@jbrowse/plugin-alignments 2.2.0 → 2.2.1

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 (154) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  2. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  3. package/dist/BamAdapter/BamAdapter.d.ts +1 -1
  4. package/dist/BamAdapter/BamAdapter.js +1 -0
  5. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  6. package/dist/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  8. package/dist/BamAdapter/MismatchParser.d.ts +2 -2
  9. package/dist/BamAdapter/MismatchParser.js +4 -7
  10. package/dist/BamAdapter/MismatchParser.js.map +1 -1
  11. package/dist/BamAdapter/configSchema.js +1 -1
  12. package/dist/BamAdapter/configSchema.js.map +1 -1
  13. package/dist/BamAdapter/index.js +7 -5
  14. package/dist/BamAdapter/index.js.map +1 -1
  15. package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  16. package/dist/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  17. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  18. package/dist/CramAdapter/CramTestAdapters.d.ts +1 -1
  19. package/dist/CramAdapter/CramTestAdapters.js +1 -1
  20. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  21. package/dist/CramAdapter/configSchema.js +2 -2
  22. package/dist/CramAdapter/configSchema.js.map +1 -1
  23. package/dist/CramAdapter/index.js +7 -5
  24. package/dist/CramAdapter/index.js.map +1 -1
  25. package/dist/CramAdapter/util.d.ts +18 -0
  26. package/dist/CramAdapter/util.js +241 -0
  27. package/dist/CramAdapter/util.js.map +1 -0
  28. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  29. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  30. package/dist/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  31. package/dist/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  32. package/dist/LinearAlignmentsDisplay/models/model.js +7 -7
  33. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  34. package/dist/LinearPileupDisplay/configSchema.d.ts +4 -4
  35. package/dist/LinearPileupDisplay/configSchema.js +2 -2
  36. package/dist/LinearPileupDisplay/configSchema.js.map +1 -1
  37. package/dist/LinearPileupDisplay/index.d.ts +3 -0
  38. package/dist/LinearPileupDisplay/index.js +3 -0
  39. package/dist/LinearPileupDisplay/index.js.map +1 -1
  40. package/dist/LinearPileupDisplay/model.d.ts +19 -9
  41. package/dist/LinearPileupDisplay/model.js +25 -30
  42. package/dist/LinearPileupDisplay/model.js.map +1 -1
  43. package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  44. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
  45. package/dist/PileupRPC/rpcMethods.d.ts +1 -1
  46. package/dist/PileupRPC/rpcMethods.js +12 -7
  47. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  48. package/dist/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  49. package/dist/PileupRenderer/PileupRenderer.js +32 -28
  50. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  51. package/dist/PileupRenderer/index.js +8 -6
  52. package/dist/PileupRenderer/index.js.map +1 -1
  53. package/dist/SNPCoverageAdapter/configSchema.d.ts +2 -3
  54. package/dist/SNPCoverageAdapter/configSchema.js +6 -3
  55. package/dist/SNPCoverageAdapter/configSchema.js.map +1 -1
  56. package/dist/SNPCoverageAdapter/index.d.ts +1 -2
  57. package/dist/SNPCoverageAdapter/index.js +17 -14
  58. package/dist/SNPCoverageAdapter/index.js.map +1 -1
  59. package/dist/index.d.ts +3 -2
  60. package/dist/index.js +4 -2
  61. package/dist/index.js.map +1 -1
  62. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +12 -13
  63. package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js.map +1 -1
  64. package/esm/BamAdapter/BamAdapter.d.ts +1 -1
  65. package/esm/BamAdapter/BamAdapter.js +1 -0
  66. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  67. package/esm/BamAdapter/BamSlightlyLazyFeature.js +1 -0
  68. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  69. package/esm/BamAdapter/MismatchParser.d.ts +2 -2
  70. package/esm/BamAdapter/MismatchParser.js +4 -7
  71. package/esm/BamAdapter/MismatchParser.js.map +1 -1
  72. package/esm/BamAdapter/configSchema.js +1 -1
  73. package/esm/BamAdapter/configSchema.js.map +1 -1
  74. package/esm/BamAdapter/index.js +7 -5
  75. package/esm/BamAdapter/index.js.map +1 -1
  76. package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts +1 -10
  77. package/esm/CramAdapter/CramSlightlyLazyFeature.js +5 -218
  78. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  79. package/esm/CramAdapter/CramTestAdapters.d.ts +1 -1
  80. package/esm/CramAdapter/CramTestAdapters.js +1 -1
  81. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  82. package/esm/CramAdapter/configSchema.js +2 -2
  83. package/esm/CramAdapter/configSchema.js.map +1 -1
  84. package/esm/CramAdapter/index.js +7 -5
  85. package/esm/CramAdapter/index.js.map +1 -1
  86. package/esm/CramAdapter/util.d.ts +18 -0
  87. package/esm/CramAdapter/util.js +236 -0
  88. package/esm/CramAdapter/util.js.map +1 -0
  89. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +1 -1
  90. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  91. package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts +1 -1
  92. package/esm/LinearAlignmentsDisplay/models/model.d.ts +5 -5
  93. package/esm/LinearAlignmentsDisplay/models/model.js +7 -7
  94. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  95. package/esm/LinearPileupDisplay/configSchema.d.ts +4 -4
  96. package/esm/LinearPileupDisplay/configSchema.js +2 -2
  97. package/esm/LinearPileupDisplay/configSchema.js.map +1 -1
  98. package/esm/LinearPileupDisplay/index.d.ts +3 -0
  99. package/esm/LinearPileupDisplay/index.js +1 -0
  100. package/esm/LinearPileupDisplay/index.js.map +1 -1
  101. package/esm/LinearPileupDisplay/model.d.ts +19 -9
  102. package/esm/LinearPileupDisplay/model.js +25 -30
  103. package/esm/LinearPileupDisplay/model.js.map +1 -1
  104. package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
  105. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +1 -1
  106. package/esm/PileupRPC/rpcMethods.d.ts +1 -1
  107. package/esm/PileupRPC/rpcMethods.js +12 -7
  108. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  109. package/esm/PileupRenderer/PileupLayoutSession.d.ts +1 -1
  110. package/esm/PileupRenderer/PileupRenderer.js +32 -28
  111. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  112. package/esm/PileupRenderer/index.js +8 -6
  113. package/esm/PileupRenderer/index.js.map +1 -1
  114. package/esm/SNPCoverageAdapter/configSchema.d.ts +2 -3
  115. package/esm/SNPCoverageAdapter/configSchema.js +6 -3
  116. package/esm/SNPCoverageAdapter/configSchema.js.map +1 -1
  117. package/esm/SNPCoverageAdapter/index.d.ts +1 -2
  118. package/esm/SNPCoverageAdapter/index.js +17 -15
  119. package/esm/SNPCoverageAdapter/index.js.map +1 -1
  120. package/esm/index.d.ts +3 -2
  121. package/esm/index.js +2 -2
  122. package/esm/index.js.map +1 -1
  123. package/package.json +3 -2
  124. package/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx +17 -16
  125. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +1 -473
  126. package/src/AlignmentsFeatureDetail/index.test.js +6 -4
  127. package/src/BamAdapter/BamAdapter.ts +3 -2
  128. package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -1
  129. package/src/BamAdapter/MismatchParser.test.ts +21 -12
  130. package/src/BamAdapter/MismatchParser.ts +7 -10
  131. package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap +135 -135
  132. package/src/BamAdapter/configSchema.ts +1 -1
  133. package/src/BamAdapter/index.ts +7 -8
  134. package/src/CombinationTest.test.ts +107 -0
  135. package/src/CramAdapter/CramSlightlyLazyFeature.ts +10 -219
  136. package/src/CramAdapter/CramTestAdapters.ts +1 -1
  137. package/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap +31 -31
  138. package/src/CramAdapter/__snapshots__/util.test.ts.snap +14 -0
  139. package/src/CramAdapter/configSchema.ts +2 -3
  140. package/src/CramAdapter/index.ts +7 -8
  141. package/src/CramAdapter/util.test.ts +26 -0
  142. package/src/CramAdapter/util.ts +251 -0
  143. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +3 -1
  144. package/src/LinearAlignmentsDisplay/models/model.tsx +8 -7
  145. package/src/LinearPileupDisplay/configSchema.ts +3 -5
  146. package/src/LinearPileupDisplay/index.ts +5 -0
  147. package/src/LinearPileupDisplay/model.ts +31 -30
  148. package/src/PileupRPC/rpcMethods.ts +15 -20
  149. package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts} +48 -54
  150. package/src/PileupRenderer/index.ts +8 -9
  151. package/src/SNPCoverageAdapter/configSchema.ts +14 -13
  152. package/src/SNPCoverageAdapter/index.ts +17 -18
  153. package/src/__snapshots__/index.test.ts.snap +1 -1
  154. package/src/index.ts +11 -4
package/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap CHANGED
@@ -1,8 +1,8 @@
1
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  // Jest Snapshot v1, https://goo.gl/fbAQLP
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  exports[`adapter can fetch features from volvox.bam 1`] = `
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- Array [
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- Object {
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+ [
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+ {
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  "CIGAR": "100M",
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  "MD": "22A32C15T12A15",
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  "MQ": 37,
@@ -29,7 +29,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-10158054",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "66G33",
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  "MQ": 37,
@@ -56,7 +56,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-10158322",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "25G23C1C24A23",
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  "MQ": 37,
@@ -83,7 +83,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-10158581",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "42C57",
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  "MQ": 37,
@@ -110,7 +110,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-10158847",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "49G11G38",
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  "MQ": 37,
@@ -137,7 +137,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-12607066",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "22T13C63",
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  "MQ": 37,
@@ -164,7 +164,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-12607328",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "35C3G60",
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  "MQ": 37,
@@ -191,7 +191,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-12607590",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "100",
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  "MQ": 37,
@@ -218,7 +218,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-12607851",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "52G43A3",
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  "MQ": 37,
@@ -245,7 +245,7 @@ Array [
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  "type": "match",
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  "uniqueId": "test-12608107",
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  },
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- Object {
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+ {
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  "CIGAR": "100M",
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  "MD": "92C7",
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  "MQ": 37,
@@ -276,825 +276,825 @@ Array [
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  `;
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  exports[`test usage of BamSlightlyLazyFeature for extended CIGAR 1`] = `
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- Array [
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- Object {
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+ [
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+ {
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  "base": "S2666",
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  "cliplen": 2666,
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  "length": 1,
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  "start": 0,
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  "type": "softclip",
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  },
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- Object {
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+ {
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  "base": "*",
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  "length": 1,
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  "start": 33,
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  "type": "deletion",
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  },
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- Object {
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+ {
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  "base": "G",
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  "length": 1,
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  "qual": 93,
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  "start": 40,
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  "type": "mismatch",
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  },
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- Object {
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+ {
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  "base": "*",
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  "length": 1,
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  "start": 75,
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  "type": "deletion",
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  },
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- Object {
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+ {
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  "base": "*",
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  "length": 1,
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  "start": 90,
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  "type": "deletion",
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  },
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- Object {
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+ {
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  "base": "1",
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  "length": 0,
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  "start": 108,
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- Object {
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+ {
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- Object {
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+ {
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  "base": "*",
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  "start": 146,
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- Object {
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+ {
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  "base": "3",
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  "length": 0,
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- Object {
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+ {
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- Object {
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+ {
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  "base": "C",
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  "length": 1,
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  "qual": 93,
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- Object {
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- Object {
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- Object {
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