@jbrowse/plugin-alignments 2.4.0 → 2.4.1

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Files changed (112) hide show
  1. package/dist/BamAdapter/BamAdapter.js +2 -2
  2. package/dist/BamAdapter/BamAdapter.js.map +1 -1
  3. package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
  4. package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  5. package/dist/CramAdapter/CramAdapter.js +2 -2
  6. package/dist/CramAdapter/CramAdapter.js.map +1 -1
  7. package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
  8. package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  9. package/dist/CramAdapter/util.js +10 -10
  10. package/dist/CramAdapter/util.js.map +1 -1
  11. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
  12. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  13. package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -3
  14. package/dist/LinearAlignmentsDisplay/models/model.js +3 -4
  15. package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
  16. package/dist/LinearPileupDisplay/index.d.ts +2 -3
  17. package/dist/LinearPileupDisplay/index.js +4 -2
  18. package/dist/LinearPileupDisplay/index.js.map +1 -1
  19. package/dist/LinearPileupDisplay/model.d.ts +7 -9
  20. package/dist/LinearPileupDisplay/model.js +4 -4
  21. package/dist/LinearPileupDisplay/model.js.map +1 -1
  22. package/dist/LinearReadArcsDisplay/model.d.ts +2 -2
  23. package/dist/LinearReadCloudDisplay/model.d.ts +2 -2
  24. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
  25. package/dist/MismatchParser/index.js +4 -6
  26. package/dist/MismatchParser/index.js.map +1 -1
  27. package/dist/NestedFrequencyTable.js +3 -13
  28. package/dist/NestedFrequencyTable.js.map +1 -1
  29. package/dist/PileupRPC/rpcMethods.d.ts +3 -4
  30. package/dist/PileupRPC/rpcMethods.js +6 -6
  31. package/dist/PileupRPC/rpcMethods.js.map +1 -1
  32. package/dist/PileupRenderer/PileupRenderer.d.ts +6 -4
  33. package/dist/PileupRenderer/PileupRenderer.js +30 -34
  34. package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
  35. package/dist/PileupRenderer/components/PileupRendering.js +2 -2
  36. package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
  37. package/dist/PileupRenderer/configSchema.js +1 -1
  38. package/dist/PileupRenderer/configSchema.js.map +1 -1
  39. package/dist/PileupRenderer/sortUtil.js +5 -4
  40. package/dist/PileupRenderer/sortUtil.js.map +1 -1
  41. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
  42. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
  43. package/dist/index.d.ts +3 -5
  44. package/dist/index.js +6 -6
  45. package/dist/index.js.map +1 -1
  46. package/esm/BamAdapter/BamAdapter.js +2 -2
  47. package/esm/BamAdapter/BamAdapter.js.map +1 -1
  48. package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
  49. package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
  50. package/esm/CramAdapter/CramAdapter.js +2 -2
  51. package/esm/CramAdapter/CramAdapter.js.map +1 -1
  52. package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
  53. package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
  54. package/esm/CramAdapter/util.js +10 -10
  55. package/esm/CramAdapter/util.js.map +1 -1
  56. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
  57. package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
  58. package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -3
  59. package/esm/LinearAlignmentsDisplay/models/model.js +3 -4
  60. package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
  61. package/esm/LinearPileupDisplay/index.d.ts +2 -3
  62. package/esm/LinearPileupDisplay/index.js +2 -1
  63. package/esm/LinearPileupDisplay/index.js.map +1 -1
  64. package/esm/LinearPileupDisplay/model.d.ts +7 -9
  65. package/esm/LinearPileupDisplay/model.js +4 -4
  66. package/esm/LinearPileupDisplay/model.js.map +1 -1
  67. package/esm/LinearReadArcsDisplay/model.d.ts +2 -2
  68. package/esm/LinearReadCloudDisplay/model.d.ts +2 -2
  69. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +2 -2
  70. package/esm/MismatchParser/index.js +4 -6
  71. package/esm/MismatchParser/index.js.map +1 -1
  72. package/esm/NestedFrequencyTable.js +3 -13
  73. package/esm/NestedFrequencyTable.js.map +1 -1
  74. package/esm/PileupRPC/rpcMethods.d.ts +3 -4
  75. package/esm/PileupRPC/rpcMethods.js +3 -4
  76. package/esm/PileupRPC/rpcMethods.js.map +1 -1
  77. package/esm/PileupRenderer/PileupRenderer.d.ts +6 -4
  78. package/esm/PileupRenderer/PileupRenderer.js +30 -34
  79. package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
  80. package/esm/PileupRenderer/components/PileupRendering.js +2 -2
  81. package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
  82. package/esm/PileupRenderer/configSchema.js +1 -1
  83. package/esm/PileupRenderer/configSchema.js.map +1 -1
  84. package/esm/PileupRenderer/sortUtil.js +5 -4
  85. package/esm/PileupRenderer/sortUtil.js.map +1 -1
  86. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
  87. package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
  88. package/esm/index.d.ts +3 -5
  89. package/esm/index.js +3 -3
  90. package/esm/index.js.map +1 -1
  91. package/package.json +2 -2
  92. package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
  93. package/src/BamAdapter/BamAdapter.ts +2 -2
  94. package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
  95. package/src/CramAdapter/CramAdapter.ts +2 -2
  96. package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
  97. package/src/CramAdapter/util.ts +10 -10
  98. package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +2 -2
  99. package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
  100. package/src/LinearAlignmentsDisplay/models/model.tsx +3 -4
  101. package/src/LinearPileupDisplay/index.ts +2 -4
  102. package/src/LinearPileupDisplay/model.ts +4 -4
  103. package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
  104. package/src/MismatchParser/index.ts +3 -5
  105. package/src/NestedFrequencyTable.ts +3 -11
  106. package/src/PileupRPC/rpcMethods.ts +3 -9
  107. package/src/PileupRenderer/PileupRenderer.ts +47 -61
  108. package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
  109. package/src/PileupRenderer/configSchema.ts +1 -1
  110. package/src/PileupRenderer/sortUtil.ts +5 -4
  111. package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
  112. package/src/index.ts +5 -10
package/dist/LinearReadArcsDisplay/model.d.ts CHANGED
@@ -156,7 +156,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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- readonly height: any;
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+ readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
@@ -186,7 +186,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  clearRegionStats(): void;
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- setHeight(displayHeight: number): any;
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+ setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
package/dist/LinearReadCloudDisplay/model.d.ts CHANGED
@@ -163,7 +163,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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- readonly height: any;
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+ readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
@@ -193,7 +193,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  clearRegionStats(): void;
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- setHeight(displayHeight: number): any;
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+ setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -175,7 +175,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
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  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
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  } & {
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- readonly height: any;
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+ readonly height: number;
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
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  } & {
@@ -205,7 +205,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  clearRegionStats(): void;
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- setHeight(displayHeight: number): any;
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+ setHeight(displayHeight: number): number;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
package/dist/MismatchParser/index.js CHANGED
@@ -287,18 +287,17 @@ function getModificationTypes(mm) {
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  const mods = mm.split(';');
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  return mods
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  .filter(mod => !!mod)
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- .map(mod => {
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+ .flatMap(mod => {
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  const [basemod] = mod.split(',');
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  const matches = basemod.match(modificationRegex);
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  if (!matches) {
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  throw new Error(`bad format for MM tag: ${mm}`);
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  }
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- const [, , , typestr] = matches;
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+ const typestr = matches[3];
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  // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
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  // split, and they can also be chemical codes (ChEBI) e.g. C+16061
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  return typestr.split(/(\d+|.)/).filter(f => !!f);
300
- })
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- .flat();
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+ });
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  }
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  exports.getModificationTypes = getModificationTypes;
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  function getOrientedCigar(flip, cigar) {
@@ -313,8 +312,7 @@ function getOrientedCigar(flip, cigar) {
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  else if (op === 'I') {
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  op = 'D';
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  }
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- ret.push(len);
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- ret.push(op);
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+ ret.push(len, op);
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  }
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  return ret;
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  }
package/dist/MismatchParser/index.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/NestedFrequencyTable.js CHANGED
@@ -22,12 +22,7 @@ class NestedFrequencyTable {
22
22
  if (!amount) {
23
23
  amount = 1;
24
24
  }
25
- if (!slotName) {
26
- slotName = 'default';
27
- }
28
- else {
29
- slotName = slotName.toString();
30
- }
25
+ slotName = slotName ? slotName.toString() : 'default';
31
26
  if (this.categories[slotName]) {
32
27
  this.categories[slotName] = Math.max(0, this.categories[slotName] - amount);
33
28
  return this.categories[slotName];
@@ -39,12 +34,7 @@ class NestedFrequencyTable {
39
34
  if (!amount) {
40
35
  amount = 1;
41
36
  }
42
- if (!slotName) {
43
- slotName = 'default';
44
- }
45
- else {
46
- slotName = slotName.toString();
47
- }
37
+ slotName = slotName ? slotName.toString() : 'default';
48
38
  this.categories[slotName] = (this.categories[slotName] || 0) + amount;
49
39
  return this.categories[slotName];
50
40
  }
@@ -58,7 +48,7 @@ class NestedFrequencyTable {
58
48
  if (typeof path === 'string') {
59
49
  path = path.split('/');
60
50
  }
61
- if (!path.length) {
51
+ if (path.length === 0) {
62
52
  return this;
63
53
  }
64
54
  const slotName = path[0].toString();
package/dist/NestedFrequencyTable.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"NestedFrequencyTable.js","sourceRoot":"","sources":["../src/NestedFrequencyTable.ts"],"names":[],"mappings":";;AAAA,uDAAuD;AACvD,iDAAiD;AACjD,sDAAsD;AACtD,MAAqB,oBAAoB;IAGvC,YAAY,WAAW,GAAG,EAAE;QAC1B,IAAI,CAAC,UAAU,GAAG,EAAE,GAAG,WAAW,EAAE,CAAA;IACtC,CAAC;IAED,yCAAyC;IACzC,KAAK;QACH,+BAA+B;QAC/B,IAAI,CAAC,GAAG,CAAC,CAAA;QAET,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,UAAU,EAAE;YAC/B,MAAM,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAC5B,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;SAC7B;QAED,OAAO,CAAC,CAAA;IACV,CAAC;IAED,6CAA6C;IAC7C,SAAS,CAAC,QAAgB,EAAE,MAAc;QACxC,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,GAAG,CAAC,CAAA;SACX;QAED,IAAI,CAAC,QAAQ,EAAE;YACb,QAAQ,GAAG,SAAS,CAAA;SACrB;aAAM;YACL,QAAQ,GAAG,QAAQ,CAAC,QAAQ,EAAE,CAAA;SAC/B;QAED,IAAI,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE;YAC7B,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC,GAAG,CAClC,CAAC,EACD,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,MAAM,CACnC,CAAA;YACD,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;SACjC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,6CAA6C;IAC7C,SAAS,CAAC,QAAgB,EAAE,MAAc;QACxC,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,GAAG,CAAC,CAAA;SACX;QAED,IAAI,CAAC,QAAQ,EAAE;YACb,QAAQ,GAAG,SAAS,CAAA;SACrB;aAAM;YACL,QAAQ,GAAG,QAAQ,CAAC,QAAQ,EAAE,CAAA;SAC/B;QAED,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QACrE,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;IAClC,CAAC;IAED,6DAA6D;IAC7D,mBAAmB;IACnB,GAAG,CAAC,QAAgB;QAClB,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;IACvC,CAAC;IAED,4CAA4C;IAC5C,SAAS,CAAC,IAAuB;QAC/B,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE;YAC5B,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;SACvB;QAED,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,OAAO,IAAI,CAAA;SACZ;QAED,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAA;QACnC,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YAC7B,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,IAAI,oBAAoB,CAClD,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAClC,CAAA;SACF;QACD,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;QAEhC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;YACnB,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SACrC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,KAAK,EAAE;aAChB,WAAW,CAAC,CAAC,CAAC;aACd,QAAQ,EAAE;aACV,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;IAC1B,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,KAAK,EAAE,CAAA;IACrB,CAAC;IAED,wDAAwD;IACxD,EAAE;IACF,mDAAmD;IACnD,uBAAuB;IACvB,eAAe;IACf,EAAE;IACF,OAAO,CAAC,IAAc,EAAE,GAAQ;QAC9B,IAAI,GAAG,EAAE;YACP,KAAK,MAAM,QAAQ,IAAI,IAAI,CAAC,UAAU,EAAE;gBACtC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,CAAC,CAAA;aACpD;SACF;aAAM;YACL,KAAK,MAAM,QAAQ,IAAI,IAAI,CAAC,UAAU,EAAE;gBACtC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,CAAC,CAAA;aAC1C;SACF;IACH,CAAC;CACF;AArHD,uCAqHC"}
1
+ {"version":3,"file":"NestedFrequencyTable.js","sourceRoot":"","sources":["../src/NestedFrequencyTable.ts"],"names":[],"mappings":";;AAAA,uDAAuD;AACvD,iDAAiD;AACjD,sDAAsD;AACtD,MAAqB,oBAAoB;IAGvC,YAAY,WAAW,GAAG,EAAE;QAC1B,IAAI,CAAC,UAAU,GAAG,EAAE,GAAG,WAAW,EAAE,CAAA;IACtC,CAAC;IAED,yCAAyC;IACzC,KAAK;QACH,+BAA+B;QAC/B,IAAI,CAAC,GAAG,CAAC,CAAA;QAET,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,UAAU,EAAE;YAC/B,MAAM,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAC5B,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;SAC7B;QAED,OAAO,CAAC,CAAA;IACV,CAAC;IAED,6CAA6C;IAC7C,SAAS,CAAC,QAAgB,EAAE,MAAc;QACxC,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,GAAG,CAAC,CAAA;SACX;QAED,QAAQ,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;QAErD,IAAI,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE;YAC7B,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC,GAAG,CAClC,CAAC,EACD,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,MAAM,CACnC,CAAA;YACD,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;SACjC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,6CAA6C;IAC7C,SAAS,CAAC,QAAgB,EAAE,MAAc;QACxC,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,GAAG,CAAC,CAAA;SACX;QAED,QAAQ,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;QAErD,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAA;QACrE,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;IAClC,CAAC;IAED,6DAA6D;IAC7D,mBAAmB;IACnB,GAAG,CAAC,QAAgB;QAClB,OAAO,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;IACvC,CAAC;IAED,4CAA4C;IAC5C,SAAS,CAAC,IAAuB;QAC/B,IAAI,OAAO,IAAI,KAAK,QAAQ,EAAE;YAC5B,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;SACvB;QAED,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;YACrB,OAAO,IAAI,CAAA;SACZ;QAED,MAAM,QAAQ,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAA;QACnC,IAAI,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YAC7B,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,IAAI,oBAAoB,CAClD,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAClC,CAAA;SACF;QACD,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAA;QAEhC,IAAI,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;YACnB,OAAO,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;SACrC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,KAAK,EAAE;aAChB,WAAW,CAAC,CAAC,CAAC;aACd,QAAQ,EAAE;aACV,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;IAC1B,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,KAAK,EAAE,CAAA;IACrB,CAAC;IAED,wDAAwD;IACxD,EAAE;IACF,mDAAmD;IACnD,uBAAuB;IACvB,eAAe;IACf,EAAE;IACF,OAAO,CAAC,IAAc,EAAE,GAAQ;QAC9B,IAAI,GAAG,EAAE;YACP,KAAK,MAAM,QAAQ,IAAI,IAAI,CAAC,UAAU,EAAE;gBACtC,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,CAAC,CAAA;aACpD;SACF;aAAM;YACL,KAAK,MAAM,QAAQ,IAAI,IAAI,CAAC,UAAU,EAAE;gBACtC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,QAAQ,CAAC,CAAA;aAC1C;SACF;IACH,CAAC;CACF;AA7GD,uCA6GC"}
package/dist/PileupRPC/rpcMethods.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- import PileupGetReducedFeatures from './methods/GetReducedFeatures';
2
- import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
3
- import PileupGetVisibleModifications from './methods/GetVisibleModifications';
4
- export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
1
+ export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures';
2
+ export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications';
3
+ export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag';
package/dist/PileupRPC/rpcMethods.js CHANGED
@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.PileupGetGlobalValueForTag = exports.PileupGetVisibleModifications = exports.PileupGetReducedFeatures = void 0;
7
- const GetReducedFeatures_1 = __importDefault(require("./methods/GetReducedFeatures"));
8
- exports.PileupGetReducedFeatures = GetReducedFeatures_1.default;
9
- const GetGlobalValueForTag_1 = __importDefault(require("./methods/GetGlobalValueForTag"));
10
- exports.PileupGetGlobalValueForTag = GetGlobalValueForTag_1.default;
11
- const GetVisibleModifications_1 = __importDefault(require("./methods/GetVisibleModifications"));
12
- exports.PileupGetVisibleModifications = GetVisibleModifications_1.default;
7
+ var GetReducedFeatures_1 = require("./methods/GetReducedFeatures");
8
+ Object.defineProperty(exports, "PileupGetReducedFeatures", { enumerable: true, get: function () { return __importDefault(GetReducedFeatures_1).default; } });
9
+ var GetVisibleModifications_1 = require("./methods/GetVisibleModifications");
10
+ Object.defineProperty(exports, "PileupGetVisibleModifications", { enumerable: true, get: function () { return __importDefault(GetVisibleModifications_1).default; } });
11
+ var GetGlobalValueForTag_1 = require("./methods/GetGlobalValueForTag");
12
+ Object.defineProperty(exports, "PileupGetGlobalValueForTag", { enumerable: true, get: function () { return __importDefault(GetGlobalValueForTag_1).default; } });
13
13
  //# sourceMappingURL=rpcMethods.js.map
package/dist/PileupRPC/rpcMethods.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,sFAAmE;AAKjE,mCALK,4BAAwB,CAKL;AAJ1B,0FAAuE;AAMrE,qCANK,8BAA0B,CAML;AAL5B,gGAA6E;AAI3E,wCAJK,iCAA6B,CAIL"}
1
+ {"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":";;;;;;AAAA,mEAAkF;AAAzE,+IAAA,OAAO,OAA4B;AAC5C,6EAA4F;AAAnF,yJAAA,OAAO,OAAiC;AACjD,uEAAsF;AAA7E,mJAAA,OAAO,OAA8B"}
package/dist/PileupRenderer/PileupRenderer.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  /// <reference types="react" />
2
2
  import { Theme } from '@mui/material/styles';
3
- import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
3
+ import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
4
4
  import { Region, Feature } from '@jbrowse/core/util';
5
5
  import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
6
6
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
@@ -100,7 +100,7 @@ export default class PileupRenderer extends BoxRendererType {
100
100
  canvasWidth: number;
101
101
  }): void;
102
102
  drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
103
- drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
103
+ drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }: {
104
104
  ctx: CanvasRenderingContext2D;
105
105
  feat: LayoutFeature;
106
106
  renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -110,8 +110,9 @@ export default class PileupRenderer extends BoxRendererType {
110
110
  charHeight: number;
111
111
  defaultColor: boolean;
112
112
  canvasWidth: number;
113
+ theme: Theme;
113
114
  }): void;
114
- drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
115
+ drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, theme, }: {
115
116
  ctx: CanvasRenderingContext2D;
116
117
  feat: LayoutFeature;
117
118
  renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
@@ -129,6 +130,7 @@ export default class PileupRenderer extends BoxRendererType {
129
130
  charWidth: number;
130
131
  charHeight: number;
131
132
  canvasWidth: number;
133
+ theme: Theme;
132
134
  }): void;
133
135
  drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
134
136
  ctx: CanvasRenderingContext2D;
@@ -175,4 +177,4 @@ export default class PileupRenderer extends BoxRendererType {
175
177
  }>;
176
178
  createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
177
179
  }
178
- export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsSerialized, ResultsDeserialized, };
180
+ export { type RenderArgs, type RenderResults, type RenderArgsSerialized, type ResultsSerialized, type ResultsDeserialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
package/dist/PileupRenderer/PileupRenderer.js CHANGED
@@ -116,14 +116,16 @@ class PileupRenderer extends BoxRendererType_1.default {
116
116
  }
117
117
  }
118
118
  }
119
- const [leftPx, rightPx] = (0, util_1.bpSpanPx)(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx);
119
+ const s = feature.get('start') - expansionBefore;
120
+ const e = feature.get('end') + expansionAfter;
121
+ const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
120
122
  if (displayMode === 'compact') {
121
123
  heightPx /= 3;
122
124
  }
123
125
  if (feature.get('refName') !== region.refName) {
124
126
  throw new Error(`feature ${feature.id()} is not on the current region's reference sequence ${region.refName}`);
125
127
  }
126
- const topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
128
+ const topPx = layout.addRect(feature.id(), s, e, heightPx, feature);
127
129
  if (topPx === null) {
128
130
  return null;
129
131
  }
@@ -289,10 +291,9 @@ class PileupRenderer extends BoxRendererType_1.default {
289
291
  const modifications = (0, MismatchParser_1.getModificationPositions)(mm, seq, strand);
290
292
  // probIndex applies across multiple modifications e.g.
291
293
  let probIndex = 0;
292
- for (let i = 0; i < modifications.length; i++) {
293
- const { type, positions } = modifications[i];
294
+ for (const { type, positions } of modifications) {
294
295
  const col = modificationTagMap[type] || 'black';
295
- // @ts-ignore
296
+ // @ts-expect-error
296
297
  const base = Color(col);
297
298
  for (const readPos of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
298
299
  const r = start + readPos;
@@ -399,7 +400,7 @@ class PileupRenderer extends BoxRendererType_1.default {
399
400
  ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
400
401
  }
401
402
  }
402
- drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
403
+ drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }) {
403
404
  const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
404
405
  const { tag = '', type: colorType = '' } = colorBy || {};
405
406
  const { feature } = feat;
@@ -454,30 +455,23 @@ class PileupRenderer extends BoxRendererType_1.default {
454
455
  }
455
456
  break;
456
457
  }
457
- case 'insertSizeAndPairOrientation':
458
+ case 'insertSizeAndPairOrientation': {
458
459
  break;
460
+ }
459
461
  case 'modifications':
460
- case 'methylation':
462
+ case 'methylation': {
461
463
  // this coloring is similar to igv.js, and is helpful to color negative
462
464
  // strand reads differently because their c-g will be flipped (e.g. g-c
463
465
  // read right to left)
464
- if (feature.get('flags') & 16) {
465
- ctx.fillStyle = '#c8dcc8';
466
- }
467
- else {
468
- ctx.fillStyle = '#c8c8c8';
469
- }
466
+ ctx.fillStyle = feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8';
470
467
  break;
471
- case 'normal':
472
- default:
473
- if (defaultColor) {
474
- // avoid a readConfObject call here
475
- ctx.fillStyle = '#c8c8c8';
476
- }
477
- else {
478
- ctx.fillStyle = (0, configuration_1.readConfObject)(config, 'color', { feature });
479
- }
468
+ }
469
+ default: {
470
+ ctx.fillStyle = defaultColor
471
+ ? 'lightgrey'
472
+ : (0, configuration_1.readConfObject)(config, 'color', { feature });
480
473
  break;
474
+ }
481
475
  }
482
476
  this.drawRect(ctx, feat, renderArgs);
483
477
  // second pass for color types that render per-base things that go over the
@@ -527,7 +521,7 @@ class PileupRenderer extends BoxRendererType_1.default {
527
521
  break;
528
522
  }
529
523
  }
530
- drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
524
+ drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, theme, }) {
531
525
  const { Color, bpPerPx, regions } = renderArgs;
532
526
  const { heightPx, topPx, feature } = feat;
533
527
  const [region] = regions;
@@ -556,30 +550,30 @@ class PileupRenderer extends BoxRendererType_1.default {
556
550
  if (mismatch.type === 'mismatch') {
557
551
  if (!drawSNPsMuted) {
558
552
  const baseColor = colorForBase[mismatch.base] || '#888';
559
- fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth, !mismatchAlpha
560
- ? baseColor
561
- : mismatch.qual !== undefined
562
- ? // @ts-ignore
553
+ fillRect(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, mismatchAlpha
554
+ ? mismatch.qual === undefined
555
+ ? baseColor
556
+ : // @ts-expect-error
563
557
  Color(baseColor)
564
558
  .alpha(Math.min(1, mismatch.qual / 50))
565
559
  .hsl()
566
560
  .string()
567
- : baseColor);
561
+ : baseColor);
568
562
  }
569
563
  if (widthPx >= charWidth && heightPx >= heightLim) {
570
564
  // normal SNP coloring
571
565
  const contrastColor = drawSNPsMuted
572
566
  ? 'black'
573
567
  : contrastForBase[mismatch.base] || 'black';
574
- ctx.fillStyle = !mismatchAlpha
575
- ? contrastColor
576
- : mismatch.qual !== undefined
577
- ? // @ts-ignore
568
+ ctx.fillStyle = mismatchAlpha
569
+ ? mismatch.qual === undefined
570
+ ? contrastColor
571
+ : // @ts-expect-error
578
572
  Color(contrastColor)
579
573
  .alpha(Math.min(1, mismatch.qual / 50))
580
574
  .hsl()
581
575
  .string()
582
- : contrastColor;
576
+ : contrastColor;
583
577
  ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
584
578
  }
585
579
  }
@@ -736,6 +730,7 @@ class PileupRenderer extends BoxRendererType_1.default {
736
730
  charWidth,
737
731
  charHeight,
738
732
  canvasWidth,
733
+ theme,
739
734
  });
740
735
  this.drawMismatches({
741
736
  ctx,
@@ -751,6 +746,7 @@ class PileupRenderer extends BoxRendererType_1.default {
751
746
  colorForBase,
752
747
  contrastForBase,
753
748
  canvasWidth,
749
+ theme,
754
750
  });
755
751
  if (showSoftClip) {
756
752
  this.drawSoftClipping({
package/dist/PileupRenderer/PileupRenderer.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/PileupRenderer/components/PileupRendering.js CHANGED
@@ -138,10 +138,10 @@ function PileupRendering(props) {
138
138
  }
139
139
  }
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140
  function callMouseHandler(handlerName, event) {
141
- // @ts-ignore
141
+ // @ts-expect-error
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142
  // eslint-disable-next-line react/destructuring-assignment
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143
  const featureHandler = props[`onFeature${handlerName}`];
144
- // @ts-ignore
144
+ // @ts-expect-error
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  // eslint-disable-next-line react/destructuring-assignment
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  const canvasHandler = props[`on${handlerName}`];
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  if (featureHandler && featureIdUnderMouse) {