@jbrowse/plugin-alignments 1.6.9 → 1.7.3

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Files changed (131) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts +6 -6
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +216 -0
  3. package/dist/AlignmentsFeatureDetail/index.d.ts +13 -13
  4. package/dist/AlignmentsFeatureDetail/index.js +63 -0
  5. package/dist/AlignmentsFeatureDetail/index.test.js +60 -0
  6. package/dist/AlignmentsTrack/index.d.ts +2 -2
  7. package/dist/AlignmentsTrack/index.js +37 -0
  8. package/dist/BamAdapter/BamAdapter.d.ts +40 -30
  9. package/dist/BamAdapter/BamAdapter.js +598 -0
  10. package/dist/BamAdapter/BamAdapter.test.js +177 -0
  11. package/dist/BamAdapter/BamSlightlyLazyFeature.d.ts +33 -33
  12. package/dist/BamAdapter/BamSlightlyLazyFeature.js +176 -0
  13. package/dist/BamAdapter/MismatchParser.d.ts +28 -28
  14. package/dist/BamAdapter/MismatchParser.js +384 -0
  15. package/dist/BamAdapter/MismatchParser.test.js +259 -0
  16. package/dist/BamAdapter/configSchema.d.ts +2 -2
  17. package/dist/BamAdapter/configSchema.js +48 -0
  18. package/dist/BamAdapter/index.d.ts +3 -3
  19. package/dist/BamAdapter/index.js +36 -0
  20. package/dist/CramAdapter/CramAdapter.d.ts +52 -43
  21. package/dist/CramAdapter/CramAdapter.js +660 -0
  22. package/dist/CramAdapter/CramAdapter.test.js +138 -0
  23. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +49 -49
  24. package/dist/CramAdapter/CramSlightlyLazyFeature.js +447 -0
  25. package/dist/CramAdapter/CramTestAdapters.d.ts +29 -29
  26. package/dist/CramAdapter/CramTestAdapters.js +234 -0
  27. package/dist/CramAdapter/configSchema.d.ts +3 -3
  28. package/dist/CramAdapter/configSchema.js +40 -0
  29. package/dist/CramAdapter/index.d.ts +3 -3
  30. package/dist/CramAdapter/index.js +36 -0
  31. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts +9 -9
  32. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +97 -0
  33. package/dist/HtsgetBamAdapter/configSchema.d.ts +2 -2
  34. package/dist/HtsgetBamAdapter/configSchema.js +31 -0
  35. package/dist/HtsgetBamAdapter/index.d.ts +3 -3
  36. package/dist/HtsgetBamAdapter/index.js +42 -0
  37. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +7 -7
  38. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +69 -0
  39. package/dist/LinearAlignmentsDisplay/index.d.ts +2 -2
  40. package/dist/LinearAlignmentsDisplay/index.js +31 -0
  41. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +4 -4
  42. package/dist/LinearAlignmentsDisplay/models/configSchema.js +25 -0
  43. package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +83 -0
  44. package/dist/LinearAlignmentsDisplay/models/model.d.ts +105 -105
  45. package/dist/LinearAlignmentsDisplay/models/model.js +250 -0
  46. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +14 -14
  47. package/dist/LinearPileupDisplay/components/ColorByModifications.js +123 -0
  48. package/dist/LinearPileupDisplay/components/ColorByTag.d.ts +9 -9
  49. package/dist/LinearPileupDisplay/components/ColorByTag.js +98 -0
  50. package/dist/LinearPileupDisplay/components/FilterByTag.d.ts +18 -18
  51. package/dist/LinearPileupDisplay/components/FilterByTag.js +203 -0
  52. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts +13 -13
  53. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +32 -0
  54. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +16 -16
  55. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +99 -0
  56. package/dist/LinearPileupDisplay/components/SetMaxHeight.d.ts +10 -10
  57. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +90 -0
  58. package/dist/LinearPileupDisplay/components/SortByTag.d.ts +9 -9
  59. package/dist/LinearPileupDisplay/components/SortByTag.js +95 -0
  60. package/dist/LinearPileupDisplay/configSchema.d.ts +6 -6
  61. package/dist/LinearPileupDisplay/configSchema.js +47 -0
  62. package/dist/LinearPileupDisplay/configSchema.test.js +92 -0
  63. package/dist/LinearPileupDisplay/index.d.ts +2 -2
  64. package/dist/LinearPileupDisplay/index.js +30 -0
  65. package/dist/LinearPileupDisplay/model.d.ts +319 -321
  66. package/dist/LinearPileupDisplay/model.js +602 -0
  67. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +10 -10
  68. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +63 -0
  69. package/dist/LinearSNPCoverageDisplay/index.d.ts +2 -2
  70. package/dist/LinearSNPCoverageDisplay/index.js +30 -0
  71. package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts +2 -2
  72. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +57 -0
  73. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +62 -0
  74. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +346 -96
  75. package/dist/LinearSNPCoverageDisplay/models/model.js +237 -0
  76. package/dist/NestedFrequencyTable.d.ts +14 -14
  77. package/dist/NestedFrequencyTable.js +152 -0
  78. package/dist/PileupRPC/rpcMethods.d.ts +34 -34
  79. package/dist/PileupRPC/rpcMethods.js +285 -0
  80. package/dist/PileupRenderer/PileupLayoutSession.d.ts +29 -29
  81. package/dist/PileupRenderer/PileupLayoutSession.js +79 -0
  82. package/dist/PileupRenderer/PileupRenderer.d.ts +125 -125
  83. package/dist/PileupRenderer/PileupRenderer.js +1220 -0
  84. package/dist/PileupRenderer/components/PileupRendering.d.ts +23 -23
  85. package/dist/PileupRenderer/components/PileupRendering.js +270 -0
  86. package/dist/PileupRenderer/components/PileupRendering.test.js +36 -0
  87. package/dist/PileupRenderer/configSchema.d.ts +2 -2
  88. package/dist/PileupRenderer/configSchema.js +72 -0
  89. package/dist/PileupRenderer/index.d.ts +2 -2
  90. package/dist/PileupRenderer/index.js +25 -0
  91. package/dist/PileupRenderer/sortUtil.d.ts +8 -8
  92. package/dist/PileupRenderer/sortUtil.js +112 -0
  93. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts +67 -71
  94. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +606 -0
  95. package/dist/SNPCoverageAdapter/configSchema.d.ts +3 -3
  96. package/dist/SNPCoverageAdapter/configSchema.js +22 -0
  97. package/dist/SNPCoverageAdapter/index.d.ts +3 -3
  98. package/dist/SNPCoverageAdapter/index.js +45 -0
  99. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +20 -20
  100. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +296 -0
  101. package/dist/SNPCoverageRenderer/configSchema.d.ts +2 -2
  102. package/dist/SNPCoverageRenderer/configSchema.js +40 -0
  103. package/dist/SNPCoverageRenderer/index.d.ts +3 -3
  104. package/dist/SNPCoverageRenderer/index.js +34 -0
  105. package/dist/declare.d.js +1 -0
  106. package/dist/index.d.ts +10 -10
  107. package/dist/index.js +154 -6
  108. package/dist/index.test.js +26 -0
  109. package/dist/shared.d.ts +25 -25
  110. package/dist/shared.js +96 -0
  111. package/dist/util.d.ts +19 -19
  112. package/dist/util.js +135 -0
  113. package/package.json +5 -8
  114. package/src/BamAdapter/BamAdapter.ts +35 -8
  115. package/src/CramAdapter/CramAdapter.ts +42 -15
  116. package/src/LinearPileupDisplay/components/SetMaxHeight.tsx +1 -1
  117. package/src/LinearPileupDisplay/model.ts +2 -22
  118. package/src/LinearSNPCoverageDisplay/models/model.ts +6 -36
  119. package/src/PileupRenderer/PileupRenderer.tsx +3 -6
  120. package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts +11 -17
  121. package/dist/AlignmentsFeatureDetail/index.test.d.ts +0 -1
  122. package/dist/LinearAlignmentsDisplay/models/configSchema.test.d.ts +0 -1
  123. package/dist/LinearPileupDisplay/configSchema.test.d.ts +0 -1
  124. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.d.ts +0 -1
  125. package/dist/PileupRenderer/components/PileupRendering.test.d.ts +0 -1
  126. package/dist/plugin-alignments.cjs.development.js +0 -8438
  127. package/dist/plugin-alignments.cjs.development.js.map +0 -1
  128. package/dist/plugin-alignments.cjs.production.min.js +0 -2
  129. package/dist/plugin-alignments.cjs.production.min.js.map +0 -1
  130. package/dist/plugin-alignments.esm.js +0 -8430
  131. package/dist/plugin-alignments.esm.js.map +0 -1

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