@gmod/bam 4.0.0 → 5.0.0

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 (68) hide show
  1. package/CHANGELOG.md +4 -4
  2. package/README.md +7 -11
  3. package/dist/bai.d.ts +1 -1
  4. package/dist/bai.js +151 -169
  5. package/dist/bai.js.map +1 -1
  6. package/dist/bamFile.d.ts +4 -5
  7. package/dist/bamFile.js +271 -350
  8. package/dist/bamFile.js.map +1 -1
  9. package/dist/chunk.d.ts +1 -1
  10. package/dist/chunk.js +5 -0
  11. package/dist/chunk.js.map +1 -1
  12. package/dist/csi.d.ts +1 -1
  13. package/dist/csi.js +140 -145
  14. package/dist/csi.js.map +1 -1
  15. package/dist/htsget.d.ts +1 -2
  16. package/dist/htsget.js +131 -161
  17. package/dist/htsget.js.map +1 -1
  18. package/dist/indexFile.d.ts +1 -1
  19. package/dist/indexFile.js +2 -0
  20. package/dist/indexFile.js.map +1 -1
  21. package/dist/nullIndex.js +2 -13
  22. package/dist/nullIndex.js.map +1 -1
  23. package/dist/record.d.ts +5 -5
  24. package/dist/record.js +44 -37
  25. package/dist/record.js.map +1 -1
  26. package/dist/util.d.ts +4 -2
  27. package/dist/util.js +25 -15
  28. package/dist/util.js.map +1 -1
  29. package/dist/virtualOffset.d.ts +1 -1
  30. package/dist/virtualOffset.js +2 -0
  31. package/dist/virtualOffset.js.map +1 -1
  32. package/esm/bai.d.ts +1 -1
  33. package/esm/bai.js +13 -13
  34. package/esm/bai.js.map +1 -1
  35. package/esm/bamFile.d.ts +4 -5
  36. package/esm/bamFile.js +49 -50
  37. package/esm/bamFile.js.map +1 -1
  38. package/esm/chunk.d.ts +1 -1
  39. package/esm/chunk.js +5 -0
  40. package/esm/chunk.js.map +1 -1
  41. package/esm/csi.d.ts +1 -1
  42. package/esm/csi.js +26 -28
  43. package/esm/csi.js.map +1 -1
  44. package/esm/htsget.d.ts +1 -2
  45. package/esm/htsget.js +21 -11
  46. package/esm/htsget.js.map +1 -1
  47. package/esm/indexFile.d.ts +1 -1
  48. package/esm/indexFile.js +2 -0
  49. package/esm/indexFile.js.map +1 -1
  50. package/esm/record.d.ts +5 -5
  51. package/esm/record.js +44 -37
  52. package/esm/record.js.map +1 -1
  53. package/esm/util.d.ts +4 -2
  54. package/esm/util.js +20 -1
  55. package/esm/util.js.map +1 -1
  56. package/esm/virtualOffset.d.ts +1 -1
  57. package/esm/virtualOffset.js +2 -0
  58. package/esm/virtualOffset.js.map +1 -1
  59. package/package.json +6 -6
  60. package/src/bai.ts +11 -8
  61. package/src/bamFile.ts +22 -41
  62. package/src/chunk.ts +1 -1
  63. package/src/csi.ts +22 -19
  64. package/src/htsget.ts +18 -9
  65. package/src/indexFile.ts +1 -1
  66. package/src/record.ts +44 -43
  67. package/src/util.ts +23 -3
  68. package/src/virtualOffset.ts +1 -1
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/chunk.d.ts CHANGED
@@ -4,7 +4,7 @@ export default class Chunk {
4
4
  maxv: VirtualOffset;
5
5
  bin: number;
6
6
  _fetchedSize?: number | undefined;
7
- buffer?: Buffer;
7
+ buffer?: Uint8Array;
8
8
  constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
9
9
  toUniqueString(): string;
10
10
  toString(): string;
package/dist/chunk.js CHANGED
@@ -2,6 +2,11 @@
2
2
  Object.defineProperty(exports, "__esModule", { value: true });
3
3
  // little class representing a chunk in the index
4
4
  class Chunk {
5
+ minv;
6
+ maxv;
7
+ bin;
8
+ _fetchedSize;
9
+ buffer;
5
10
  constructor(minv, maxv, bin, _fetchedSize) {
6
11
  this.minv = minv;
7
12
  this.maxv = maxv;
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;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;AAlCD,wBAkCC"}
1
+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAAa;IAE1B,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;AAlCD,wBAkCC"}
package/dist/csi.d.ts CHANGED
@@ -9,7 +9,7 @@ export default class CSI extends IndexFile {
9
9
  setupP?: ReturnType<CSI['_parse']>;
10
10
  lineCount(refId: number, opts?: BaseOpts): Promise<number>;
11
11
  indexCov(): Promise<never[]>;
12
- parseAuxData(bytes: Buffer, offset: number): {
12
+ parseAuxData(bytes: Uint8Array, offset: number): {
13
13
  refNameToId: Record<string, number>;
14
14
  refIdToName: string[];
15
15
  columnNumbers: {
package/dist/csi.js CHANGED
@@ -15,22 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
15
15
  }) : function(o, v) {
16
16
  o["default"] = v;
17
17
  });
18
- var __importStar = (this && this.__importStar) || function (mod) {
19
- if (mod && mod.__esModule) return mod;
20
- var result = {};
21
- if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
22
- __setModuleDefault(result, mod);
23
- return result;
24
- };
25
- var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
26
- function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
27
- return new (P || (P = Promise))(function (resolve, reject) {
28
- function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
29
- function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
30
- function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
31
- step((generator = generator.apply(thisArg, _arguments || [])).next());
32
- });
33
- };
18
+ var __importStar = (this && this.__importStar) || (function () {
19
+ var ownKeys = function(o) {
20
+ ownKeys = Object.getOwnPropertyNames || function (o) {
21
+ var ar = [];
22
+ for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
23
+ return ar;
24
+ };
25
+ return ownKeys(o);
26
+ };
27
+ return function (mod) {
28
+ if (mod && mod.__esModule) return mod;
29
+ var result = {};
30
+ if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
31
+ __setModuleDefault(result, mod);
32
+ return result;
33
+ };
34
+ })();
34
35
  var __importDefault = (this && this.__importDefault) || function (mod) {
35
36
  return (mod && mod.__esModule) ? mod : { "default": mod };
36
37
  };
@@ -43,149 +44,148 @@ const indexFile_1 = __importDefault(require("./indexFile"));
43
44
  const CSI1_MAGIC = 21582659; // CSI\1
44
45
  const CSI2_MAGIC = 38359875; // CSI\2
45
46
  function lshift(num, bits) {
46
- return num * Math.pow(2, bits);
47
+ return num * 2 ** bits;
47
48
  }
48
49
  function rshift(num, bits) {
49
- return Math.floor(num / Math.pow(2, bits));
50
+ return Math.floor(num / 2 ** bits);
50
51
  }
51
52
  class CSI extends indexFile_1.default {
52
- constructor() {
53
- super(...arguments);
54
- this.maxBinNumber = 0;
55
- this.depth = 0;
56
- this.minShift = 0;
53
+ maxBinNumber = 0;
54
+ depth = 0;
55
+ minShift = 0;
56
+ setupP;
57
+ async lineCount(refId, opts) {
58
+ const indexData = await this.parse(opts);
59
+ return indexData.indices[refId]?.stats?.lineCount || 0;
57
60
  }
58
- lineCount(refId, opts) {
59
- return __awaiter(this, void 0, void 0, function* () {
60
- var _a, _b;
61
- const indexData = yield this.parse(opts);
62
- return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
63
- });
64
- }
65
- indexCov() {
66
- return __awaiter(this, void 0, void 0, function* () {
67
- return [];
68
- });
61
+ async indexCov() {
62
+ return [];
69
63
  }
70
64
  parseAuxData(bytes, offset) {
71
- const formatFlags = bytes.readInt32LE(offset);
65
+ const dataView = new DataView(bytes.buffer);
66
+ const formatFlags = dataView.getUint32(offset, true);
72
67
  const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
73
68
  const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
74
69
  if (!format) {
75
70
  throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
76
71
  }
77
72
  const columnNumbers = {
78
- ref: bytes.readInt32LE(offset + 4),
79
- start: bytes.readInt32LE(offset + 8),
80
- end: bytes.readInt32LE(offset + 12),
73
+ ref: dataView.getInt32(offset + 4, true),
74
+ start: dataView.getInt32(offset + 8, true),
75
+ end: dataView.getInt32(offset + 12, true),
81
76
  };
82
- const metaValue = bytes.readInt32LE(offset + 16);
77
+ const metaValue = dataView.getInt32(offset + 16, true);
83
78
  const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
84
- const skipLines = bytes.readInt32LE(offset + 20);
85
- const nameSectionLength = bytes.readInt32LE(offset + 24);
86
- return Object.assign({ columnNumbers,
79
+ const skipLines = dataView.getInt32(offset + 20, true);
80
+ const nameSectionLength = dataView.getInt32(offset + 24, true);
81
+ return {
82
+ columnNumbers,
87
83
  coordinateType,
88
84
  metaValue,
89
85
  metaChar,
90
86
  skipLines,
91
87
  format,
92
- formatFlags }, (0, util_1.parseNameBytes)(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq));
88
+ formatFlags,
89
+ ...(0, util_1.parseNameBytes)(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq),
90
+ };
93
91
  }
94
92
  // fetch and parse the index
95
- _parse(opts) {
96
- return __awaiter(this, void 0, void 0, function* () {
97
- const buffer = yield this.filehandle.readFile(opts);
98
- const bytes = yield (0, bgzf_filehandle_1.unzip)(buffer);
99
- let csiVersion;
100
- // check TBI magic numbers
101
- if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
102
- csiVersion = 1;
103
- }
104
- else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
105
- csiVersion = 2;
106
- }
107
- else {
108
- throw new Error('Not a CSI file');
109
- // TODO: do we need to support big-endian CSI files?
110
- }
111
- this.minShift = bytes.readInt32LE(4);
112
- this.depth = bytes.readInt32LE(8);
113
- this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
114
- const auxLength = bytes.readInt32LE(12);
115
- const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
116
- const refCount = bytes.readInt32LE(16 + auxLength);
117
- // read the indexes for each reference sequence
118
- let curr = 16 + auxLength + 4;
119
- let firstDataLine;
120
- const indices = new Array(refCount);
121
- for (let i = 0; i < refCount; i++) {
122
- // the binning index
123
- const binCount = bytes.readInt32LE(curr);
93
+ async _parse(opts) {
94
+ const buffer = await this.filehandle.readFile(opts);
95
+ const bytes = await (0, bgzf_filehandle_1.unzip)(buffer);
96
+ const dataView = new DataView(bytes.buffer);
97
+ let csiVersion;
98
+ const magic = dataView.getUint32(0, true);
99
+ if (magic === CSI1_MAGIC) {
100
+ csiVersion = 1;
101
+ }
102
+ else if (magic === CSI2_MAGIC) {
103
+ csiVersion = 2;
104
+ }
105
+ else {
106
+ throw new Error(`Not a CSI file ${magic}`);
107
+ // TODO: do we need to support big-endian CSI files?
108
+ }
109
+ this.minShift = dataView.getInt32(4, true);
110
+ this.depth = dataView.getInt32(8, true);
111
+ this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
112
+ const auxLength = dataView.getInt32(12, true);
113
+ const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
114
+ const refCount = dataView.getInt32(16 + auxLength, true);
115
+ // read the indexes for each reference sequence
116
+ let curr = 16 + auxLength + 4;
117
+ let firstDataLine;
118
+ const indices = new Array(refCount);
119
+ for (let i = 0; i < refCount; i++) {
120
+ // the binning index
121
+ const binCount = dataView.getInt32(curr, true);
122
+ curr += 4;
123
+ const binIndex = {};
124
+ let stats; // < provided by parsing a pseudo-bin, if present
125
+ for (let j = 0; j < binCount; j++) {
126
+ const bin = dataView.getUint32(curr, true);
124
127
  curr += 4;
125
- const binIndex = {};
126
- let stats; // < provided by parsing a pseudo-bin, if present
127
- for (let j = 0; j < binCount; j++) {
128
- const bin = bytes.readUInt32LE(curr);
128
+ if (bin > this.maxBinNumber) {
129
+ stats = (0, util_1.parsePseudoBin)(bytes, curr + 28);
130
+ curr += 28 + 16;
131
+ }
132
+ else {
133
+ firstDataLine = (0, util_1.findFirstData)(firstDataLine, (0, virtualOffset_1.fromBytes)(bytes, curr));
134
+ curr += 8;
135
+ const chunkCount = dataView.getInt32(curr, true);
129
136
  curr += 4;
130
- if (bin > this.maxBinNumber) {
131
- stats = (0, util_1.parsePseudoBin)(bytes, curr + 28);
132
- curr += 28 + 16;
133
- }
134
- else {
135
- firstDataLine = (0, util_1.findFirstData)(firstDataLine, (0, virtualOffset_1.fromBytes)(bytes, curr));
137
+ const chunks = new Array(chunkCount);
138
+ for (let k = 0; k < chunkCount; k += 1) {
139
+ const u = (0, virtualOffset_1.fromBytes)(bytes, curr);
136
140
  curr += 8;
137
- const chunkCount = bytes.readInt32LE(curr);
138
- curr += 4;
139
- const chunks = new Array(chunkCount);
140
- for (let k = 0; k < chunkCount; k += 1) {
141
- const u = (0, virtualOffset_1.fromBytes)(bytes, curr);
142
- curr += 8;
143
- const v = (0, virtualOffset_1.fromBytes)(bytes, curr);
144
- curr += 8;
145
- firstDataLine = (0, util_1.findFirstData)(firstDataLine, u);
146
- chunks[k] = new chunk_1.default(u, v, bin);
147
- }
148
- binIndex[bin] = chunks;
141
+ const v = (0, virtualOffset_1.fromBytes)(bytes, curr);
142
+ curr += 8;
143
+ firstDataLine = (0, util_1.findFirstData)(firstDataLine, u);
144
+ chunks[k] = new chunk_1.default(u, v, bin);
149
145
  }
146
+ binIndex[bin] = chunks;
150
147
  }
151
- indices[i] = { binIndex, stats };
152
148
  }
153
- return Object.assign({ csiVersion,
154
- firstDataLine,
155
- indices,
156
- refCount, csi: true, maxBlockSize: 1 << 16 }, aux);
157
- });
149
+ indices[i] = { binIndex, stats };
150
+ }
151
+ return {
152
+ csiVersion,
153
+ firstDataLine,
154
+ indices,
155
+ refCount,
156
+ csi: true,
157
+ maxBlockSize: 1 << 16,
158
+ ...aux,
159
+ };
158
160
  }
159
- blocksForRange(refId_1, min_1, max_1) {
160
- return __awaiter(this, arguments, void 0, function* (refId, min, max, opts = {}) {
161
- if (min < 0) {
162
- min = 0;
163
- }
164
- const indexData = yield this.parse(opts);
165
- const ba = indexData.indices[refId];
166
- // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
167
- if (!ba) {
168
- return [];
169
- }
170
- const overlappingBins = this.reg2bins(min, max);
171
- if (overlappingBins.length === 0) {
172
- return [];
173
- }
174
- const chunks = [];
175
- // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
176
- for (const [start, end] of overlappingBins) {
177
- for (let bin = start; bin <= end; bin++) {
178
- // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
179
- if (ba.binIndex[bin]) {
180
- const binChunks = ba.binIndex[bin];
181
- for (const c of binChunks) {
182
- chunks.push(c);
183
- }
161
+ async blocksForRange(refId, min, max, opts = {}) {
162
+ if (min < 0) {
163
+ min = 0;
164
+ }
165
+ const indexData = await this.parse(opts);
166
+ const ba = indexData.indices[refId];
167
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
168
+ if (!ba) {
169
+ return [];
170
+ }
171
+ const overlappingBins = this.reg2bins(min, max);
172
+ if (overlappingBins.length === 0) {
173
+ return [];
174
+ }
175
+ const chunks = [];
176
+ // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
177
+ for (const [start, end] of overlappingBins) {
178
+ for (let bin = start; bin <= end; bin++) {
179
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
180
+ if (ba.binIndex[bin]) {
181
+ const binChunks = ba.binIndex[bin];
182
+ for (const c of binChunks) {
183
+ chunks.push(c);
184
184
  }
185
185
  }
186
186
  }
187
- return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
188
- });
187
+ }
188
+ return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
189
189
  }
190
190
  /**
191
191
  * calculate the list of bins that may overlap with region [beg,end)
@@ -196,8 +196,8 @@ class CSI extends indexFile_1.default {
196
196
  if (beg < 1) {
197
197
  beg = 1;
198
198
  }
199
- if (end > Math.pow(2, 50)) {
200
- end = Math.pow(2, 34);
199
+ if (end > 2 ** 50) {
200
+ end = 2 ** 34;
201
201
  } // 17 GiB ought to be enough for anybody
202
202
  end -= 1;
203
203
  let l = 0;
@@ -214,23 +214,18 @@ class CSI extends indexFile_1.default {
214
214
  }
215
215
  return bins;
216
216
  }
217
- parse() {
218
- return __awaiter(this, arguments, void 0, function* (opts = {}) {
219
- if (!this.setupP) {
220
- this.setupP = this._parse(opts).catch((e) => {
221
- this.setupP = undefined;
222
- throw e;
223
- });
224
- }
225
- return this.setupP;
226
- });
217
+ async parse(opts = {}) {
218
+ if (!this.setupP) {
219
+ this.setupP = this._parse(opts).catch((e) => {
220
+ this.setupP = undefined;
221
+ throw e;
222
+ });
223
+ }
224
+ return this.setupP;
227
225
  }
228
- hasRefSeq(seqId_1) {
229
- return __awaiter(this, arguments, void 0, function* (seqId, opts = {}) {
230
- var _a;
231
- const header = yield this.parse(opts);
232
- return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
233
- });
226
+ async hasRefSeq(seqId, opts = {}) {
227
+ const header = await this.parse(opts);
228
+ return !!header.indices[seqId]?.binIndex;
234
229
  }
235
230
  }
236
231
  exports.default = CSI;
package/dist/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/htsget.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- import { Buffer } from 'buffer';
2
1
  import { BaseOpts, BamOpts } from './util';
3
2
  import BamFile from './bamFile';
4
3
  import Chunk from './chunk';
@@ -14,7 +13,7 @@ export default class HtsgetFile extends BamFile {
14
13
  chunk: Chunk;
15
14
  opts: BaseOpts;
16
15
  }): Promise<{
17
- data: Buffer;
16
+ data: Uint8Array<ArrayBufferLike>;
18
17
  cpositions: never[];
19
18
  dpositions: never[];
20
19
  chunk: Chunk;