@gmod/tabix 1.6.1 → 2.0.0

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Files changed (39) hide show
  1. package/CHANGELOG.md +3 -3
  2. package/dist/csi.d.ts +3 -4
  3. package/dist/csi.js +56 -38
  4. package/dist/csi.js.map +1 -1
  5. package/dist/indexFile.d.ts +1 -1
  6. package/dist/indexFile.js +1 -2
  7. package/dist/indexFile.js.map +1 -1
  8. package/dist/tabix-bundle.js +1 -2
  9. package/dist/tabixIndexedFile.d.ts +3 -5
  10. package/dist/tabixIndexedFile.js +24 -32
  11. package/dist/tabixIndexedFile.js.map +1 -1
  12. package/dist/tbi.d.ts +2 -3
  13. package/dist/tbi.js +46 -33
  14. package/dist/tbi.js.map +1 -1
  15. package/dist/virtualOffset.d.ts +1 -2
  16. package/dist/virtualOffset.js +1 -4
  17. package/dist/virtualOffset.js.map +1 -1
  18. package/esm/csi.d.ts +3 -4
  19. package/esm/csi.js +39 -31
  20. package/esm/csi.js.map +1 -1
  21. package/esm/indexFile.d.ts +1 -1
  22. package/esm/indexFile.js +1 -2
  23. package/esm/indexFile.js.map +1 -1
  24. package/esm/tabixIndexedFile.d.ts +3 -5
  25. package/esm/tabixIndexedFile.js +16 -24
  26. package/esm/tabixIndexedFile.js.map +1 -1
  27. package/esm/tbi.d.ts +2 -3
  28. package/esm/tbi.js +29 -26
  29. package/esm/tbi.js.map +1 -1
  30. package/esm/virtualOffset.d.ts +1 -2
  31. package/esm/virtualOffset.js +1 -4
  32. package/esm/virtualOffset.js.map +1 -1
  33. package/package.json +4 -7
  34. package/src/csi.ts +49 -40
  35. package/src/indexFile.ts +1 -1
  36. package/src/tabixIndexedFile.ts +15 -33
  37. package/src/tbi.ts +33 -29
  38. package/src/virtualOffset.ts +1 -6
  39. package/dist/tabix-bundle.js.LICENSE.txt +0 -8
package/esm/csi.js CHANGED
@@ -6,6 +6,11 @@ import { longToNumber, optimizeChunks } from './util';
6
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  import IndexFile from './indexFile';
7
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  const CSI1_MAGIC = 21582659; // CSI\1
8
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  const CSI2_MAGIC = 38359875; // CSI\2
9
+ const formats = {
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+ 0: 'generic',
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+ 1: 'SAM',
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+ 2: 'VCF',
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+ };
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  function lshift(num, bits) {
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  return num * 2 ** bits;
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  }
@@ -39,22 +44,23 @@ export default class CSI extends IndexFile {
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  throw new Error('CSI indexes do not support indexcov');
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  }
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  parseAuxData(bytes, offset) {
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- const formatFlags = bytes.readInt32LE(offset);
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+ const dataView = new DataView(bytes.buffer);
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+ const formatFlags = dataView.getInt32(offset, true);
43
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  const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
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- const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
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+ const format = formats[(formatFlags & 0xf)];
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  if (!format) {
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  throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
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  }
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  const columnNumbers = {
49
- ref: bytes.readInt32LE(offset + 4),
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- start: bytes.readInt32LE(offset + 8),
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- end: bytes.readInt32LE(offset + 12),
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+ ref: dataView.getInt32(offset + 4, true),
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+ start: dataView.getInt32(offset + 8, true),
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+ end: dataView.getInt32(offset + 12, true),
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  };
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- const metaValue = bytes.readInt32LE(offset + 16);
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+ const metaValue = dataView.getInt32(offset + 16, true);
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  const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
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- const skipLines = bytes.readInt32LE(offset + 20);
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- const nameSectionLength = bytes.readInt32LE(offset + 24);
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- const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
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+ const skipLines = dataView.getInt32(offset + 20, true);
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+ const nameSectionLength = dataView.getInt32(offset + 24, true);
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+ const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
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  return {
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  refIdToName,
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  refNameToId,
@@ -70,11 +76,11 @@ export default class CSI extends IndexFile {
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  let currNameStart = 0;
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  const refIdToName = [];
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  const refNameToId = {};
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+ const decoder = new TextDecoder('utf8');
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  for (let i = 0; i < namesBytes.length; i += 1) {
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  if (!namesBytes[i]) {
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  if (currNameStart < i) {
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- let refName = namesBytes.toString('utf8', currNameStart, i);
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- refName = this.renameRefSeq(refName);
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+ const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
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  refIdToName[currRefId] = refName;
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  refNameToId[refName] = currRefId;
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  }
@@ -82,28 +88,31 @@ export default class CSI extends IndexFile {
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  currRefId += 1;
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  }
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  }
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- return { refNameToId, refIdToName };
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+ return {
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+ refNameToId,
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+ refIdToName,
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+ };
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  }
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  // fetch and parse the index
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  async _parse(opts = {}) {
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  const bytes = await unzip(await this.filehandle.readFile(opts));
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+ const dataView = new DataView(bytes.buffer);
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  // check TBI magic numbers
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  let csiVersion;
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- if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
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+ if (dataView.getUint32(0, true) === CSI1_MAGIC) {
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  csiVersion = 1;
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  }
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- else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
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+ else if (dataView.getUint32(0, true) === CSI2_MAGIC) {
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  csiVersion = 2;
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  }
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  else {
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  throw new Error('Not a CSI file');
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- // TODO: do we need to support big-endian CSI files?
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  }
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- this.minShift = bytes.readInt32LE(4);
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- this.depth = bytes.readInt32LE(8);
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+ this.minShift = dataView.getInt32(4, true);
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+ this.depth = dataView.getInt32(8, true);
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  this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
105
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  const maxRefLength = 2 ** (this.minShift + this.depth * 3);
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- const auxLength = bytes.readInt32LE(12);
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+ const auxLength = dataView.getInt32(12, true);
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  const aux = auxLength && auxLength >= 30
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  ? this.parseAuxData(bytes, 16)
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  : {
@@ -114,35 +123,33 @@ export default class CSI extends IndexFile {
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  coordinateType: 'zero-based-half-open',
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  format: 'generic',
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  };
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- const refCount = bytes.readInt32LE(16 + auxLength);
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+ const refCount = dataView.getInt32(16 + auxLength, true);
118
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  // read the indexes for each reference sequence
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  let firstDataLine;
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  let currOffset = 16 + auxLength + 4;
121
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  const indices = new Array(refCount).fill(0).map(() => {
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- // the binning index
123
- const binCount = bytes.readInt32LE(currOffset);
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+ const binCount = dataView.getInt32(currOffset, true);
124
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  currOffset += 4;
125
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  const binIndex = {};
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- let stats; // < provided by parsing a pseudo-bin, if present
134
+ let stats;
127
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  for (let j = 0; j < binCount; j += 1) {
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- const bin = bytes.readUInt32LE(currOffset);
136
+ const bin = dataView.getUint32(currOffset, true);
129
137
  if (bin > this.maxBinNumber) {
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- // this is a fake bin that actually has stats information
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- // about the reference sequence in it
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+ // this is a fake bin that actually has stats information about the
139
+ // reference sequence in it
132
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  stats = this.parsePseudoBin(bytes, currOffset + 4);
133
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  currOffset += 4 + 8 + 4 + 16 + 16;
134
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  }
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  else {
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  const loffset = fromBytes(bytes, currOffset + 4);
137
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  firstDataLine = this._findFirstData(firstDataLine, loffset);
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- const chunkCount = bytes.readInt32LE(currOffset + 12);
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+ const chunkCount = dataView.getInt32(currOffset + 12, true);
139
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  currOffset += 16;
140
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  const chunks = new Array(chunkCount);
141
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  for (let k = 0; k < chunkCount; k += 1) {
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  const u = fromBytes(bytes, currOffset);
143
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  const v = 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(u, v, bin);
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  }
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  binIndex[bin] = chunks;
@@ -164,8 +171,9 @@ export default class CSI extends IndexFile {
164
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  };
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  }
166
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  parsePseudoBin(bytes, offset) {
167
- const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
168
- return { lineCount };
174
+ return {
175
+ lineCount: longToNumber(Long.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true)),
176
+ };
169
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  }
170
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  async blocksForRange(refName, min, max, opts = {}) {
171
179
  if (min < 0) {
@@ -180,8 +188,8 @@ export default class CSI extends IndexFile {
180
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  if (!ba) {
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  return [];
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  }
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- // const { linearIndex, binIndex } = indexes
184
- const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
191
+ // List of bin #s that overlap min, max
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+ const overlappingBins = this.reg2bins(min, max);
185
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  const chunks = [];
186
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  // Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
187
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  for (const [start, end] of overlappingBins) {
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
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package/esm/indexFile.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { GenericFilehandle } from 'generic-filehandle';
1
+ import { GenericFilehandle } from 'generic-filehandle2';
2
2
  import VirtualOffset from './virtualOffset';
3
3
  import Chunk from './chunk';
4
4
  export interface Options {
package/esm/indexFile.js CHANGED
@@ -27,9 +27,8 @@ export default class IndexFile {
27
27
  return this.parseP;
28
28
  }
29
29
  async hasRefSeq(seqId, opts = {}) {
30
- var _a;
31
30
  const idx = await this.parse(opts);
32
- return !!((_a = idx.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
31
+ return !!idx.indices[seqId]?.binIndex;
33
32
  }
34
33
  }
35
34
  //# sourceMappingURL=indexFile.js.map
package/esm/indexFile.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,CAAA,MAAA,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,QAAQ,CAAA,CAAA;IACvC,CAAC;CACF"}
1
+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAoBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}
package/esm/tabixIndexedFile.d.ts CHANGED
@@ -1,5 +1,4 @@
1
- import { Buffer } from 'buffer';
2
- import { GenericFilehandle } from 'generic-filehandle';
1
+ import { GenericFilehandle } from 'generic-filehandle2';
3
2
  import { Options, IndexData } from './indexFile';
4
3
  import Chunk from './chunk';
5
4
  type GetLinesCallback = (line: string, fileOffset: number) => void;
@@ -83,7 +82,7 @@ export default class TabixIndexedFile {
83
82
  * get a buffer containing the "header" region of the file, which are the
84
83
  * bytes up to the first non-meta line
85
84
  */
86
- getHeaderBuffer(opts?: Options): Promise<Buffer>;
85
+ getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBuffer>>;
87
86
  /**
88
87
  * get a string containing the "header" region of the file, is the portion up
89
88
  * to the first non-meta line
@@ -128,13 +127,12 @@ export default class TabixIndexedFile {
128
127
  * @returns number of data lines present on that reference sequence
129
128
  */
130
129
  lineCount(refName: string, opts?: Options): Promise<number>;
131
- _readRegion(pos: number, size: number, opts?: Options): Promise<Buffer>;
132
130
  /**
133
131
  * read and uncompress the data in a chunk (composed of one or more
134
132
  * contiguous bgzip blocks) of the file
135
133
  */
136
134
  readChunk(c: Chunk, opts?: Options): Promise<{
137
- buffer: Buffer;
135
+ buffer: Uint8Array<ArrayBuffer>;
138
136
  cpositions: number[];
139
137
  dpositions: number[];
140
138
  }>;
package/esm/tabixIndexedFile.js CHANGED
@@ -1,7 +1,6 @@
1
1
  import AbortablePromiseCache from '@gmod/abortable-promise-cache';
2
2
  import LRU from 'quick-lru';
3
- import { Buffer } from 'buffer';
4
- import { RemoteFile, LocalFile } from 'generic-filehandle';
3
+ import { RemoteFile, LocalFile } from 'generic-filehandle2';
5
4
  import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
6
5
  import { checkAbortSignal } from './util';
7
6
  import TBI from './tbi';
@@ -10,7 +9,6 @@ function isASCII(str) {
10
9
  // eslint-disable-next-line no-control-regex
11
10
  return /^[\u0000-\u007F]*$/.test(str);
12
11
  }
13
- const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
14
12
  export default class TabixIndexedFile {
15
13
  /**
16
14
  * @param {object} args
@@ -119,7 +117,6 @@ export default class TabixIndexedFile {
119
117
  * rejected on error
120
118
  */
121
119
  async getLines(refName, s, e, opts) {
122
- var _a, _b;
123
120
  let signal;
124
121
  let options = {};
125
122
  let callback;
@@ -133,8 +130,8 @@ export default class TabixIndexedFile {
133
130
  }
134
131
  const metadata = await this.index.getMetadata(options);
135
132
  checkAbortSignal(signal);
136
- const start = s !== null && s !== void 0 ? s : 0;
137
- const end = e !== null && e !== void 0 ? e : metadata.maxRefLength;
133
+ const start = s ?? 0;
134
+ const end = e ?? metadata.maxRefLength;
138
135
  if (!(start <= end)) {
139
136
  throw new TypeError('invalid start and end coordinates. start must be less than or equal to end');
140
137
  }
@@ -143,17 +140,18 @@ export default class TabixIndexedFile {
143
140
  }
144
141
  const chunks = await this.index.blocksForRange(refName, start, end, options);
145
142
  checkAbortSignal(signal);
143
+ const decoder = new TextDecoder('utf8');
146
144
  // now go through each chunk and parse and filter the lines out of it
147
145
  for (const c of chunks) {
148
146
  const { buffer, cpositions, dpositions } = await this.chunkCache.get(c.toString(), c, signal);
149
147
  checkAbortSignal(signal);
150
148
  let blockStart = 0;
151
149
  let pos = 0;
152
- const str = (_a = decoder === null || decoder === void 0 ? void 0 : decoder.decode(buffer)) !== null && _a !== void 0 ? _a : buffer.toString();
153
150
  // fast path, Buffer is just ASCII chars and not gigantor, can be
154
151
  // converted to string and processed directly. if it is not ASCII or
155
152
  // gigantic (chrome max str len is 512Mb), we have to decode line by line
156
- const strIsASCII = buffer.length < 500000000 && isASCII(str);
153
+ const str = decoder.decode(buffer);
154
+ const strIsASCII = isASCII(str);
157
155
  while (blockStart < str.length) {
158
156
  let line;
159
157
  let n;
@@ -165,12 +163,12 @@ export default class TabixIndexedFile {
165
163
  line = str.slice(blockStart, n);
166
164
  }
167
165
  else {
168
- n = buffer.indexOf('\n', blockStart);
166
+ n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
169
167
  if (n === -1) {
170
168
  break;
171
169
  }
172
170
  const b = buffer.slice(blockStart, n);
173
- line = (_b = decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) !== null && _b !== void 0 ? _b : b.toString();
171
+ line = decoder.decode(b);
174
172
  }
175
173
  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
176
174
  if (dpositions) {
@@ -217,10 +215,10 @@ export default class TabixIndexedFile {
217
215
  async getHeaderBuffer(opts = {}) {
218
216
  const { firstDataLine, metaChar, maxBlockSize } = await this.getMetadata(opts);
219
217
  checkAbortSignal(opts.signal);
220
- const maxFetch = ((firstDataLine === null || firstDataLine === void 0 ? void 0 : firstDataLine.blockPosition) || 0) + maxBlockSize;
221
- // TODO: what if we don't have a firstDataLine, and the header
222
- // actually takes up more than one block? this case is not covered here
223
- const buf = await this._readRegion(0, maxFetch, opts);
218
+ const maxFetch = (firstDataLine?.blockPosition || 0) + maxBlockSize;
219
+ // TODO: what if we don't have a firstDataLine, and the header actually
220
+ // takes up more than one block? this case is not covered here
221
+ const buf = await this.filehandle.read(maxFetch, 0, opts);
224
222
  const bytes = await unzip(buf);
225
223
  // trim off lines after the last non-meta line
226
224
  if (metaChar) {
@@ -247,8 +245,9 @@ export default class TabixIndexedFile {
247
245
  * @returns {Promise} for a string
248
246
  */
249
247
  async getHeader(opts = {}) {
248
+ const decoder = new TextDecoder('utf8');
250
249
  const bytes = await this.getHeaderBuffer(opts);
251
- return bytes.toString('utf8');
250
+ return decoder.decode(bytes);
252
251
  }
253
252
  /**
254
253
  * get an array of reference sequence names, in the order in which they occur
@@ -398,20 +397,13 @@ export default class TabixIndexedFile {
398
397
  async lineCount(refName, opts = {}) {
399
398
  return this.index.lineCount(refName, opts);
400
399
  }
401
- async _readRegion(pos, size, opts = {}) {
402
- const b = Buffer.alloc(size);
403
- const { bytesRead, buffer } = await this.filehandle.read(b, 0, size, pos, opts);
404
- return buffer.subarray(0, bytesRead);
405
- }
406
400
  /**
407
401
  * read and uncompress the data in a chunk (composed of one or more
408
402
  * contiguous bgzip blocks) of the file
409
403
  */
410
404
  async readChunk(c, opts = {}) {
411
- // fetch the uncompressed data, uncompress carefully a block at a time, and
412
- // stop when done
413
- const data = await this._readRegion(c.minv.blockPosition, c.fetchedSize(), opts);
414
- return unzipChunkSlice(data, c);
405
+ const ret = await this.filehandle.read(c.fetchedSize(), c.minv.blockPosition, opts);
406
+ return unzipChunkSlice(ret, c);
415
407
  }
416
408
  }
417
409
  //# sourceMappingURL=tabixIndexedFile.js.map
package/esm/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/tbi.d.ts CHANGED
@@ -1,4 +1,3 @@
1
- import { Buffer } from 'buffer';
2
1
  import VirtualOffset from './virtualOffset';
3
2
  import Chunk from './chunk';
4
3
  import IndexFile, { Options } from './indexFile';
@@ -28,10 +27,10 @@ export default class TabixIndex extends IndexFile {
28
27
  refNameToId: Record<string, number>;
29
28
  maxBlockSize: number;
30
29
  }>;
31
- parsePseudoBin(bytes: Buffer, offset: number): {
30
+ parsePseudoBin(bytes: Uint8Array, offset: number): {
32
31
  lineCount: number;
33
32
  };
34
- _parseNameBytes(namesBytes: Buffer): {
33
+ _parseNameBytes(namesBytes: Uint8Array): {
35
34
  refNameToId: Record<string, number>;
36
35
  refIdToName: string[];
37
36
  };
package/esm/tbi.js CHANGED
@@ -33,25 +33,21 @@ export default class TabixIndex extends IndexFile {
33
33
  if (!idx) {
34
34
  return -1;
35
35
  }
36
- const { stats } = indexData.indices[refId];
37
- if (stats) {
38
- return stats.lineCount;
39
- }
40
- return -1;
36
+ return indexData.indices[refId].stats?.lineCount ?? -1;
41
37
  }
42
38
  // fetch and parse the index
43
39
  async _parse(opts = {}) {
44
40
  const buf = await this.filehandle.readFile(opts);
45
41
  const bytes = await unzip(buf);
46
42
  checkAbortSignal(opts.signal);
47
- // check TBI magic numbers
48
- if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
43
+ const dataView = new DataView(bytes.buffer);
44
+ const magic = dataView.getUint32(0, true);
45
+ if (magic !== TBI_MAGIC /* "TBI\1" */) {
49
46
  throw new Error('Not a TBI file');
50
- // TODO: do we need to support big-endian TBI files?
51
47
  }
52
48
  // number of reference sequences in the index
53
- const refCount = bytes.readInt32LE(4);
54
- const formatFlags = bytes.readInt32LE(8);
49
+ const refCount = dataView.getUint32(4, true);
50
+ const formatFlags = dataView.getUint32(8, true);
55
51
  const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
56
52
  const formatOpts = {
57
53
  0: 'generic',
@@ -63,36 +59,36 @@ export default class TabixIndex extends IndexFile {
63
59
  throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
64
60
  }
65
61
  const columnNumbers = {
66
- ref: bytes.readInt32LE(12),
67
- start: bytes.readInt32LE(16),
68
- end: bytes.readInt32LE(20),
62
+ ref: dataView.getInt32(12, true),
63
+ start: dataView.getInt32(16, true),
64
+ end: dataView.getInt32(20, true),
69
65
  };
70
- const metaValue = bytes.readInt32LE(24);
66
+ const metaValue = dataView.getInt32(24, true);
71
67
  const depth = 5;
72
68
  const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
73
69
  const maxRefLength = 2 ** (14 + depth * 3);
74
70
  const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
75
- const skipLines = bytes.readInt32LE(28);
71
+ const skipLines = dataView.getInt32(28, true);
76
72
  // read sequence dictionary
77
- const nameSectionLength = bytes.readInt32LE(32);
73
+ const nameSectionLength = dataView.getInt32(32, true);
78
74
  const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
79
75
  // read the indexes for each reference sequence
80
76
  let currOffset = 36 + nameSectionLength;
81
77
  let firstDataLine;
82
78
  const indices = new Array(refCount).fill(0).map(() => {
83
79
  // the binning index
84
- const binCount = bytes.readInt32LE(currOffset);
80
+ const binCount = dataView.getInt32(currOffset, true);
85
81
  currOffset += 4;
86
82
  const binIndex = {};
87
83
  let stats;
88
84
  for (let j = 0; j < binCount; j += 1) {
89
- const bin = bytes.readUInt32LE(currOffset);
85
+ const bin = dataView.getUint32(currOffset, true);
90
86
  currOffset += 4;
91
87
  if (bin > maxBinNumber + 1) {
92
88
  throw new Error('tabix index contains too many bins, please use a CSI index');
93
89
  }
94
90
  else if (bin === maxBinNumber + 1) {
95
- const chunkCount = bytes.readInt32LE(currOffset);
91
+ const chunkCount = dataView.getInt32(currOffset, true);
96
92
  currOffset += 4;
97
93
  if (chunkCount === 2) {
98
94
  stats = this.parsePseudoBin(bytes, currOffset);
@@ -100,7 +96,7 @@ export default class TabixIndex extends IndexFile {
100
96
  currOffset += 16 * chunkCount;
101
97
  }
102
98
  else {
103
- const chunkCount = bytes.readInt32LE(currOffset);
99
+ const chunkCount = dataView.getInt32(currOffset, true);
104
100
  currOffset += 4;
105
101
  const chunks = new Array(chunkCount);
106
102
  for (let k = 0; k < chunkCount; k += 1) {
@@ -114,7 +110,7 @@ export default class TabixIndex extends IndexFile {
114
110
  }
115
111
  }
116
112
  // the linear index
117
- const linearCount = bytes.readInt32LE(currOffset);
113
+ const linearCount = dataView.getInt32(currOffset, true);
118
114
  currOffset += 4;
119
115
  const linearIndex = new Array(linearCount);
120
116
  for (let k = 0; k < linearCount; k += 1) {
@@ -122,7 +118,11 @@ export default class TabixIndex extends IndexFile {
122
118
  currOffset += 8;
123
119
  firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
124
120
  }
125
- return { binIndex, linearIndex, stats };
121
+ return {
122
+ binIndex,
123
+ linearIndex,
124
+ stats,
125
+ };
126
126
  });
127
127
  return {
128
128
  indices,
@@ -140,7 +140,7 @@ export default class TabixIndex extends IndexFile {
140
140
  };
141
141
  }
142
142
  parsePseudoBin(bytes, offset) {
143
- const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
143
+ const lineCount = longToNumber(Long.fromBytesLE(bytes.subarray(offset + 16, offset + 24), true));
144
144
  return { lineCount };
145
145
  }
146
146
  _parseNameBytes(namesBytes) {
@@ -148,11 +148,11 @@ export default class TabixIndex extends IndexFile {
148
148
  let currNameStart = 0;
149
149
  const refIdToName = [];
150
150
  const refNameToId = {};
151
+ const decoder = new TextDecoder('utf8');
151
152
  for (let i = 0; i < namesBytes.length; i += 1) {
152
153
  if (!namesBytes[i]) {
153
154
  if (currNameStart < i) {
154
- let refName = namesBytes.toString('utf8', currNameStart, i);
155
- refName = this.renameRefSeq(refName);
155
+ const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
156
156
  refIdToName[currRefId] = refName;
157
157
  refNameToId[refName] = currRefId;
158
158
  }
@@ -160,7 +160,10 @@ export default class TabixIndex extends IndexFile {
160
160
  currRefId += 1;
161
161
  }
162
162
  }
163
- return { refNameToId, refIdToName };
163
+ return {
164
+ refNameToId,
165
+ refIdToName,
166
+ };
164
167
  }
165
168
  async blocksForRange(refName, min, max, opts = {}) {
166
169
  if (min < 0) {