@gmod/cram 1.7.4 → 2.0.1

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 (104) hide show
  1. package/CHANGELOG.md +9 -2
  2. package/README.md +343 -24
  3. package/dist/craiIndex.js.map +1 -1
  4. package/dist/cram-bundle.js +1 -1
  5. package/dist/cram-bundle.js.LICENSE.txt +6 -0
  6. package/dist/cramFile/codecs/beta.js.map +1 -1
  7. package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
  8. package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
  9. package/dist/cramFile/codecs/external.js.map +1 -1
  10. package/dist/cramFile/codecs/gamma.js.map +1 -1
  11. package/dist/cramFile/codecs/getBits.js.map +1 -1
  12. package/dist/cramFile/codecs/huffman.js.map +1 -1
  13. package/dist/cramFile/codecs/index.js.map +1 -1
  14. package/dist/cramFile/codecs/subexp.js.map +1 -1
  15. package/dist/cramFile/container/compressionScheme.js.map +1 -1
  16. package/dist/cramFile/container/index.js.map +1 -1
  17. package/dist/cramFile/file.d.ts +10 -3
  18. package/dist/cramFile/file.js +56 -50
  19. package/dist/cramFile/file.js.map +1 -1
  20. package/dist/cramFile/record.js.map +1 -1
  21. package/dist/cramFile/sectionParsers.d.ts +1 -0
  22. package/dist/cramFile/sectionParsers.js +7 -7
  23. package/dist/cramFile/sectionParsers.js.map +1 -1
  24. package/dist/cramFile/slice/decodeRecord.js +1 -1
  25. package/dist/cramFile/slice/decodeRecord.js.map +1 -1
  26. package/dist/cramFile/slice/index.js.map +1 -1
  27. package/dist/cramFile/util.d.ts +1 -0
  28. package/dist/cramFile/util.js.map +1 -1
  29. package/dist/indexedCramFile.js.map +1 -1
  30. package/dist/io/index.js.map +1 -1
  31. package/dist/rans/constants.d.ts +4 -3
  32. package/dist/rans/constants.js.map +1 -1
  33. package/dist/rans/d04.js +1 -0
  34. package/dist/rans/d04.js.map +1 -1
  35. package/dist/rans/d14.js +1 -0
  36. package/dist/rans/d14.js.map +1 -1
  37. package/dist/rans/decoding.d.ts +16 -19
  38. package/dist/rans/decoding.js +1 -0
  39. package/dist/rans/decoding.js.map +1 -1
  40. package/dist/rans/frequencies.d.ts +2 -2
  41. package/dist/rans/frequencies.js +1 -0
  42. package/dist/rans/frequencies.js.map +1 -1
  43. package/dist/rans/index.js +1 -0
  44. package/dist/rans/index.js.map +1 -1
  45. package/dist/sam.d.ts +5 -6
  46. package/dist/sam.js +23 -7
  47. package/dist/sam.js.map +1 -1
  48. package/dist/typescript.js.map +1 -1
  49. package/dist/unzip.d.ts +1 -0
  50. package/esm/craiIndex.js.map +1 -1
  51. package/esm/cramFile/codecs/beta.js.map +1 -1
  52. package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
  53. package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
  54. package/esm/cramFile/codecs/external.js.map +1 -1
  55. package/esm/cramFile/codecs/gamma.js.map +1 -1
  56. package/esm/cramFile/codecs/getBits.js.map +1 -1
  57. package/esm/cramFile/codecs/huffman.js.map +1 -1
  58. package/esm/cramFile/codecs/index.js.map +1 -1
  59. package/esm/cramFile/codecs/subexp.js.map +1 -1
  60. package/esm/cramFile/container/compressionScheme.js.map +1 -1
  61. package/esm/cramFile/container/index.js.map +1 -1
  62. package/esm/cramFile/file.d.ts +10 -3
  63. package/esm/cramFile/file.js +17 -13
  64. package/esm/cramFile/file.js.map +1 -1
  65. package/esm/cramFile/record.js.map +1 -1
  66. package/esm/cramFile/sectionParsers.d.ts +1 -0
  67. package/esm/cramFile/sectionParsers.js +7 -7
  68. package/esm/cramFile/sectionParsers.js.map +1 -1
  69. package/esm/cramFile/slice/decodeRecord.js +1 -1
  70. package/esm/cramFile/slice/decodeRecord.js.map +1 -1
  71. package/esm/cramFile/slice/index.js.map +1 -1
  72. package/esm/cramFile/util.d.ts +1 -0
  73. package/esm/cramFile/util.js.map +1 -1
  74. package/esm/indexedCramFile.js.map +1 -1
  75. package/esm/io/index.js.map +1 -1
  76. package/esm/rans/constants.d.ts +4 -3
  77. package/esm/rans/constants.js.map +1 -1
  78. package/esm/rans/d04.js +1 -0
  79. package/esm/rans/d04.js.map +1 -1
  80. package/esm/rans/d14.js +1 -0
  81. package/esm/rans/d14.js.map +1 -1
  82. package/esm/rans/decoding.d.ts +16 -19
  83. package/esm/rans/decoding.js +1 -0
  84. package/esm/rans/decoding.js.map +1 -1
  85. package/esm/rans/frequencies.d.ts +2 -2
  86. package/esm/rans/frequencies.js +1 -0
  87. package/esm/rans/frequencies.js.map +1 -1
  88. package/esm/rans/index.js +1 -0
  89. package/esm/rans/index.js.map +1 -1
  90. package/esm/sam.d.ts +5 -6
  91. package/esm/sam.js +23 -7
  92. package/esm/sam.js.map +1 -1
  93. package/esm/typescript.js.map +1 -1
  94. package/esm/unzip.d.ts +1 -0
  95. package/package.json +11 -10
  96. package/src/cramFile/container/index.ts +4 -1
  97. package/src/cramFile/file.ts +23 -19
  98. package/src/rans/{d04.js → d04.ts} +1 -0
  99. package/src/rans/{d14.js → d14.ts} +1 -0
  100. package/src/rans/{decoding.js → decoding.ts} +1 -0
  101. package/src/rans/{frequencies.js → frequencies.ts} +1 -0
  102. package/src/rans/{index.js → index.ts} +1 -0
  103. package/src/sam.ts +30 -14
  104. /package/src/rans/{constants.js → constants.ts} +0 -0
package/esm/rans/d14.js CHANGED
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { TF_SHIFT } from './constants';
2
3
  import Decoding from './decoding';
3
4
  export default function uncompress(
@@ -1 +1 @@
1
- {"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AACtC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,gBAAgB,CAAC,MAAM;AACvB,2BAA2B,CAAC,CAAC;AAC7B,yBAAyB,CAAC,IAAI;IAE9B,MAAM,SAAS,CAAC,UAAU,GAAG,MAAM,CAAC,SAAS,EAAE,CAAA;IAC/C,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,IAAI,GAAG,UAAU,IAAI,CAAC,CAAA;IACtC,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,IAAI,CAAA;IACvB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,OAAO,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE;QACpD,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAElE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAEjE,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAE1C,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;KACR;IAED,YAAY;IACZ,OAAO,EAAE,GAAG,UAAU,EAAE,EAAE,IAAI,CAAC,EAAE;QAC/B,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,EAAE,GAAG,EAAE,CAAA;KACR;AACH,CAAC"}
1
+ {"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AACtC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,gBAAgB,CAAC,MAAM;AACvB,2BAA2B,CAAC,CAAC;AAC7B,yBAAyB,CAAC,IAAI;IAE9B,MAAM,SAAS,CAAC,UAAU,GAAG,MAAM,CAAC,SAAS,EAAE,CAAA;IAC/C,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,IAAI,GAAG,UAAU,IAAI,CAAC,CAAA;IACtC,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,IAAI,CAAA;IACvB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,OAAO,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC;QACrD,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAElE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAEjE,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAE1C,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;IACT,CAAC;IAED,YAAY;IACZ,OAAO,EAAE,GAAG,UAAU,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC;QAChC,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,EAAE,GAAG,EAAE,CAAA;IACT,CAAC;AACH,CAAC"}
@@ -1,30 +1,27 @@
1
- export default Decode;
2
- declare namespace Decode {
3
- export { FC };
4
- export { AriDecoder };
5
- export { Symbol };
6
- export { symbolInit };
7
- export { advanceStep };
8
- export { advanceSymbolStep };
9
- export { get };
10
- export { advanceSymbol };
11
- export { renormalize };
12
- }
13
1
  declare class FC {
14
- F: any;
15
- C: any;
2
+ constructor();
16
3
  }
17
4
  declare class AriDecoder {
18
- fc: any[];
19
- R: any;
5
+ constructor();
20
6
  }
21
7
  declare class Symbol {
22
- start: any;
23
- freq: any;
8
+ constructor();
24
9
  }
25
10
  declare function symbolInit(sym: any, start: any, freq: any): void;
26
11
  declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
27
12
  declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
28
- declare function get(r: any, scaleBits: any): number;
13
+ declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
29
14
  declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
30
15
  declare function renormalize(r: any, pptr: any): any;
16
+ declare const Decode: {
17
+ FC: typeof FC;
18
+ AriDecoder: typeof AriDecoder;
19
+ Symbol: typeof Symbol;
20
+ symbolInit: typeof symbolInit;
21
+ advanceStep: typeof advanceStep;
22
+ advanceSymbolStep: typeof advanceSymbolStep;
23
+ get: typeof get;
24
+ advanceSymbol: typeof advanceSymbol;
25
+ renormalize: typeof renormalize;
26
+ };
27
+ export default Decode;
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors';
2
3
  import { RANS_BYTE_L } from './constants';
3
4
  class FC {
@@ -1 +1 @@
1
- {"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAA;AAEzC,MAAM,EAAE;IACN,YAAY;IACZ;QACE,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;QAClB,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;IACpB,CAAC;CACF;AAED,MAAM,UAAU;IACd,+BAA+B;IAC/B,YAAY;IAEZ;QACE,IAAI,CAAC,EAAE,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC1C,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,EAAE,CAAA;SACtB;QACD,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;IACf,CAAC;CACF;AAED,MAAM,MAAM;IACV,gCAAgC;IAChC,iCAAiC;IACjC;QACE,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACtB,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;IACvB,CAAC;CACF;AAED,oEAAoE;AACpE,SAAS,UAAU,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI;IAClC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE;QACvB,MAAM,IAAI,kBAAkB,CAAC,kCAAkC,CAAC,CAAA;KACjE;IACD,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE;QAChC,MAAM,IAAI,kBAAkB,CAAC,iCAAiC,CAAC,CAAA;KAChE;IACD,GAAG,CAAC,KAAK,GAAG,KAAK,CAAA;IACjB,GAAG,CAAC,IAAI,GAAG,IAAI,CAAA;AACjB,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,wCAAwC;AACxC,wBAAwB,CAAC,SAAS,WAAW;AAC3C,eAAe,CAAC,CAAC;AACjB,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,OAAO,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;AACrD,CAAC;AAED,wDAAwD;AACxD,iBAAiB,CAAC,SAAS,iBAAiB;AAC1C,eAAe,CAAC,CAAC;AACjB,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,WAAW,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACvD,CAAC;AAED,0EAA0E;AAC1E,gBAAgB,CAAC,SAAS,GAAG,CAAC,eAAe,CAAC,CAAC,EAAE,eAAe,CAAC,SAAS;IACxE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,CAAA;AACnC,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,iEAAiE;AACjE,wBAAwB,CAAC,SAAS,OAAO;AACvC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;AAC3B,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;IAEhD,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE;QACnB,GAAG;YACD,eAAe,CAAC,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;YAC3C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;SACjB,QAAQ,CAAC,GAAG,WAAW,EAAC;KAC1B;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,oDAAoD;AACpD,iBAAiB,CAAC,SAAS,aAAa;AACtC,eAAe,CAAC,CAAC;AACjB,sBAAsB,CAAC,IAAI;AAC3B,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACzD,CAAC;AAED,gBAAgB;AAChB,iBAAiB,CAAC,SAAS,WAAW;AACpC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;IAE3B,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE;QACnB,GAAG;YACD,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;SACnC,QAAQ,CAAC,GAAG,WAAW,EAAC;KAC1B;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,MAAM,GAAG;IACb,EAAE;IACF,UAAU;IACV,MAAM;IACN,UAAU;IACV,WAAW;IACX,iBAAiB;IACjB,GAAG;IACH,aAAa;IACb,WAAW;CACZ,CAAA;AAED,eAAe,MAAM,CAAA"}
1
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@@ -1,2 +1,2 @@
1
- export function readStatsO0(cp: any, decoder: any, syms: any): void;
2
- export function readStatsO1(cp: any, D: any, syms: any): void;
1
+ export declare function readStatsO0(cp: any, decoder: any, syms: any): void;
2
+ export declare function readStatsO1(cp: any, D: any, syms: any): void;
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors';
2
3
  import { TOTFREQ } from './constants';
3
4
  import Decoding from './decoding';
@@ -1 +1 @@
1
- {"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAA;AACrC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE;QACX,MAAM,IAAI,kBAAkB,CAAC,kBAAkB,CAAC,CAAA;KACjD;AACH,CAAC;AAED,MAAM,UAAU,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,yBAAyB,CAAC,OAAO;AACjC,8BAA8B,CAAC,IAAI;IAEnC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;IACvB,GAAG;QACD,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;YACzB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,CAAA;SAClC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACjC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;YAC1B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;YACvB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,CAAA;SACrE;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnB,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAE9D,gCAAgC;QAChC,IAAI,CAAC,OAAO,CAAC,CAAC,EAAE;YACd,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;SAC/B;QACD,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEzC,CAAC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEpB,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;YAC/D,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACtB;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE;YACpB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,OAAO,CAAC,CAAA;AACrB,CAAC;AAED,MAAM,UAAU,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,4BAA4B,CAAC,CAAC;AAC9B,gCAAgC,CAAC,IAAI;IAErC,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;IACvB,GAAG;QACD,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACvB,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;YAChB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;SACjC;QACD,GAAG;YACD,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,CAAA;aAC/B;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YAC9B,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;gBACpB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;aAC/D;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAEhB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAA;aACvB;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,aAAa,EAAE,CAAA;aAC1C;YAED,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAE3D,gCAAgC;YAChC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBAClB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;aAC5B;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACjB,MAAM,CAAC,CAAC,IAAI,OAAO,CAAC,CAAA;YAEpB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;gBAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACvB;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE;gBACrB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;aACP;iBAAM;gBACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACpB;SACF,QAAQ,CAAC,KAAK,CAAC,EAAC;QAEjB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;YAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACvB;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE;YACrB,IAAI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;AACnB,CAAC"}
1
+ 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package/esm/rans/index.js CHANGED
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors';
2
3
  import Decoding from './decoding';
3
4
  import { readStatsO0, readStatsO1 } from './frequencies';
@@ -1 +1 @@
1
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1
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package/esm/sam.d.ts CHANGED
@@ -1,8 +1,7 @@
1
- export type HeaderDataItem = {
1
+ export declare function parseHeaderText(text: string): {
2
2
  tag: string;
3
- data: Array<{
3
+ data: {
4
4
  tag: string;
5
- value: string;
6
- }>;
7
- };
8
- export declare function parseHeaderText(text: string): HeaderDataItem[];
5
+ value: string | undefined;
6
+ }[];
7
+ }[];
package/esm/sam.js CHANGED
@@ -1,16 +1,32 @@
1
1
  export function parseHeaderText(text) {
2
2
  const lines = text.split(/\r?\n/);
3
3
  const data = [];
4
- lines.forEach(line => {
4
+ for (const line of lines) {
5
5
  const [tag, ...fields] = line.split(/\t/);
6
- const parsedFields = fields.map(f => {
7
- const [fieldTag, value] = f.split(':', 2);
8
- return { tag: fieldTag, value };
9
- });
10
6
  if (tag) {
11
- data.push({ tag: tag.substr(1), data: parsedFields });
7
+ data.push({
8
+ tag: tag.slice(1),
9
+ data: fields.map(f => {
10
+ const r = f.indexOf(':');
11
+ if (r !== -1) {
12
+ return {
13
+ tag: f.slice(0, r),
14
+ value: f.slice(r + 1),
15
+ };
16
+ }
17
+ else {
18
+ // @CO lines are not comma separated.
19
+ // See "samtools view -H c2\#pad.3.0.cram"
20
+ // so, just store value tag itself
21
+ return {
22
+ tag: f,
23
+ value: undefined,
24
+ };
25
+ }
26
+ }),
27
+ });
12
28
  }
13
- });
29
+ }
14
30
  return data;
15
31
  }
16
32
  //# sourceMappingURL=sam.js.map
package/esm/sam.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAKA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAAqB,EAAE,CAAA;IACjC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}
1
+ {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;wBACb,OAAO;4BACL,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB,CAAA;oBACH,CAAC;yBAAM,CAAC;wBACN,qCAAqC;wBACrC,0CAA0C;wBAC1C,kCAAkC;wBAClC,OAAO;4BACL,GAAG,EAAE,CAAC;4BACN,KAAK,EAAE,SAAS;yBACjB,CAAA;oBACH,CAAC;gBACH,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
@@ -1 +1 @@
1
- {"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE;QACjC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;KAC9C;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
1
+ {"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QAClC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;IAC/C,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
package/esm/unzip.d.ts CHANGED
@@ -1,2 +1,3 @@
1
+ /// <reference types="node" />
1
2
  import { gunzipSync } from 'zlib';
2
3
  export { gunzipSync as unzip };
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/cram",
3
- "version": "1.7.4",
3
+ "version": "2.0.1",
4
4
  "description": "read CRAM files with pure Javascript",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/cram-js",
@@ -23,7 +23,7 @@
23
23
  "scripts": {
24
24
  "test": "jest",
25
25
  "lint": "eslint src test",
26
- "docs": "documentation readme --shallow src/indexedCramFile.js --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/craiIndex.js --section=CraiIndex; documentation readme --shallow errors.js '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/cramFile/record.js --section=CramRecord",
26
+ "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex; documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
27
27
  "prebuild": "npm run clean",
28
28
  "clean": "rimraf dist esm",
29
29
  "build:esm": "tsc --target es2018 --outDir esm",
@@ -50,34 +50,35 @@
50
50
  "long": "^4.0.0",
51
51
  "md5": "^2.2.1",
52
52
  "pako": "^1.0.4",
53
- "quick-lru": "^4.0.1"
53
+ "quick-lru": "^4.0.1",
54
+ "xz-decompress": "^0.2.1"
54
55
  },
55
56
  "devDependencies": {
56
57
  "@babel/plugin-transform-modules-commonjs": "^7.18.2",
57
58
  "@babel/preset-typescript": "^7.17.12",
58
- "@gmod/indexedfasta": "^2.0.2",
59
+ "@gmod/indexedfasta": "^2.1.0",
59
60
  "@types/buffer-crc32": "^0.2.2",
60
61
  "@types/jest": "^29.2.4",
61
62
  "@types/long": "^4.0.2",
62
63
  "@types/md5": "^2.3.2",
63
64
  "@types/pako": "^1.0.3",
64
- "@typescript-eslint/eslint-plugin": "^5.46.1",
65
- "@typescript-eslint/parser": "^5.46.1",
65
+ "@typescript-eslint/eslint-plugin": "^6.9.1",
66
+ "@typescript-eslint/parser": "^6.9.1",
66
67
  "buffer": "^6.0.3",
67
68
  "documentation": "^14.0.1",
68
69
  "eslint": "^8.30.0",
69
- "eslint-config-prettier": "^8.5.0",
70
+ "eslint-config-prettier": "^9.0.0",
70
71
  "eslint-plugin-import": "^2.25.4",
71
- "eslint-plugin-prettier": "^4.0.0",
72
+ "eslint-plugin-prettier": "^5.0.1",
72
73
  "glob": "^10.3.1",
73
74
  "jest": "^29.3.1",
74
75
  "mock-fs": "^5.2.0",
75
- "prettier": "^2.8.1",
76
+ "prettier": "^3.0.3",
76
77
  "rimraf": "^5.0.1",
77
78
  "ts-jest": "^29.0.3",
78
79
  "typescript": "^5.0.3",
79
80
  "url": "^0.11.0",
80
- "webpack": "5.88.1",
81
+ "webpack": "^5.89.0",
81
82
  "webpack-cli": "^5.0.1"
82
83
  },
83
84
  "publishConfig": {
@@ -6,7 +6,10 @@ import CramContainerCompressionScheme from './compressionScheme'
6
6
  import CramFile from '../file'
7
7
 
8
8
  export default class CramContainer {
9
- constructor(public file: CramFile, public filePosition: number) {}
9
+ constructor(
10
+ public file: CramFile,
11
+ public filePosition: number,
12
+ ) {}
10
13
 
11
14
  // memoize
12
15
  getHeader() {
@@ -1,9 +1,11 @@
1
1
  import { unzip } from '../unzip'
2
2
  import crc32 from 'buffer-crc32'
3
3
  import QuickLRU from 'quick-lru'
4
+ import htscodecs from '@jkbonfield/htscodecs'
5
+ import { Parser } from '@gmod/binary-parser'
4
6
  // @ts-expect-error
5
7
  import bzip2 from 'bzip2'
6
-
8
+ import { XzReadableStream } from 'xz-decompress'
7
9
  import { CramMalformedError, CramUnimplementedError } from '../errors'
8
10
  import ransuncompress from '../rans'
9
11
  import {
@@ -12,16 +14,24 @@ import {
12
14
  cramFileDefinition as cramFileDefinitionParser,
13
15
  getSectionParsers,
14
16
  } from './sectionParsers'
15
- import htscodecs from '@jkbonfield/htscodecs'
17
+
16
18
  import CramContainer from './container'
17
19
 
18
20
  import { open } from '../io'
19
21
  import { parseItem, tinyMemoize } from './util'
20
22
  import { parseHeaderText } from '../sam'
21
- import { Parser } from '@gmod/binary-parser'
22
23
  import CramRecord from './record'
23
24
  import { Filehandle } from './filehandle'
24
25
 
26
+ function bufferToStream(buf: Buffer) {
27
+ return new ReadableStream({
28
+ start(controller) {
29
+ controller.enqueue(buf)
30
+ controller.close()
31
+ },
32
+ })
33
+ }
34
+
25
35
  //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
26
36
  function getEndianness() {
27
37
  const uInt32 = new Uint32Array([0x11223344])
@@ -99,17 +109,6 @@ export default class CramFile {
99
109
  }
100
110
  }
101
111
 
102
- // toString() {
103
- // if (this.file.filename) {
104
- // return this.file.filename
105
- // }
106
- // if (this.file.url) {
107
- // return this.file.url
108
- // }
109
- //
110
- // return '(cram file)'
111
- // }
112
-
113
112
  // can just read this object like a filehandle
114
113
  read(
115
114
  buffer: Buffer,
@@ -247,9 +246,8 @@ export default class CramFile {
247
246
  let containerCount = 0
248
247
  let position = sectionParsers.cramFileDefinition.maxLength
249
248
  while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
250
- const currentHeader = await this.getContainerAtPosition(
251
- position,
252
- ).getHeader()
249
+ const currentHeader =
250
+ await this.getContainerAtPosition(position).getHeader()
253
251
  if (!currentHeader) {
254
252
  break
255
253
  }
@@ -319,7 +317,7 @@ export default class CramFile {
319
317
  return data
320
318
  }
321
319
 
322
- _uncompress(
320
+ async _uncompress(
323
321
  compressionMethod: CompressionMethod,
324
322
  inputBuffer: Buffer,
325
323
  outputBuffer: Buffer,
@@ -340,6 +338,12 @@ export default class CramFile {
340
338
  size -= chunk.length
341
339
  }
342
340
  } while (chunk != -1)
341
+ } else if (compressionMethod === 'lzma') {
342
+ const decompressedResponse = new Response(
343
+ new XzReadableStream(bufferToStream(inputBuffer)),
344
+ )
345
+ const ret = Buffer.from(await decompressedResponse.arrayBuffer())
346
+ ret.copy(outputBuffer)
343
347
  } else if (compressionMethod === 'rans') {
344
348
  ransuncompress(inputBuffer, outputBuffer)
345
349
  //htscodecs r4x8 is slower, but compatible.
@@ -386,7 +390,7 @@ export default class CramFile {
386
390
  blockContentPosition,
387
391
  )
388
392
 
389
- this._uncompress(
393
+ await this._uncompress(
390
394
  blockHeader.compressionMethod,
391
395
  compressedData,
392
396
  uncompressedData,
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors'
2
3
 
3
4
  import { TF_SHIFT } from './constants'
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { TF_SHIFT } from './constants'
2
3
  import Decoding from './decoding'
3
4
 
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors'
2
3
 
3
4
  import { RANS_BYTE_L } from './constants'
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors'
2
3
 
3
4
  import { TOTFREQ } from './constants'
@@ -1,3 +1,4 @@
1
+ //@ts-nocheck
1
2
  import { CramMalformedError } from '../errors'
2
3
 
3
4
  import Decoding from './decoding'
package/src/sam.ts CHANGED
@@ -1,20 +1,36 @@
1
- export type HeaderDataItem = {
2
- tag: string
3
- data: Array<{ tag: string; value: string }>
4
- }
5
-
6
- export function parseHeaderText(text: string): HeaderDataItem[] {
1
+ export function parseHeaderText(text: string) {
7
2
  const lines = text.split(/\r?\n/)
8
- const data: HeaderDataItem[] = []
9
- lines.forEach(line => {
3
+ const data: {
4
+ tag: string
5
+ data: {
6
+ tag: string
7
+ value: string | undefined
8
+ }[]
9
+ }[] = []
10
+ for (const line of lines) {
10
11
  const [tag, ...fields] = line.split(/\t/)
11
- const parsedFields = fields.map(f => {
12
- const [fieldTag, value] = f.split(':', 2)
13
- return { tag: fieldTag, value }
14
- })
15
12
  if (tag) {
16
- data.push({ tag: tag.substr(1), data: parsedFields })
13
+ data.push({
14
+ tag: tag.slice(1),
15
+ data: fields.map(f => {
16
+ const r = f.indexOf(':')
17
+ if (r !== -1) {
18
+ return {
19
+ tag: f.slice(0, r),
20
+ value: f.slice(r + 1),
21
+ }
22
+ } else {
23
+ // @CO lines are not comma separated.
24
+ // See "samtools view -H c2\#pad.3.0.cram"
25
+ // so, just store value tag itself
26
+ return {
27
+ tag: f,
28
+ value: undefined,
29
+ }
30
+ }
31
+ }),
32
+ })
17
33
  }
18
- })
34
+ }
19
35
  return data
20
36
  }
File without changes