@gmod/tabix 1.5.10 → 1.5.12

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Files changed (54) hide show
  1. package/CHANGELOG.md +15 -5
  2. package/dist/chunk.d.ts +0 -6
  3. package/dist/chunk.js +1 -6
  4. package/dist/chunk.js.map +1 -1
  5. package/dist/csi.d.ts +7 -16
  6. package/dist/csi.js +4 -7
  7. package/dist/csi.js.map +1 -1
  8. package/dist/index.d.ts +3 -4
  9. package/dist/index.js +7 -7
  10. package/dist/index.js.map +1 -1
  11. package/dist/indexFile.d.ts +2 -6
  12. package/dist/indexFile.js +4 -3
  13. package/dist/indexFile.js.map +1 -1
  14. package/dist/tabixIndexedFile.d.ts +3 -4
  15. package/dist/tabixIndexedFile.js +27 -48
  16. package/dist/tabixIndexedFile.js.map +1 -1
  17. package/dist/tbi.d.ts +4 -9
  18. package/dist/tbi.js +2 -3
  19. package/dist/tbi.js.map +1 -1
  20. package/dist/util.js +1 -6
  21. package/dist/util.js.map +1 -1
  22. package/dist/virtualOffset.d.ts +1 -0
  23. package/dist/virtualOffset.js.map +1 -1
  24. package/esm/chunk.d.ts +0 -6
  25. package/esm/chunk.js +1 -6
  26. package/esm/chunk.js.map +1 -1
  27. package/esm/csi.d.ts +7 -16
  28. package/esm/csi.js +4 -5
  29. package/esm/csi.js.map +1 -1
  30. package/esm/index.d.ts +3 -4
  31. package/esm/index.js +3 -4
  32. package/esm/index.js.map +1 -1
  33. package/esm/indexFile.d.ts +2 -6
  34. package/esm/indexFile.js +4 -3
  35. package/esm/indexFile.js.map +1 -1
  36. package/esm/tabixIndexedFile.d.ts +3 -4
  37. package/esm/tabixIndexedFile.js +26 -47
  38. package/esm/tabixIndexedFile.js.map +1 -1
  39. package/esm/tbi.d.ts +4 -9
  40. package/esm/tbi.js +2 -3
  41. package/esm/tbi.js.map +1 -1
  42. package/esm/util.js +1 -6
  43. package/esm/util.js.map +1 -1
  44. package/esm/virtualOffset.d.ts +1 -0
  45. package/esm/virtualOffset.js.map +1 -1
  46. package/package.json +16 -16
  47. package/src/chunk.ts +1 -6
  48. package/src/csi.ts +7 -7
  49. package/src/index.ts +3 -5
  50. package/src/indexFile.ts +4 -4
  51. package/src/tabixIndexedFile.ts +33 -52
  52. package/src/tbi.ts +6 -6
  53. package/src/util.ts +1 -5
  54. package/src/virtualOffset.ts +1 -0
package/CHANGELOG.md CHANGED
@@ -1,18 +1,28 @@
1
- ## [1.5.10](https://github.com/GMOD/tabix-js/compare/v1.5.9...v1.5.10) (2023-03-30)
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+ ## [1.5.12](https://github.com/GMOD/tabix-js/compare/v1.5.11...v1.5.12) (2024-01-09)
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2
 
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- - Remove stray console.log
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+ - Add missing abort signal to the abortable-promise-cache fetch for tabix chunks
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+ (#143)
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- ## [1.5.9](https://github.com/GMOD/tabix-js/compare/v1.5.8...v1.5.9) (2023-03-27)
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+ ## [1.5.11](https://github.com/GMOD/tabix-js/compare/v1.5.10...v1.5.11) (2023-07-10)
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+ ### Features
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11
 
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+ - explicit buffer import ([#140](https://github.com/GMOD/tabix-js/issues/140))
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+ ([fb80ac8](https://github.com/GMOD/tabix-js/commit/fb80ac813a0d40255556de3ab28dae1940f59c1d))
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14
 
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- - Revert the Buffer::slice -> Buffer::subarray change due to use with polyfills
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+ * Add explicit buffer import
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16
 
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- ## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
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+ ## [1.5.10](https://github.com/GMOD/tabix-js/compare/v1.5.9...v1.5.10) (2023-03-30)
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18
 
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+ - Remove stray console.log
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+
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+ ## [1.5.9](https://github.com/GMOD/tabix-js/compare/v1.5.8...v1.5.9) (2023-03-27)
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+ - Revert the Buffer::slice -> Buffer::subarray change due to use with polyfills
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+
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+ ## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
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  - Make yieldTime optional
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package/dist/chunk.d.ts CHANGED
@@ -4,12 +4,6 @@ export default class Chunk {
4
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  maxv: VirtualOffset;
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  bin: number;
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  _fetchedSize?: number;
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- /**
8
- * @param {VirtualOffset} minv
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- * @param {VirtualOffset} maxv
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- * @param {number} bin
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- * @param {number} [fetchedSize]
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- */
13
7
  constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
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8
  toUniqueString(): string;
15
9
  toString(): string;
package/dist/chunk.js CHANGED
@@ -2,12 +2,6 @@
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2
  Object.defineProperty(exports, "__esModule", { value: true });
3
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  // little class representing a chunk in the index
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  class Chunk {
5
- /**
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- * @param {VirtualOffset} minv
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- * @param {VirtualOffset} maxv
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- * @param {number} bin
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- * @param {number} [fetchedSize]
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- */
11
5
  constructor(minv, maxv, bin, fetchedSize = undefined) {
12
6
  this.minv = minv;
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7
  this.maxv = maxv;
@@ -15,6 +9,7 @@ class Chunk {
15
9
  this._fetchedSize = fetchedSize;
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  }
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  toUniqueString() {
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+ // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
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  return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
19
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  }
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  toString() {
package/dist/chunk.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB;;;;;OAKG;IACH,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAhDD,wBAgDC"}
1
+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,4EAA4E;QAC5E,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AA3CD,wBA2CC"}
package/dist/csi.d.ts CHANGED
@@ -1,4 +1,5 @@
1
1
  /// <reference types="node" />
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+ import { Buffer } from 'buffer';
2
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  import VirtualOffset from './virtualOffset';
3
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  import Chunk from './chunk';
4
5
  import IndexFile, { Options } from './indexFile';
@@ -8,12 +9,10 @@ export default class CSI extends IndexFile {
8
9
  private minShift;
9
10
  constructor(args: any);
10
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  lineCount(refName: string, opts?: Options): Promise<number>;
11
- indexCov(): Promise<void>;
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+ indexCov(): void;
12
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  parseAuxData(bytes: Buffer, offset: number): {
13
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  refIdToName: string[];
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- refNameToId: {
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- [key: string]: number;
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- };
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+ refNameToId: Record<string, number>;
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  skipLines: number;
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  metaChar: string | null;
19
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  columnNumbers: {
@@ -25,9 +24,7 @@ export default class CSI extends IndexFile {
25
24
  coordinateType: string;
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  };
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  _parseNameBytes(namesBytes: Buffer): {
28
- refNameToId: {
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- [key: string]: number;
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- };
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+ refNameToId: Record<string, number>;
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28
  refIdToName: string[];
32
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  };
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  _parse(opts?: Options): Promise<{
@@ -37,9 +34,7 @@ export default class CSI extends IndexFile {
37
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  firstDataLine: VirtualOffset | undefined;
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  csiVersion: number;
39
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  indices: {
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- binIndex: {
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- [key: string]: Chunk[];
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- };
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+ binIndex: Record<string, Chunk[]>;
43
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  stats: {
44
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  lineCount: number;
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  } | undefined;
@@ -48,9 +43,7 @@ export default class CSI extends IndexFile {
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  maxBinNumber: number;
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  maxRefLength: number;
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  refIdToName: string[];
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- refNameToId: {
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- [key: string]: number;
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- };
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+ refNameToId: Record<string, number>;
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47
  skipLines: number;
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  metaChar: string | null;
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  columnNumbers: {
@@ -67,9 +60,7 @@ export default class CSI extends IndexFile {
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  firstDataLine: VirtualOffset | undefined;
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  csiVersion: number;
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  indices: {
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- binIndex: {
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- [key: string]: Chunk[];
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- };
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+ binIndex: Record<string, Chunk[]>;
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  stats: {
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  lineCount: number;
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  } | undefined;
package/dist/csi.js CHANGED
@@ -75,9 +75,7 @@ class CSI extends indexFile_1.default {
75
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  });
76
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  }
77
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  indexCov() {
78
- return __awaiter(this, void 0, void 0, function* () {
79
- throw new Error('CSI indexes do not support indexcov');
80
- });
78
+ throw new Error('CSI indexes do not support indexcov');
81
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  }
82
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  parseAuxData(bytes, offset) {
83
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  const formatFlags = bytes.readInt32LE(offset);
@@ -128,7 +126,7 @@ class CSI extends indexFile_1.default {
128
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  // fetch and parse the index
129
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  _parse(opts = {}) {
130
128
  return __awaiter(this, void 0, void 0, function* () {
131
- const bytes = yield (0, bgzf_filehandle_1.unzip)((yield this.filehandle.readFile(opts)));
129
+ const bytes = yield (0, bgzf_filehandle_1.unzip)(yield this.filehandle.readFile(opts));
132
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  // check TBI magic numbers
133
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  let csiVersion;
134
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  if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
@@ -222,9 +220,8 @@ class CSI extends indexFile_1.default {
222
220
  for (const [start, end] of overlappingBins) {
223
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  for (let bin = start; bin <= end; bin++) {
224
222
  if (ba.binIndex[bin]) {
225
- const binChunks = ba.binIndex[bin];
226
- for (let c = 0; c < binChunks.length; ++c) {
227
- chunks.push(new chunk_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
223
+ for (const c of ba.binIndex[bin]) {
224
+ chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
228
225
  }
229
226
  }
230
227
  }
package/dist/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/index.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- import TabixIndexedFile from './tabixIndexedFile';
2
- import TBI from './tbi';
3
- import CSI from './csi';
4
- export { TabixIndexedFile, TBI, CSI };
1
+ export { default as TabixIndexedFile } from './tabixIndexedFile';
2
+ export { default as CSI } from './csi';
3
+ export { default as TBI } from './tbi';
package/dist/index.js CHANGED
@@ -3,11 +3,11 @@ 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.CSI = exports.TBI = exports.TabixIndexedFile = void 0;
7
- const tabixIndexedFile_1 = __importDefault(require("./tabixIndexedFile"));
8
- exports.TabixIndexedFile = tabixIndexedFile_1.default;
9
- const tbi_1 = __importDefault(require("./tbi"));
10
- exports.TBI = tbi_1.default;
11
- const csi_1 = __importDefault(require("./csi"));
12
- exports.CSI = csi_1.default;
6
+ exports.TBI = exports.CSI = exports.TabixIndexedFile = void 0;
7
+ var tabixIndexedFile_1 = require("./tabixIndexedFile");
8
+ Object.defineProperty(exports, "TabixIndexedFile", { enumerable: true, get: function () { return __importDefault(tabixIndexedFile_1).default; } });
9
+ var csi_1 = require("./csi");
10
+ Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_1).default; } });
11
+ var tbi_1 = require("./tbi");
12
+ Object.defineProperty(exports, "TBI", { enumerable: true, get: function () { return __importDefault(tbi_1).default; } });
13
13
  //# sourceMappingURL=index.js.map
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAAiD;AAIxC,2BAJF,0BAAgB,CAIE;AAHzB,gDAAuB;AAGI,cAHpB,aAAG,CAGoB;AAF9B,gDAAuB;AAES,cAFzB,aAAG,CAEyB"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,uDAAgE;AAAvD,qIAAA,OAAO,OAAoB;AACpC,6BAAsC;AAA7B,2GAAA,OAAO,OAAO;AACvB,6BAAsC;AAA7B,2GAAA,OAAO,OAAO"}
package/dist/indexFile.d.ts CHANGED
@@ -6,9 +6,7 @@ export interface Options {
6
6
  signal?: AbortSignal;
7
7
  }
8
8
  export interface IndexData {
9
- refNameToId: {
10
- [key: string]: number;
11
- };
9
+ refNameToId: Record<string, number>;
12
10
  refIdToName: string[];
13
11
  metaChar: string | null;
14
12
  columnNumbers: {
@@ -32,9 +30,7 @@ export default abstract class IndexFile {
32
30
  protected abstract _parse(opts: Options): Promise<IndexData>;
33
31
  getMetadata(opts?: Options): Promise<{
34
32
  [key: string]: any;
35
- refNameToId: {
36
- [key: string]: number;
37
- };
33
+ refNameToId: Record<string, number>;
38
34
  refIdToName: string[];
39
35
  metaChar: string | null;
40
36
  columnNumbers: {
package/dist/indexFile.js CHANGED
@@ -27,8 +27,7 @@ class IndexFile {
27
27
  }
28
28
  getMetadata(opts = {}) {
29
29
  return __awaiter(this, void 0, void 0, function* () {
30
- // eslint-disable-next-line @typescript-eslint/no-unused-vars
31
- const _a = yield this.parse(opts), { indices } = _a, rest = __rest(_a, ["indices"]);
30
+ const _a = yield this.parse(opts), { indices: _indices } = _a, rest = __rest(_a, ["indices"]);
32
31
  return rest;
33
32
  });
34
33
  }
@@ -54,8 +53,10 @@ class IndexFile {
54
53
  });
55
54
  }
56
55
  hasRefSeq(seqId, opts = {}) {
56
+ var _a;
57
57
  return __awaiter(this, void 0, void 0, function* () {
58
- return !!((yield this.parse(opts)).indices[seqId] || {}).binIndex;
58
+ const idx = yield this.parse(opts);
59
+ return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
59
60
  });
60
61
  }
61
62
  }
package/dist/indexFile.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;AAoBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMY,WAAW,CAAC,OAAgB,EAAE;;YACzC,6DAA6D;YAC7D,MAAM,KAAuB,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAA7C,EAAE,OAAO,OAAoC,EAA/B,IAAI,cAAlB,WAAoB,CAAyB,CAAA;YACnD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE;YACd,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;SACf;aAAM;YACL,OAAO,aAAa,CAAA;SACrB;IACH,CAAC;IAEK,KAAK,CAAC,OAAgB,EAAE;;YAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;YAC/C,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;QACnE,CAAC;KAAA;CACF;AA3DD,4BA2DC"}
1
+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;AAoBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMY,WAAW,CAAC,OAAgB,EAAE;;YACzC,MAAM,KAAiC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAvD,EAAE,OAAO,EAAE,QAAQ,OAAoC,EAA/B,IAAI,cAA5B,WAA8B,CAAyB,CAAA;YAC7D,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAEK,KAAK,CAAC,OAAgB,EAAE;;YAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;gBACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;;YAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;;KACtC;CACF;AA3DD,4BA2DC"}
package/dist/tabixIndexedFile.d.ts CHANGED
@@ -1,4 +1,5 @@
1
1
  /// <reference types="node" />
2
+ import { Buffer } from 'buffer';
2
3
  import { GenericFilehandle } from 'generic-filehandle';
3
4
  import { Options, IndexData } from './indexFile';
4
5
  import Chunk from './chunk';
@@ -47,12 +48,10 @@ export default class TabixIndexedFile {
47
48
  * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
48
49
  * @returns promise that is resolved when the whole read is finished, rejected on error
49
50
  */
50
- getLines(refName: string, start: number, end: number, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
51
+ getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
51
52
  getMetadata(opts?: Options): Promise<{
52
53
  [key: string]: any;
53
- refNameToId: {
54
- [key: string]: number;
55
- };
54
+ refNameToId: Record<string, number>;
56
55
  refIdToName: string[];
57
56
  metaChar: string | null;
58
57
  columnNumbers: {
package/dist/tabixIndexedFile.js CHANGED
@@ -14,12 +14,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
14
14
  Object.defineProperty(exports, "__esModule", { value: true });
15
15
  const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
16
16
  const quick_lru_1 = __importDefault(require("quick-lru"));
17
+ const buffer_1 = require("buffer");
17
18
  const generic_filehandle_1 = require("generic-filehandle");
18
19
  const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
19
20
  const util_1 = require("./util");
20
21
  const tbi_1 = __importDefault(require("./tbi"));
21
22
  const csi_1 = __importDefault(require("./csi"));
22
- const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
23
+ const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
23
24
  function timeout(time) {
24
25
  return new Promise(resolve => setTimeout(resolve, time));
25
26
  }
@@ -95,12 +96,13 @@ class TabixIndexedFile {
95
96
  * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
96
97
  * @returns promise that is resolved when the whole read is finished, rejected on error
97
98
  */
98
- getLines(refName, start, end, opts) {
99
+ getLines(refName, s, e, opts) {
100
+ var _a;
99
101
  return __awaiter(this, void 0, void 0, function* () {
100
102
  let signal;
101
103
  let options = {};
102
104
  let callback;
103
- if (typeof opts === 'undefined') {
105
+ if (opts === undefined) {
104
106
  throw new TypeError('line callback must be provided');
105
107
  }
106
108
  if (typeof opts === 'function') {
@@ -118,12 +120,8 @@ class TabixIndexedFile {
118
120
  }
119
121
  const metadata = yield this.index.getMetadata(options);
120
122
  (0, util_1.checkAbortSignal)(signal);
121
- if (!start) {
122
- start = 0;
123
- }
124
- if (!end) {
125
- end = metadata.maxRefLength;
126
- }
123
+ const start = s !== null && s !== void 0 ? s : 0;
124
+ const end = e !== null && e !== void 0 ? e : metadata.maxRefLength;
127
125
  if (!(start <= end)) {
128
126
  throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
129
127
  }
@@ -134,18 +132,17 @@ class TabixIndexedFile {
134
132
  (0, util_1.checkAbortSignal)(signal);
135
133
  // check the chunks for any that are over the size limit. if
136
134
  // any are, don't fetch any of them
137
- for (let i = 0; i < chunks.length; i += 1) {
138
- const size = chunks[i].fetchedSize();
135
+ for (const chunk of chunks) {
136
+ const size = chunk.fetchedSize();
139
137
  if (size > this.chunkSizeLimit) {
140
138
  throw new Error(`Too much data. Chunk size ${size.toLocaleString()} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit.toLocaleString()}.`);
141
139
  }
142
140
  }
143
141
  // now go through each chunk and parse and filter the lines out of it
144
142
  let last = Date.now();
145
- for (let chunkNum = 0; chunkNum < chunks.length; chunkNum += 1) {
143
+ for (const c of chunks) {
146
144
  let previousStartCoordinate;
147
- const c = chunks[chunkNum];
148
- const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c);
145
+ const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c, signal);
149
146
  (0, util_1.checkAbortSignal)(signal);
150
147
  let blockStart = 0;
151
148
  let pos = 0;
@@ -155,7 +152,7 @@ class TabixIndexedFile {
155
152
  break;
156
153
  }
157
154
  const b = buffer.slice(blockStart, n);
158
- const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
155
+ const line = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _a !== void 0 ? _a : b.toString();
159
156
  if (dpositions) {
160
157
  while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
161
158
  pos--;
@@ -219,17 +216,8 @@ class TabixIndexedFile {
219
216
  const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
220
217
  // TODO: what if we don't have a firstDataLine, and the header
221
218
  // actually takes up more than one block? this case is not covered here
222
- let bytes = yield this._readRegion(0, maxFetch, opts);
223
- (0, util_1.checkAbortSignal)(opts.signal);
224
- try {
225
- bytes = yield (0, bgzf_filehandle_1.unzip)(bytes);
226
- }
227
- catch (e) {
228
- console.error(e);
229
- throw new Error(
230
- //@ts-ignore
231
- `error decompressing block ${e.code} at 0 (length ${maxFetch}) ${e}`);
232
- }
219
+ const buf = yield this._readRegion(0, maxFetch, opts);
220
+ const bytes = yield (0, bgzf_filehandle_1.unzip)(buf);
233
221
  // trim off lines after the last non-meta line
234
222
  if (metaChar) {
235
223
  // trim backward from the end
@@ -244,7 +232,7 @@ class TabixIndexedFile {
244
232
  lastNewline = i;
245
233
  }
246
234
  }
247
- bytes = bytes.slice(0, lastNewline + 1);
235
+ return bytes.slice(0, lastNewline + 1);
248
236
  }
249
237
  return bytes;
250
238
  });
@@ -285,7 +273,7 @@ class TabixIndexedFile {
285
273
  checkLine(metadata, regionRefName, regionStart, regionEnd, line) {
286
274
  const { columnNumbers, metaChar, coordinateType, format } = metadata;
287
275
  // skip meta lines
288
- if (line.charAt(0) === metaChar) {
276
+ if (metaChar && line.startsWith(metaChar)) {
289
277
  return { overlaps: false };
290
278
  }
291
279
  // check ref/start/end using column metadata from index
@@ -338,14 +326,10 @@ class TabixIndexedFile {
338
326
  refSeq = line.slice(currentColumnStart, i);
339
327
  }
340
328
  else if (currentColumnNumber === end) {
341
- let endCoordinate;
342
329
  // this will never match if there is no end column
343
- if (format === 'VCF') {
344
- endCoordinate = this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i));
345
- }
346
- else {
347
- endCoordinate = parseInt(line.slice(currentColumnStart, i), 10);
348
- }
330
+ const endCoordinate = format === 'VCF'
331
+ ? this._getVcfEnd(startCoordinate, refSeq, line.slice(currentColumnStart, i))
332
+ : parseInt(line.slice(currentColumnStart, i), 10);
349
333
  if (endCoordinate <= regionStart) {
350
334
  return { overlaps: false };
351
335
  }
@@ -361,12 +345,12 @@ class TabixIndexedFile {
361
345
  }
362
346
  _getVcfEnd(startCoordinate, refSeq, info) {
363
347
  let endCoordinate = startCoordinate + refSeq.length;
364
- // ignore TRA features as they specify CHR2 and END
365
- // as being on a different chromosome
366
- // if CHR2 is on the same chromosome, still ignore it
367
- // because there should be another pairwise feature
368
- // at the end of this one
369
- const isTRA = info.indexOf('SVTYPE=TRA') !== -1;
348
+ // ignore TRA features as they specify CHR2 and END as being on a different
349
+ // chromosome
350
+ //
351
+ // if CHR2 is on the same chromosome, still ignore it because there should
352
+ // be another pairwise feature at the end of this one
353
+ const isTRA = info.includes('SVTYPE=TRA');
370
354
  if (info[0] !== '.' && !isTRA) {
371
355
  let prevChar = ';';
372
356
  for (let j = 0; j < info.length; j += 1) {
@@ -398,7 +382,7 @@ class TabixIndexedFile {
398
382
  }
399
383
  _readRegion(pos, size, opts = {}) {
400
384
  return __awaiter(this, void 0, void 0, function* () {
401
- const b = Buffer.alloc(size);
385
+ const b = buffer_1.Buffer.alloc(size);
402
386
  const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
403
387
  return buffer.slice(0, bytesRead);
404
388
  });
@@ -412,12 +396,7 @@ class TabixIndexedFile {
412
396
  // fetch the uncompressed data, uncompress carefully a block at a time,
413
397
  // and stop when done
414
398
  const data = yield this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
415
- try {
416
- return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
417
- }
418
- catch (e) {
419
- throw new Error(`error decompressing c ${c.toString()} ${e}`);
420
- }
399
+ return (0, bgzf_filehandle_1.unzipChunkSlice)(data, c);
421
400
  });
422
401
  }
423
402
  }
package/dist/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/tbi.d.ts CHANGED
@@ -1,4 +1,5 @@
1
1
  /// <reference types="node" />
2
+ import { Buffer } from 'buffer';
2
3
  import VirtualOffset from './virtualOffset';
3
4
  import Chunk from './chunk';
4
5
  import IndexFile, { Options } from './indexFile';
@@ -6,9 +7,7 @@ export default class TabixIndex extends IndexFile {
6
7
  lineCount(refName: string, opts?: Options): Promise<any>;
7
8
  _parse(opts?: Options): Promise<{
8
9
  indices: {
9
- binIndex: {
10
- [key: number]: Chunk[];
11
- };
10
+ binIndex: Record<number, Chunk[]>;
12
11
  linearIndex: any[];
13
12
  stats: {
14
13
  lineCount: number;
@@ -27,18 +26,14 @@ export default class TabixIndex extends IndexFile {
27
26
  coordinateType: string;
28
27
  format: string;
29
28
  refIdToName: string[];
30
- refNameToId: {
31
- [key: string]: number;
32
- };
29
+ refNameToId: Record<string, number>;
33
30
  maxBlockSize: number;
34
31
  }>;
35
32
  parsePseudoBin(bytes: Buffer, offset: number): {
36
33
  lineCount: number;
37
34
  };
38
35
  _parseNameBytes(namesBytes: Buffer): {
39
- refNameToId: {
40
- [key: string]: number;
41
- };
36
+ refNameToId: Record<string, number>;
42
37
  refIdToName: string[];
43
38
  };
44
39
  blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
package/dist/tbi.js CHANGED
@@ -231,9 +231,8 @@ class TabixIndex extends indexFile_1.default {
231
231
  for (const [start, end] of overlappingBins) {
232
232
  for (let bin = start; bin <= end; bin++) {
233
233
  if (ba.binIndex[bin]) {
234
- const binChunks = ba.binIndex[bin];
235
- for (let c = 0; c < binChunks.length; ++c) {
236
- chunks.push(new chunk_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
234
+ for (const c of ba.binIndex[bin]) {
235
+ chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
237
236
  }
238
237
  }
239
238
  }