@gmod/cram 2.0.4 → 3.0.0

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 (64) hide show
  1. package/CHANGELOG.md +10 -0
  2. package/dist/cram-bundle.js +1 -1
  3. package/dist/cramFile/codecs/byteArrayLength.js +1 -1
  4. package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
  5. package/dist/cramFile/codecs/external.js +1 -1
  6. package/dist/cramFile/codecs/external.js.map +1 -1
  7. package/dist/cramFile/codecs/huffman.js +2 -1
  8. package/dist/cramFile/codecs/huffman.js.map +1 -1
  9. package/dist/cramFile/container/compressionScheme.d.ts +0 -3
  10. package/dist/cramFile/container/compressionScheme.js +0 -4
  11. package/dist/cramFile/container/compressionScheme.js.map +1 -1
  12. package/dist/cramFile/container/index.d.ts +56 -3
  13. package/dist/cramFile/container/index.js +15 -9
  14. package/dist/cramFile/container/index.js.map +1 -1
  15. package/dist/cramFile/file.d.ts +24 -59
  16. package/dist/cramFile/file.js +21 -26
  17. package/dist/cramFile/file.js.map +1 -1
  18. package/dist/cramFile/record.d.ts +1 -1
  19. package/dist/cramFile/sectionParsers.d.ts +195 -48
  20. package/dist/cramFile/sectionParsers.js +621 -303
  21. package/dist/cramFile/sectionParsers.js.map +1 -1
  22. package/dist/cramFile/slice/index.d.ts +23 -1
  23. package/dist/cramFile/slice/index.js +9 -6
  24. package/dist/cramFile/slice/index.js.map +1 -1
  25. package/dist/cramFile/util.d.ts +6 -4
  26. package/dist/cramFile/util.js +88 -6
  27. package/dist/cramFile/util.js.map +1 -1
  28. package/esm/cramFile/codecs/byteArrayLength.js +1 -1
  29. package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
  30. package/esm/cramFile/codecs/external.js +1 -1
  31. package/esm/cramFile/codecs/external.js.map +1 -1
  32. package/esm/cramFile/codecs/huffman.js +2 -1
  33. package/esm/cramFile/codecs/huffman.js.map +1 -1
  34. package/esm/cramFile/container/compressionScheme.d.ts +0 -3
  35. package/esm/cramFile/container/compressionScheme.js +0 -4
  36. package/esm/cramFile/container/compressionScheme.js.map +1 -1
  37. package/esm/cramFile/container/index.d.ts +56 -3
  38. package/esm/cramFile/container/index.js +15 -9
  39. package/esm/cramFile/container/index.js.map +1 -1
  40. package/esm/cramFile/file.d.ts +24 -59
  41. package/esm/cramFile/file.js +22 -25
  42. package/esm/cramFile/file.js.map +1 -1
  43. package/esm/cramFile/record.d.ts +1 -1
  44. package/esm/cramFile/sectionParsers.d.ts +195 -48
  45. package/esm/cramFile/sectionParsers.js +620 -303
  46. package/esm/cramFile/sectionParsers.js.map +1 -1
  47. package/esm/cramFile/slice/index.d.ts +23 -1
  48. package/esm/cramFile/slice/index.js +10 -7
  49. package/esm/cramFile/slice/index.js.map +1 -1
  50. package/esm/cramFile/util.d.ts +6 -4
  51. package/esm/cramFile/util.js +87 -6
  52. package/esm/cramFile/util.js.map +1 -1
  53. package/package.json +7 -8
  54. package/src/cramFile/codecs/byteArrayLength.ts +1 -2
  55. package/src/cramFile/codecs/external.ts +1 -1
  56. package/src/cramFile/codecs/huffman.ts +2 -1
  57. package/src/cramFile/container/compressionScheme.ts +1 -8
  58. package/src/cramFile/container/index.ts +21 -10
  59. package/src/cramFile/file.ts +28 -43
  60. package/src/cramFile/record.ts +1 -1
  61. package/src/cramFile/sectionParsers.ts +668 -390
  62. package/src/cramFile/slice/index.ts +11 -5
  63. package/src/cramFile/util.ts +90 -91
  64. package/src/typings/binary-parser.d.ts +0 -44
@@ -2,23 +2,24 @@ import { CramMalformedError } from '../../errors';
2
2
  import { itf8Size, parseItem, tinyMemoize } from '../util';
3
3
  import CramSlice from '../slice';
4
4
  import CramContainerCompressionScheme from './compressionScheme';
5
+ import { getSectionParsers } from '../sectionParsers';
5
6
  export default class CramContainer {
6
7
  constructor(file, filePosition) {
7
8
  this.file = file;
8
9
  this.filePosition = filePosition;
9
10
  }
10
- // memoize
11
11
  getHeader() {
12
12
  return this._readContainerHeader(this.filePosition);
13
13
  }
14
- // memoize
15
14
  async getCompressionHeaderBlock() {
16
15
  const containerHeader = await this.getHeader();
17
- // if there are no records in the container, there will be no compression header
18
- if (!containerHeader.numRecords) {
16
+ // if there are no records in the container, there will be no compression
17
+ // header
18
+ if (!(containerHeader === null || containerHeader === void 0 ? void 0 : containerHeader.numRecords)) {
19
19
  return null;
20
20
  }
21
- const sectionParsers = await this.file.getSectionParsers();
21
+ const { majorVersion } = await this.file.getDefinition();
22
+ const sectionParsers = getSectionParsers(majorVersion);
22
23
  const block = await this.getFirstBlock();
23
24
  if (block === undefined) {
24
25
  return undefined;
@@ -34,10 +35,13 @@ export default class CramContainer {
34
35
  }
35
36
  async getFirstBlock() {
36
37
  const containerHeader = await this.getHeader();
38
+ if (!containerHeader) {
39
+ return undefined;
40
+ }
37
41
  return this.file.readBlock(containerHeader._endPosition);
38
42
  }
39
- // parses the compression header data into a CramContainerCompressionScheme object
40
- // memoize
43
+ // parses the compression header data into a CramContainerCompressionScheme
44
+ // object
41
45
  async getCompressionScheme() {
42
46
  const header = await this.getCompressionHeaderBlock();
43
47
  if (!header) {
@@ -51,10 +55,12 @@ export default class CramContainer {
51
55
  return new CramSlice(this, slicePosition, sliceSize);
52
56
  }
53
57
  async _readContainerHeader(position) {
54
- const sectionParsers = await this.file.getSectionParsers();
58
+ const { majorVersion } = await this.file.getDefinition();
59
+ const sectionParsers = getSectionParsers(majorVersion);
55
60
  const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
56
61
  const { size: fileSize } = await this.file.stat();
57
62
  if (position >= fileSize) {
63
+ console.warn(`position:${position}>=fileSize:${fileSize} in cram container`);
58
64
  return undefined;
59
65
  }
60
66
  // parse the container header. do it in 2 pieces because you cannot tell
@@ -64,7 +70,7 @@ export default class CramContainer {
64
70
  const header1 = parseItem(bytes1, cramContainerHeader1.parser);
65
71
  const numLandmarksSize = itf8Size(header1.numLandmarks);
66
72
  if (position + header1.length >= fileSize) {
67
- console.warn(`${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
73
+ console.warn(`container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
68
74
  return undefined;
69
75
  }
70
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  const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAGhE,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,UAAU;IACV,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,gFAAgF;QAChF,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE,CAAC;YAChC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;QAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,yDAAyD,CACnG,CAAA;QACH,CAAC;QACD,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,kFAAkF;IAClF,UAAU;IACV,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,iBAAiB,EAAE,CAAA;QAC1D,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;QACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACzE,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAQ,CAAA;QACrE,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,OAAO,CAAC,IAAI,CACV,GAAG,IAAI,CAAC,IAAI,yBAAyB,QAAQ,4CAA4C,OAAO,CAAC,MAAM,yEAAyE,CACjL,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;QACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,CAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,UAAU,CAAA,EAAE,CAAC;YACjC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,yDAAyD,CACnG,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;YACrB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,CAAC,IAAI,CACV,YAAY,QAAQ,cAAc,QAAQ,oBAAoB,CAC/D,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;QACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACzE,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,OAAO,CAAC,IAAI,CACV,uBAAuB,QAAQ,4CAA4C,OAAO,CAAC,MAAM,yEAAyE,CACnK,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;QACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}
@@ -1,5 +1,4 @@
1
1
  import QuickLRU from 'quick-lru';
2
- import { Parser } from '@gmod/binary-parser';
3
2
  import { BlockHeader, CompressionMethod } from './sectionParsers';
4
3
  import CramContainer from './container';
5
4
  import CramRecord from './record';
@@ -38,7 +37,12 @@ export default class CramFile {
38
37
  buffer: Buffer;
39
38
  }>;
40
39
  stat(): Promise<import("generic-filehandle").Stats>;
41
- getDefinition(): Promise<any>;
40
+ getDefinition(): Promise<{
41
+ magic: string;
42
+ majorVersion: number;
43
+ minorVersion: number;
44
+ fileId: string;
45
+ }>;
42
46
  getSamHeader(): Promise<{
43
47
  tag: string;
44
48
  data: {
@@ -47,60 +51,6 @@ export default class CramFile {
47
51
  }[];
48
52
  }[]>;
49
53
  getHeaderText(): Promise<string | undefined>;
50
- getSectionParsers(): Promise<{
51
- cramFileDefinition: {
52
- parser: Parser<{
53
- magic: string;
54
- majorVersion: number;
55
- minorVersion: number;
56
- fileId: string;
57
- }>;
58
- maxLength: number;
59
- };
60
- cramContainerHeader1: {
61
- parser: Parser<{
62
- length: number;
63
- refSeqId: number;
64
- refSeqStart: number;
65
- alignmentSpan: number;
66
- numRecords: number;
67
- recordCounter: number;
68
- numBases: number;
69
- numBlocks: number;
70
- numLandmarks: number;
71
- }>;
72
- maxLength: number;
73
- };
74
- cramContainerHeader2: {
75
- parser: Parser<{
76
- numLandmarks: number;
77
- landmarks: number[];
78
- crc32: number;
79
- }>;
80
- maxLength: (x: number) => number;
81
- };
82
- cramBlockHeader: {
83
- parser: Parser<BlockHeader>;
84
- maxLength: number;
85
- };
86
- cramBlockCrc32: {
87
- parser: Parser<{
88
- crc32: number;
89
- }>;
90
- maxLength: number;
91
- };
92
- cramCompressionHeader: {
93
- parser: Parser<import("./sectionParsers").CramCompressionHeader>;
94
- };
95
- cramMappedSliceHeader: {
96
- parser: Parser<import("./sectionParsers").MappedSliceHeader>;
97
- maxLength: (numContentIds: number) => number;
98
- };
99
- cramUnmappedSliceHeader: {
100
- parser: Parser<import("./sectionParsers").UnmappedSliceHeader>;
101
- maxLength: (numContentIds: number) => number;
102
- };
103
- }>;
104
54
  getContainerById(containerNumber: number): Promise<CramContainer | undefined>;
105
55
  checkCrc32(position: number, length: number, recordedCrc32: number, description: string): Promise<void>;
106
56
  /**
@@ -108,11 +58,26 @@ export default class CramFile {
108
58
  */
109
59
  containerCount(): Promise<number | undefined>;
110
60
  getContainerAtPosition(position: number): CramContainer;
111
- readBlockHeader(position: number): Promise<import("./util").ParsedItem<BlockHeader> | undefined>;
61
+ readBlockHeader(position: number): Promise<({
62
+ uncompressedSize: number;
63
+ compressedSize: number;
64
+ contentId: number;
65
+ contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
66
+ compressionMethod: CompressionMethod;
67
+ } & {
68
+ _endPosition: number;
69
+ _size: number;
70
+ }) | undefined>;
112
71
  _parseSection<T>(section: {
113
- parser: Parser<T>;
114
72
  maxLength: number;
115
- }, position: number, size?: number, preReadBuffer?: undefined): Promise<import("./util").ParsedItem<T> | undefined>;
73
+ parser: (buffer: Buffer, offset: number) => {
74
+ offset: number;
75
+ value: T;
76
+ };
77
+ }, position: number, size?: number, preReadBuffer?: undefined): Promise<(T & {
78
+ _endPosition: number;
79
+ _size: number;
80
+ }) | undefined>;
116
81
  _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): Promise<void>;
117
82
  readBlock(position: number): Promise<CramFileBlock | undefined>;
118
83
  }
@@ -7,7 +7,7 @@ import bzip2 from 'bzip2';
7
7
  import { XzReadableStream } from 'xz-decompress';
8
8
  import { CramMalformedError, CramUnimplementedError } from '../errors';
9
9
  import ransuncompress from '../rans';
10
- import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';
10
+ import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
11
11
  import CramContainer from './container';
12
12
  import { open } from '../io';
13
13
  import { parseItem, tinyMemoize } from './util';
@@ -20,18 +20,18 @@ function bufferToStream(buf) {
20
20
  },
21
21
  });
22
22
  }
23
- //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
23
+ // source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
24
24
  function getEndianness() {
25
25
  const uInt32 = new Uint32Array([0x11223344]);
26
26
  const uInt8 = new Uint8Array(uInt32.buffer);
27
27
  if (uInt8[0] === 0x44) {
28
- return 0; //little-endian
28
+ return 0; // little-endian
29
29
  }
30
30
  else if (uInt8[0] === 0x11) {
31
- return 1; //big-endian
31
+ return 1; // big-endian
32
32
  }
33
33
  else {
34
- return 2; //mixed-endian?
34
+ return 2; // mixed-endian?
35
35
  }
36
36
  }
37
37
  export default class CramFile {
@@ -65,10 +65,10 @@ export default class CramFile {
65
65
  }
66
66
  // memoized
67
67
  async getDefinition() {
68
- const headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength);
69
- await this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0);
70
- const definition = cramFileDefinitionParser.parser.parse(headbytes)
71
- .result;
68
+ const { maxLength, parser } = cramFileDefinition();
69
+ const headbytes = Buffer.allocUnsafe(maxLength);
70
+ await this.file.read(headbytes, 0, maxLength, 0);
71
+ const definition = parser(headbytes).value;
72
72
  if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
73
73
  throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
74
74
  }
@@ -99,19 +99,15 @@ export default class CramFile {
99
99
  await this.getSamHeader();
100
100
  return this.header;
101
101
  }
102
- // memoize
103
- async getSectionParsers() {
104
- const { majorVersion } = await this.getDefinition();
105
- return getSectionParsers(majorVersion);
106
- }
107
102
  async getContainerById(containerNumber) {
108
- const sectionParsers = await this.getSectionParsers();
103
+ const { majorVersion } = await this.getDefinition();
104
+ const sectionParsers = getSectionParsers(majorVersion);
109
105
  let position = sectionParsers.cramFileDefinition.maxLength;
110
106
  const { size: fileSize } = await this.file.stat();
111
107
  const { cramContainerHeader1 } = sectionParsers;
112
108
  // skip with a series of reads to the proper container
113
109
  let currentContainer;
114
- for (let i = 0; i <= containerNumber; i += 1) {
110
+ for (let i = 0; i <= containerNumber; i++) {
115
111
  // if we are about to go off the end of the file
116
112
  // and have not found that container, it does not exist
117
113
  if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
@@ -122,13 +118,12 @@ export default class CramFile {
122
118
  if (!currentHeader) {
123
119
  throw new CramMalformedError(`container ${containerNumber} not found in file`);
124
120
  }
125
- // if this is the first container, read all the blocks in the
126
- // container to determine its length, because we cannot trust
127
- // the container header's given length due to a bug somewhere
128
- // in htslib
121
+ // if this is the first container, read all the blocks in the container
122
+ // to determine its length, because we cannot trust the container
123
+ // header's given length due to a bug somewhere in htslib
129
124
  if (i === 0) {
130
125
  position = currentHeader._endPosition;
131
- for (let j = 0; j < currentHeader.numBlocks; j += 1) {
126
+ for (let j = 0; j < currentHeader.numBlocks; j++) {
132
127
  const block = await this.readBlock(position);
133
128
  if (block === undefined) {
134
129
  return undefined;
@@ -155,7 +150,8 @@ export default class CramFile {
155
150
  * @returns {Promise[number]} the number of containers in the file
156
151
  */
157
152
  async containerCount() {
158
- const sectionParsers = await this.getSectionParsers();
153
+ const { majorVersion } = await this.getDefinition();
154
+ const sectionParsers = getSectionParsers(majorVersion);
159
155
  const { size: fileSize } = await this.file.stat();
160
156
  const { cramContainerHeader1 } = sectionParsers;
161
157
  let containerCount = 0;
@@ -170,7 +166,7 @@ export default class CramFile {
170
166
  // header's given length due to a bug somewhere in htslib
171
167
  if (containerCount === 0) {
172
168
  position = currentHeader._endPosition;
173
- for (let j = 0; j < currentHeader.numBlocks; j += 1) {
169
+ for (let j = 0; j < currentHeader.numBlocks; j++) {
174
170
  const block = await this.readBlock(position);
175
171
  if (block === undefined) {
176
172
  return undefined;
@@ -190,7 +186,8 @@ export default class CramFile {
190
186
  return new CramContainer(this, position);
191
187
  }
192
188
  async readBlockHeader(position) {
193
- const sectionParsers = await this.getSectionParsers();
189
+ const { majorVersion } = await this.getDefinition();
190
+ const sectionParsers = getSectionParsers(majorVersion);
194
191
  const { cramBlockHeader } = sectionParsers;
195
192
  const { size: fileSize } = await this.file.stat();
196
193
  if (position + cramBlockHeader.maxLength >= fileSize) {
@@ -266,7 +263,7 @@ export default class CramFile {
266
263
  }
267
264
  async readBlock(position) {
268
265
  const { majorVersion } = await this.getDefinition();
269
- const sectionParsers = await this.getSectionParsers();
266
+ const sectionParsers = getSectionParsers(majorVersion);
270
267
  const blockHeader = await this.readBlockHeader(position);
271
268
  if (blockHeader === undefined) {
272
269
  return undefined;
@@ -1 +1 @@
1
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@@ -1,5 +1,5 @@
1
1
  import CramContainerCompressionScheme from './container/compressionScheme';
2
- import decodeRecord from './slice/decodeRecord';
2
+ import type decodeRecord from './slice/decodeRecord';
3
3
  export interface RefRegion {
4
4
  start: number;
5
5
  end: number;