@gmod/tabix 1.5.4 → 1.5.5
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.
- package/CHANGELOG.md +6 -0
- package/README.md +37 -37
- package/dist/chunk.js +12 -14
- package/dist/chunk.js.map +1 -1
- package/dist/csi.js +170 -253
- package/dist/csi.js.map +1 -1
- package/dist/index.js +3 -3
- package/dist/index.js.map +1 -1
- package/dist/indexFile.js +27 -73
- package/dist/indexFile.js.map +1 -1
- package/dist/tabixIndexedFile.d.ts +1 -1
- package/dist/tabixIndexedFile.js +205 -306
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +185 -256
- package/dist/tbi.js.map +1 -1
- package/dist/util.js +10 -64
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.js +13 -20
- package/dist/virtualOffset.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +1 -1
- package/package.json +6 -7
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package/dist/tbi.js
CHANGED
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@@ -1,19 +1,4 @@
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1
1
|
"use strict";
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|
2
|
-
var __extends = (this && this.__extends) || (function () {
|
|
3
|
-
var extendStatics = function (d, b) {
|
|
4
|
-
extendStatics = Object.setPrototypeOf ||
|
|
5
|
-
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
-
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
-
return extendStatics(d, b);
|
|
8
|
-
};
|
|
9
|
-
return function (d, b) {
|
|
10
|
-
if (typeof b !== "function" && b !== null)
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47
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* calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
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class TabixIndex extends indexFile_1.default {
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|
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lineCount(refName, opts = {}) {
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|
63
|
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|
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|
+
const indexData = yield this.parse(opts);
|
|
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|
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|
|
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|
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return -1;
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|
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|
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}
|
|
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|
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const refId = indexData.refNameToId[refName];
|
|
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|
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const idx = indexData.indices[refId];
|
|
70
|
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if (!idx) {
|
|
71
|
+
return -1;
|
|
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|
+
}
|
|
73
|
+
const { stats } = indexData.indices[refId];
|
|
74
|
+
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|
|
75
|
+
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|
|
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|
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}
|
|
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|
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|
|
132
78
|
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|
|
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|
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}
|
|
79
|
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}
|
|
134
80
|
// memoize
|
|
135
81
|
// fetch and parse the index
|
|
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|
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|
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|
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|
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|
82
|
+
_parse(opts = {}) {
|
|
83
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
84
|
+
const bytes = yield (0, bgzf_filehandle_1.unzip)((yield this.filehandle.readFile(opts)));
|
|
85
|
+
(0, util_1.checkAbortSignal)(opts.signal);
|
|
86
|
+
// check TBI magic numbers
|
|
87
|
+
if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
|
|
88
|
+
throw new Error('Not a TBI file');
|
|
89
|
+
// TODO: do we need to support big-endian TBI files?
|
|
90
|
+
}
|
|
91
|
+
// number of reference sequences in the index
|
|
92
|
+
const refCount = bytes.readInt32LE(4);
|
|
93
|
+
const formatFlags = bytes.readInt32LE(8);
|
|
94
|
+
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
95
|
+
const formatOpts = {
|
|
96
|
+
0: 'generic',
|
|
97
|
+
1: 'SAM',
|
|
98
|
+
2: 'VCF',
|
|
99
|
+
};
|
|
100
|
+
const format = formatOpts[formatFlags & 0xf];
|
|
101
|
+
if (!format) {
|
|
102
|
+
throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
|
|
103
|
+
}
|
|
104
|
+
const columnNumbers = {
|
|
105
|
+
ref: bytes.readInt32LE(12),
|
|
106
|
+
start: bytes.readInt32LE(16),
|
|
107
|
+
end: bytes.readInt32LE(20),
|
|
108
|
+
};
|
|
109
|
+
const metaValue = bytes.readInt32LE(24);
|
|
110
|
+
const depth = 5;
|
|
111
|
+
const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
|
|
112
|
+
const maxRefLength = Math.pow(2, (14 + depth * 3));
|
|
113
|
+
const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
|
|
114
|
+
const skipLines = bytes.readInt32LE(28);
|
|
115
|
+
// read sequence dictionary
|
|
116
|
+
const nameSectionLength = bytes.readInt32LE(32);
|
|
117
|
+
const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
|
|
118
|
+
// read the indexes for each reference sequence
|
|
119
|
+
let currOffset = 36 + nameSectionLength;
|
|
120
|
+
let firstDataLine;
|
|
121
|
+
const indices = new Array(refCount).fill(0).map(() => {
|
|
122
|
+
// the binning index
|
|
123
|
+
const binCount = bytes.readInt32LE(currOffset);
|
|
124
|
+
currOffset += 4;
|
|
125
|
+
const binIndex = {};
|
|
126
|
+
let stats;
|
|
127
|
+
for (let j = 0; j < binCount; j += 1) {
|
|
128
|
+
const bin = bytes.readUInt32LE(currOffset);
|
|
129
|
+
currOffset += 4;
|
|
130
|
+
if (bin > maxBinNumber + 1) {
|
|
131
|
+
throw new Error('tabix index contains too many bins, please use a CSI index');
|
|
132
|
+
}
|
|
133
|
+
else if (bin === maxBinNumber + 1) {
|
|
134
|
+
const chunkCount = bytes.readInt32LE(currOffset);
|
|
135
|
+
currOffset += 4;
|
|
136
|
+
if (chunkCount === 2) {
|
|
137
|
+
stats = this.parsePseudoBin(bytes, currOffset);
|
|
154
138
|
}
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
158
|
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|
|
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|
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|
|
160
|
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|
|
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|
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|
|
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|
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|
|
163
|
-
|
|
164
|
-
|
|
165
|
-
|
|
139
|
+
currOffset += 16 * chunkCount;
|
|
140
|
+
}
|
|
141
|
+
else {
|
|
142
|
+
const chunkCount = bytes.readInt32LE(currOffset);
|
|
143
|
+
currOffset += 4;
|
|
144
|
+
const chunks = new Array(chunkCount);
|
|
145
|
+
for (let k = 0; k < chunkCount; k += 1) {
|
|
146
|
+
const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
|
|
147
|
+
const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
|
|
148
|
+
currOffset += 16;
|
|
149
|
+
firstDataLine = this._findFirstData(firstDataLine, u);
|
|
150
|
+
chunks[k] = new chunk_1.default(u, v, bin);
|
|
166
151
|
}
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
start: bytes.readInt32LE(16),
|
|
170
|
-
end: bytes.readInt32LE(20),
|
|
171
|
-
};
|
|
172
|
-
metaValue = bytes.readInt32LE(24);
|
|
173
|
-
depth = 5;
|
|
174
|
-
maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
|
|
175
|
-
maxRefLength = Math.pow(2, (14 + depth * 3));
|
|
176
|
-
metaChar = metaValue ? String.fromCharCode(metaValue) : null;
|
|
177
|
-
skipLines = bytes.readInt32LE(28);
|
|
178
|
-
nameSectionLength = bytes.readInt32LE(32);
|
|
179
|
-
_b = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength)), refNameToId = _b.refNameToId, refIdToName = _b.refIdToName;
|
|
180
|
-
currOffset = 36 + nameSectionLength;
|
|
181
|
-
indices = new Array(refCount).fill(0).map(function () {
|
|
182
|
-
// the binning index
|
|
183
|
-
var binCount = bytes.readInt32LE(currOffset);
|
|
184
|
-
currOffset += 4;
|
|
185
|
-
var binIndex = {};
|
|
186
|
-
var stats;
|
|
187
|
-
for (var j = 0; j < binCount; j += 1) {
|
|
188
|
-
var bin = bytes.readUInt32LE(currOffset);
|
|
189
|
-
currOffset += 4;
|
|
190
|
-
if (bin > maxBinNumber + 1) {
|
|
191
|
-
throw new Error('tabix index contains too many bins, please use a CSI index');
|
|
192
|
-
}
|
|
193
|
-
else if (bin === maxBinNumber + 1) {
|
|
194
|
-
var chunkCount = bytes.readInt32LE(currOffset);
|
|
195
|
-
currOffset += 4;
|
|
196
|
-
if (chunkCount === 2) {
|
|
197
|
-
stats = _this.parsePseudoBin(bytes, currOffset);
|
|
198
|
-
}
|
|
199
|
-
currOffset += 16 * chunkCount;
|
|
200
|
-
}
|
|
201
|
-
else {
|
|
202
|
-
var chunkCount = bytes.readInt32LE(currOffset);
|
|
203
|
-
currOffset += 4;
|
|
204
|
-
var chunks = new Array(chunkCount);
|
|
205
|
-
for (var k = 0; k < chunkCount; k += 1) {
|
|
206
|
-
var u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
|
|
207
|
-
var v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
|
|
208
|
-
currOffset += 16;
|
|
209
|
-
firstDataLine = _this._findFirstData(firstDataLine, u);
|
|
210
|
-
chunks[k] = new chunk_1.default(u, v, bin);
|
|
211
|
-
}
|
|
212
|
-
binIndex[bin] = chunks;
|
|
213
|
-
}
|
|
214
|
-
}
|
|
215
|
-
// the linear index
|
|
216
|
-
var linearCount = bytes.readInt32LE(currOffset);
|
|
217
|
-
currOffset += 4;
|
|
218
|
-
var linearIndex = new Array(linearCount);
|
|
219
|
-
for (var k = 0; k < linearCount; k += 1) {
|
|
220
|
-
linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
|
|
221
|
-
currOffset += 8;
|
|
222
|
-
firstDataLine = _this._findFirstData(firstDataLine, linearIndex[k]);
|
|
223
|
-
}
|
|
224
|
-
return { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
|
|
225
|
-
});
|
|
226
|
-
return [2 /*return*/, {
|
|
227
|
-
indices: indices,
|
|
228
|
-
metaChar: metaChar,
|
|
229
|
-
maxBinNumber: maxBinNumber,
|
|
230
|
-
maxRefLength: maxRefLength,
|
|
231
|
-
skipLines: skipLines,
|
|
232
|
-
firstDataLine: firstDataLine,
|
|
233
|
-
columnNumbers: columnNumbers,
|
|
234
|
-
coordinateType: coordinateType,
|
|
235
|
-
format: format,
|
|
236
|
-
refIdToName: refIdToName,
|
|
237
|
-
refNameToId: refNameToId,
|
|
238
|
-
maxBlockSize: 1 << 16,
|
|
239
|
-
}];
|
|
152
|
+
binIndex[bin] = chunks;
|
|
153
|
+
}
|
|
240
154
|
}
|
|
155
|
+
// the linear index
|
|
156
|
+
const linearCount = bytes.readInt32LE(currOffset);
|
|
157
|
+
currOffset += 4;
|
|
158
|
+
const linearIndex = new Array(linearCount);
|
|
159
|
+
for (let k = 0; k < linearCount; k += 1) {
|
|
160
|
+
linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
|
|
161
|
+
currOffset += 8;
|
|
162
|
+
firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
|
|
163
|
+
}
|
|
164
|
+
return { binIndex, linearIndex, stats };
|
|
241
165
|
});
|
|
166
|
+
return {
|
|
167
|
+
indices,
|
|
168
|
+
metaChar,
|
|
169
|
+
maxBinNumber,
|
|
170
|
+
maxRefLength,
|
|
171
|
+
skipLines,
|
|
172
|
+
firstDataLine,
|
|
173
|
+
columnNumbers,
|
|
174
|
+
coordinateType,
|
|
175
|
+
format,
|
|
176
|
+
refIdToName,
|
|
177
|
+
refNameToId,
|
|
178
|
+
maxBlockSize: 1 << 16,
|
|
179
|
+
};
|
|
242
180
|
});
|
|
243
|
-
}
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
-
|
|
299
|
-
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
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|
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|
|
301
|
-
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|
|
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|
-
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|
|
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|
-
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|
|
304
|
-
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|
|
305
|
-
for (c = 0; c < binChunks.length; ++c) {
|
|
306
|
-
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|
|
307
|
-
}
|
|
308
|
-
}
|
|
309
|
-
}
|
|
310
|
-
}
|
|
311
|
-
nintv = ba.linearIndex.length;
|
|
312
|
-
lowest = null;
|
|
313
|
-
minLin = Math.min(min >> 14, nintv - 1);
|
|
314
|
-
maxLin = Math.min(max >> 14, nintv - 1);
|
|
315
|
-
for (i = minLin; i <= maxLin; ++i) {
|
|
316
|
-
vp = ba.linearIndex[i];
|
|
317
|
-
if (vp) {
|
|
318
|
-
if (!lowest || vp.compareTo(lowest) < 0) {
|
|
319
|
-
lowest = vp;
|
|
320
|
-
}
|
|
321
|
-
}
|
|
203
|
+
return { refNameToId, refIdToName };
|
|
204
|
+
}
|
|
205
|
+
blocksForRange(refName, min, max, opts = {}) {
|
|
206
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
207
|
+
if (min < 0) {
|
|
208
|
+
min = 0;
|
|
209
|
+
}
|
|
210
|
+
const indexData = yield this.parse(opts);
|
|
211
|
+
if (!indexData) {
|
|
212
|
+
return [];
|
|
213
|
+
}
|
|
214
|
+
const refId = indexData.refNameToId[refName];
|
|
215
|
+
const ba = indexData.indices[refId];
|
|
216
|
+
if (!ba) {
|
|
217
|
+
return [];
|
|
218
|
+
}
|
|
219
|
+
const minOffset = ba.linearIndex.length
|
|
220
|
+
? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
|
|
221
|
+
? ba.linearIndex.length - 1
|
|
222
|
+
: min >> TAD_LIDX_SHIFT]
|
|
223
|
+
: new virtualOffset_1.default(0, 0);
|
|
224
|
+
if (!minOffset) {
|
|
225
|
+
console.warn('querying outside of possible tabix range');
|
|
226
|
+
}
|
|
227
|
+
// const { linearIndex, binIndex } = indexes
|
|
228
|
+
const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
|
|
229
|
+
const chunks = [];
|
|
230
|
+
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
231
|
+
for (const [start, end] of overlappingBins) {
|
|
232
|
+
for (let bin = start; bin <= end; bin++) {
|
|
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));
|
|
322
237
|
}
|
|
323
|
-
|
|
238
|
+
}
|
|
324
239
|
}
|
|
325
|
-
}
|
|
240
|
+
}
|
|
241
|
+
// Use the linear index to find minimum file position of chunks that could
|
|
242
|
+
// contain alignments in the region
|
|
243
|
+
const nintv = ba.linearIndex.length;
|
|
244
|
+
let lowest = null;
|
|
245
|
+
const minLin = Math.min(min >> 14, nintv - 1);
|
|
246
|
+
const maxLin = Math.min(max >> 14, nintv - 1);
|
|
247
|
+
for (let i = minLin; i <= maxLin; ++i) {
|
|
248
|
+
const vp = ba.linearIndex[i];
|
|
249
|
+
if (vp) {
|
|
250
|
+
if (!lowest || vp.compareTo(lowest) < 0) {
|
|
251
|
+
lowest = vp;
|
|
252
|
+
}
|
|
253
|
+
}
|
|
254
|
+
}
|
|
255
|
+
return (0, util_1.optimizeChunks)(chunks, lowest);
|
|
326
256
|
});
|
|
327
|
-
}
|
|
328
|
-
|
|
329
|
-
}(indexFile_1.default));
|
|
257
|
+
}
|
|
258
|
+
}
|
|
330
259
|
exports.default = TabixIndex;
|
|
331
260
|
//# sourceMappingURL=tbi.js.map
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"
|
|
1
|
+
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