@gmod/bam 1.1.12 → 1.1.13

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 (22) hide show
  1. package/CHANGELOG.md +12 -11
  2. package/dist/bai.d.ts +1 -1
  3. package/dist/bai.js +37 -49
  4. package/dist/bai.js.map +1 -1
  5. package/dist/bamFile.js +7 -7
  6. package/dist/bamFile.js.map +1 -1
  7. package/dist/csi.js +1 -6
  8. package/dist/csi.js.map +1 -1
  9. package/dist/record.d.ts +8 -8
  10. package/dist/record.js +29 -37
  11. package/dist/record.js.map +1 -1
  12. package/esm/bai.d.ts +1 -1
  13. package/esm/bai.js +2 -3
  14. package/esm/bai.js.map +1 -1
  15. package/esm/bamFile.js +7 -7
  16. package/esm/bamFile.js.map +1 -1
  17. package/esm/csi.js +1 -6
  18. package/esm/csi.js.map +1 -1
  19. package/esm/record.d.ts +8 -8
  20. package/esm/record.js +28 -36
  21. package/esm/record.js.map +1 -1
  22. package/package.json +13 -18
package/CHANGELOG.md CHANGED
@@ -1,37 +1,38 @@
1
- <a name="1.1.12"></a>
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- ## [1.1.12](https://github.com/GMOD/bam-js/compare/v1.1.11...v1.1.12) (2022-02-17)
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+ ## [1.1.13](https://github.com/GMOD/bam-js/compare/v1.1.12...v1.1.13) (2022-02-25)
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+
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+
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+
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+ - Optimize qual and sequence string record functions for less GC pressure
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+ <a name="1.1.12"></a>
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+ ## [1.1.12](https://github.com/GMOD/bam-js/compare/v1.1.11...v1.1.12) (2022-02-17)
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  - Add blocksForRange method to BamFile class to help stats estimation in JBrowse 2
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  <a name="1.1.11"></a>
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- ## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)
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-
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+ ## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)
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  - Cache setup of index file parsing
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  <a name="1.1.10"></a>
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- ## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
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-
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+ ## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
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- - Make _refID and flags public fields
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+ - Make \_refID and flags public fields
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  - Small internal changes to the handling of opts
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  <a name="1.1.9"></a>
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- ## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
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-
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+ ## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
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  - Add ESM module export in package.json (smaller bundle size for consumers)
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  - Cache BAI readFile result for compatibility with node.js native filehandles (which otherwise fail if re-reading the filehandle twice)
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  <a name="1.1.8"></a>
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- ## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
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-
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+ ## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
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  - Fix types for yieldThreadTime
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package/dist/bai.d.ts CHANGED
@@ -9,7 +9,7 @@ export default class BAI extends IndexFile {
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  };
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  lineCount(refId: number, opts?: BaseOpts): Promise<any>;
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  fetchBai(opts?: BaseOpts): Promise<Buffer>;
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- _parse(opts?: BaseOpts): Promise<{
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+ _parse(): Promise<{
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  [key: string]: any;
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  }>;
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  indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
package/dist/bai.js CHANGED
@@ -117,8 +117,7 @@ var BAI = /** @class */ (function (_super) {
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  return this.baiP;
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  };
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  // fetch and parse the index
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- BAI.prototype._parse = function (opts) {
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- if (opts === void 0) { opts = {}; }
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+ BAI.prototype._parse = function () {
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  return __awaiter(this, void 0, void 0, function () {
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  var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, linearCount, linearIndex, k;
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  return __generator(this, function (_a) {
@@ -140,58 +139,47 @@ var BAI = /** @class */ (function (_super) {
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  // read the indexes for each reference sequence
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  data.indices = new Array(data.refCount);
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  currOffset = 8;
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- i = 0;
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- _a.label = 2;
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- case 2:
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- if (!(i < data.refCount)) return [3 /*break*/, 5];
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- return [4 /*yield*/, (0, util_1.abortBreakPoint)(opts.signal)
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- // the binning index
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- ];
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- case 3:
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- _a.sent();
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- binCount = bytes.readInt32LE(currOffset);
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- stats = void 0;
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- currOffset += 4;
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- binIndex = {};
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- for (j = 0; j < binCount; j += 1) {
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- bin = bytes.readUInt32LE(currOffset);
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+ for (i = 0; i < data.refCount; i += 1) {
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+ binCount = bytes.readInt32LE(currOffset);
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+ stats = void 0;
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  currOffset += 4;
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- if (bin === binLimit + 1) {
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- currOffset += 4;
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- stats = this.parsePseudoBin(bytes, currOffset);
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- currOffset += 32;
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- }
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- else if (bin > binLimit + 1) {
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- throw new Error('bai index contains too many bins, please use CSI');
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- }
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- else {
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- chunkCount = bytes.readInt32LE(currOffset);
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+ binIndex = {};
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+ for (j = 0; j < binCount; j += 1) {
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+ bin = bytes.readUInt32LE(currOffset);
169
149
  currOffset += 4;
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- chunks = new Array(chunkCount);
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- for (k = 0; k < chunkCount; k += 1) {
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- u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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- v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
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- currOffset += 16;
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- this._findFirstData(data, u);
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- chunks[k] = new chunk_1.default(u, v, bin);
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+ if (bin === binLimit + 1) {
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+ currOffset += 4;
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+ stats = this.parsePseudoBin(bytes, currOffset);
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+ currOffset += 32;
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+ }
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+ else if (bin > binLimit + 1) {
156
+ throw new Error('bai index contains too many bins, please use CSI');
157
+ }
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+ else {
159
+ chunkCount = bytes.readInt32LE(currOffset);
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+ currOffset += 4;
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+ chunks = new Array(chunkCount);
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+ for (k = 0; k < chunkCount; k += 1) {
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+ u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
164
+ v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
165
+ currOffset += 16;
166
+ this._findFirstData(data, u);
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+ chunks[k] = new chunk_1.default(u, v, bin);
168
+ }
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+ binIndex[bin] = chunks;
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170
  }
178
- binIndex[bin] = chunks;
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  }
172
+ linearCount = bytes.readInt32LE(currOffset);
173
+ currOffset += 4;
174
+ linearIndex = new Array(linearCount);
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+ for (k = 0; k < linearCount; k += 1) {
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+ linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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+ currOffset += 8;
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+ this._findFirstData(data, linearIndex[k]);
179
+ }
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+ data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
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  }
181
- linearCount = bytes.readInt32LE(currOffset);
182
- currOffset += 4;
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- linearIndex = new Array(linearCount);
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- for (k = 0; k < linearCount; k += 1) {
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- linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
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- currOffset += 8;
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- this._findFirstData(data, linearIndex[k]);
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- }
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- data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };
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- _a.label = 4;
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- case 4:
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- i += 1;
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- return [3 /*break*/, 2];
194
- case 5: return [2 /*return*/, data];
182
+ return [2 /*return*/, data];
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  }
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  });
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  });
package/dist/bai.js.map CHANGED
@@ -1 +1 @@
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package/dist/bamFile.js CHANGED
@@ -164,10 +164,10 @@ var BamFile = /** @class */ (function () {
164
164
  throw new Error('Error reading header');
165
165
  }
166
166
  if (bytesRead < ret) {
167
- buffer = buffer.slice(0, bytesRead);
167
+ buffer = buffer.subarray(0, bytesRead);
168
168
  }
169
169
  else {
170
- buffer = buffer.slice(0, ret);
170
+ buffer = buffer.subarray(0, ret);
171
171
  }
172
172
  return [3 /*break*/, 5];
173
173
  case 3: return [4 /*yield*/, this.bam.readFile(opts)];
@@ -226,10 +226,10 @@ var BamFile = /** @class */ (function () {
226
226
  throw new Error('Error reading refseqs from header');
227
227
  }
228
228
  if (bytesRead < refSeqBytes) {
229
- buffer = buffer.slice(0, bytesRead);
229
+ buffer = buffer.subarray(0, bytesRead);
230
230
  }
231
231
  else {
232
- buffer = buffer.slice(0, refSeqBytes);
232
+ buffer = buffer.subarray(0, refSeqBytes);
233
233
  }
234
234
  return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)];
235
235
  case 2:
@@ -573,10 +573,10 @@ var BamFile = /** @class */ (function () {
573
573
  buffer = res.buffer;
574
574
  (0, util_1.checkAbortSignal)(signal);
575
575
  if (bytesRead < bufsize) {
576
- buffer = buffer.slice(0, bytesRead);
576
+ buffer = buffer.subarray(0, bytesRead);
577
577
  }
578
578
  else {
579
- buffer = buffer.slice(0, bufsize);
579
+ buffer = buffer.subarray(0, bufsize);
580
580
  }
581
581
  return [4 /*yield*/, (0, bgzf_filehandle_1.unzipChunkSlice)(buffer, chunk)];
582
582
  case 2:
@@ -635,7 +635,7 @@ var BamFile = /** @class */ (function () {
635
635
  (blockStart - dpositions[pos]) +
636
636
  chunk.minv.dataPosition +
637
637
  1
638
- : buffer_crc32_1.default.signed(ba.slice(blockStart, blockEnd)),
638
+ : buffer_crc32_1.default.signed(ba.subarray(blockStart, blockEnd)),
639
639
  });
640
640
  sink.push(feature);
641
641
  if (!(this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime)) return [3 /*break*/, 3];
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/csi.js CHANGED
@@ -148,7 +148,7 @@ var CSI = /** @class */ (function (_super) {
148
148
  data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
149
149
  data.skipLines = bytes.readInt32LE(offset + 20);
150
150
  var nameSectionLength = bytes.readInt32LE(offset + 24);
151
- Object.assign(data, this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
151
+ Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
152
152
  return data;
153
153
  };
154
154
  CSI.prototype._parseNameBytes = function (namesBytes) {
@@ -257,11 +257,6 @@ var CSI = /** @class */ (function (_super) {
257
257
  });
258
258
  };
259
259
  CSI.prototype.parsePseudoBin = function (bytes, offset) {
260
- // const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
261
- // const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
262
- // const three = longToNumber(
263
- // Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
264
- // )
265
260
  var lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
266
261
  return { lineCount: lineCount };
267
262
  };
package/dist/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ {"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAC7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAgF;AAEhF,0DAAmC;AAEnC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,KAAa;;;;;4BACT,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA9B,SAAS,GAAG,SAAkB;wBACpC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IAEK,sBAAQ,GAAd;;;gBACE,sBAAO,EAAE,EAAA;;;KACV;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,IAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,4CAAqC,IAAI,CAAC,WAAW,CAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAA8B;;;;;;;wBACnC,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBACzD,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;;wBAA9C,MAAM,GAAG,CAAC,SAAoC,CAAW;wBACjD,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC;4BAEjC,0BAA0B;0BAFO;;wBAA3B,KAAK,GAAG,SAAmB;wBAEjC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACrD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACvC,IAAI,SAAS,EAAE;4BACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;yBAC7D;wBACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAEjD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC1B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAClC,oBAAoB;0BADc;;wBAAlC,SAAkC,CAAA;wBAE5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC3C,KAAK,SAAA,CAAA;wBACT,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;gCAC3B,yDAAyD;gCACzD,qCAAqC;gCACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;6BAClC;iCAAM;gCACC,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,G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package/dist/record.d.ts CHANGED
@@ -30,12 +30,12 @@ export default class BamRecord {
30
30
  strand(): 1 | -1;
31
31
  multi_segment_next_segment_strand(): 1 | -1 | undefined;
32
32
  name(): any;
33
- _read_name(): any;
33
+ _read_name(): string;
34
34
  /**
35
35
  * Get the value of a tag, parsing the tags as far as necessary.
36
36
  * Only called if we have not already parsed that field.
37
37
  */
38
- _parseTag(tagName?: string): any;
38
+ _parseTag(tagName?: string): string | number | undefined;
39
39
  _parseAllTags(): void;
40
40
  _parseCigar(cigar: string): (string | number)[][];
41
41
  /**
@@ -76,12 +76,12 @@ export default class BamRecord {
76
76
  getReadBases(): string;
77
77
  seq(): string;
78
78
  getPairOrientation(): string | null;
79
- _bin_mq_nl(): any;
80
- _flag_nc(): any;
81
- seq_length(): any;
82
- _next_refid(): any;
83
- _next_pos(): any;
84
- template_length(): any;
79
+ _bin_mq_nl(): number;
80
+ _flag_nc(): number;
81
+ seq_length(): number;
82
+ _next_refid(): number;
83
+ _next_pos(): number;
84
+ template_length(): number;
85
85
  toJSON(): {
86
86
  [key: string]: any;
87
87
  };
package/dist/record.js CHANGED
@@ -5,24 +5,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  /* eslint-disable @typescript-eslint/no-empty-function */
7
7
  var constants_1 = __importDefault(require("./constants"));
8
- var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('').map(function (s) { return s.charCodeAt(0); });
8
+ var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
9
9
  var CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
10
10
  /**
11
11
  * Class of each BAM record returned by this API.
12
12
  */
13
13
  var BamRecord = /** @class */ (function () {
14
14
  function BamRecord(args) {
15
- this._tagOffset = undefined;
15
+ this.data = {};
16
16
  this._tagList = [];
17
17
  this._allTagsParsed = false;
18
+ var bytes = args.bytes, fileOffset = args.fileOffset;
19
+ var byteArray = bytes.byteArray, start = bytes.start;
18
20
  this.data = {};
19
- this.bytes = {
20
- start: args.bytes.start,
21
- end: args.bytes.end,
22
- byteArray: args.bytes.byteArray,
23
- };
24
- this._id = args.fileOffset;
25
- var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
21
+ this.bytes = bytes;
22
+ this._id = fileOffset;
26
23
  this._refID = byteArray.readInt32LE(start + 4);
27
24
  this.data.start = byteArray.readInt32LE(start + 8);
28
25
  this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
@@ -73,7 +70,7 @@ var BamRecord = /** @class */ (function () {
73
70
  }
74
71
  });
75
72
  var seen = {};
76
- tags = tags.filter(function (t) {
73
+ return tags.filter(function (t) {
77
74
  if ((t in _this.data && _this.data[t] === undefined) ||
78
75
  t === 'CG' ||
79
76
  t === 'cg') {
@@ -84,7 +81,6 @@ var BamRecord = /** @class */ (function () {
84
81
  seen[lt] = true;
85
82
  return !s;
86
83
  });
87
- return tags;
88
84
  };
89
85
  BamRecord.prototype.parent = function () {
90
86
  return undefined;
@@ -114,18 +110,14 @@ var BamRecord = /** @class */ (function () {
114
110
  if (this.isSegmentUnmapped()) {
115
111
  return undefined;
116
112
  }
117
- var byteArray = this.bytes.byteArray;
118
- var p = this.bytes.start +
113
+ var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
114
+ var p = start +
119
115
  36 +
120
116
  this.get('_l_read_name') +
121
117
  this.get('_n_cigar_op') * 4 +
122
118
  this.get('_seq_bytes');
123
119
  var lseq = this.get('seq_length');
124
- var qseq = Buffer.allocUnsafe(lseq);
125
- for (var j = 0; j < lseq; ++j) {
126
- qseq[j] = byteArray[p + j];
127
- }
128
- return qseq;
120
+ return byteArray.subarray(p, p + lseq);
129
121
  };
130
122
  BamRecord.prototype.strand = function () {
131
123
  return this.isReverseComplemented() ? -1 : 1;
@@ -141,7 +133,8 @@ var BamRecord = /** @class */ (function () {
141
133
  };
142
134
  BamRecord.prototype._read_name = function () {
143
135
  var nl = this.get('_l_read_name');
144
- return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
136
+ var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
137
+ return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
145
138
  };
146
139
  /**
147
140
  * Get the value of a tag, parsing the tags as far as necessary.
@@ -154,9 +147,9 @@ var BamRecord = /** @class */ (function () {
154
147
  if (this._allTagsParsed) {
155
148
  return undefined;
156
149
  }
157
- var byteArray = this.bytes.byteArray;
150
+ var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
158
151
  var p = this._tagOffset ||
159
- this.bytes.start +
152
+ start +
160
153
  36 +
161
154
  this.get('_l_read_name') +
162
155
  this.get('_n_cigar_op') * 4 +
@@ -452,25 +445,24 @@ var BamRecord = /** @class */ (function () {
452
445
  return this.seq();
453
446
  };
454
447
  BamRecord.prototype.seq = function () {
455
- var byteArray = this.bytes.byteArray;
456
- var p = this.bytes.start +
457
- 36 +
458
- this.get('_l_read_name') +
459
- this.get('_n_cigar_op') * 4;
448
+ var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
449
+ var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
460
450
  var seqBytes = this.get('_seq_bytes');
461
451
  var len = this.get('seq_length');
462
- var buf = '';
463
- var i = 0;
464
- for (var j = 0; j < seqBytes; ++j) {
465
- var sb = byteArray[p + j];
466
- buf += String.fromCharCode(SEQRET_DECODER[(sb & 0xf0) >> 4]);
467
- i++;
468
- if (i < len) {
469
- buf += String.fromCharCode(SEQRET_DECODER[sb & 0x0f]);
470
- i++;
471
- }
452
+ var buf = [];
453
+ for (var j = 0; j < seqBytes - 1; ++j) {
454
+ var sb_1 = byteArray[p + j];
455
+ buf.push(SEQRET_DECODER[(sb_1 & 0xf0) >> 4]);
456
+ buf.push(SEQRET_DECODER[sb_1 & 0x0f]);
457
+ }
458
+ // there are two bases per byte, so this handles the case where it is odd
459
+ // length
460
+ var sb = byteArray[p + seqBytes - 1];
461
+ buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
462
+ if (len % 2 === 0) {
463
+ buf.push(SEQRET_DECODER[sb & 0x0f]);
472
464
  }
473
- return buf;
465
+ return buf.join('');
474
466
  };
475
467
  // adapted from igv.js
476
468
  BamRecord.prototype.getPairOrientation = function () {
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bai.d.ts CHANGED
@@ -9,7 +9,7 @@ export default class BAI extends IndexFile {
9
9
  };
10
10
  lineCount(refId: number, opts?: BaseOpts): Promise<any>;
11
11
  fetchBai(opts?: BaseOpts): Promise<Buffer>;
12
- _parse(opts?: BaseOpts): Promise<{
12
+ _parse(): Promise<{
13
13
  [key: string]: any;
14
14
  }>;
15
15
  indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
package/esm/bai.js CHANGED
@@ -2,7 +2,7 @@ import Long from 'long';
2
2
  import { fromBytes } from './virtualOffset';
3
3
  import Chunk from './chunk';
4
4
  import IndexFile from './indexFile';
5
- import { longToNumber, abortBreakPoint, optimizeChunks } from './util';
5
+ import { longToNumber, optimizeChunks } from './util';
6
6
  const BAI_MAGIC = 21578050; // BAI\1
7
7
  function roundDown(n, multiple) {
8
8
  return n - (n % multiple);
@@ -34,7 +34,7 @@ export default class BAI extends IndexFile {
34
34
  return this.baiP;
35
35
  }
36
36
  // fetch and parse the index
37
- async _parse(opts = {}) {
37
+ async _parse() {
38
38
  const data = { bai: true, maxBlockSize: 1 << 16 };
39
39
  const bytes = await this.fetchBai();
40
40
  // check BAI magic numbers
@@ -48,7 +48,6 @@ export default class BAI extends IndexFile {
48
48
  data.indices = new Array(data.refCount);
49
49
  let currOffset = 8;
50
50
  for (let i = 0; i < data.refCount; i += 1) {
51
- await abortBreakPoint(opts.signal);
52
51
  // the binning index
53
52
  const binCount = bytes.readInt32LE(currOffset);
54
53
  let stats;
package/esm/bai.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,KAAK,MAAM,SAAS,CAAA;AAE3B,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EAAE,YAAY,EAAE,cAAc,EAAY,MAAM,QAAQ,CAAA;AAE/D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAGxC,cAAc,CAAC,KAAa,EAAE,MAAc;QAC1C,MAAM,SAAS,GAAG,YAAY,CAC5B,IAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,EAAE,CAAA;IACtB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACnC,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACjC,IAAI,CAAC,KAAK,EAAE;YACV,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,IAAI,EAAE,CAAA;QAC7B,OAAO,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAA;IACzD,CAAC;IAED,QAAQ,CAAC,OAAiB,EAAE;QAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE;YACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACnD,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;gBACrB,MAAM,CAAC,CAAA;YACT,CAAC,CAAoB,CAAA;SACtB;QACD,OAAO,IAAI,CAAC,IAAI,CAAA;IAClB,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM;QACV,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;QACzE,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QAEnC,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;YACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;SAClC;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;oBACxB,UAAU,IAAI,CAAC,CAAA;oBACf,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC9C,UAAU,IAAI,EAAE,CAAA;iBACjB;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;oBAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;iBACpE;qBAAM;oBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;wBAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;qBACjC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;iBACvB;aACF;YAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YACjD,UAAU,IAAI,CAAC,CAAA;YACf,sDAAsD;YACtD,oDAAoD;YACpD,qCAAqC;YACrC,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;gBACvC,WAAW,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;aAC1C;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;SACnD;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;QAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;QACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACvC,IAAI,CAAC,MAAM,EAAE;YACX,OAAO,EAAE,CAAA;SACV;QACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QAC1C,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;YACvB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvD,IAAI,MAAM,CAAA;QACV,IAAI,KAAK,EAAE;YACT,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;SAChC;aAAM;YACL,MAAM,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SAC3C;QACD,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;YACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;SAC1D;QACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GA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package/esm/bamFile.js CHANGED
@@ -77,10 +77,10 @@ export default class BamFile {
77
77
  throw new Error('Error reading header');
78
78
  }
79
79
  if (bytesRead < ret) {
80
- buffer = buffer.slice(0, bytesRead);
80
+ buffer = buffer.subarray(0, bytesRead);
81
81
  }
82
82
  else {
83
- buffer = buffer.slice(0, ret);
83
+ buffer = buffer.subarray(0, ret);
84
84
  }
85
85
  }
86
86
  else {
@@ -114,10 +114,10 @@ export default class BamFile {
114
114
  throw new Error('Error reading refseqs from header');
115
115
  }
116
116
  if (bytesRead < refSeqBytes) {
117
- buffer = buffer.slice(0, bytesRead);
117
+ buffer = buffer.subarray(0, bytesRead);
118
118
  }
119
119
  else {
120
- buffer = buffer.slice(0, refSeqBytes);
120
+ buffer = buffer.subarray(0, refSeqBytes);
121
121
  }
122
122
  const uncba = await unzip(buffer);
123
123
  const nRef = uncba.readInt32LE(start);
@@ -303,10 +303,10 @@ export default class BamFile {
303
303
  let { buffer } = res;
304
304
  checkAbortSignal(signal);
305
305
  if (bytesRead < bufsize) {
306
- buffer = buffer.slice(0, bytesRead);
306
+ buffer = buffer.subarray(0, bytesRead);
307
307
  }
308
308
  else {
309
- buffer = buffer.slice(0, bufsize);
309
+ buffer = buffer.subarray(0, bufsize);
310
310
  }
311
311
  const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer, chunk);
312
312
  checkAbortSignal(signal);
@@ -354,7 +354,7 @@ export default class BamFile {
354
354
  (blockStart - dpositions[pos]) +
355
355
  chunk.minv.dataPosition +
356
356
  1
357
- : crc32.signed(ba.slice(blockStart, blockEnd)),
357
+ : crc32.signed(ba.subarray(blockStart, blockEnd)),
358
358
  });
359
359
  sink.push(feature);
360
360
  if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/csi.js CHANGED
@@ -58,7 +58,7 @@ export default class CSI extends IndexFile {
58
58
  data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
59
59
  data.skipLines = bytes.readInt32LE(offset + 20);
60
60
  const nameSectionLength = bytes.readInt32LE(offset + 24);
61
- Object.assign(data, this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
61
+ Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
62
62
  return data;
63
63
  }
64
64
  _parseNameBytes(namesBytes) {
@@ -143,11 +143,6 @@ export default class CSI extends IndexFile {
143
143
  return data;
144
144
  }
145
145
  parsePseudoBin(bytes, offset) {
146
- // const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
147
- // const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
148
- // const three = longToNumber(
149
- // Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
150
- // )
151
146
  const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
152
147
  return { lineCount };
153
148
  }
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/esm/record.d.ts CHANGED
@@ -30,12 +30,12 @@ export default class BamRecord {
30
30
  strand(): 1 | -1;
31
31
  multi_segment_next_segment_strand(): 1 | -1 | undefined;
32
32
  name(): any;
33
- _read_name(): any;
33
+ _read_name(): string;
34
34
  /**
35
35
  * Get the value of a tag, parsing the tags as far as necessary.
36
36
  * Only called if we have not already parsed that field.
37
37
  */
38
- _parseTag(tagName?: string): any;
38
+ _parseTag(tagName?: string): string | number | undefined;
39
39
  _parseAllTags(): void;
40
40
  _parseCigar(cigar: string): (string | number)[][];
41
41
  /**
@@ -76,12 +76,12 @@ export default class BamRecord {
76
76
  getReadBases(): string;
77
77
  seq(): string;
78
78
  getPairOrientation(): string | null;
79
- _bin_mq_nl(): any;
80
- _flag_nc(): any;
81
- seq_length(): any;
82
- _next_refid(): any;
83
- _next_pos(): any;
84
- template_length(): any;
79
+ _bin_mq_nl(): number;
80
+ _flag_nc(): number;
81
+ seq_length(): number;
82
+ _next_refid(): number;
83
+ _next_pos(): number;
84
+ template_length(): number;
85
85
  toJSON(): {
86
86
  [key: string]: any;
87
87
  };
package/esm/record.js CHANGED
@@ -1,23 +1,20 @@
1
1
  /* eslint-disable @typescript-eslint/no-empty-function */
2
2
  import Constants from './constants';
3
- const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('').map(s => s.charCodeAt(0));
3
+ const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
4
4
  const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
5
5
  /**
6
6
  * Class of each BAM record returned by this API.
7
7
  */
8
8
  export default class BamRecord {
9
9
  constructor(args) {
10
- this._tagOffset = undefined;
10
+ this.data = {};
11
11
  this._tagList = [];
12
12
  this._allTagsParsed = false;
13
+ const { bytes, fileOffset } = args;
14
+ const { byteArray, start } = bytes;
13
15
  this.data = {};
14
- this.bytes = {
15
- start: args.bytes.start,
16
- end: args.bytes.end,
17
- byteArray: args.bytes.byteArray,
18
- };
19
- this._id = args.fileOffset;
20
- const { start, byteArray } = this.bytes;
16
+ this.bytes = bytes;
17
+ this._id = fileOffset;
21
18
  this._refID = byteArray.readInt32LE(start + 4);
22
19
  this.data.start = byteArray.readInt32LE(start + 8);
23
20
  this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
@@ -67,7 +64,7 @@ export default class BamRecord {
67
64
  }
68
65
  });
69
66
  const seen = {};
70
- tags = tags.filter(t => {
67
+ return tags.filter(t => {
71
68
  if ((t in this.data && this.data[t] === undefined) ||
72
69
  t === 'CG' ||
73
70
  t === 'cg') {
@@ -78,7 +75,6 @@ export default class BamRecord {
78
75
  seen[lt] = true;
79
76
  return !s;
80
77
  });
81
- return tags;
82
78
  }
83
79
  parent() {
84
80
  return undefined;
@@ -108,18 +104,14 @@ export default class BamRecord {
108
104
  if (this.isSegmentUnmapped()) {
109
105
  return undefined;
110
106
  }
111
- const { byteArray } = this.bytes;
112
- const p = this.bytes.start +
107
+ const { start, byteArray } = this.bytes;
108
+ const p = start +
113
109
  36 +
114
110
  this.get('_l_read_name') +
115
111
  this.get('_n_cigar_op') * 4 +
116
112
  this.get('_seq_bytes');
117
113
  const lseq = this.get('seq_length');
118
- const qseq = Buffer.allocUnsafe(lseq);
119
- for (let j = 0; j < lseq; ++j) {
120
- qseq[j] = byteArray[p + j];
121
- }
122
- return qseq;
114
+ return byteArray.subarray(p, p + lseq);
123
115
  }
124
116
  strand() {
125
117
  return this.isReverseComplemented() ? -1 : 1;
@@ -135,7 +127,8 @@ export default class BamRecord {
135
127
  }
136
128
  _read_name() {
137
129
  const nl = this.get('_l_read_name');
138
- return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
130
+ const { byteArray, start } = this.bytes;
131
+ return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
139
132
  }
140
133
  /**
141
134
  * Get the value of a tag, parsing the tags as far as necessary.
@@ -148,9 +141,9 @@ export default class BamRecord {
148
141
  if (this._allTagsParsed) {
149
142
  return undefined;
150
143
  }
151
- const { byteArray } = this.bytes;
144
+ const { byteArray, start } = this.bytes;
152
145
  let p = this._tagOffset ||
153
- this.bytes.start +
146
+ start +
154
147
  36 +
155
148
  this.get('_l_read_name') +
156
149
  this.get('_n_cigar_op') * 4 +
@@ -446,25 +439,24 @@ export default class BamRecord {
446
439
  return this.seq();
447
440
  }
448
441
  seq() {
449
- const { byteArray } = this.bytes;
450
- const p = this.bytes.start +
451
- 36 +
452
- this.get('_l_read_name') +
453
- this.get('_n_cigar_op') * 4;
442
+ const { start, byteArray } = this.bytes;
443
+ const p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
454
444
  const seqBytes = this.get('_seq_bytes');
455
445
  const len = this.get('seq_length');
456
- let buf = '';
457
- let i = 0;
458
- for (let j = 0; j < seqBytes; ++j) {
446
+ const buf = [];
447
+ for (let j = 0; j < seqBytes - 1; ++j) {
459
448
  const sb = byteArray[p + j];
460
- buf += String.fromCharCode(SEQRET_DECODER[(sb & 0xf0) >> 4]);
461
- i++;
462
- if (i < len) {
463
- buf += String.fromCharCode(SEQRET_DECODER[sb & 0x0f]);
464
- i++;
465
- }
449
+ buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
450
+ buf.push(SEQRET_DECODER[sb & 0x0f]);
451
+ }
452
+ // there are two bases per byte, so this handles the case where it is odd
453
+ // length
454
+ const sb = byteArray[p + seqBytes - 1];
455
+ buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
456
+ if (len % 2 === 0) {
457
+ buf.push(SEQRET_DECODER[sb & 0x0f]);
466
458
  }
467
- return buf;
459
+ return buf.join('');
468
460
  }
469
461
  // adapted from igv.js
470
462
  getPairOrientation() {
package/esm/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/bam",
3
- "version": "1.1.12",
3
+ "version": "1.1.13",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -39,34 +39,29 @@
39
39
  ],
40
40
  "dependencies": {
41
41
  "@gmod/bgzf-filehandle": "^1.3.3",
42
- "abortable-promise-cache": "^1.4.0",
43
42
  "buffer-crc32": "^0.2.13",
44
43
  "cross-fetch": "^3.0.2",
45
- "es6-promisify": "^6.0.1",
46
44
  "generic-filehandle": "^2.0.0",
47
45
  "long": "^4.0.0",
48
- "object.entries-ponyfill": "^1.0.1",
49
- "quick-lru": "^2.0.0",
50
- "range-parser": "^1.2.1"
46
+ "object.entries-ponyfill": "^1.0.1"
51
47
  },
52
48
  "devDependencies": {
53
49
  "@types/buffer-crc32": "^0.2.0",
54
- "@types/jest": "^27.0.2",
50
+ "@types/jest": "^27.4.1",
55
51
  "@types/long": "^4.0.0",
56
- "@types/node": "^12.7.8",
57
- "@types/range-parser": "^1.2.3",
58
- "@typescript-eslint/eslint-plugin": "^5.7.0",
59
- "@typescript-eslint/parser": "^5.7.0",
60
- "eslint": "^7.0.0",
61
- "eslint-config-prettier": "^8.3.0",
62
- "eslint-plugin-import": "^2.25.3",
52
+ "@types/node": "^17.0.21",
53
+ "@typescript-eslint/eslint-plugin": "^5.12.1",
54
+ "@typescript-eslint/parser": "^5.12.1",
55
+ "eslint": "^8.9.0",
56
+ "eslint-config-prettier": "^8.4.0",
57
+ "eslint-plugin-import": "^2.25.4",
63
58
  "eslint-plugin-prettier": "^4.0.0",
64
- "jest": "^27.3.1",
59
+ "jest": "^27.5.1",
65
60
  "prettier": "^2.4.1",
66
61
  "rimraf": "^3.0.2",
67
- "standard-changelog": "^1.0.0",
68
- "ts-jest": "^27.0.7",
69
- "typescript": "^4.4.4"
62
+ "standard-changelog": "^2.0.27",
63
+ "ts-jest": "^27.1.3",
64
+ "typescript": "^4.5.5"
70
65
  },
71
66
  "publishConfig": {
72
67
  "access": "public"