@gmod/bam 1.1.9 → 1.1.10

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Files changed (10) hide show
  1. package/CHANGELOG.md +8 -0
  2. package/dist/bamFile.js +32 -37
  3. package/dist/bamFile.js.map +1 -1
  4. package/dist/record.d.ts +2 -2
  5. package/dist/record.js.map +1 -1
  6. package/esm/bamFile.js +10 -15
  7. package/esm/bamFile.js.map +1 -1
  8. package/esm/record.d.ts +2 -2
  9. package/esm/record.js.map +1 -1
  10. package/package.json +1 -2
package/CHANGELOG.md CHANGED
@@ -1,3 +1,11 @@
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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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+
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+
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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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+
1
9
  <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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11
 
package/dist/bamFile.js CHANGED
@@ -312,21 +312,13 @@ var BamFile = /** @class */ (function () {
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  });
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  };
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  BamFile.prototype.streamRecordsForRange = function (chr, min, max, opts) {
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- if (opts === void 0) { opts = {
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- viewAsPairs: false,
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- pairAcrossChr: false,
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- maxInsertSize: 200000,
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- }; }
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+ if (opts === void 0) { opts = {}; }
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  return __asyncGenerator(this, arguments, function streamRecordsForRange_1() {
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- var chrId, chunks, i, size, totalSize;
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+ var signal, chrId, chunks, i, size, totalSize;
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  return __generator(this, function (_a) {
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  switch (_a.label) {
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  case 0:
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- // todo regularize refseq names
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- opts.viewAsPairs = opts.viewAsPairs || false;
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- opts.pairAcrossChr = opts.pairAcrossChr || false;
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- opts.maxInsertSize =
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- opts.maxInsertSize !== undefined ? opts.maxInsertSize : 200000;
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+ signal = opts.signal;
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  chrId = this.chrToIndex && this.chrToIndex[chr];
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  if (!!(chrId >= 0)) return [3 /*break*/, 1];
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  chunks = [];
@@ -343,7 +335,7 @@ var BamFile = /** @class */ (function () {
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  _a.label = 4;
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  case 4:
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  if (!(i < chunks.length)) return [3 /*break*/, 7];
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- return [4 /*yield*/, __await((0, util_1.abortBreakPoint)(opts.signal))];
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+ return [4 /*yield*/, __await((0, util_1.abortBreakPoint)(signal))];
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  case 5:
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  _a.sent();
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  size = chunks[i].fetchedSize();
@@ -372,14 +364,15 @@ var BamFile = /** @class */ (function () {
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  };
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  BamFile.prototype._fetchChunkFeatures = function (chunks, chrId, min, max, opts) {
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  return __asyncGenerator(this, arguments, function _fetchChunkFeatures_1() {
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- var featPromises, done, i, _a, data, cpositions, dpositions, chunk, promise, i;
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- return __generator(this, function (_b) {
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- switch (_b.label) {
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+ var _a, viewAsPairs, featPromises, done, i, _b, data, cpositions, dpositions, chunk, promise, i;
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+ return __generator(this, function (_c) {
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+ switch (_c.label) {
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  case 0:
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+ _a = opts.viewAsPairs, viewAsPairs = _a === void 0 ? false : _a;
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  featPromises = [];
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  done = false;
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  i = 0;
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- _b.label = 1;
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+ _c.label = 1;
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  case 1:
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  if (!(i < chunks.length)) return [3 /*break*/, 5];
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  return [4 /*yield*/, __await(this._readChunk({
@@ -387,7 +380,7 @@ var BamFile = /** @class */ (function () {
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  opts: opts,
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  }))];
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  case 2:
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- _a = _b.sent(), data = _a.data, cpositions = _a.cpositions, dpositions = _a.dpositions, chunk = _a.chunk;
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+ _b = _c.sent(), data = _b.data, cpositions = _b.cpositions, dpositions = _b.dpositions, chunk = _b.chunk;
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  promise = this.readBamFeatures(data, cpositions, dpositions, chunk).then(function (records) {
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  var recs = [];
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  for (var i_1 = 0; i_1 < records.length; i_1 += 1) {
@@ -409,36 +402,36 @@ var BamFile = /** @class */ (function () {
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  featPromises.push(promise);
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  return [4 /*yield*/, __await(promise)];
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  case 3:
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- _b.sent();
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+ _c.sent();
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  if (done) {
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  return [3 /*break*/, 5];
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  }
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- _b.label = 4;
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+ _c.label = 4;
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  case 4:
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  i++;
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  return [3 /*break*/, 1];
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  case 5:
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  (0, util_1.checkAbortSignal)(opts.signal);
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  i = 0;
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- _b.label = 6;
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+ _c.label = 6;
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  case 6:
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  if (!(i < featPromises.length)) return [3 /*break*/, 10];
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  return [4 /*yield*/, __await(featPromises[i])];
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- case 7: return [4 /*yield*/, _b.sent()];
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+ case 7: return [4 /*yield*/, _c.sent()];
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  case 8:
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- _b.sent();
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- _b.label = 9;
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+ _c.sent();
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+ _c.label = 9;
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  case 9:
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  i++;
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  return [3 /*break*/, 6];
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  case 10:
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  (0, util_1.checkAbortSignal)(opts.signal);
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- if (!opts.viewAsPairs) return [3 /*break*/, 13];
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+ if (!viewAsPairs) return [3 /*break*/, 13];
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  return [4 /*yield*/, __await(this.fetchPairs(chrId, featPromises, opts))];
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- case 11: return [4 /*yield*/, _b.sent()];
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+ case 11: return [4 /*yield*/, _c.sent()];
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  case 12:
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- _b.sent();
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- _b.label = 13;
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+ _c.sent();
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+ _c.label = 13;
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  case 13: return [2 /*return*/];
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  }
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  });
@@ -446,11 +439,12 @@ var BamFile = /** @class */ (function () {
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  };
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  BamFile.prototype.fetchPairs = function (chrId, featPromises, opts) {
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  return __awaiter(this, void 0, void 0, function () {
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- var unmatedPairs, readIds, matePromises, mateBlocks, mateChunks, i, mateTotalSize, mateFeatPromises, newMateFeats, featuresRet, newMates;
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+ var _a, pairAcrossChr, _b, maxInsertSize, unmatedPairs, readIds, matePromises, mateBlocks, mateChunks, i, mateTotalSize, mateFeatPromises, newMateFeats, featuresRet, newMates;
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  var _this = this;
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- return __generator(this, function (_a) {
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- switch (_a.label) {
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+ return __generator(this, function (_c) {
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+ switch (_c.label) {
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  case 0:
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+ _a = opts.pairAcrossChr, pairAcrossChr = _a === void 0 ? false : _a, _b = opts.maxInsertSize, maxInsertSize = _b === void 0 ? 200000 : _b;
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  unmatedPairs = {};
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  readIds = {};
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  return [4 /*yield*/, Promise.all(featPromises.map(function (f) { return __awaiter(_this, void 0, void 0, function () {
@@ -481,7 +475,7 @@ var BamFile = /** @class */ (function () {
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  });
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  }); }))];
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  case 1:
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- _a.sent();
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+ _c.sent();
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  matePromises = [];
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  return [4 /*yield*/, Promise.all(featPromises.map(function (f) { return __awaiter(_this, void 0, void 0, function () {
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  var ret, i, name_2;
@@ -493,10 +487,10 @@ var BamFile = /** @class */ (function () {
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  for (i = 0; i < ret.length; i++) {
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  name_2 = ret[i].name();
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  if (unmatedPairs[name_2] &&
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- (opts.pairAcrossChr ||
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+ (pairAcrossChr ||
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  (ret[i]._next_refid() === chrId &&
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  Math.abs(ret[i].get('start') - ret[i]._next_pos()) <
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- (opts.maxInsertSize || 200000)))) {
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+ maxInsertSize))) {
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  matePromises.push(this.index.blocksForRange(ret[i]._next_refid(), ret[i]._next_pos(), ret[i]._next_pos() + 1, opts));
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  }
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  }
@@ -505,15 +499,16 @@ var BamFile = /** @class */ (function () {
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  });
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  }); }))];
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  case 2:
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- _a.sent();
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+ _c.sent();
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  return [4 /*yield*/, Promise.all(matePromises)];
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  case 3:
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- mateBlocks = _a.sent();
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+ mateBlocks = _c.sent();
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  mateChunks = [];
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  for (i = 0; i < mateBlocks.length; i++) {
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  mateChunks = mateChunks.concat(mateBlocks[i]);
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  }
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- // filter out duplicate chunks (the blocks are lists of chunks, blocks are concatenated, then filter dup chunks)
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+ // filter out duplicate chunks (the blocks are lists of chunks, blocks are
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+ // concatenated, then filter dup chunks)
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  mateChunks = mateChunks
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  .sort()
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  .filter(function (item, pos, ary) { return !pos || item.toString() !== ary[pos - 1].toString(); });
@@ -549,7 +544,7 @@ var BamFile = /** @class */ (function () {
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  }); });
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  return [4 /*yield*/, Promise.all(mateFeatPromises)];
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  case 4:
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- newMateFeats = _a.sent();
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+ newMateFeats = _c.sent();
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  featuresRet = [];
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  if (newMateFeats.length) {
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  newMates = newMateFeats.reduce(function (result, current) {
package/dist/bamFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/record.d.ts CHANGED
@@ -5,12 +5,12 @@
5
5
  export default class BamRecord {
6
6
  private data;
7
7
  private bytes;
8
- private flags;
9
8
  private _id;
10
- private _refID;
11
9
  private _tagOffset;
12
10
  private _tagList;
13
11
  private _allTagsParsed;
12
+ flags: any;
13
+ _refID: number;
14
14
  constructor(args: any);
15
15
  get(field: string): any;
16
16
  end(): any;
package/dist/record.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/bamFile.js CHANGED
@@ -150,16 +150,8 @@ export default class BamFile {
150
150
  }
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151
  return records;
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152
  }
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- async *streamRecordsForRange(chr, min, max, opts = {
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- viewAsPairs: false,
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- pairAcrossChr: false,
156
- maxInsertSize: 200000,
157
- }) {
158
- // todo regularize refseq names
159
- opts.viewAsPairs = opts.viewAsPairs || false;
160
- opts.pairAcrossChr = opts.pairAcrossChr || false;
161
- opts.maxInsertSize =
162
- opts.maxInsertSize !== undefined ? opts.maxInsertSize : 200000;
153
+ async *streamRecordsForRange(chr, min, max, opts = {}) {
154
+ const { signal } = opts;
163
155
  const chrId = this.chrToIndex && this.chrToIndex[chr];
164
156
  let chunks;
165
157
  if (!(chrId >= 0)) {
@@ -172,7 +164,7 @@ export default class BamFile {
172
164
  }
173
165
  }
174
166
  for (let i = 0; i < chunks.length; i += 1) {
175
- await abortBreakPoint(opts.signal);
167
+ await abortBreakPoint(signal);
176
168
  const size = chunks[i].fetchedSize();
177
169
  if (size > this.chunkSizeLimit) {
178
170
  throw new Error(`Too many BAM features. BAM chunk size ${size} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit}`);
@@ -187,6 +179,7 @@ export default class BamFile {
187
179
  yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
188
180
  }
189
181
  async *_fetchChunkFeatures(chunks, chrId, min, max, opts) {
182
+ const { viewAsPairs = false } = opts;
190
183
  const featPromises = [];
191
184
  let done = false;
192
185
  for (let i = 0; i < chunks.length; i++) {
@@ -223,11 +216,12 @@ export default class BamFile {
223
216
  yield featPromises[i];
224
217
  }
225
218
  checkAbortSignal(opts.signal);
226
- if (opts.viewAsPairs) {
219
+ if (viewAsPairs) {
227
220
  yield this.fetchPairs(chrId, featPromises, opts);
228
221
  }
229
222
  }
230
223
  async fetchPairs(chrId, featPromises, opts) {
224
+ const { pairAcrossChr = false, maxInsertSize = 200000 } = opts;
231
225
  const unmatedPairs = {};
232
226
  const readIds = {};
233
227
  await Promise.all(featPromises.map(async (f) => {
@@ -254,10 +248,10 @@ export default class BamFile {
254
248
  for (let i = 0; i < ret.length; i++) {
255
249
  const name = ret[i].name();
256
250
  if (unmatedPairs[name] &&
257
- (opts.pairAcrossChr ||
251
+ (pairAcrossChr ||
258
252
  (ret[i]._next_refid() === chrId &&
259
253
  Math.abs(ret[i].get('start') - ret[i]._next_pos()) <
260
- (opts.maxInsertSize || 200000)))) {
254
+ maxInsertSize))) {
261
255
  matePromises.push(this.index.blocksForRange(ret[i]._next_refid(), ret[i]._next_pos(), ret[i]._next_pos() + 1, opts));
262
256
  }
263
257
  }
@@ -267,7 +261,8 @@ export default class BamFile {
267
261
  for (let i = 0; i < mateBlocks.length; i++) {
268
262
  mateChunks = mateChunks.concat(mateBlocks[i]);
269
263
  }
270
- // filter out duplicate chunks (the blocks are lists of chunks, blocks are concatenated, then filter dup chunks)
264
+ // filter out duplicate chunks (the blocks are lists of chunks, blocks are
265
+ // concatenated, then filter dup chunks)
271
266
  mateChunks = mateChunks
272
267
  .sort()
273
268
  .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
package/esm/bamFile.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/record.d.ts CHANGED
@@ -5,12 +5,12 @@
5
5
  export default class BamRecord {
6
6
  private data;
7
7
  private bytes;
8
- private flags;
9
8
  private _id;
10
- private _refID;
11
9
  private _tagOffset;
12
10
  private _tagList;
13
11
  private _allTagsParsed;
12
+ flags: any;
13
+ _refID: number;
14
14
  constructor(args: any);
15
15
  get(field: string): any;
16
16
  end(): any;
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": "1.1.9",
3
+ "version": "1.1.10",
4
4
  "description": "Parser for BAM and BAM index (bai) files",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/bam-js",
@@ -58,7 +58,6 @@
58
58
  "@typescript-eslint/eslint-plugin": "^5.7.0",
59
59
  "@typescript-eslint/parser": "^5.7.0",
60
60
  "eslint": "^7.0.0",
61
- "eslint-config-airbnb-base": "^15.0.0",
62
61
  "eslint-config-prettier": "^8.3.0",
63
62
  "eslint-plugin-import": "^2.25.3",
64
63
  "eslint-plugin-prettier": "^4.0.0",