@jbrowse/plugin-alignments 2.13.1 → 2.15.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (155) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +5 -3
  2. package/dist/AlignmentsFeatureDetail/BreakendOptionDialog.js +12 -4
  3. package/dist/AlignmentsFeatureDetail/Formatter.js +6 -2
  4. package/dist/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js +4 -2
  5. package/dist/AlignmentsFeatureDetail/getSAFeatures.js +4 -4
  6. package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js +2 -2
  7. package/dist/BamAdapter/BamAdapter.js +12 -18
  8. package/dist/BamAdapter/BamSlightlyLazyFeature.js +0 -1
  9. package/dist/CramAdapter/CramAdapter.d.ts +1 -1
  10. package/dist/CramAdapter/CramAdapter.js +7 -6
  11. package/dist/CramAdapter/CramTestAdapters.js +8 -2
  12. package/dist/GuessAlignmentsTypes/index.js +2 -2
  13. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -2
  14. package/dist/LinearAlignmentsDisplay/models/model.d.ts +13 -20
  15. package/dist/LinearAlignmentsDisplay/models/model.js +13 -3
  16. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +9 -4
  17. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +41 -22
  18. package/dist/LinearPileupDisplay/components/{ColorByModifications.js → ColorByModificationsDialog.js} +3 -1
  19. package/dist/LinearPileupDisplay/components/{ColorByTag.js → ColorByTagDialog.js} +4 -2
  20. package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts +11 -0
  21. package/dist/LinearPileupDisplay/components/GroupByDialog.js +129 -0
  22. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +1 -3
  23. package/dist/LinearPileupDisplay/components/{SetFeatureHeight.js → SetFeatureHeightDialog.js} +9 -3
  24. package/{esm/LinearPileupDisplay/components/SetMaxHeight.d.ts → dist/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts} +1 -1
  25. package/dist/LinearPileupDisplay/components/{SetMaxHeight.js → SetMaxHeightDialog.js} +7 -3
  26. package/dist/LinearPileupDisplay/components/{SortByTag.d.ts → SortByTagDialog.d.ts} +1 -1
  27. package/dist/LinearPileupDisplay/components/{SortByTag.js → SortByTagDialog.js} +7 -3
  28. package/dist/LinearPileupDisplay/configSchema.js +0 -1
  29. package/dist/LinearPileupDisplay/model.d.ts +58 -46
  30. package/dist/LinearPileupDisplay/model.js +69 -41
  31. package/dist/LinearReadArcsDisplay/components/ReactComponent.js +1 -0
  32. package/dist/LinearReadArcsDisplay/model.d.ts +2 -2
  33. package/dist/LinearReadArcsDisplay/model.js +37 -13
  34. package/dist/LinearReadCloudDisplay/components/ReactComponent.js +4 -1
  35. package/dist/LinearReadCloudDisplay/drawPairChains.js +3 -3
  36. package/dist/LinearReadCloudDisplay/model.d.ts +4 -8
  37. package/dist/LinearReadCloudDisplay/model.js +16 -6
  38. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  39. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
  40. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
  41. package/dist/LinearSNPCoverageDisplay/models/model.js +15 -5
  42. package/dist/MismatchParser/index.js +12 -10
  43. package/dist/PileupRPC/base.d.ts +1 -1
  44. package/dist/PileupRPC/methods/GetGlobalValueForTag.d.ts +1 -1
  45. package/dist/PileupRPC/methods/GetReducedFeatures.d.ts +3 -3
  46. package/dist/PileupRPC/methods/GetVisibleModifications.d.ts +1 -1
  47. package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  48. package/dist/PileupRenderer/PileupLayoutSession.js +3 -2
  49. package/dist/PileupRenderer/PileupRenderer.d.ts +1 -1
  50. package/dist/PileupRenderer/PileupRenderer.js +16 -13
  51. package/dist/PileupRenderer/colorBy.js +3 -5
  52. package/dist/PileupRenderer/components/PileupRendering.d.ts +1 -1
  53. package/dist/PileupRenderer/components/PileupRendering.js +65 -60
  54. package/dist/PileupRenderer/getAlignmentShapeColor.js +24 -16
  55. package/dist/PileupRenderer/layoutFeature.js +6 -1
  56. package/dist/PileupRenderer/layoutFeatures.js +1 -7
  57. package/dist/PileupRenderer/makeImageData.d.ts +1 -1
  58. package/dist/PileupRenderer/makeImageData.js +1 -0
  59. package/dist/PileupRenderer/renderAlignmentShape.js +1 -1
  60. package/dist/PileupRenderer/renderMismatches.js +1 -1
  61. package/dist/PileupRenderer/renderSoftClipping.js +1 -1
  62. package/dist/PileupRenderer/util.js +3 -5
  63. package/dist/SNPCoverageAdapter/generateCoverageBins.js +4 -10
  64. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -2
  65. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +2 -5
  66. package/dist/index.js +3 -1
  67. package/dist/shared/BaseDisplayComponent.js +3 -1
  68. package/dist/shared/{FilterByTag.js → FilterByTagDialog.js} +16 -6
  69. package/dist/shared/color.js +2 -2
  70. package/dist/shared/index.d.ts +24 -20
  71. package/dist/shared/index.js +4 -5
  72. package/dist/shared/renderSvg.js +1 -3
  73. package/dist/util.d.ts +1 -1
  74. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +5 -3
  75. package/esm/AlignmentsFeatureDetail/BreakendOptionDialog.js +12 -4
  76. package/esm/AlignmentsFeatureDetail/Formatter.js +6 -2
  77. package/esm/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.js +4 -2
  78. package/esm/AlignmentsFeatureDetail/getSAFeatures.js +4 -4
  79. package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.js +2 -2
  80. package/esm/BamAdapter/BamAdapter.js +12 -18
  81. package/esm/BamAdapter/BamSlightlyLazyFeature.js +0 -1
  82. package/esm/CramAdapter/CramAdapter.d.ts +1 -1
  83. package/esm/CramAdapter/CramAdapter.js +7 -6
  84. package/esm/CramAdapter/CramTestAdapters.js +8 -2
  85. package/esm/GuessAlignmentsTypes/index.js +2 -2
  86. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts +2 -2
  87. package/esm/LinearAlignmentsDisplay/models/model.d.ts +13 -20
  88. package/esm/LinearAlignmentsDisplay/models/model.js +13 -3
  89. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +9 -4
  90. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +42 -23
  91. package/esm/LinearPileupDisplay/components/{ColorByModifications.js → ColorByModificationsDialog.js} +3 -1
  92. package/esm/LinearPileupDisplay/components/{ColorByTag.js → ColorByTagDialog.js} +4 -2
  93. package/esm/LinearPileupDisplay/components/GroupByDialog.d.ts +11 -0
  94. package/esm/LinearPileupDisplay/components/GroupByDialog.js +104 -0
  95. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +1 -3
  96. package/esm/LinearPileupDisplay/components/{SetFeatureHeight.js → SetFeatureHeightDialog.js} +9 -3
  97. package/{dist/LinearPileupDisplay/components/SetMaxHeight.d.ts → esm/LinearPileupDisplay/components/SetMaxHeightDialog.d.ts} +1 -1
  98. package/esm/LinearPileupDisplay/components/{SetMaxHeight.js → SetMaxHeightDialog.js} +7 -3
  99. package/esm/LinearPileupDisplay/components/{SortByTag.d.ts → SortByTagDialog.d.ts} +1 -1
  100. package/esm/LinearPileupDisplay/components/{SortByTag.js → SortByTagDialog.js} +7 -3
  101. package/esm/LinearPileupDisplay/configSchema.js +0 -1
  102. package/esm/LinearPileupDisplay/model.d.ts +58 -46
  103. package/esm/LinearPileupDisplay/model.js +69 -41
  104. package/esm/LinearReadArcsDisplay/components/ReactComponent.js +1 -0
  105. package/esm/LinearReadArcsDisplay/model.d.ts +2 -2
  106. package/esm/LinearReadArcsDisplay/model.js +37 -13
  107. package/esm/LinearReadCloudDisplay/components/ReactComponent.js +4 -1
  108. package/esm/LinearReadCloudDisplay/drawPairChains.js +3 -3
  109. package/esm/LinearReadCloudDisplay/model.d.ts +4 -8
  110. package/esm/LinearReadCloudDisplay/model.js +16 -6
  111. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  112. package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
  113. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
  114. package/esm/LinearSNPCoverageDisplay/models/model.js +15 -5
  115. package/esm/MismatchParser/index.js +12 -10
  116. package/esm/PileupRPC/base.d.ts +1 -1
  117. package/esm/PileupRPC/methods/GetGlobalValueForTag.d.ts +1 -1
  118. package/esm/PileupRPC/methods/GetReducedFeatures.d.ts +3 -3
  119. package/esm/PileupRPC/methods/GetVisibleModifications.d.ts +1 -1
  120. package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  121. package/esm/PileupRenderer/PileupLayoutSession.js +3 -2
  122. package/esm/PileupRenderer/PileupRenderer.d.ts +1 -1
  123. package/esm/PileupRenderer/PileupRenderer.js +16 -13
  124. package/esm/PileupRenderer/colorBy.js +3 -5
  125. package/esm/PileupRenderer/components/PileupRendering.d.ts +1 -1
  126. package/esm/PileupRenderer/components/PileupRendering.js +65 -60
  127. package/esm/PileupRenderer/getAlignmentShapeColor.js +24 -16
  128. package/esm/PileupRenderer/layoutFeature.js +6 -1
  129. package/esm/PileupRenderer/layoutFeatures.js +1 -7
  130. package/esm/PileupRenderer/makeImageData.d.ts +1 -1
  131. package/esm/PileupRenderer/makeImageData.js +1 -0
  132. package/esm/PileupRenderer/renderAlignmentShape.js +1 -1
  133. package/esm/PileupRenderer/renderMismatches.js +1 -1
  134. package/esm/PileupRenderer/renderSoftClipping.js +1 -1
  135. package/esm/PileupRenderer/util.js +3 -5
  136. package/esm/SNPCoverageAdapter/generateCoverageBins.js +4 -10
  137. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts +2 -2
  138. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +2 -5
  139. package/esm/index.js +3 -1
  140. package/esm/shared/BaseDisplayComponent.js +3 -1
  141. package/esm/shared/{FilterByTag.js → FilterByTagDialog.js} +16 -6
  142. package/esm/shared/color.js +2 -2
  143. package/esm/shared/index.d.ts +24 -20
  144. package/esm/shared/index.js +4 -5
  145. package/esm/shared/renderSvg.js +1 -3
  146. package/esm/util.d.ts +1 -1
  147. package/package.json +6 -6
  148. /package/dist/LinearPileupDisplay/components/{ColorByModifications.d.ts → ColorByModificationsDialog.d.ts} +0 -0
  149. /package/dist/LinearPileupDisplay/components/{ColorByTag.d.ts → ColorByTagDialog.d.ts} +0 -0
  150. /package/dist/LinearPileupDisplay/components/{SetFeatureHeight.d.ts → SetFeatureHeightDialog.d.ts} +0 -0
  151. /package/dist/shared/{FilterByTag.d.ts → FilterByTagDialog.d.ts} +0 -0
  152. /package/esm/LinearPileupDisplay/components/{ColorByModifications.d.ts → ColorByModificationsDialog.d.ts} +0 -0
  153. /package/esm/LinearPileupDisplay/components/{ColorByTag.d.ts → ColorByTagDialog.d.ts} +0 -0
  154. /package/esm/LinearPileupDisplay/components/{SetFeatureHeight.d.ts → SetFeatureHeightDialog.d.ts} +0 -0
  155. /package/esm/shared/{FilterByTag.d.ts → FilterByTagDialog.d.ts} +0 -0
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.13.1",
3
+ "version": "2.15.0",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -24,7 +24,7 @@
24
24
  ],
25
25
  "scripts": {
26
26
  "build": "npm-run-all build:*",
27
- "test": "cd ../..; jest plugins/alignments",
27
+ "test": "cd ../..; jest --passWithNoTests plugins/alignments",
28
28
  "prepublishOnly": "yarn test",
29
29
  "prepack": "yarn build && yarn useDist",
30
30
  "postpack": "yarn useSrc",
@@ -37,8 +37,8 @@
37
37
  },
38
38
  "dependencies": {
39
39
  "@gmod/bam": "^2.0.0",
40
- "@gmod/cram": "^2.0.0",
41
- "@mui/icons-material": "^5.0.1",
40
+ "@gmod/cram": "^3.0.3",
41
+ "@mui/icons-material": "^6.0.0",
42
42
  "canvas2svg": "^1.0.16",
43
43
  "clone": "^2.1.2",
44
44
  "copy-to-clipboard": "^3.3.1",
@@ -49,7 +49,7 @@
49
49
  "@jbrowse/core": "^2.0.0",
50
50
  "@jbrowse/plugin-linear-genome-view": "^2.0.0",
51
51
  "@jbrowse/plugin-wiggle": "^2.0.0",
52
- "@mui/material": "^5.0.0",
52
+ "@mui/material": "^6.0.0",
53
53
  "mobx": "^6.0.0",
54
54
  "mobx-react": "^9.0.0",
55
55
  "mobx-state-tree": "^5.0.0",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
66
+ "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
67
67
  }