@gmod/tabix 1.5.5 → 1.5.6

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Files changed (7) hide show
  1. package/CHANGELOG.md +6 -0
  2. package/dist/tabixIndexedFile.js +21 -12
  3. package/dist/tabixIndexedFile.js.map +1 -1
  4. package/esm/tabixIndexedFile.js +21 -12
  5. package/esm/tabixIndexedFile.js.map +1 -1
  6. package/package.json +1 -1
  7. package/src/tabixIndexedFile.ts +23 -16
package/CHANGELOG.md CHANGED
@@ -1,3 +1,9 @@
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+ ## [1.5.6](https://github.com/GMOD/tabix-js/compare/v1.5.5...v1.5.6) (2023-02-28)
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+
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+
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+
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+ - Add fix for fileOffset being stable in presence of Unicode characters (#137)
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+
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  ## [1.5.5](https://github.com/GMOD/tabix-js/compare/v1.5.4...v1.5.5) (2022-12-17)
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package/dist/tabixIndexedFile.js CHANGED
@@ -19,6 +19,7 @@ const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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  const util_1 = require("./util");
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  const tbi_1 = __importDefault(require("./tbi"));
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  const csi_1 = __importDefault(require("./csi"));
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+ const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
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  function timeout(time) {
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  return new Promise(resolve => {
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  setTimeout(resolve, time);
@@ -150,19 +151,24 @@ class TabixIndexedFile {
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  let previousStartCoordinate;
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  const c = chunks[chunkNum];
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  const { buffer, cpositions, dpositions } = yield this.chunkCache.get(c.toString(), c, signal);
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- const lines = (typeof TextDecoder !== 'undefined'
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- ? new TextDecoder('utf-8').decode(buffer)
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- : buffer.toString()).split('\n');
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- lines.pop();
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  (0, util_1.checkAbortSignal)(signal);
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- let blockStart = c.minv.dataPosition;
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- let pos;
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- for (let i = 0; i < lines.length; i += 1) {
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- const line = lines[i];
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- for (pos = 0; blockStart >= dpositions[pos]; pos += 1) { }
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+ let blockStart = 0;
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+ let pos = 0;
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+ while (blockStart < buffer.length) {
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+ const n = buffer.indexOf('\n', blockStart);
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+ if (n === -1) {
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+ break;
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+ }
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+ const b = buffer.subarray(blockStart, n);
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+ const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
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+ if (dpositions) {
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+ while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
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+ pos--;
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+ }
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  // filter the line for whether it is within the requested range
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  const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
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- // do a small check just to make sure that the lines are really sorted by start coordinate
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+ // do a small check just to make sure that the lines are really sorted
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+ // by start coordinate
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  if (previousStartCoordinate !== undefined &&
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  startCoordinate !== undefined &&
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  previousStartCoordinate > startCoordinate) {
@@ -179,7 +185,10 @@ class TabixIndexedFile {
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  // then the blockStart-dpositions is an uncompressed file offset from
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  // that bgzip block boundary, and since the cpositions are multiplied by
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  // (1 << 8) these uncompressed offsets get a unique space
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- cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]));
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+ cpositions[pos] * (1 << 8) +
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+ (blockStart - dpositions[pos]) +
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+ c.minv.dataPosition +
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+ 1);
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  }
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  else if (startCoordinate !== undefined && startCoordinate >= end) {
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  // the lines were overlapping the region, but now have stopped, so
@@ -187,13 +196,13 @@ class TabixIndexedFile {
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  // processing data now
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  return;
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  }
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- blockStart += line.length + 1;
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  // yield if we have emitted beyond the yield limit
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  if (last - Date.now() > 500) {
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  last = Date.now();
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  (0, util_1.checkAbortSignal)(signal);
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  yield timeout(1);
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  }
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+ blockStart = n + 1;
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  }
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  }
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  });
package/dist/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/tabixIndexedFile.js CHANGED
@@ -5,6 +5,7 @@ import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
5
5
  import { checkAbortSignal } from './util';
6
6
  import TBI from './tbi';
7
7
  import CSI from './csi';
8
+ const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined;
8
9
  function timeout(time) {
9
10
  return new Promise(resolve => {
10
11
  setTimeout(resolve, time);
@@ -135,19 +136,24 @@ export default class TabixIndexedFile {
135
136
  let previousStartCoordinate;
136
137
  const c = chunks[chunkNum];
137
138
  const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
138
- const lines = (typeof TextDecoder !== 'undefined'
139
- ? new TextDecoder('utf-8').decode(buffer)
140
- : buffer.toString()).split('\n');
141
- lines.pop();
142
139
  checkAbortSignal(signal);
143
- let blockStart = c.minv.dataPosition;
144
- let pos;
145
- for (let i = 0; i < lines.length; i += 1) {
146
- const line = lines[i];
147
- for (pos = 0; blockStart >= dpositions[pos]; pos += 1) { }
140
+ let blockStart = 0;
141
+ let pos = 0;
142
+ while (blockStart < buffer.length) {
143
+ const n = buffer.indexOf('\n', blockStart);
144
+ if (n === -1) {
145
+ break;
146
+ }
147
+ const b = buffer.subarray(blockStart, n);
148
+ const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
149
+ if (dpositions) {
150
+ while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
151
+ pos--;
152
+ }
148
153
  // filter the line for whether it is within the requested range
149
154
  const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
150
- // do a small check just to make sure that the lines are really sorted by start coordinate
155
+ // do a small check just to make sure that the lines are really sorted
156
+ // by start coordinate
151
157
  if (previousStartCoordinate !== undefined &&
152
158
  startCoordinate !== undefined &&
153
159
  previousStartCoordinate > startCoordinate) {
@@ -164,7 +170,10 @@ export default class TabixIndexedFile {
164
170
  // then the blockStart-dpositions is an uncompressed file offset from
165
171
  // that bgzip block boundary, and since the cpositions are multiplied by
166
172
  // (1 << 8) these uncompressed offsets get a unique space
167
- cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]));
173
+ cpositions[pos] * (1 << 8) +
174
+ (blockStart - dpositions[pos]) +
175
+ c.minv.dataPosition +
176
+ 1);
168
177
  }
169
178
  else if (startCoordinate !== undefined && startCoordinate >= end) {
170
179
  // the lines were overlapping the region, but now have stopped, so
@@ -172,13 +181,13 @@ export default class TabixIndexedFile {
172
181
  // processing data now
173
182
  return;
174
183
  }
175
- blockStart += line.length + 1;
176
184
  // yield if we have emitted beyond the yield limit
177
185
  if (last - Date.now() > 500) {
178
186
  last = Date.now();
179
187
  checkAbortSignal(signal);
180
188
  await timeout(1);
181
189
  }
190
+ blockStart = n + 1;
182
191
  }
183
192
  }
184
193
  }
package/esm/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/tabix",
3
- "version": "1.5.5",
3
+ "version": "1.5.6",
4
4
  "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/tabix-js",
package/src/tabixIndexedFile.ts CHANGED
@@ -11,6 +11,9 @@ import CSI from './csi'
11
11
 
12
12
  type GetLinesCallback = (line: string, fileOffset: number) => void
13
13
 
14
+ const decoder =
15
+ typeof TextDecoder !== 'undefined' ? new TextDecoder('utf-8') : undefined
16
+
14
17
  interface GetLinesOpts {
15
18
  [key: string]: unknown
16
19
  signal?: AbortSignal
@@ -188,21 +191,21 @@ export default class TabixIndexedFile {
188
191
  signal,
189
192
  )
190
193
 
191
- const lines = (
192
- typeof TextDecoder !== 'undefined'
193
- ? new TextDecoder('utf-8').decode(buffer)
194
- : buffer.toString()
195
- ).split('\n')
196
- lines.pop()
197
-
198
194
  checkAbortSignal(signal)
199
- let blockStart = c.minv.dataPosition
200
- let pos
201
-
202
- for (let i = 0; i < lines.length; i += 1) {
203
- const line = lines[i]
195
+ let blockStart = 0
196
+ let pos = 0
197
+ while (blockStart < buffer.length) {
198
+ const n = buffer.indexOf('\n', blockStart)
199
+ if (n === -1) {
200
+ break
201
+ }
202
+ const b = buffer.subarray(blockStart, n)
203
+ const line = decoder?.decode(b) || b.toString()
204
204
 
205
- for (pos = 0; blockStart >= dpositions[pos]; pos += 1) {}
205
+ if (dpositions) {
206
+ while (blockStart + c.minv.dataPosition >= dpositions[pos++]) {}
207
+ pos--
208
+ }
206
209
 
207
210
  // filter the line for whether it is within the requested range
208
211
  const { startCoordinate, overlaps } = this.checkLine(
@@ -213,7 +216,8 @@ export default class TabixIndexedFile {
213
216
  line,
214
217
  )
215
218
 
216
- // do a small check just to make sure that the lines are really sorted by start coordinate
219
+ // do a small check just to make sure that the lines are really sorted
220
+ // by start coordinate
217
221
  if (
218
222
  previousStartCoordinate !== undefined &&
219
223
  startCoordinate !== undefined &&
@@ -236,7 +240,10 @@ export default class TabixIndexedFile {
236
240
  // then the blockStart-dpositions is an uncompressed file offset from
237
241
  // that bgzip block boundary, and since the cpositions are multiplied by
238
242
  // (1 << 8) these uncompressed offsets get a unique space
239
- cpositions[pos] * (1 << 8) + (blockStart - dpositions[pos]),
243
+ cpositions[pos] * (1 << 8) +
244
+ (blockStart - dpositions[pos]) +
245
+ c.minv.dataPosition +
246
+ 1,
240
247
  )
241
248
  } else if (startCoordinate !== undefined && startCoordinate >= end) {
242
249
  // the lines were overlapping the region, but now have stopped, so
@@ -244,7 +251,6 @@ export default class TabixIndexedFile {
244
251
  // processing data now
245
252
  return
246
253
  }
247
- blockStart += line.length + 1
248
254
 
249
255
  // yield if we have emitted beyond the yield limit
250
256
  if (last - Date.now() > 500) {
@@ -252,6 +258,7 @@ export default class TabixIndexedFile {
252
258
  checkAbortSignal(signal)
253
259
  await timeout(1)
254
260
  }
261
+ blockStart = n + 1
255
262
  }
256
263
  }
257
264
  }