@gmod/cram 2.0.1 → 2.0.2

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Files changed (109) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/craiIndex.d.ts +2 -2
  3. package/dist/craiIndex.js +5 -9
  4. package/dist/craiIndex.js.map +1 -1
  5. package/dist/cram-bundle.js +1 -1
  6. package/dist/cramFile/codecs/_base.d.ts +6 -6
  7. package/dist/cramFile/codecs/external.js +1 -0
  8. package/dist/cramFile/codecs/external.js.map +1 -1
  9. package/dist/cramFile/codecs/huffman.d.ts +0 -1
  10. package/dist/cramFile/codecs/huffman.js +1 -3
  11. package/dist/cramFile/codecs/huffman.js.map +1 -1
  12. package/dist/cramFile/container/compressionScheme.js +1 -1
  13. package/dist/cramFile/container/compressionScheme.js.map +1 -1
  14. package/dist/cramFile/encoding.d.ts +20 -20
  15. package/dist/cramFile/file.d.ts +6 -6
  16. package/dist/cramFile/filehandle.d.ts +1 -2
  17. package/dist/cramFile/index.d.ts +1 -2
  18. package/dist/cramFile/index.js +3 -3
  19. package/dist/cramFile/index.js.map +1 -1
  20. package/dist/cramFile/record.d.ts +6 -6
  21. package/dist/cramFile/record.js +7 -4
  22. package/dist/cramFile/record.js.map +1 -1
  23. package/dist/cramFile/sectionParsers.d.ts +8 -8
  24. package/dist/cramFile/sectionParsers.js +3 -4
  25. package/dist/cramFile/sectionParsers.js.map +1 -1
  26. package/dist/cramFile/slice/decodeRecord.js +6 -10
  27. package/dist/cramFile/slice/decodeRecord.js.map +1 -1
  28. package/dist/cramFile/slice/index.js +24 -22
  29. package/dist/cramFile/slice/index.js.map +1 -1
  30. package/dist/cramFile/util.js +1 -1
  31. package/dist/cramFile/util.js.map +1 -1
  32. package/dist/index.d.ts +3 -4
  33. package/dist/index.js +7 -30
  34. package/dist/index.js.map +1 -1
  35. package/dist/indexedCramFile.d.ts +6 -6
  36. package/dist/indexedCramFile.js +13 -18
  37. package/dist/indexedCramFile.js.map +1 -1
  38. package/dist/io/index.d.ts +2 -1
  39. package/dist/io/index.js +4 -3
  40. package/dist/io/index.js.map +1 -1
  41. package/dist/sam.js +10 -13
  42. package/dist/sam.js.map +1 -1
  43. package/dist/unzip.d.ts +1 -2
  44. package/dist/unzip.js +1 -1
  45. package/dist/unzip.js.map +1 -1
  46. package/esm/craiIndex.d.ts +2 -2
  47. package/esm/craiIndex.js +5 -9
  48. package/esm/craiIndex.js.map +1 -1
  49. package/esm/cramFile/codecs/_base.d.ts +6 -6
  50. package/esm/cramFile/codecs/external.js +1 -0
  51. package/esm/cramFile/codecs/external.js.map +1 -1
  52. package/esm/cramFile/codecs/huffman.d.ts +0 -1
  53. package/esm/cramFile/codecs/huffman.js +1 -3
  54. package/esm/cramFile/codecs/huffman.js.map +1 -1
  55. package/esm/cramFile/container/compressionScheme.js +1 -1
  56. package/esm/cramFile/container/compressionScheme.js.map +1 -1
  57. package/esm/cramFile/encoding.d.ts +20 -20
  58. package/esm/cramFile/file.d.ts +6 -6
  59. package/esm/cramFile/filehandle.d.ts +1 -2
  60. package/esm/cramFile/index.d.ts +1 -2
  61. package/esm/cramFile/index.js +1 -2
  62. package/esm/cramFile/index.js.map +1 -1
  63. package/esm/cramFile/record.d.ts +6 -6
  64. package/esm/cramFile/record.js +7 -4
  65. package/esm/cramFile/record.js.map +1 -1
  66. package/esm/cramFile/sectionParsers.d.ts +8 -8
  67. package/esm/cramFile/sectionParsers.js +3 -4
  68. package/esm/cramFile/sectionParsers.js.map +1 -1
  69. package/esm/cramFile/slice/decodeRecord.js +6 -10
  70. package/esm/cramFile/slice/decodeRecord.js.map +1 -1
  71. package/esm/cramFile/slice/index.js +24 -22
  72. package/esm/cramFile/slice/index.js.map +1 -1
  73. package/esm/cramFile/util.js +1 -1
  74. package/esm/cramFile/util.js.map +1 -1
  75. package/esm/index.d.ts +3 -4
  76. package/esm/index.js +3 -4
  77. package/esm/index.js.map +1 -1
  78. package/esm/indexedCramFile.d.ts +6 -6
  79. package/esm/indexedCramFile.js +13 -18
  80. package/esm/indexedCramFile.js.map +1 -1
  81. package/esm/io/index.d.ts +2 -1
  82. package/esm/io/index.js +2 -1
  83. package/esm/io/index.js.map +1 -1
  84. package/esm/sam.js +10 -13
  85. package/esm/sam.js.map +1 -1
  86. package/esm/unzip.d.ts +1 -2
  87. package/esm/unzip.js +1 -2
  88. package/esm/unzip.js.map +1 -1
  89. package/package.json +11 -11
  90. package/src/craiIndex.ts +8 -13
  91. package/src/cramFile/codecs/_base.ts +3 -3
  92. package/src/cramFile/codecs/external.ts +1 -0
  93. package/src/cramFile/codecs/huffman.ts +7 -8
  94. package/src/cramFile/container/compressionScheme.ts +1 -1
  95. package/src/cramFile/encoding.ts +10 -10
  96. package/src/cramFile/file.ts +5 -5
  97. package/src/cramFile/filehandle.ts +1 -3
  98. package/src/cramFile/index.ts +1 -2
  99. package/src/cramFile/record.ts +13 -10
  100. package/src/cramFile/sectionParsers.ts +8 -9
  101. package/src/cramFile/slice/decodeRecord.ts +15 -17
  102. package/src/cramFile/slice/index.ts +26 -23
  103. package/src/cramFile/util.ts +1 -1
  104. package/src/index.ts +3 -5
  105. package/src/indexedCramFile.ts +19 -23
  106. package/src/io/index.ts +3 -1
  107. package/src/sam.ts +12 -14
  108. package/src/typings/binary-parser.d.ts +1 -1
  109. package/src/unzip.ts +1 -2
package/dist/cramFile/codecs/_base.d.ts CHANGED
@@ -1,24 +1,24 @@
1
1
  import CramSlice from '../slice';
2
2
  import { CramFileBlock } from '../file';
3
3
  import { DataType } from './dataSeriesTypes';
4
- export type DataTypeMapping = {
4
+ export interface DataTypeMapping {
5
5
  byte: number;
6
6
  int: number;
7
7
  long: number;
8
8
  byteArray: Uint8Array;
9
- };
10
- export type Cursor = {
9
+ }
10
+ export interface Cursor {
11
11
  bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
12
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  bytePosition: number;
13
- };
14
- export type Cursors = {
13
+ }
14
+ export interface Cursors {
15
15
  lastAlignmentStart: number;
16
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  coreBlock: Cursor;
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17
  externalBlocks: {
18
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  map: Map<any, any>;
19
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  getCursor: (contentId: number) => Cursor;
20
20
  };
21
- };
21
+ }
22
22
  export default abstract class CramCodec<TResult extends DataType = DataType, TParameters = unknown> {
23
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  parameters: TParameters;
24
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  dataType: DataType;
package/dist/cramFile/codecs/external.js CHANGED
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
+ /* eslint-disable @typescript-eslint/unbound-method */
6
7
  const errors_1 = require("../../errors");
7
8
  const _base_1 = __importDefault(require("./_base"));
8
9
  const util_1 = require("../util");
package/dist/cramFile/codecs/external.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}
1
+ {"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,sDAAsD;AACtD,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}
package/dist/cramFile/codecs/huffman.d.ts CHANGED
@@ -5,7 +5,6 @@ import { CramFileBlock } from '../file';
5
5
  export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
6
6
  private codes;
7
7
  private codeBook;
8
- private sortedByValue;
9
8
  private sortedCodes;
10
9
  private sortedValuesByBitCode;
11
10
  private sortedBitCodes;
package/dist/cramFile/codecs/huffman.js CHANGED
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
+ /* eslint-disable @typescript-eslint/unbound-method */
6
7
  const errors_1 = require("../../errors");
7
8
  const _base_1 = __importDefault(require("./_base"));
8
9
  const getBits_1 = require("./getBits");
@@ -16,7 +17,6 @@ class HuffmanIntCodec extends _base_1.default {
16
17
  super(parameters, dataType);
17
18
  this.codes = {};
18
19
  this.codeBook = {};
19
- this.sortedByValue = [];
20
20
  this.sortedCodes = [];
21
21
  this.sortedValuesByBitCode = [];
22
22
  this.sortedBitCodes = [];
@@ -78,8 +78,6 @@ class HuffmanIntCodec extends _base_1.default {
78
78
  }
79
79
  buildCaches() {
80
80
  this.sortedCodes = Object.values(this.codes).sort((a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode);
81
- // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
82
- this.sortedByValue = Object.values(this.codes).sort((a, b) => a.value - b.value);
83
81
  this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value);
84
82
  this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode);
85
83
  this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength);
package/dist/cramFile/codecs/huffman.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/cramFile/container/compressionScheme.js CHANGED
@@ -123,7 +123,7 @@ class CramContainerCompressionScheme {
123
123
  toJSON() {
124
124
  const data = {};
125
125
  Object.keys(this).forEach(k => {
126
- if (/Cache$/.test(k)) {
126
+ if (k.endsWith('Cache')) {
127
127
  return;
128
128
  }
129
129
  data[k] = this[k];
package/dist/cramFile/container/compressionScheme.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ {"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":";;AAAA,sCAA4C;AAI5C,yCAAiD;AAMjD,sDAAsD;AACtD,aAAa;AACb,MAAM,eAAe,GAAG;IACtB,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,gBAAgB;IAChB,gBAAgB;CACR,CAAA;AAIV,SAAS,uBAAuB,CAAC,SAAmB;IAClD,MAAM,MAAM,GAAe,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAqB,8BAA8B;IAcjD,YAAY,OAA8B;QARnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAOnD,+BAA+B;QAC/B,iEAAiE;QACjE,IAAI,CAAC,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAChD,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QACtC,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAClD,IAAI,CAAC,gBAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAC/C,IAAI,CAAC,kBAAkB,GAAG,uBAAuB,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;QAC1E,IAAI,CAAC,kBAAkB,GAAG,OAAO,CAAC,kBAAkB,CAAA;QACpD,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAA;QACtC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;QACxC,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,CAAA;QAC1B,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;IAC1C,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE,CAAC;YACjC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE,CAAC;gBACjB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAA,yBAAgB,EAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAiB;QAC3B,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CACnB,cAA2B;QAE3B,IAAI,CAAC,GACH,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,CAAA;QAC3C,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,2BAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,IAAA,yBAAgB,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;YACjE,CAAC;QACH,CAAC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAQ,EAAE,CAAA;QACpB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;gBACxB,OAAM;YACR,CAAC;YACD,IAAI,CAAC,CAAC,CAAC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package/dist/cramFile/encoding.d.ts CHANGED
@@ -1,24 +1,24 @@
1
- export type NullEncoding = {
1
+ export interface NullEncoding {
2
2
  codecId: 0;
3
3
  parametersBytes: number;
4
4
  parameters: Record<string, never>;
5
- };
6
- export type ExternalCramEncoding = {
5
+ }
6
+ export interface ExternalCramEncoding {
7
7
  codecId: 1;
8
8
  parametersBytes: number;
9
9
  parameters: {
10
10
  blockContentId: number;
11
11
  };
12
- };
13
- export type GolombEncoding = {
12
+ }
13
+ export interface GolombEncoding {
14
14
  codecId: 2;
15
15
  parametersBytes: number;
16
16
  parameters: {
17
17
  offset: number;
18
18
  M: number;
19
19
  };
20
- };
21
- export type HuffmanEncoding = {
20
+ }
21
+ export interface HuffmanEncoding {
22
22
  codecId: 3;
23
23
  parametersBytes: number;
24
24
  parameters: {
@@ -27,52 +27,52 @@ export type HuffmanEncoding = {
27
27
  numLengths: number;
28
28
  bitLengths: number[];
29
29
  };
30
- };
31
- export type ByteArrayLengthEncoding = {
30
+ }
31
+ export interface ByteArrayLengthEncoding {
32
32
  codecId: 4;
33
33
  parametersBytes: number;
34
34
  parameters: {
35
35
  lengthsEncoding: CramEncoding;
36
36
  valuesEncoding: CramEncoding;
37
37
  };
38
- };
39
- export type ByteArrayStopCramEncoding = {
38
+ }
39
+ export interface ByteArrayStopCramEncoding {
40
40
  codecId: 5;
41
41
  parametersBytes: number;
42
42
  parameters: {
43
43
  stopByte: number;
44
44
  blockContentId: number;
45
45
  };
46
- };
47
- export type BetaEncoding = {
46
+ }
47
+ export interface BetaEncoding {
48
48
  codecId: 6;
49
49
  parametersBytes: number;
50
50
  parameters: {
51
51
  offset: number;
52
52
  length: number;
53
53
  };
54
- };
55
- export type SubexpEncoding = {
54
+ }
55
+ export interface SubexpEncoding {
56
56
  codecId: 7;
57
57
  parametersBytes: number;
58
58
  parameters: {
59
59
  offset: number;
60
60
  K: number;
61
61
  };
62
- };
63
- export type GolombRiceEncoding = {
62
+ }
63
+ export interface GolombRiceEncoding {
64
64
  codecId: 8;
65
65
  parametersBytes: number;
66
66
  parameters: {
67
67
  offset: number;
68
68
  log2m: number;
69
69
  };
70
- };
71
- export type GammaEncoding = {
70
+ }
71
+ export interface GammaEncoding {
72
72
  codecId: 9;
73
73
  parametersBytes: number;
74
74
  parameters: {
75
75
  offset: number;
76
76
  };
77
- };
77
+ }
78
78
  export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;
package/dist/cramFile/file.d.ts CHANGED
@@ -6,16 +6,16 @@ import { BlockHeader, CompressionMethod } from './sectionParsers';
6
6
  import CramContainer from './container';
7
7
  import CramRecord from './record';
8
8
  import { Filehandle } from './filehandle';
9
- export type CramFileSource = {
9
+ export interface CramFileSource {
10
10
  filehandle?: Filehandle;
11
11
  url?: string;
12
12
  path?: string;
13
- };
13
+ }
14
14
  export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
15
15
  export type CramFileArgs = CramFileSource & {
16
- checkSequenceMD5: boolean;
16
+ checkSequenceMD5?: boolean;
17
17
  cacheSize?: number;
18
- seqFetch: SeqFetch;
18
+ seqFetch?: SeqFetch;
19
19
  };
20
20
  export type CramFileBlock = BlockHeader & {
21
21
  _endPosition: number;
@@ -27,9 +27,9 @@ export type CramFileBlock = BlockHeader & {
27
27
  export default class CramFile {
28
28
  private file;
29
29
  validateChecksums: boolean;
30
- fetchReferenceSequenceCallback: SeqFetch;
30
+ fetchReferenceSequenceCallback?: SeqFetch;
31
31
  options: {
32
- checkSequenceMD5: boolean;
32
+ checkSequenceMD5?: boolean;
33
33
  cacheSize: number;
34
34
  };
35
35
  featureCache: QuickLRU<string, Promise<CramRecord[]>>;
package/dist/cramFile/filehandle.d.ts CHANGED
@@ -1,2 +1 @@
1
- import { GenericFilehandle } from 'generic-filehandle';
2
- export { GenericFilehandle as Filehandle };
1
+ export { GenericFilehandle as Filehandle } from 'generic-filehandle';
package/dist/cramFile/index.d.ts CHANGED
@@ -1,3 +1,2 @@
1
- import CramFile from './file';
2
1
  export { default as CramRecord } from './record';
3
- export default CramFile;
2
+ export { default } from './file';
package/dist/cramFile/index.js CHANGED
@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
3
3
  return (mod && mod.__esModule) ? mod : { "default": mod };
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.CramRecord = void 0;
7
- const file_1 = __importDefault(require("./file"));
6
+ exports.default = exports.CramRecord = void 0;
8
7
  var record_1 = require("./record");
9
8
  Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return __importDefault(record_1).default; } });
10
- exports.default = file_1.default;
9
+ var file_1 = require("./file");
10
+ Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(file_1).default; } });
11
11
  //# sourceMappingURL=index.js.map
package/dist/cramFile/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,kDAA6B;AAC7B,mCAAgD;AAAvC,qHAAA,OAAO,OAAc;AAE9B,kBAAe,cAAQ,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAgD;AAAvC,qHAAA,OAAO,OAAc;AAE9B,+BAAgC;AAAvB,gHAAA,OAAO,OAAA"}
package/dist/cramFile/record.d.ts CHANGED
@@ -1,25 +1,25 @@
1
1
  import CramContainerCompressionScheme from './container/compressionScheme';
2
2
  import decodeRecord from './slice/decodeRecord';
3
- export type RefRegion = {
3
+ export interface RefRegion {
4
4
  start: number;
5
5
  end: number;
6
6
  seq: string;
7
- };
8
- export type ReadFeature = {
7
+ }
8
+ export interface ReadFeature {
9
9
  code: string;
10
10
  pos: number;
11
11
  refPos: number;
12
12
  data: any;
13
13
  ref?: string;
14
14
  sub?: string;
15
- };
16
- export type MateRecord = {
15
+ }
16
+ export interface MateRecord {
17
17
  readName?: string;
18
18
  sequenceId: number;
19
19
  alignmentStart: number;
20
20
  flags?: number;
21
21
  uniqueId?: number;
22
- };
22
+ }
23
23
  export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
24
24
  export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
25
25
  export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];
package/dist/cramFile/record.js CHANGED
@@ -17,7 +17,7 @@ function decodeReadSequence(cramRecord, refRegion) {
17
17
  const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
18
18
  if (!cramRecord.readFeatures) {
19
19
  return refRegion.seq
20
- .substr(regionSeqOffset, cramRecord.lengthOnRef)
20
+ .slice(regionSeqOffset, regionSeqOffset + (cramRecord.lengthOnRef || 0))
21
21
  .toUpperCase();
22
22
  }
23
23
  let bases = '';
@@ -81,14 +81,17 @@ function decodeReadSequence(cramRecord, refRegion) {
81
81
  }
82
82
  else if (currentReadFeature < cramRecord.readFeatures.length) {
83
83
  // put down a chunk of sequence up to the next read feature
84
- const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
84
+ const chunk = refRegion.seq.slice(regionPos, regionPos +
85
+ cramRecord.readFeatures[currentReadFeature].pos -
86
+ bases.length -
87
+ 1);
85
88
  bases += chunk;
86
89
  regionPos += chunk.length;
87
90
  }
88
91
  }
89
92
  else {
90
93
  // put down a chunk of reference up to the full read length
91
- const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
94
+ const chunk = refRegion.seq.slice(regionPos, regionPos + cramRecord.readLength - bases.length);
92
95
  bases += chunk;
93
96
  regionPos += chunk.length;
94
97
  }
@@ -368,7 +371,7 @@ class CramRecord {
368
371
  toJSON() {
369
372
  const data = {};
370
373
  Object.keys(this).forEach(k => {
371
- if (k.charAt(0) === '_') {
374
+ if (k.startsWith('_')) {
372
375
  return;
373
376
  }
374
377
  data[k] = this[k];
package/dist/cramFile/record.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/cramFile/sectionParsers.d.ts CHANGED
@@ -9,7 +9,7 @@ declare const cramFileDefinition: {
9
9
  maxLength: number;
10
10
  };
11
11
  export type CramTagDictionary = string[][];
12
- export type CramPreservationMap = {
12
+ export interface CramPreservationMap {
13
13
  MI: boolean;
14
14
  UI: boolean;
15
15
  PI: boolean;
@@ -18,8 +18,8 @@ export type CramPreservationMap = {
18
18
  RR: boolean;
19
19
  SM: [number, number, number, number, number];
20
20
  TD: CramTagDictionary;
21
- };
22
- export type MappedSliceHeader = {
21
+ }
22
+ export interface MappedSliceHeader {
23
23
  refSeqId: number;
24
24
  refSeqStart: number;
25
25
  refSeqSpan: number;
@@ -30,24 +30,24 @@ export type MappedSliceHeader = {
30
30
  contentIds: number[];
31
31
  refBaseBlockId: number;
32
32
  md5: TupleOf<number, 16>;
33
- };
34
- export type UnmappedSliceHeader = {
33
+ }
34
+ export interface UnmappedSliceHeader {
35
35
  numRecords: number;
36
36
  recordCounter: number;
37
37
  numBlocks: number;
38
38
  numContentIds: number;
39
39
  contentIds: number[];
40
40
  md5: TupleOf<number, 16>;
41
- };
41
+ }
42
42
  export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
43
43
  export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
44
- export type BlockHeader = {
44
+ export interface BlockHeader {
45
45
  compressionMethod: CompressionMethod;
46
46
  contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';
47
47
  contentId: number;
48
48
  compressedSize: number;
49
49
  uncompressedSize: number;
50
- };
50
+ }
51
51
  export type CramCompressionHeader = ParsedItem<{
52
52
  preservation: CramPreservationMap;
53
53
  dataSeriesEncoding: DataSeriesEncodingMap;
package/dist/cramFile/sectionParsers.js CHANGED
@@ -65,7 +65,7 @@ const cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents
65
65
  const str = buffer.toString('utf8', stringStart, stringEnd);
66
66
  const tags = [];
67
67
  for (let i = 0; i < str.length; i += 3) {
68
- tags.push(str.substr(i, 3));
68
+ tags.push(str.slice(i, i + 3));
69
69
  }
70
70
  return tags;
71
71
  }
@@ -121,8 +121,7 @@ const cramPreservationMap = new binary_parser_1.Parser()
121
121
  /* istanbul ignore next */
122
122
  function formatMap(data) {
123
123
  const map = {};
124
- for (let i = 0; i < data.ents.length; i += 1) {
125
- const { key, value } = data.ents[i];
124
+ for (const { key, value } of data.ents) {
126
125
  if (map[key]) {
127
126
  console.warn(`duplicate key ${key} in map`);
128
127
  }
@@ -206,7 +205,7 @@ const versionedParsers = {
206
205
  const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
207
206
  return { parser, maxLength: maxLengthFunc };
208
207
  },
209
- cramEncoding(majorVersion) {
208
+ cramEncoding(_majorVersion) {
210
209
  const parser = new binary_parser_1.Parser()
211
210
  .namely('cramEncoding')
212
211
  .itf8('codecId')
package/dist/cramFile/sectionParsers.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/cramFile/slice/decodeRecord.js CHANGED
@@ -186,15 +186,11 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
186
186
  // in javascript land.
187
187
  const cramFlags = decodeDataSeries('CF');
188
188
  if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent)) {
189
- throw new Error();
190
- }
191
- let sequenceId;
192
- if (majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2) {
193
- sequenceId = decodeDataSeries('RI');
194
- }
195
- else {
196
- sequenceId = sliceHeader.parsedContent.refSeqId;
189
+ throw new Error('slice header not mapped');
197
190
  }
191
+ const sequenceId = majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2
192
+ ? decodeDataSeries('RI')
193
+ : sliceHeader.parsedContent.refSeqId;
198
194
  const readLength = decodeDataSeries('RL');
199
195
  // if APDelta, will calculate the true start in a second pass
200
196
  let alignmentStart = decodeDataSeries('AP');
@@ -257,8 +253,8 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
257
253
  const ntags = TN.length;
258
254
  for (let i = 0; i < ntags; i += 1) {
259
255
  const tagId = TN[i];
260
- const tagName = tagId.substr(0, 2);
261
- const tagType = tagId.substr(2, 1);
256
+ const tagName = tagId.slice(0, 2);
257
+ const tagType = tagId.slice(2, 3);
262
258
  const tagCodec = compressionScheme.getCodecForTag(tagId);
263
259
  if (!tagCodec) {
264
260
  throw new errors_1.CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);