",
79
- "seq_length": 100,
80
- "start": 5444,
81
- "strand": 1,
82
- "template_length": 0,
83
- "type": "match",
84
- "uniqueId": "test-10158581",
85
- },
86
- {
87
- "CIGAR": "100M",
88
- "MD": "42C57",
89
- "MQ": 37,
90
- "NM": 1,
91
- "X0": 1,
92
- "X1": 0,
93
- "XG": 0,
94
- "XM": 1,
95
- "XO": 0,
96
- "XT": "U",
97
- "clipPos": 0,
98
- "end": 5553,
99
- "flags": 0,
100
- "length_on_ref": 100,
101
- "name": "ctgA_5454_5906_0:1:0_2:0:0_d8a",
102
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
103
- "refName": "ctgA",
104
- "score": 37,
105
- "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT",
106
- "seq_length": 100,
107
- "start": 5453,
108
- "strand": 1,
109
- "template_length": 0,
110
- "type": "match",
111
- "uniqueId": "test-10158847",
112
- },
113
- {
114
- "CIGAR": "100M",
115
- "MD": "49G11G38",
116
- "MQ": 37,
117
- "NM": 2,
118
- "X0": 1,
119
- "X1": 0,
120
- "XG": 0,
121
- "XM": 2,
122
- "XO": 0,
123
- "XT": "U",
124
- "clipPos": 0,
125
- "end": 5554,
126
- "flags": 0,
127
- "length_on_ref": 100,
128
- "name": "ctgA_5455_5964_2:0:0_2:0:0_23e2",
129
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
130
- "refName": "ctgA",
131
- "score": 37,
132
- "seq": "GACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCCGCCGCTGTCCGACGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTA",
133
- "seq_length": 100,
134
- "start": 5454,
135
- "strand": 1,
136
- "template_length": 0,
137
- "type": "match",
138
- "uniqueId": "test-12607066",
139
- },
140
- {
141
- "CIGAR": "100M",
142
- "MD": "22T13C63",
143
- "MQ": 37,
144
- "NM": 2,
145
- "X0": 1,
146
- "X1": 0,
147
- "XG": 0,
148
- "XM": 2,
149
- "XO": 0,
150
- "XT": "U",
151
- "clipPos": 0,
152
- "end": 5559,
153
- "flags": 16,
154
- "length_on_ref": 100,
155
- "name": "ctgA_5153_5559_3:0:0_1:1:0_11ac",
156
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
157
- "refName": "ctgA",
158
- "score": 37,
159
- "seq": "TTCATGACGAGCGCGCTATATGACGGCATCTGCGCCGCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT",
160
- "seq_length": 100,
161
- "start": 5459,
162
- "strand": -1,
163
- "template_length": 0,
164
- "type": "match",
165
- "uniqueId": "test-12607328",
166
- },
167
- {
168
- "CIGAR": "100M",
169
- "MD": "35C3G60",
170
- "MQ": 37,
171
- "NM": 2,
172
- "X0": 1,
173
- "X1": 0,
174
- "XG": 0,
175
- "XM": 2,
176
- "XO": 0,
177
- "XT": "U",
178
- "clipPos": 0,
179
- "end": 5560,
180
- "flags": 0,
181
- "length_on_ref": 100,
182
- "name": "ctgA_5461_5986_1:1:0_3:0:0_200e",
183
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
184
- "refName": "ctgA",
185
- "score": 37,
186
- "seq": "TCATGACGAGCGCGCTATATGTCGGCATCTGCGCCGCATCAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTA",
187
- "seq_length": 100,
188
- "start": 5460,
189
- "strand": 1,
190
- "template_length": 0,
191
- "type": "match",
192
- "uniqueId": "test-12607590",
193
- },
194
- {
195
- "CIGAR": "100M",
196
- "MD": "100",
197
- "MQ": 37,
198
- "NM": 0,
199
- "X0": 1,
200
- "X1": 0,
201
- "XG": 0,
202
- "XM": 0,
203
- "XO": 0,
204
- "XT": "U",
205
- "clipPos": 0,
206
- "end": 5568,
207
- "flags": 0,
208
- "length_on_ref": 100,
209
- "name": "ctgA_5469_5932_0:0:0_2:0:0_6f8",
210
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
211
- "refName": "ctgA",
212
- "score": 37,
213
- "seq": "AGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGAT",
214
- "seq_length": 100,
215
- "start": 5468,
216
- "strand": 1,
217
- "template_length": 0,
218
- "type": "match",
219
- "uniqueId": "test-12607851",
220
- },
221
- {
222
- "CIGAR": "100M",
223
- "MD": "52G43A3",
224
- "MQ": 37,
225
- "NM": 2,
226
- "X0": 1,
227
- "X1": 0,
228
- "XG": 0,
229
- "XM": 2,
230
- "XO": 0,
231
- "XT": "U",
232
- "clipPos": 0,
233
- "end": 5594,
234
- "flags": 16,
235
- "length_on_ref": 100,
236
- "name": "ctgA_5079_5594_1:0:0_2:0:0_d64",
237
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
238
- "refName": "ctgA",
239
- "score": 37,
240
- "seq": "CCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCTAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCTCACA",
241
- "seq_length": 100,
242
- "start": 5494,
243
- "strand": -1,
244
- "template_length": 0,
245
- "type": "match",
246
- "uniqueId": "test-12608107",
247
- },
248
- {
249
- "CIGAR": "100M",
250
- "MD": "92C7",
251
- "MQ": 37,
252
- "NM": 1,
253
- "X0": 1,
254
- "X1": 0,
255
- "XG": 0,
256
- "XM": 1,
257
- "XO": 0,
258
- "XT": "U",
259
- "clipPos": 0,
260
- "end": 5596,
261
- "flags": 0,
262
- "length_on_ref": 100,
263
- "name": "ctgA_5497_6082_1:0:0_2:0:0_b2",
264
- "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
265
- "refName": "ctgA",
266
- "score": 37,
267
- "seq": "CATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTGTAACAGG",
268
- "seq_length": 100,
269
- "start": 5496,
270
- "strand": 1,
271
- "template_length": 0,
272
- "type": "match",
273
- "uniqueId": "test-12608367",
274
- },
275
- ]
276
- `;
277
-
278
- exports[`test usage of BamSlightlyLazyFeature for extended CIGAR 1`] = `
279
- [
280
- {
281
- "base": "S2666",
282
- "cliplen": 2666,
283
- "length": 1,
284
- "start": 0,
285
- "type": "softclip",
286
- },
287
- {
288
- "base": "*",
289
- "length": 1,
290
- "start": 33,
291
- "type": "deletion",
292
- },
293
- {
294
- "base": "G",
295
- "length": 1,
296
- "qual": 93,
297
- "start": 40,
298
- "type": "mismatch",
299
- },
300
- {
301
- "base": "*",
302
- "length": 1,
303
- "start": 75,
304
- "type": "deletion",
305
- },
306
- {
307
- "base": "*",
308
- "length": 1,
309
- "start": 90,
310
- "type": "deletion",
311
- },
312
- {
313
- "base": "1",
314
- "length": 0,
315
- "start": 108,
316
- "type": "insertion",
317
- },
318
- {
319
- "base": "*",
320
- "length": 1,
321
- "start": 132,
322
- "type": "deletion",
323
- },
324
- {
325
- "base": "*",
326
- "length": 1,
327
- "start": 146,
328
- "type": "deletion",
329
- },
330
- {
331
- "base": "3",
332
- "length": 0,
333
- "start": 177,
334
- "type": "insertion",
335
- },
336
- {
337
- "base": "1",
338
- "length": 0,
339
- "start": 209,
340
- "type": "insertion",
341
- },
342
- {
343
- "base": "C",
344
- "length": 1,
345
- "qual": 93,
346
- "start": 216,
347
- "type": "mismatch",
348
- },
349
- {
350
- "base": "C",
351
- "length": 1,
352
- "qual": 93,
353
- "start": 222,
354
- "type": "mismatch",
355
- },
356
- {
357
- "base": "C",
358
- "length": 1,
359
- "qual": 93,
360
- "start": 228,
361
- "type": "mismatch",
362
- },
363
- {
364
- "base": "*",
365
- "length": 1,
366
- "start": 230,
367
- "type": "deletion",
368
- },
369
- {
370
- "base": "C",
371
- "length": 1,
372
- "qual": 93,
373
- "start": 235,
374
- "type": "mismatch",
375
- },
376
- {
377
- "base": "C",
378
- "length": 1,
379
- "qual": 93,
380
- "start": 241,
381
- "type": "mismatch",
382
- },
383
- {
384
- "base": "*",
385
- "length": 1,
386
- "start": 247,
387
- "type": "deletion",
388
- },
389
- {
390
- "base": "C",
391
- "length": 1,
392
- "qual": 93,
393
- "start": 248,
394
- "type": "mismatch",
395
- },
396
- {
397
- "base": "*",
398
- "length": 1,
399
- "start": 254,
400
- "type": "deletion",
401
- },
402
- {
403
- "base": "C",
404
- "length": 1,
405
- "qual": 93,
406
- "start": 255,
407
- "type": "mismatch",
408
- },
409
- {
410
- "base": "*",
411
- "length": 1,
412
- "start": 263,
413
- "type": "deletion",
414
- },
415
- {
416
- "base": "1",
417
- "length": 0,
418
- "start": 284,
419
- "type": "insertion",
420
- },
421
- {
422
- "base": "T",
423
- "length": 1,
424
- "qual": 93,
425
- "start": 289,
426
- "type": "mismatch",
427
- },
428
- {
429
- "base": "T",
430
- "length": 1,
431
- "qual": 93,
432
- "start": 290,
433
- "type": "mismatch",
434
- },
435
- {
436
- "base": "*",
437
- "length": 1,
438
- "start": 293,
439
- "type": "deletion",
440
- },
441
- {
442
- "base": "A",
443
- "length": 1,
444
- "qual": 93,
445
- "start": 294,
446
- "type": "mismatch",
447
- },
448
- {
449
- "base": "T",
450
- "length": 1,
451
- "qual": 93,
452
- "start": 296,
453
- "type": "mismatch",
454
- },
455
- {
456
- "base": "T",
457
- "length": 1,
458
- "qual": 93,
459
- "start": 302,
460
- "type": "mismatch",
461
- },
462
- {
463
- "base": "G",
464
- "length": 1,
465
- "qual": 93,
466
- "start": 308,
467
- "type": "mismatch",
468
- },
469
- {
470
- "base": "G",
471
- "length": 1,
472
- "qual": 93,
473
- "start": 314,
474
- "type": "mismatch",
475
- },
476
- {
477
- "base": "G",
478
- "length": 1,
479
- "qual": 93,
480
- "start": 320,
481
- "type": "mismatch",
482
- },
483
- {
484
- "base": "G",
485
- "length": 1,
486
- "qual": 93,
487
- "start": 326,
488
- "type": "mismatch",
489
- },
490
- {
491
- "base": "*",
492
- "length": 1,
493
- "start": 329,
494
- "type": "deletion",
495
- },
496
- {
497
- "base": "G",
498
- "length": 1,
499
- "qual": 93,
500
- "start": 333,
501
- "type": "mismatch",
502
- },
503
- {
504
- "base": "1",
505
- "length": 0,
506
- "start": 339,
507
- "type": "insertion",
508
- },
509
- {
510
- "base": "1",
511
- "length": 0,
512
- "start": 345,
513
- "type": "insertion",
514
- },
515
- {
516
- "base": "2",
517
- "length": 0,
518
- "start": 352,
519
- "type": "insertion",
520
- },
521
- {
522
- "base": "*",
523
- "length": 1,
524
- "start": 375,
525
- "type": "deletion",
526
- },
527
- {
528
- "base": "G",
529
- "length": 1,
530
- "qual": 93,
531
- "start": 384,
532
- "type": "mismatch",
533
- },
534
- {
535
- "base": "67",
536
- "length": 0,
537
- "start": 403,
538
- "type": "insertion",
539
- },
540
- {
541
- "base": "1",
542
- "length": 0,
543
- "start": 427,
544
- "type": "insertion",
545
- },
546
- {
547
- "base": "1",
548
- "length": 0,
549
- "start": 433,
550
- "type": "insertion",
551
- },
552
- {
553
- "base": "*",
554
- "length": 1,
555
- "start": 439,
556
- "type": "deletion",
557
- },
558
- {
559
- "base": "T",
560
- "length": 1,
561
- "qual": 93,
562
- "start": 491,
563
- "type": "mismatch",
564
- },
565
- {
566
- "base": "G",
567
- "length": 1,
568
- "qual": 93,
569
- "start": 621,
570
- "type": "mismatch",
571
- },
572
- {
573
- "base": "C",
574
- "length": 1,
575
- "qual": 93,
576
- "start": 622,
577
- "type": "mismatch",
578
- },
579
- {
580
- "base": "7",
581
- "length": 0,
582
- "start": 626,
583
- "type": "insertion",
584
- },
585
- {
586
- "base": "1",
587
- "length": 0,
588
- "start": 627,
589
- "type": "insertion",
590
- },
591
- {
592
- "base": "G",
593
- "length": 1,
594
- "qual": 93,
595
- "start": 800,
596
- "type": "mismatch",
597
- },
598
- {
599
- "base": "G",
600
- "length": 1,
601
- "qual": 93,
602
- "start": 802,
603
- "type": "mismatch",
604
- },
605
- {
606
- "base": "G",
607
- "length": 1,
608
- "qual": 93,
609
- "start": 803,
610
- "type": "mismatch",
611
- },
612
- {
613
- "base": "C",
614
- "length": 1,
615
- "qual": 93,
616
- "start": 804,
617
- "type": "mismatch",
618
- },
619
- {
620
- "base": "*",
621
- "length": 1,
622
- "start": 807,
623
- "type": "deletion",
624
- },
625
- {
626
- "base": "G",
627
- "length": 1,
628
- "qual": 93,
629
- "start": 808,
630
- "type": "mismatch",
631
- },
632
- {
633
- "base": "C",
634
- "length": 1,
635
- "qual": 93,
636
- "start": 809,
637
- "type": "mismatch",
638
- },
639
- {
640
- "base": "C",
641
- "length": 1,
642
- "qual": 93,
643
- "start": 814,
644
- "type": "mismatch",
645
- },
646
- {
647
- "base": "4",
648
- "length": 0,
649
- "start": 818,
650
- "type": "insertion",
651
- },
652
- {
653
- "base": "C",
654
- "length": 1,
655
- "qual": 93,
656
- "start": 820,
657
- "type": "mismatch",
658
- },
659
- {
660
- "base": "4",
661
- "length": 0,
662
- "start": 822,
663
- "type": "insertion",
664
- },
665
- {
666
- "base": "8",
667
- "length": 0,
668
- "start": 828,
669
- "type": "insertion",
670
- },
671
- {
672
- "base": "C",
673
- "length": 1,
674
- "qual": 93,
675
- "start": 828,
676
- "type": "mismatch",
677
- },
678
- {
679
- "base": "G",
680
- "length": 1,
681
- "qual": 93,
682
- "start": 883,
683
- "type": "mismatch",
684
- },
685
- {
686
- "base": "47",
687
- "length": 0,
688
- "start": 889,
689
- "type": "insertion",
690
- },
691
- {
692
- "base": "A",
693
- "length": 1,
694
- "qual": 93,
695
- "start": 896,
696
- "type": "mismatch",
697
- },
698
- {
699
- "base": "G",
700
- "length": 1,
701
- "qual": 93,
702
- "start": 926,
703
- "type": "mismatch",
704
- },
705
- {
706
- "base": "T",
707
- "length": 1,
708
- "qual": 93,
709
- "start": 930,
710
- "type": "mismatch",
711
- },
712
- {
713
- "base": "T",
714
- "length": 1,
715
- "qual": 93,
716
- "start": 933,
717
- "type": "mismatch",
718
- },
719
- {
720
- "base": "C",
721
- "length": 1,
722
- "qual": 93,
723
- "start": 935,
724
- "type": "mismatch",
725
- },
726
- {
727
- "base": "1",
728
- "length": 0,
729
- "start": 968,
730
- "type": "insertion",
731
- },
732
- {
733
- "base": "C",
734
- "length": 1,
735
- "qual": 93,
736
- "start": 1001,
737
- "type": "mismatch",
738
- },
739
- {
740
- "base": "T",
741
- "length": 1,
742
- "qual": 93,
743
- "start": 1016,
744
- "type": "mismatch",
745
- },
746
- {
747
- "base": "G",
748
- "length": 1,
749
- "qual": 39,
750
- "start": 1018,
751
- "type": "mismatch",
752
- },
753
- {
754
- "base": "A",
755
- "length": 1,
756
- "qual": 93,
757
- "start": 1034,
758
- "type": "mismatch",
759
- },
760
- {
761
- "base": "1",
762
- "length": 0,
763
- "start": 1063,
764
- "type": "insertion",
765
- },
766
- {
767
- "base": "2",
768
- "length": 0,
769
- "start": 1068,
770
- "type": "insertion",
771
- },
772
- {
773
- "base": "G",
774
- "length": 1,
775
- "qual": 93,
776
- "start": 1074,
777
- "type": "mismatch",
778
- },
779
- {
780
- "base": "G",
781
- "length": 1,
782
- "qual": 93,
783
- "start": 1078,
784
- "type": "mismatch",
785
- },
786
- {
787
- "base": "C",
788
- "length": 1,
789
- "qual": 93,
790
- "start": 1112,
791
- "type": "mismatch",
792
- },
793
- {
794
- "base": "G",
795
- "length": 1,
796
- "qual": 93,
797
- "start": 1133,
798
- "type": "mismatch",
799
- },
800
- {
801
- "base": "C",
802
- "length": 1,
803
- "qual": 93,
804
- "start": 1153,
805
- "type": "mismatch",
806
- },
807
- {
808
- "base": "A",
809
- "length": 1,
810
- "qual": 93,
811
- "start": 1166,
812
- "type": "mismatch",
813
- },
814
- {
815
- "base": "A",
816
- "length": 1,
817
- "qual": 93,
818
- "start": 1390,
819
- "type": "mismatch",
820
- },
821
- {
822
- "base": "G",
823
- "length": 1,
824
- "qual": 93,
825
- "start": 1408,
826
- "type": "mismatch",
827
- },
828
- {
829
- "base": "G",
830
- "length": 1,
831
- "qual": 93,
832
- "start": 1456,
833
- "type": "mismatch",
834
- },
835
- {
836
- "base": "G",
837
- "length": 1,
838
- "qual": 93,
839
- "start": 1507,
840
- "type": "mismatch",
841
- },
842
- {
843
- "base": "T",
844
- "length": 1,
845
- "qual": 93,
846
- "start": 1541,
847
- "type": "mismatch",
848
- },
849
- {
850
- "base": "T",
851
- "length": 1,
852
- "qual": 93,
853
- "start": 1564,
854
- "type": "mismatch",
855
- },
856
- {
857
- "base": "A",
858
- "length": 1,
859
- "qual": 93,
860
- "start": 1771,
861
- "type": "mismatch",
862
- },
863
- {
864
- "base": "C",
865
- "length": 1,
866
- "qual": 93,
867
- "start": 2197,
868
- "type": "mismatch",
869
- },
870
- {
871
- "base": "A",
872
- "length": 1,
873
- "qual": 93,
874
- "start": 2382,
875
- "type": "mismatch",
876
- },
877
- {
878
- "base": "A",
879
- "length": 1,
880
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