@apollo-annotation/shared 0.3.6 → 0.3.8

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Files changed (94) hide show
  1. package/dist/Changes/AddAssemblyAliasesChange.d.ts +16 -0
  2. package/dist/Changes/AddAssemblyAliasesChange.js +50 -0
  3. package/dist/Changes/AddAssemblyAliasesChange.js.map +1 -0
  4. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js +1 -1
  5. package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map +1 -1
  6. package/dist/Changes/AddAssemblyFromFileChange.js +1 -1
  7. package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -1
  8. package/dist/Changes/AddFeatureChange.d.ts +1 -0
  9. package/dist/Changes/AddFeatureChange.js +5 -25
  10. package/dist/Changes/AddFeatureChange.js.map +1 -1
  11. package/dist/Changes/AddRefSeqAliasesChange.js +2 -4
  12. package/dist/Changes/AddRefSeqAliasesChange.js.map +1 -1
  13. package/dist/Changes/DeleteFeatureChange.d.ts +9 -8
  14. package/dist/Changes/DeleteFeatureChange.js +37 -32
  15. package/dist/Changes/DeleteFeatureChange.js.map +1 -1
  16. package/dist/Changes/FeatureAttributeChange.d.ts +2 -1
  17. package/dist/Changes/FeatureAttributeChange.js +14 -6
  18. package/dist/Changes/FeatureAttributeChange.js.map +1 -1
  19. package/dist/Changes/ImportJBrowseConfigChange.d.ts +3 -0
  20. package/dist/Changes/ImportJBrowseConfigChange.js +17 -13
  21. package/dist/Changes/ImportJBrowseConfigChange.js.map +1 -1
  22. package/dist/Changes/LocationEndChange.js +40 -37
  23. package/dist/Changes/LocationEndChange.js.map +1 -1
  24. package/dist/Changes/LocationStartChange.js +40 -37
  25. package/dist/Changes/LocationStartChange.js.map +1 -1
  26. package/dist/Changes/MergeExonsChange.d.ts +29 -0
  27. package/dist/Changes/MergeExonsChange.js +114 -0
  28. package/dist/Changes/MergeExonsChange.js.map +1 -0
  29. package/dist/Changes/MergeTranscriptsChange.d.ts +34 -0
  30. package/dist/Changes/MergeTranscriptsChange.js +245 -0
  31. package/dist/Changes/MergeTranscriptsChange.js.map +1 -0
  32. package/dist/Changes/SplitExonChange.d.ts +33 -0
  33. package/dist/Changes/SplitExonChange.js +142 -0
  34. package/dist/Changes/SplitExonChange.js.map +1 -0
  35. package/dist/Changes/UndoMergeExonsChange.d.ts +27 -0
  36. package/dist/Changes/UndoMergeExonsChange.js +104 -0
  37. package/dist/Changes/UndoMergeExonsChange.js.map +1 -0
  38. package/dist/Changes/UndoMergeTranscriptsChange.d.ts +27 -0
  39. package/dist/Changes/UndoMergeTranscriptsChange.js +104 -0
  40. package/dist/Changes/UndoMergeTranscriptsChange.js.map +1 -0
  41. package/dist/Changes/UndoSplitExonChange.d.ts +32 -0
  42. package/dist/Changes/UndoSplitExonChange.js +111 -0
  43. package/dist/Changes/UndoSplitExonChange.js.map +1 -0
  44. package/dist/Changes/index.d.ts +21 -0
  45. package/dist/Changes/index.js +21 -0
  46. package/dist/Changes/index.js.map +1 -1
  47. package/dist/Checks/CDSCheck.d.ts +1 -1
  48. package/dist/Checks/CDSCheck.js +8 -9
  49. package/dist/Checks/CDSCheck.js.map +1 -1
  50. package/dist/Checks/TranscriptCheck.d.ts +9 -0
  51. package/dist/Checks/TranscriptCheck.js +109 -0
  52. package/dist/Checks/TranscriptCheck.js.map +1 -0
  53. package/dist/Checks/index.d.ts +1 -0
  54. package/dist/Checks/index.js +1 -0
  55. package/dist/Checks/index.js.map +1 -1
  56. package/dist/GFF3/annotationFeatureToGFF3.js +7 -1
  57. package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
  58. package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -1
  59. package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
  60. package/dist/Validations/ParentChildValidation.js +3 -1
  61. package/dist/Validations/ParentChildValidation.js.map +1 -1
  62. package/dist/tsconfig.tsbuildinfo +1 -1
  63. package/dist/util.d.ts +5 -0
  64. package/dist/util.js +46 -0
  65. package/dist/util.js.map +1 -1
  66. package/package.json +7 -7
  67. package/src/Changes/AddAssemblyAliasesChange.ts +69 -0
  68. package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +2 -1
  69. package/src/Changes/AddAssemblyFromFileChange.ts +1 -1
  70. package/src/Changes/AddFeatureChange.ts +5 -29
  71. package/src/Changes/AddRefSeqAliasesChange.ts +2 -4
  72. package/src/Changes/DeleteFeatureChange.ts +42 -36
  73. package/src/Changes/FeatureAttributeChange.ts +16 -7
  74. package/src/Changes/ImportJBrowseConfigChange.ts +33 -18
  75. package/src/Changes/LocationEndChange.ts +41 -50
  76. package/src/Changes/LocationStartChange.ts +41 -50
  77. package/src/Changes/MergeExonsChange.ts +201 -0
  78. package/src/Changes/MergeTranscriptsChange.ts +394 -0
  79. package/src/Changes/SplitExonChange.ts +249 -0
  80. package/src/Changes/UndoMergeExonsChange.ts +149 -0
  81. package/src/Changes/UndoMergeTranscriptsChange.ts +153 -0
  82. package/src/Changes/UndoSplitExonChange.ts +174 -0
  83. package/src/Changes/index.ts +21 -0
  84. package/src/Checks/CDSCheck.ts +10 -10
  85. package/src/Checks/TranscriptCheck.ts +139 -0
  86. package/src/Checks/index.ts +1 -0
  87. package/src/GFF3/annotationFeatureToGFF3.ts +7 -1
  88. package/src/GFF3/gff3ToAnnotationFeature.test.ts +1 -1
  89. package/src/Validations/ParentChildValidation.ts +3 -2
  90. package/src/util.ts +53 -0
  91. package/test_data/example01.json +20 -20
  92. package/test_data/example02.json +38 -38
  93. package/test_data/example04.json +57 -57
  94. package/test_data/gene_representations.gff3 +1054 -276
package/test_data/example04.json CHANGED
@@ -2,77 +2,77 @@
2
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  "_id": "66e0555fae0bd7cfcd69912d",
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  "refSeq": "chr1",
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  "type": "gene",
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- "min": 30999,
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- "max": 39000,
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+ "min": 60999,
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+ "max": 69000,
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  "strand": 1,
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  "children": {
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  "66e0555fae0bd7cfcd699120": {
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  "_id": "66e0555fae0bd7cfcd699120",
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  "refSeq": "chr1",
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  "type": "mRNA",
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- "min": 31049,
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- "max": 39000,
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+ "min": 61049,
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+ "max": 69000,
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  "strand": 1,
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  "children": {
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  "66e0555fae0bd7cfcd69911b": {
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  "_id": "66e0555fae0bd7cfcd69911b",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 31049,
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- "max": 31499,
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+ "min": 61049,
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+ "max": 61499,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40001"]
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+ "gff_id": ["exon60001"]
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  }
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  },
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  "66e0555fae0bd7cfcd69911c": {
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  "_id": "66e0555fae0bd7cfcd69911c",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 32999,
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- "max": 33902,
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+ "min": 62999,
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+ "max": 63902,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40003"]
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+ "gff_id": ["exon60003"]
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  }
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  },
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  "66e0555fae0bd7cfcd69911d": {
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  "_id": "66e0555fae0bd7cfcd69911d",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 34999,
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- "max": 35500,
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+ "min": 64999,
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+ "max": 65500,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40004"]
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+ "gff_id": ["exon60004"]
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  }
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  },
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  "66e0555fae0bd7cfcd69911e": {
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  "_id": "66e0555fae0bd7cfcd69911e",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 36999,
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- "max": 39000,
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+ "min": 66999,
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+ "max": 69000,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40005"]
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+ "gff_id": ["exon60005"]
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  }
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  },
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  "66e0555fae0bd7cfcd69911f": {
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  "_id": "66e0555fae0bd7cfcd69911f",
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  "refSeq": "chr1",
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  "type": "CDS",
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- "min": 31200,
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- "max": 37600,
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+ "min": 61200,
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+ "max": 67600,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["cds40001"],
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+ "gff_id": ["cds60001"],
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  "gff_name": ["edenprotein.1"]
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  }
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  }
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  },
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  "attributes": {
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- "gff_id": ["mRNA40001"],
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+ "gff_id": ["mRNA60001"],
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  "gff_name": ["EDEN.1"]
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  }
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  },
@@ -80,58 +80,58 @@
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  "_id": "66e0555fae0bd7cfcd699125",
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  "refSeq": "chr1",
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  "type": "mRNA",
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- "min": 31049,
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- "max": 39000,
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+ "min": 61049,
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+ "max": 69000,
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  "strand": 1,
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  "children": {
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  "66e0555fae0bd7cfcd699121": {
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  "_id": "66e0555fae0bd7cfcd699121",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 31049,
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- "max": 31499,
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+ "min": 61049,
92
+ "max": 61499,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40001"]
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+ "gff_id": ["exon60001"]
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  }
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  },
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  "66e0555fae0bd7cfcd699122": {
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  "_id": "66e0555fae0bd7cfcd699122",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 34999,
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- "max": 35500,
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+ "min": 64999,
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+ "max": 65500,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40004"]
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+ "gff_id": ["exon60004"]
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  }
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  },
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  "66e0555fae0bd7cfcd699123": {
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  "_id": "66e0555fae0bd7cfcd699123",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 36999,
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- "max": 39000,
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+ "min": 66999,
114
+ "max": 69000,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40005"]
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+ "gff_id": ["exon60005"]
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  }
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  },
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  "66e0555fae0bd7cfcd699124": {
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  "_id": "66e0555fae0bd7cfcd699124",
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  "refSeq": "chr1",
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  "type": "CDS",
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- "min": 31200,
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- "max": 37600,
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+ "min": 61200,
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+ "max": 67600,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["cds40002"],
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+ "gff_id": ["cds60002"],
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  "gff_name": ["edenprotein.2"]
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  }
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  }
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  },
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  "attributes": {
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- "gff_id": ["mRNA40002"],
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+ "gff_id": ["mRNA60002"],
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  "gff_name": ["EDEN.2"]
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  }
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  },
@@ -139,63 +139,63 @@
139
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  "_id": "66e0555fae0bd7cfcd69912c",
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  "refSeq": "chr1",
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  "type": "mRNA",
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- "min": 31299,
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- "max": 39000,
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+ "min": 61299,
143
+ "max": 69000,
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  "strand": 1,
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  "children": {
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  "66e0555fae0bd7cfcd699126": {
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  "_id": "66e0555fae0bd7cfcd699126",
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  "refSeq": "chr1",
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  "type": "exon",
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- "min": 31299,
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- "max": 31499,
150
+ "min": 61299,
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+ "max": 61499,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40002"]
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+ "gff_id": ["exon60002"]
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  }
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  },
157
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  "66e0555fae0bd7cfcd699127": {
158
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  "_id": "66e0555fae0bd7cfcd699127",
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  "refSeq": "chr1",
160
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  "type": "exon",
161
- "min": 32999,
162
- "max": 33902,
161
+ "min": 62999,
162
+ "max": 63902,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40003"]
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+ "gff_id": ["exon60003"]
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  }
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  },
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  "66e0555fae0bd7cfcd699128": {
169
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  "_id": "66e0555fae0bd7cfcd699128",
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  "refSeq": "chr1",
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  "type": "exon",
172
- "min": 34999,
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- "max": 35500,
172
+ "min": 64999,
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+ "max": 65500,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40004"]
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+ "gff_id": ["exon60004"]
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  }
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  },
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  "66e0555fae0bd7cfcd699129": {
180
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  "_id": "66e0555fae0bd7cfcd699129",
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  "refSeq": "chr1",
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  "type": "exon",
183
- "min": 36999,
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- "max": 39000,
183
+ "min": 66999,
184
+ "max": 69000,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["exon40005"]
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+ "gff_id": ["exon60005"]
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  }
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  },
190
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  "66e0555fae0bd7cfcd69912a": {
191
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  "_id": "66e0555fae0bd7cfcd69912a",
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  "refSeq": "chr1",
193
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  "type": "CDS",
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- "min": 33300,
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- "max": 37600,
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+ "min": 63300,
195
+ "max": 67600,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["cds40003"],
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+ "gff_id": ["cds60003"],
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  "gff_name": ["edenprotein.3"]
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  }
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  },
@@ -203,23 +203,23 @@
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  "_id": "66e0555fae0bd7cfcd69912b",
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  "refSeq": "chr1",
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  "type": "CDS",
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- "min": 33390,
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- "max": 37600,
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+ "min": 63390,
207
+ "max": 67600,
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  "strand": 1,
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  "attributes": {
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- "gff_id": ["cds40004"],
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+ "gff_id": ["cds60004"],
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  "gff_name": ["edenprotein.4"]
212
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  }
213
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  }
214
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  },
215
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  "attributes": {
216
- "gff_id": ["mRNA40003"],
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+ "gff_id": ["mRNA60003"],
217
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  "gff_name": ["EDEN.3"]
218
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  }
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  }
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  },
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  "attributes": {
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- "gff_id": ["gene40001"],
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+ "gff_id": ["gene60001"],
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  "gff_name": ["EDEN"]
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  }
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  }