@gmod/bam 2.0.1 → 2.0.3

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 (54) hide show
  1. package/CHANGELOG.md +13 -1
  2. package/dist/bai.d.ts +3 -7
  3. package/dist/bai.js +10 -10
  4. package/dist/bai.js.map +1 -1
  5. package/dist/bamFile.d.ts +1 -4
  6. package/dist/bamFile.js +17 -17
  7. package/dist/bamFile.js.map +1 -1
  8. package/dist/chunk.d.ts +0 -1
  9. package/dist/chunk.js +1 -1
  10. package/dist/chunk.js.map +1 -1
  11. package/dist/csi.d.ts +6 -17
  12. package/dist/csi.js +8 -8
  13. package/dist/csi.js.map +1 -1
  14. package/dist/htsget.d.ts +0 -1
  15. package/dist/htsget.js +5 -6
  16. package/dist/htsget.js.map +1 -1
  17. package/dist/record.d.ts +1 -5
  18. package/dist/record.js +2 -3
  19. package/dist/record.js.map +1 -1
  20. package/dist/sam.js +1 -2
  21. package/dist/sam.js.map +1 -1
  22. package/dist/util.d.ts +1 -4
  23. package/dist/util.js +10 -11
  24. package/dist/util.js.map +1 -1
  25. package/dist/virtualOffset.d.ts +0 -1
  26. package/dist/virtualOffset.js +1 -2
  27. package/dist/virtualOffset.js.map +1 -1
  28. package/esm/bai.d.ts +3 -7
  29. package/esm/bai.js.map +1 -1
  30. package/esm/bamFile.d.ts +1 -4
  31. package/esm/bamFile.js +2 -2
  32. package/esm/bamFile.js.map +1 -1
  33. package/esm/chunk.d.ts +0 -1
  34. package/esm/chunk.js +1 -1
  35. package/esm/chunk.js.map +1 -1
  36. package/esm/csi.d.ts +6 -17
  37. package/esm/csi.js.map +1 -1
  38. package/esm/htsget.d.ts +0 -1
  39. package/esm/htsget.js +0 -1
  40. package/esm/htsget.js.map +1 -1
  41. package/esm/record.d.ts +1 -5
  42. package/esm/record.js +2 -3
  43. package/esm/record.js.map +1 -1
  44. package/esm/util.d.ts +1 -4
  45. package/esm/util.js.map +1 -1
  46. package/esm/virtualOffset.d.ts +0 -1
  47. package/package.json +7 -8
  48. package/src/bai.ts +2 -2
  49. package/src/bamFile.ts +7 -7
  50. package/src/chunk.ts +1 -1
  51. package/src/csi.ts +3 -5
  52. package/src/htsget.ts +1 -1
  53. package/src/record.ts +5 -7
  54. package/src/util.ts +2 -2
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/sam.js CHANGED
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.parseHeaderText = void 0;
3
+ exports.parseHeaderText = parseHeaderText;
4
4
  function parseHeaderText(text) {
5
5
  const lines = text.split(/\r?\n/);
6
6
  const data = [];
@@ -20,5 +20,4 @@ function parseHeaderText(text) {
20
20
  }
21
21
  return data;
22
22
  }
23
- exports.parseHeaderText = parseHeaderText;
24
23
  //# sourceMappingURL=sam.js.map
package/dist/sam.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,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,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAlBD,0CAkBC"}
1
+ {"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;AAAA,0CAkBC;AAlBD,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,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,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
package/dist/util.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import Long from 'long';
3
2
  import Chunk from './chunk';
4
3
  import VirtualOffset from './virtualOffset';
@@ -40,8 +39,6 @@ export declare function parsePseudoBin(bytes: Buffer, offset: number): {
40
39
  };
41
40
  export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
42
41
  export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
43
- refNameToId: {
44
- [key: string]: number;
45
- };
42
+ refNameToId: Record<string, number>;
46
43
  refIdToName: string[];
47
44
  };
package/dist/util.js CHANGED
@@ -12,12 +12,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
12
12
  return (mod && mod.__esModule) ? mod : { "default": mod };
13
13
  };
14
14
  Object.defineProperty(exports, "__esModule", { value: true });
15
- exports.parseNameBytes = exports.findFirstData = exports.parsePseudoBin = exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
15
+ exports.timeout = timeout;
16
+ exports.longToNumber = longToNumber;
17
+ exports.checkAbortSignal = checkAbortSignal;
18
+ exports.abortBreakPoint = abortBreakPoint;
19
+ exports.canMergeBlocks = canMergeBlocks;
20
+ exports.makeOpts = makeOpts;
21
+ exports.optimizeChunks = optimizeChunks;
22
+ exports.parsePseudoBin = parsePseudoBin;
23
+ exports.findFirstData = findFirstData;
24
+ exports.parseNameBytes = parseNameBytes;
16
25
  const long_1 = __importDefault(require("long"));
17
26
  function timeout(ms) {
18
27
  return new Promise(resolve => setTimeout(resolve, ms));
19
28
  }
20
- exports.timeout = timeout;
21
29
  function longToNumber(long) {
22
30
  if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
23
31
  long.lessThan(Number.MIN_SAFE_INTEGER)) {
@@ -25,7 +33,6 @@ function longToNumber(long) {
25
33
  }
26
34
  return long.toNumber();
27
35
  }
28
- exports.longToNumber = longToNumber;
29
36
  /**
30
37
  * Properly check if the given AbortSignal is aborted.
31
38
  * Per the standard, if the signal reads as aborted,
@@ -54,7 +61,6 @@ function checkAbortSignal(signal) {
54
61
  }
55
62
  }
56
63
  }
57
- exports.checkAbortSignal = checkAbortSignal;
58
64
  /**
59
65
  * Skips to the next tick, then runs `checkAbortSignal`.
60
66
  * Await this to inside an otherwise synchronous loop to
@@ -67,16 +73,13 @@ function abortBreakPoint(signal) {
67
73
  checkAbortSignal(signal);
68
74
  });
69
75
  }
70
- exports.abortBreakPoint = abortBreakPoint;
71
76
  function canMergeBlocks(chunk1, chunk2) {
72
77
  return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
73
78
  chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
74
79
  }
75
- exports.canMergeBlocks = canMergeBlocks;
76
80
  function makeOpts(obj = {}) {
77
81
  return 'aborted' in obj ? { signal: obj } : obj;
78
82
  }
79
- exports.makeOpts = makeOpts;
80
83
  function optimizeChunks(chunks, lowest) {
81
84
  const mergedChunks = [];
82
85
  let lastChunk;
@@ -108,12 +111,10 @@ function optimizeChunks(chunks, lowest) {
108
111
  }
109
112
  return mergedChunks;
110
113
  }
111
- exports.optimizeChunks = optimizeChunks;
112
114
  function parsePseudoBin(bytes, offset) {
113
115
  const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
114
116
  return { lineCount };
115
117
  }
116
- exports.parsePseudoBin = parsePseudoBin;
117
118
  function findFirstData(firstDataLine, virtualOffset) {
118
119
  return firstDataLine
119
120
  ? firstDataLine.compareTo(virtualOffset) > 0
@@ -121,7 +122,6 @@ function findFirstData(firstDataLine, virtualOffset) {
121
122
  : firstDataLine
122
123
  : virtualOffset;
123
124
  }
124
- exports.findFirstData = findFirstData;
125
125
  function parseNameBytes(namesBytes, renameRefSeq = s => s) {
126
126
  let currRefId = 0;
127
127
  let currNameStart = 0;
@@ -141,5 +141,4 @@ function parseNameBytes(namesBytes, renameRefSeq = s => s) {
141
141
  }
142
142
  return { refNameToId, refIdToName };
143
143
  }
144
- exports.parseNameBytes = parseNameBytes;
145
144
  //# sourceMappingURL=util.js.map
package/dist/util.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;AAAA,gDAAuB;AAIvB,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAFD,0BAEC;AAED,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAhBD,4CAgBC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAE,GAAgB,CAAA;AAC7E,CAAC;AAFD,4BAEC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAhCD,wCAgCC;AAED,SAAgB,cAAc,CAAC,KAAa,EAAE,MAAc;IAC1D,MAAM,SAAS,GAAG,YAAY,CAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EACrD,IAAI,CACL,CACF,CAAA;IACD,OAAO,EAAE,SAAS,EAAE,CAAA;AACtB,CAAC;AARD,wCAQC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AATD,sCASC;AAED,SAAgB,cAAc,CAC5B,UAAkB,EAClB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;IACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;gBAC3D,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AArBD,wCAqBC"}
1
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package/dist/virtualOffset.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  export default class VirtualOffset {
3
2
  blockPosition: number;
4
3
  dataPosition: number;
package/dist/virtualOffset.js CHANGED
@@ -1,6 +1,6 @@
1
1
  "use strict";
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.fromBytes = void 0;
3
+ exports.fromBytes = fromBytes;
4
4
  class VirtualOffset {
5
5
  constructor(blockPosition, dataPosition) {
6
6
  this.blockPosition = blockPosition; // < offset of the compressed data block
@@ -38,5 +38,4 @@ function fromBytes(bytes, offset = 0, bigendian = false) {
38
38
  bytes[offset + 3] * 0x100 +
39
39
  bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
40
40
  }
41
- exports.fromBytes = fromBytes;
42
41
  //# sourceMappingURL=virtualOffset.js.map
package/dist/virtualOffset.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/bai.d.ts CHANGED
@@ -10,13 +10,11 @@ export default class BAI extends IndexFile {
10
10
  firstDataLine: VirtualOffset | undefined;
11
11
  maxBlockSize: number;
12
12
  indices: {
13
- binIndex: {
14
- [key: string]: Chunk[];
15
- };
13
+ binIndex: Record<string, Chunk[]>;
16
14
  linearIndex: VirtualOffset[];
17
15
  stats?: {
18
16
  lineCount: number;
19
- } | undefined;
17
+ };
20
18
  }[];
21
19
  refCount: number;
22
20
  }>;
@@ -31,9 +29,7 @@ export default class BAI extends IndexFile {
31
29
  firstDataLine: VirtualOffset | undefined;
32
30
  maxBlockSize: number;
33
31
  indices: {
34
- binIndex: {
35
- [key: string]: Chunk[];
36
- };
32
+ binIndex: Record<string, Chunk[]>;
37
33
  linearIndex: VirtualOffset[];
38
34
  stats?: {
39
35
  lineCount: number;
package/esm/bai.js.map CHANGED
@@ -1 +1 @@
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package/esm/bamFile.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import { Buffer } from 'buffer';
3
2
  import { GenericFilehandle } from 'generic-filehandle';
4
3
  import BAI from './bai';
@@ -51,9 +50,7 @@ export default class BamFile {
51
50
  }[] | undefined>;
52
51
  getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
53
52
  _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
54
- chrToIndex: {
55
- [key: string]: number;
56
- };
53
+ chrToIndex: Record<string, number>;
57
54
  indexToChr: {
58
55
  refName: string;
59
56
  length: number;
package/esm/bamFile.js CHANGED
@@ -2,7 +2,7 @@ import { Buffer } from 'buffer';
2
2
  import crc32 from 'buffer-crc32';
3
3
  import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
4
4
  import { LocalFile, RemoteFile } from 'generic-filehandle';
5
- import AbortablePromiseCache from 'abortable-promise-cache';
5
+ import AbortablePromiseCache from '@gmod/abortable-promise-cache';
6
6
  import QuickLRU from 'quick-lru';
7
7
  // locals
8
8
  import BAI from './bai';
@@ -117,7 +117,7 @@ export default class BamFile {
117
117
  buffer = res.buffer.subarray(0, Math.min(res.bytesRead, ret));
118
118
  }
119
119
  else {
120
- buffer = (await this.bam.readFile(opts));
120
+ buffer = await this.bam.readFile(opts);
121
121
  }
122
122
  const uncba = await unzip(buffer);
123
123
  if (uncba.readInt32LE(0) !== BAM_MAGIC) {
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/chunk.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import VirtualOffset from './virtualOffset';
3
2
  export default class Chunk {
4
3
  minv: VirtualOffset;
package/esm/chunk.js CHANGED
@@ -7,7 +7,7 @@ export default class Chunk {
7
7
  this._fetchedSize = _fetchedSize;
8
8
  }
9
9
  toUniqueString() {
10
- return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
10
+ return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
11
11
  }
12
12
  toString() {
13
13
  return this.toUniqueString();
package/esm/chunk.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,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,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"}
1
+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,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"}
package/esm/csi.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import VirtualOffset from './virtualOffset';
3
2
  import Chunk from './chunk';
4
3
  import { BaseOpts } from './util';
@@ -11,9 +10,7 @@ export default class CSI extends IndexFile {
11
10
  lineCount(refId: number, opts?: BaseOpts): Promise<number>;
12
11
  indexCov(): Promise<never[]>;
13
12
  parseAuxData(bytes: Buffer, offset: number): {
14
- refNameToId: {
15
- [key: string]: number;
16
- };
13
+ refNameToId: Record<string, number>;
17
14
  refIdToName: string[];
18
15
  columnNumbers: {
19
16
  ref: number;
@@ -30,9 +27,7 @@ export default class CSI extends IndexFile {
30
27
  _parse(opts: {
31
28
  signal?: AbortSignal;
32
29
  }): Promise<{
33
- refNameToId?: {
34
- [key: string]: number;
35
- } | undefined;
30
+ refNameToId?: Record<string, number> | undefined;
36
31
  refIdToName?: string[] | undefined;
37
32
  columnNumbers?: {
38
33
  ref: number;
@@ -48,12 +43,10 @@ export default class CSI extends IndexFile {
48
43
  csiVersion: number;
49
44
  firstDataLine: VirtualOffset | undefined;
50
45
  indices: {
51
- binIndex: {
52
- [key: string]: Chunk[];
53
- };
46
+ binIndex: Record<string, Chunk[]>;
54
47
  stats?: {
55
48
  lineCount: number;
56
- } | undefined;
49
+ };
57
50
  }[];
58
51
  refCount: number;
59
52
  csi: boolean;
@@ -66,9 +59,7 @@ export default class CSI extends IndexFile {
66
59
  */
67
60
  reg2bins(beg: number, end: number): number[][];
68
61
  parse(opts?: BaseOpts): Promise<{
69
- refNameToId?: {
70
- [key: string]: number;
71
- } | undefined;
62
+ refNameToId?: Record<string, number> | undefined;
72
63
  refIdToName?: string[] | undefined;
73
64
  columnNumbers?: {
74
65
  ref: number;
@@ -84,9 +75,7 @@ export default class CSI extends IndexFile {
84
75
  csiVersion: number;
85
76
  firstDataLine: VirtualOffset | undefined;
86
77
  indices: {
87
- binIndex: {
88
- [key: string]: Chunk[];
89
- };
78
+ binIndex: Record<string, Chunk[]>;
90
79
  stats?: {
91
80
  lineCount: number;
92
81
  } | undefined;
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/esm/htsget.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  import { Buffer } from 'buffer';
3
2
  import { BaseOpts, BamOpts } from './util';
4
3
  import BamFile from './bamFile';
package/esm/htsget.js CHANGED
@@ -11,7 +11,6 @@ async function concat(arr, opts) {
11
11
  else {
12
12
  //remove referer header, it is not even allowed to be specified
13
13
  // @ts-expect-error
14
- //eslint-disable-next-line @typescript-eslint/no-unused-vars
15
14
  const { referer, ...rest } = headers;
16
15
  const res = await fetch(url, {
17
16
  ...opts,
package/esm/htsget.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AAMvC,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,+DAA+D;YAC/D,mBAAmB;YACnB,4DAA4D;YAC5D,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;IACtE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
1
+ {"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAE/B,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AAMvC,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,+DAA+D;YAC/D,mBAAmB;YAEnB,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;IACtE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;QACzD,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
package/esm/record.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- /// <reference types="node" />
2
1
  /**
3
2
  * Class of each BAM record returned by this API.
4
3
  */
@@ -65,7 +64,6 @@ export default class BamRecord {
65
64
  /** @returns {boolean} true if this is a supplementary alignment */
66
65
  isSupplementary(): boolean;
67
66
  cigar(): any;
68
- _flags(): void;
69
67
  length_on_ref(): any;
70
68
  _n_cigar_op(): number;
71
69
  _l_read_name(): number;
@@ -82,7 +80,5 @@ export default class BamRecord {
82
80
  _next_refid(): number;
83
81
  _next_pos(): number;
84
82
  template_length(): number;
85
- toJSON(): {
86
- [key: string]: any;
87
- };
83
+ toJSON(): Record<string, any>;
88
84
  }