@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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