@gmod/bam - npm Package Compare versions

Comparing version 1.0.14 to 1.0.15

CHANGELOG.md

@@ -0,1 +1,9 @@
+## [1.0.15](https://github.com/GMOD/bam-js/compare/v1.0.14...v1.0.15) (2019-04-04)
+
+
+
+- Added check for too large of chromosomes in the bai bins
+- Added aborting support (thanks @rbuels)
+- Refactored index file class
+
 <a name="1.0.14"></a>
@@ -2,0 +10,0 @@ ## [1.0.14](https://github.com/GMOD/bam-js/compare/v1.0.13...v1.0.14) (2019-01-04)

dist/bai.js

@@ -1,133 +0,36 @@
-'use strict';
-
-var _regenerator = require('babel-runtime/regenerator');
-
-var _regenerator2 = _interopRequireDefault(_regenerator);
-
-var _asyncToGenerator2 = require('babel-runtime/helpers/asyncToGenerator');
-
-var _asyncToGenerator3 = _interopRequireDefault(_asyncToGenerator2);
-
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require('babel-runtime/helpers/createClass');
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var Long = require('long');
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/inherits"));var Long = require('long');
 var VirtualOffset = require('./virtualOffset');
 var Chunk = require('./chunk');
+var IndexFile = require('./indexFile');
 
 var BAI_MAGIC = 21578050; // BAI\1
+var _require = require('./util'),longToNumber = _require.longToNumber,abortBreakPoint = _require.abortBreakPoint;var
 
-var _require = require('./util'),
-    longToNumber = _require.longToNumber;
+BAI = /*#__PURE__*/function (_IndexFile) {(0, _inherits2.default)(BAI, _IndexFile);function BAI() {(0, _classCallCheck2.default)(this, BAI);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BAI).apply(this, arguments));}(0, _createClass2.default)(BAI, [{ key: "parsePseudoBin", value: function parsePseudoBin(
+    bytes, offset) {
+      var lineCount = longToNumber(
+      Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
 
-var BAI = function () {
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
-  function BAI(_ref) {
-    var filehandle = _ref.filehandle,
-        _ref$renameRefSeqs = _ref.renameRefSeqs,
-        renameRefSeqs = _ref$renameRefSeqs === undefined ? function (n) {
-      return n;
-    } : _ref$renameRefSeqs;
-    (0, _classCallCheck3.default)(this, BAI);
-
-    this.filehandle = filehandle;
-    this.renameRefSeq = renameRefSeqs;
-  }
-
-  (0, _createClass3.default)(BAI, [{
-    key: '_findFirstData',
-    value: function _findFirstData(data, virtualOffset) {
-      var currentFdl = data.firstDataLine;
-      if (currentFdl) {
-        data.firstDataLine = currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-      } else {
-        data.firstDataLine = virtualOffset;
-      }
-    }
-  }, {
-    key: 'parsePseudoBin',
-    value: function parsePseudoBin(bytes, offset) {
-      var lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true));
       return { lineCount: lineCount };
-    }
-  }, {
-    key: 'lineCount',
-    value: function () {
-      var _ref2 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee(refId) {
-        var index, ret;
-        return _regenerator2.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.parse();
+    } }, { key: "lineCount", value: function () {var _lineCount = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(
 
-              case 2:
-                _context.t0 = refId;
-                index = _context.sent.indices[_context.t0];
+      refId) {var index, ret;return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:_context.next = 2;return (
+                  this.parse());case 2:_context.t0 = refId;index = _context.sent.indices[_context.t0];if (
+                index) {_context.next = 6;break;}return _context.abrupt("return",
+                -1);case 6:
 
-                if (index) {
-                  _context.next = 6;
-                  break;
-                }
+                ret = index.stats || {};return _context.abrupt("return",
+                ret.lineCount === undefined ? -1 : ret.lineCount);case 8:case "end":return _context.stop();}}}, _callee, this);}));function lineCount(_x) {return _lineCount.apply(this, arguments);}return lineCount;}()
 
-                return _context.abrupt('return', -1);
 
-              case 6:
-                ret = index.stats || {};
-                return _context.abrupt('return', ret.lineCount === undefined ? -1 : ret.lineCount);
-
-              case 8:
-              case 'end':
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function lineCount(_x) {
-        return _ref2.apply(this, arguments);
-      }
-
-      return lineCount;
-    }()
-
-    // memoize
     // fetch and parse the index
+  }, { key: "_parse", value: function () {var _parse2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(abortSignal) {var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, nintv;return _regenerator.default.wrap(function _callee2$(_context2) {while (1) {switch (_context2.prev = _context2.next) {case 0:
+                data = { bai: true, maxBlockSize: 1 << 16 };_context2.next = 3;return (
+                  this.filehandle.readFile(abortSignal));case 3:bytes = _context2.sent;if (!(
 
-  }, {
-    key: 'parse',
-    value: function () {
-      var _ref3 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee2() {
-        var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, nintv;
-        return _regenerator2.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                data = { bai: true, maxBlockSize: 1 << 16 };
-                _context2.next = 3;
-                return this.filehandle.readFile();
 
-              case 3:
-                bytes = _context2.sent;
+                bytes.readUInt32LE(0) !== BAI_MAGIC)) {_context2.next = 6;break;}throw (
+                  new Error('Not a BAI file'));case 6:
 
-                if (!(bytes.readUInt32LE(0) !== BAI_MAGIC)) {
-                  _context2.next = 6;
-                  break;
-                }
 
-                throw new Error('Not a BAI file');
-
-              case 6:
-
                 data.refCount = bytes.readInt32LE(4);
@@ -138,110 +41,68 @@ depth = 5;
                 // read the indexes for each reference sequence
-
                 data.indices = new Array(data.refCount);
                 currOffset = 8;
+                i = 0;case 12:if (!(i < data.refCount)) {_context2.next = 49;break;}_context2.next = 15;return (
+                  abortBreakPoint(abortSignal));case 15:
 
-                for (i = 0; i < data.refCount; i += 1) {
-                  // the binning index
-                  binCount = bytes.readInt32LE(currOffset);
-                  stats = void 0;
+                // the binning index
+                binCount = bytes.readInt32LE(currOffset);
+                stats = void 0;
 
+                currOffset += 4;
+                binIndex = {};
+                j = 0;case 20:if (!(j < binCount)) {_context2.next = 41;break;}
+                bin = bytes.readUInt32LE(currOffset);
+                currOffset += 4;if (!(
+                bin === binLimit + 1)) {_context2.next = 29;break;}
+                currOffset += 4;
+                stats = this.parsePseudoBin(bytes, currOffset);
+                currOffset += 32;_context2.next = 38;break;case 29:if (!(
+                bin > binLimit + 1)) {_context2.next = 33;break;}throw (
+                  new Error('bai index contains too many bins, please use CSI'));case 33:
 
-                  currOffset += 4;
-                  binIndex = {};
+                chunkCount = bytes.readInt32LE(currOffset);
+                currOffset += 4;
+                chunks = new Array(chunkCount);
+                for (k = 0; k < chunkCount; k += 1) {
+                  u = VirtualOffset.fromBytes(bytes, currOffset);
+                  v = VirtualOffset.fromBytes(bytes, currOffset + 8);
+                  currOffset += 16;
+                  this._findFirstData(data, u);
+                  chunks[k] = new Chunk(u, v, bin);
+                }
+                binIndex[bin] = chunks;case 38:j += 1;_context2.next = 20;break;case 41:
 
-                  for (j = 0; j < binCount; j += 1) {
-                    bin = bytes.readUInt32LE(currOffset);
 
-                    if (bin > binLimit) {
-                      stats = this.parsePseudoBin(bytes, currOffset + 4);
-                    }
 
-                    chunkCount = bytes.readInt32LE(currOffset + 4);
-
-                    currOffset += 8;
-                    chunks = new Array(chunkCount);
-
-                    for (k = 0; k < chunkCount; k += 1) {
-                      u = VirtualOffset.fromBytes(bytes, currOffset);
-                      v = VirtualOffset.fromBytes(bytes, currOffset + 8);
-
-                      currOffset += 16;
-                      this._findFirstData(data, u);
-                      chunks[k] = new Chunk(u, v, bin);
-                    }
-                    binIndex[bin] = chunks;
-                  }
-
-                  nintv = bytes.readInt32LE(currOffset);
-
-                  currOffset += 4;
-                  // as we're going through the linear index, figure out
-                  // the smallest virtual offset in the indexes, which
-                  // tells us where the BAM header ends
-                  if (nintv) {
-                    this._findFirstData(bytes, VirtualOffset.fromBytes(bytes, currOffset));
-                  }
-
-                  currOffset += nintv * 8;
-
-                  data.indices[i] = { binIndex: binIndex, stats: stats };
+                nintv = bytes.readInt32LE(currOffset);
+                currOffset += 4;
+                // as we're going through the linear index, figure out
+                // the smallest virtual offset in the indexes, which
+                // tells us where the BAM header ends
+                if (nintv) {
+                  this._findFirstData(bytes, VirtualOffset.fromBytes(bytes, currOffset));
                 }
 
-                return _context2.abrupt('return', data);
+                currOffset += nintv * 8;
 
-              case 13:
-              case 'end':
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
+                data.indices[i] = { binIndex: binIndex, stats: stats };case 46:i += 1;_context2.next = 12;break;case 49:return _context2.abrupt("return",
 
-      function parse() {
-        return _ref3.apply(this, arguments);
-      }
 
-      return parse;
-    }()
-  }, {
-    key: 'blocksForRange',
-    value: function () {
-      var _ref4 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee3(refId, beg, end) {
-        var indexData, indexes, binIndex, bins, l, numOffsets, i, off, _i, chunks, j, _i2, _i3, _i4;
+                data);case 50:case "end":return _context2.stop();}}}, _callee2, this);}));function _parse(_x2) {return _parse2.apply(this, arguments);}return _parse;}() }, { key: "blocksForRange", value: function () {var _blocksForRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(
 
-        return _regenerator2.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                if (beg < 0) beg = 0;
 
-                _context3.next = 3;
-                return this.parse();
+      refId, beg, end) {var indexData, indexes, binIndex, bins, l, numOffsets, i, off, _i, chunks, j, _i2, _i3, _i4;return _regenerator.default.wrap(function _callee3$(_context3) {while (1) {switch (_context3.prev = _context3.next) {case 0:
+                if (beg < 0) beg = 0;_context3.next = 3;return (
 
-              case 3:
-                indexData = _context3.sent;
+                  this.parse());case 3:indexData = _context3.sent;if (
+                indexData) {_context3.next = 6;break;}return _context3.abrupt("return", []);case 6:
+                indexes = indexData.indices[refId];if (
+                indexes) {_context3.next = 9;break;}return _context3.abrupt("return", []);case 9:
 
-                if (indexData) {
-                  _context3.next = 6;
-                  break;
-                }
+                binIndex = indexes.binIndex;
 
-                return _context3.abrupt('return', []);
+                bins = this.reg2bins(beg, end);
 
-              case 6:
-                indexes = indexData.indices[refId];
 
-                if (indexes) {
-                  _context3.next = 9;
-                  break;
-                }
-
-                return _context3.abrupt('return', []);
-
-              case 9:
-                binIndex = indexes.binIndex;
-                bins = this.reg2bins(beg, end);
-                l = void 0;
                 numOffsets = 0;
-
                 for (i = 0; i < bins.length; i += 1) {
@@ -251,37 +112,25 @@ if (binIndex[bins[i]]) {
                   }
-                }
+                }if (!(
 
-                if (!(numOffsets === 0)) {
-                  _context3.next = 16;
-                  break;
-                }
+                numOffsets === 0)) {_context3.next = 15;break;}return _context3.abrupt("return", []);case 15:
 
-                return _context3.abrupt('return', []);
-
-              case 16:
                 off = [];
-
                 numOffsets = 0;
                 for (_i = 0; _i < bins.length; _i += 1) {
                   chunks = binIndex[bins[_i]];
+                  if (chunks)
+                  for (j = 0; j < chunks.length; j += 1) {
+                    off[numOffsets] = new Chunk(
+                    chunks[j].minv,
+                    chunks[j].maxv,
+                    chunks[j].bin);
 
-                  if (chunks) for (j = 0; j < chunks.length; j += 1) {
-                    off[numOffsets] = new Chunk(chunks[j].minv, chunks[j].maxv, chunks[j].bin);
                     numOffsets += 1;
                   }
-                }
+                }if (
 
-                if (off.length) {
-                  _context3.next = 21;
-                  break;
-                }
+                off.length) {_context3.next = 20;break;}return _context3.abrupt("return", []);case 20:
 
-                return _context3.abrupt('return', []);
+                off = off.sort(function (a, b) {return a.compareTo(b);});
 
-              case 21:
-
-                off = off.sort(function (a, b) {
-                  return a.compareTo(b);
-                });
-
                 // resolve completely contained adjacent blocks
@@ -300,7 +149,10 @@ l = 0;
                 for (_i3 = 1; _i3 < numOffsets; _i3 += 1) {
-                  if (off[_i3 - 1].maxv.compareTo(off[_i3].minv) >= 0) off[_i3 - 1].maxv = off[_i3].minv;
-                } // merge adjacent blocks
+                  if (off[_i3 - 1].maxv.compareTo(off[_i3].minv) >= 0)
+                  off[_i3 - 1].maxv = off[_i3].minv;}
+                // merge adjacent blocks
                 l = 0;
                 for (_i4 = 1; _i4 < numOffsets; _i4 += 1) {
-                  if (off[l].maxv.blockPosition === off[_i4].minv.blockPosition) off[l].maxv = off[_i4].maxv;else {
+                  if (off[l].maxv.blockPosition === off[_i4].minv.blockPosition)
+                  off[l].maxv = off[_i4].maxv;else
+                  {
                     l += 1;
@@ -311,108 +163,24 @@ off[l].minv = off[_i4].minv;
                 }
-                numOffsets = l + 1;
+                numOffsets = l + 1;return _context3.abrupt("return",
 
-                return _context3.abrupt('return', off.slice(0, numOffsets));
+                off.slice(0, numOffsets));case 29:case "end":return _context3.stop();}}}, _callee3, this);}));function blocksForRange(_x3, _x4, _x5) {return _blocksForRange.apply(this, arguments);}return blocksForRange;}()
 
-              case 30:
-              case 'end':
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
 
-      function blocksForRange(_x2, _x3, _x4) {
-        return _ref4.apply(this, arguments);
-      }
-
-      return blocksForRange;
-    }()
-
     /**
-     * @param {number} seqId
-     * @returns {Promise} true if the index contains entries for
-     * the given reference sequence ID, false otherwise
-     */
-
-  }, {
-    key: 'hasRefSeq',
-    value: function () {
-      var _ref5 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee4(seqId) {
-        return _regenerator2.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.parse();
-
-              case 2:
-                _context4.t1 = seqId;
-                _context4.t0 = _context4.sent.indices[_context4.t1];
-
-                if (_context4.t0) {
-                  _context4.next = 6;
-                  break;
-                }
-
-                _context4.t0 = {};
-
-              case 6:
-                return _context4.abrupt('return', !!_context4.t0.binIndex);
-
-              case 7:
-              case 'end':
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function hasRefSeq(_x5) {
-        return _ref5.apply(this, arguments);
-      }
-
-      return hasRefSeq;
-    }()
-
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-
-  }, {
-    key: 'reg2bins',
-    value: function reg2bins(beg, end) {
+                                                                                                                                                                                                                                * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+                                                                                                                                                                                                                                * @returns {Array[number]}
+                                                                                                                                                                                                                                */ }, { key: "reg2bins", value: function reg2bins(
+    beg, end) {
       var list = [0];
       end -= 1;
-      for (var k = 1 + (beg >> 26); k <= 1 + (end >> 26); k += 1) {
-        list.push(k);
-      }for (var _k = 9 + (beg >> 23); _k <= 9 + (end >> 23); _k += 1) {
-        list.push(_k);
-      }for (var _k2 = 73 + (beg >> 20); _k2 <= 73 + (end >> 20); _k2 += 1) {
-        list.push(_k2);
-      }for (var _k3 = 585 + (beg >> 17); _k3 <= 585 + (end >> 17); _k3 += 1) {
-        list.push(_k3);
-      }for (var _k4 = 4681 + (beg >> 14); _k4 <= 4681 + (end >> 14); _k4 += 1) {
-        list.push(_k4);
-      }return list;
-    }
-  }]);
-  return BAI;
-}();
+      for (var k = 1 + (beg >> 26); k <= 1 + (end >> 26); k += 1) {list.push(k);}
+      for (var _k = 9 + (beg >> 23); _k <= 9 + (end >> 23); _k += 1) {list.push(_k);}
+      for (var _k2 = 73 + (beg >> 20); _k2 <= 73 + (end >> 20); _k2 += 1) {list.push(_k2);}
+      for (var _k3 = 585 + (beg >> 17); _k3 <= 585 + (end >> 17); _k3 += 1) {list.push(_k3);}
+      for (var _k4 = 4681 + (beg >> 14); _k4 <= 4681 + (end >> 14); _k4 += 1) {
+        list.push(_k4);}
+      return list;
+    } }]);return BAI;}(IndexFile);
 
-// this is the stupidest possible memoization, ignores arguments.
 
-
-function tinyMemoize(_class, methodName) {
-  var method = _class.prototype[methodName];
-  if (!method) throw new Error('no method ' + methodName + ' found in class ' + _class.name);
-  var memoAttrName = '_memo_' + methodName;
-  _class.prototype[methodName] = function _tinyMemoized() {
-    if (!(memoAttrName in this)) this[memoAttrName] = method.call(this);
-    return this[memoAttrName];
-  };
-}
-// memoize index.parse()
-tinyMemoize(BAI, 'parse');
-
 module.exports = BAI;

dist/bamFile.js

@@ -1,78 +0,36 @@
-'use strict';
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/slicedToArray"));var _entries = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/object/entries"));var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/toConsumableArray"));var _promise = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/promise"));var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));var _require =
 
-var _slicedToArray2 = require('babel-runtime/helpers/slicedToArray');
+require('@gmod/bgzf-filehandle'),unzip = _require.unzip;
+var LRU = require('quick-lru');
+var BAI = require('./bai');
+var CSI = require('./csi');
+var LocalFile = require('./localFile');
+var BAMFeature = require('./record');var _require2 =
+require('./sam'),parseHeaderText = _require2.parseHeaderText;var _require3 =
+require('./util'),abortBreakPoint = _require3.abortBreakPoint,checkAbortSignal = _require3.checkAbortSignal;
 
-var _slicedToArray3 = _interopRequireDefault(_slicedToArray2);
+var BAM_MAGIC = 21840194;
 
-var _entries = require('babel-runtime/core-js/object/entries');
+var blockLen = 1 << 16;var
 
-var _entries2 = _interopRequireDefault(_entries);
+BamFile = /*#__PURE__*/function () {
+  /**
+                                     * @param {object} args
+                                     * @param {string} [args.bamPath]
+                                     * @param {FileHandle} [args.bamFilehandle]
+                                     * @param {string} [args.baiPath]
+                                     * @param {FileHandle} [args.baiFilehandle]
+                                     */
+  function BamFile(_ref)
 
-var _toConsumableArray2 = require('babel-runtime/helpers/toConsumableArray');
 
-var _toConsumableArray3 = _interopRequireDefault(_toConsumableArray2);
 
-var _promise = require('babel-runtime/core-js/promise');
 
-var _promise2 = _interopRequireDefault(_promise);
 
-var _regenerator = require('babel-runtime/regenerator');
 
-var _regenerator2 = _interopRequireDefault(_regenerator);
 
-var _asyncToGenerator2 = require('babel-runtime/helpers/asyncToGenerator');
 
-var _asyncToGenerator3 = _interopRequireDefault(_asyncToGenerator2);
 
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
 
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require('babel-runtime/helpers/createClass');
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var _require = require('@gmod/bgzf-filehandle'),
-    unzip = _require.unzip;
-
-var LRU = require('quick-lru');
-
-var BAI = require('./bai');
-var CSI = require('./csi');
-var LocalFile = require('./localFile');
-var BAMFeature = require('./record');
-
-var _require2 = require('./sam'),
-    parseHeaderText = _require2.parseHeaderText;
-
-var BAM_MAGIC = 21840194;
-
-var blockLen = 1 << 16;
-
-var BamFile = function () {
-  /**
-   * @param {object} args
-   * @param {string} [args.bamPath]
-   * @param {FileHandle} [args.bamFilehandle]
-   * @param {string} [args.baiPath]
-   * @param {FileHandle} [args.baiFilehandle]
-   */
-  function BamFile(_ref) {
-    var bamFilehandle = _ref.bamFilehandle,
-        bamPath = _ref.bamPath,
-        baiPath = _ref.baiPath,
-        baiFilehandle = _ref.baiFilehandle,
-        csiPath = _ref.csiPath,
-        csiFilehandle = _ref.csiFilehandle,
-        cacheSize = _ref.cacheSize,
-        fetchSizeLimit = _ref.fetchSizeLimit,
-        chunkSizeLimit = _ref.chunkSizeLimit,
-        _ref$renameRefSeqs = _ref.renameRefSeqs,
-        renameRefSeqs = _ref$renameRefSeqs === undefined ? function (n) {
-      return n;
-    } : _ref$renameRefSeqs;
-    (0, _classCallCheck3.default)(this, BamFile);
-
+  {var bamFilehandle = _ref.bamFilehandle,bamPath = _ref.bamPath,baiPath = _ref.baiPath,baiFilehandle = _ref.baiFilehandle,csiPath = _ref.csiPath,csiFilehandle = _ref.csiFilehandle,cacheSize = _ref.cacheSize,fetchSizeLimit = _ref.fetchSizeLimit,chunkSizeLimit = _ref.chunkSizeLimit,_ref$renameRefSeqs = _ref.renameRefSeqs,renameRefSeqs = _ref$renameRefSeqs === void 0 ? function (n) {return n;} : _ref$renameRefSeqs;(0, _classCallCheck2.default)(this, BamFile);
     this.renameRefSeq = renameRefSeqs;
@@ -90,4 +48,4 @@
       this.index = new CSI({
-        filehandle: new LocalFile(csiPath)
-      });
+        filehandle: new LocalFile(csiPath) });
+
     } else if (baiFilehandle) {
@@ -98,54 +56,34 @@ this.index = new BAI({ filehandle: baiFilehandle });
     } else {
-      this.index = new BAI({ filehandle: new LocalFile(bamPath + '.bai') });
+      this.index = new BAI({ filehandle: new LocalFile("".concat(bamPath, ".bai")) });
     }
 
-    this.featureCache = new LRU({
-      maxSize: cacheSize !== undefined ? cacheSize : 20000,
-      length: function length(featureArray) {
-        return featureArray.length;
-      }
-    });
+    this.featureCache = new _abortablePromiseCache.default({
+      cache: new LRU({
+        maxSize: cacheSize !== undefined ? cacheSize : 50 }),
 
+      fill: this._readChunk.bind(this) });
+
+
     this.fetchSizeLimit = fetchSizeLimit || 50000000;
     this.chunkSizeLimit = chunkSizeLimit || 10000000;
-  }
+  }(0, _createClass2.default)(BamFile, [{ key: "getHeader", value: function () {var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(
 
-  (0, _createClass3.default)(BamFile, [{
-    key: 'getHeader',
-    value: function () {
-      var _ref2 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee() {
-        var indexData, ret, buf, bytesRead, uncba, headLen, _ref3, chrToIndex, indexToChr;
+      abortSignal) {var indexData, ret, buf, bytesRead, uncba, headLen, _ref2, chrToIndex, indexToChr;return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:_context.next = 2;return (
+                  this.index.parse(abortSignal));case 2:indexData = _context.sent;
+                ret = indexData.firstDataLine ?
+                indexData.firstDataLine.blockPosition + 65535 :
+                undefined;if (!
 
-        return _regenerator2.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.index.parse();
+                ret) {_context.next = 14;break;}
+                buf = Buffer.alloc(ret + blockLen);_context.next = 8;return (
+                  this.bam.read(
+                  buf,
+                  0,
+                  ret + blockLen,
+                  0,
+                  abortSignal));case 8:bytesRead = _context.sent;if (
 
-              case 2:
-                indexData = _context.sent;
-                ret = indexData.firstDataLine ? indexData.firstDataLine.blockPosition + 65535 : undefined;
-                buf = void 0;
+                bytesRead) {_context.next = 11;break;}throw (
+                  new Error('Error reading header'));case 11:
 
-                if (!ret) {
-                  _context.next = 15;
-                  break;
-                }
-
-                buf = Buffer.alloc(ret + blockLen);
-                _context.next = 9;
-                return this.bam.read(buf, 0, ret + blockLen, 0);
-
-              case 9:
-                bytesRead = _context.sent;
-
-                if (bytesRead) {
-                  _context.next = 12;
-                  break;
-                }
-
-                throw new Error('Error reading header');
-
-              case 12:
                 if (bytesRead < ret) {
@@ -155,96 +93,40 @@ buf = buf.slice(0, bytesRead);
                   buf = buf.slice(0, ret);
-                }
-                _context.next = 18;
-                break;
+                }_context.next = 17;break;case 14:_context.next = 16;return (
 
-              case 15:
-                _context.next = 17;
-                return this.bam.readFile();
+                  this.bam.readFile(abortSignal));case 16:buf = _context.sent;case 17:_context.next = 19;return (
 
-              case 17:
-                buf = _context.sent;
 
-              case 18:
-                _context.next = 20;
-                return unzip(buf);
+                  unzip(buf));case 19:uncba = _context.sent;if (!(
 
-              case 20:
-                uncba = _context.sent;
-
-                if (!(uncba.readInt32LE(0) !== BAM_MAGIC)) {
-                  _context.next = 23;
-                  break;
-                }
-
-                throw new Error('Not a BAM file');
-
-              case 23:
+                uncba.readInt32LE(0) !== BAM_MAGIC)) {_context.next = 22;break;}throw new Error('Not a BAM file');case 22:
                 headLen = uncba.readInt32LE(4);
 
+                this.header = uncba.toString('utf8', 8, 8 + headLen);_context.next = 26;return (
+                  this._readRefSeqs(
+                  headLen + 8,
+                  65535,
+                  abortSignal));case 26:_ref2 = _context.sent;chrToIndex = _ref2.chrToIndex;indexToChr = _ref2.indexToChr;
 
-                this.header = uncba.toString('utf8', 8, 8 + headLen);
-                _context.next = 27;
-                return this._readRefSeqs(headLen + 8, 65535);
-
-              case 27:
-                _ref3 = _context.sent;
-                chrToIndex = _ref3.chrToIndex;
-                indexToChr = _ref3.indexToChr;
-
                 this.chrToIndex = chrToIndex;
-                this.indexToChr = indexToChr;
+                this.indexToChr = indexToChr;return _context.abrupt("return",
 
-                return _context.abrupt('return', parseHeaderText(this.header));
+                parseHeaderText(this.header));case 32:case "end":return _context.stop();}}}, _callee, this);}));function getHeader(_x) {return _getHeader.apply(this, arguments);}return getHeader;}()
 
-              case 33:
-              case 'end':
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
 
-      function getHeader() {
-        return _ref2.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-
     // the full length of the refseq block is not given in advance so this grabs a chunk and
     // doubles it if all refseqs haven't been processed
+  }, { key: "_readRefSeqs", value: function () {var _readRefSeqs2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(start, refSeqBytes, abortSignal) {var buf, bytesRead, uncba, nRef, p, chrToIndex, indexToChr, i, lName, refName, lRef;return _regenerator.default.wrap(function _callee2$(_context2) {while (1) {switch (_context2.prev = _context2.next) {case 0:
+                buf = Buffer.alloc(refSeqBytes + blockLen);if (!(
+                start > refSeqBytes)) {_context2.next = 3;break;}return _context2.abrupt("return",
+                this._readRefSeqs(start, refSeqBytes * 2));case 3:_context2.next = 5;return (
 
-  }, {
-    key: '_readRefSeqs',
-    value: function () {
-      var _ref4 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee2(start, refSeqBytes) {
-        var buf, bytesRead, uncba, nRef, p, chrToIndex, indexToChr, i, lName, refName, lRef;
-        return _regenerator2.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                buf = Buffer.alloc(refSeqBytes + blockLen);
+                  this.bam.read(
+                  buf,
+                  0,
+                  refSeqBytes + blockLen,
+                  abortSignal));case 5:bytesRead = _context2.sent;if (
 
-                if (!(start > refSeqBytes)) {
-                  _context2.next = 3;
-                  break;
-                }
+                bytesRead) {_context2.next = 8;break;}return _context2.abrupt("return",
+                new Error('Error reading refseqs from header'));case 8:
 
-                return _context2.abrupt('return', this._readRefSeqs(start, refSeqBytes * 2));
-
-              case 3:
-                _context2.next = 5;
-                return this.bam.read(buf, 0, refSeqBytes + blockLen);
-
-              case 5:
-                bytesRead = _context2.sent;
-
-                if (bytesRead) {
-                  _context2.next = 8;
-                  break;
-                }
-
-                return _context2.abrupt('return', new Error('Error reading refseqs from header'));
-
-              case 8:
                 if (bytesRead < refSeqBytes) {
@@ -254,8 +136,4 @@ buf = buf.slice(0, bytesRead);
                   buf = buf.slice(0, refSeqBytes);
-                }
-                _context2.next = 11;
-                return unzip(buf);
-
-              case 11:
-                uncba = _context2.sent;
+                }_context2.next = 11;return (
+                  unzip(buf));case 11:uncba = _context2.sent;
                 nRef = uncba.readInt32LE(start);
@@ -265,62 +143,25 @@ p = start + 4;
                 indexToChr = [];
-                i = 0;
-
-              case 17:
-                if (!(i < nRef)) {
-                  _context2.next = 31;
-                  break;
-                }
-
+                i = 0;case 17:if (!(i < nRef)) {_context2.next = 33;break;}_context2.next = 20;return (
+                  abortBreakPoint(abortSignal));case 20:
                 lName = uncba.readInt32LE(p);
                 refName = uncba.toString('utf8', p + 4, p + 4 + lName - 1);
-
                 refName = this.renameRefSeq(refName);
                 lRef = uncba.readInt32LE(p + lName + 4);
 
-
                 chrToIndex[refName] = i;
                 indexToChr.push({ refName: refName, length: lRef });
 
-                p = p + 8 + lName;
+                p = p + 8 + lName;if (!(
+                p > uncba.length)) {_context2.next = 30;break;}
+                // eslint-disable-next-line no-console
+                console.warn("BAM header is very big.  Re-fetching ".concat(
+                refSeqBytes, " bytes."));return _context2.abrupt("return",
 
-                if (!(p > uncba.length)) {
-                  _context2.next = 28;
-                  break;
-                }
+                this._readRefSeqs(start, refSeqBytes * 2));case 30:i += 1;_context2.next = 17;break;case 33:return _context2.abrupt("return",
 
-                console.warn('BAM header is very big.  Re-fetching ' + refSeqBytes + ' bytes.');
-                return _context2.abrupt('return', this._readRefSeqs(start, refSeqBytes * 2));
 
-              case 28:
-                i += 1;
-                _context2.next = 17;
-                break;
+                { chrToIndex: chrToIndex, indexToChr: indexToChr });case 34:case "end":return _context2.stop();}}}, _callee2, this);}));function _readRefSeqs(_x2, _x3, _x4) {return _readRefSeqs2.apply(this, arguments);}return _readRefSeqs;}() }, { key: "getRecordsForRange", value: function () {var _getRecordsForRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(
 
-              case 31:
-                return _context2.abrupt('return', { chrToIndex: chrToIndex, indexToChr: indexToChr });
 
-              case 32:
-              case 'end':
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function _readRefSeqs(_x, _x2) {
-        return _ref4.apply(this, arguments);
-      }
-
-      return _readRefSeqs;
-    }()
-  }, {
-    key: 'getRecordsForRange',
-    value: function () {
-      var _ref5 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee3(chr, min, max) {
-        var opts = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : {};
-        var chrId, chunks, i, size, totalSize;
-        return _regenerator2.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
+      chr, min, max) {var opts,chrId,chunks,i,size,totalSize,_args3 = arguments;return _regenerator.default.wrap(function _callee3$(_context3) {while (1) {switch (_context3.prev = _context3.next) {case 0:opts = _args3.length > 3 && _args3[3] !== undefined ? _args3[3] : {};
                 opts.viewAsPairs = opts.viewAsPairs || false;
@@ -330,106 +171,42 @@ opts.pairAcrossChr = opts.pairAcrossChr || false;
                 // todo regularize refseq names
-                chrId = this.chrToIndex && this.chrToIndex[chr];
-                chunks = void 0;
+                chrId = this.chrToIndex && this.chrToIndex[chr];if (
 
-                if (chrId >= 0) {
-                  _context3.next = 9;
-                  break;
-                }
+                chrId >= 0) {_context3.next = 9;break;}
+                chunks = [];_context3.next = 14;break;case 9:_context3.next = 11;return (
 
-                chunks = [];
-                _context3.next = 14;
-                break;
+                  this.index.blocksForRange(chrId, min - 1, max, opts));case 11:chunks = _context3.sent;if (
 
-              case 9:
-                _context3.next = 11;
-                return this.index.blocksForRange(chrId, min - 1, max);
+                chunks) {_context3.next = 14;break;}throw (
+                  new Error('Error in index fetch'));case 14:
 
-              case 11:
-                chunks = _context3.sent;
 
-                if (chunks) {
-                  _context3.next = 14;
-                  break;
-                }
 
-                throw new Error('Error in index fetch');
+                i = 0;case 15:if (!(i < chunks.length)) {_context3.next = 24;break;}_context3.next = 18;return (
+                  abortBreakPoint(opts.signal));case 18:
+                size = chunks[i].fetchedSize();if (!(
+                size > this.chunkSizeLimit)) {_context3.next = 21;break;}throw (
+                  new Error("Too many BAM features. BAM chunk size ".concat(
+                  size, " bytes exceeds chunkSizeLimit of ").concat(
+                  this.chunkSizeLimit)));case 21:i += 1;_context3.next = 15;break;case 24:
 
-              case 14:
-                i = 0;
 
-              case 15:
-                if (!(i < chunks.length)) {
-                  _context3.next = 22;
-                  break;
-                }
 
-                size = chunks[i].fetchedSize();
 
-                if (!(size > this.chunkSizeLimit)) {
-                  _context3.next = 19;
-                  break;
-                }
 
-                throw new Error('Too many BAM features. BAM chunk size ' + size + ' bytes exceeds chunkSizeLimit of ' + this.chunkSizeLimit);
+                totalSize = chunks.
+                map(function (s) {return s.fetchedSize();}).
+                reduce(function (a, b) {return a + b;}, 0);if (!(
+                totalSize > this.fetchSizeLimit)) {_context3.next = 27;break;}throw (
+                  new Error("data size of ".concat(
+                  totalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes")));case 27:return _context3.abrupt("return",
 
-              case 19:
-                i += 1;
-                _context3.next = 15;
-                break;
 
-              case 22:
-                totalSize = chunks.map(function (s) {
-                  return s.fetchedSize();
-                }).reduce(function (a, b) {
-                  return a + b;
-                }, 0);
+                this._fetchChunkFeatures(chunks, chrId, min, max, opts));case 28:case "end":return _context3.stop();}}}, _callee3, this);}));function getRecordsForRange(_x5, _x6, _x7) {return _getRecordsForRange.apply(this, arguments);}return getRecordsForRange;}() }, { key: "_fetchChunkFeatures", value: function () {var _fetchChunkFeatures2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(
 
-                if (!(totalSize > this.fetchSizeLimit)) {
-                  _context3.next = 25;
-                  break;
-                }
 
-                throw new Error('data size of ' + totalSize.toLocaleString() + ' bytes exceeded fetch size limit of ' + this.fetchSizeLimit.toLocaleString() + ' bytes');
-
-              case 25:
-                return _context3.abrupt('return', this._fetchChunkFeatures(chunks, chrId, min, max, opts));
-
-              case 26:
-              case 'end':
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRecordsForRange(_x3, _x4, _x5) {
-        return _ref5.apply(this, arguments);
-      }
-
-      return getRecordsForRange;
-    }()
-  }, {
-    key: '_fetchChunkFeatures',
-    value: function () {
-      var _ref6 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee4(chunks, chrId, min, max) {
-        var _this = this,
-            _ref7;
-
-        var opts = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : {};
-
-        var recordPromises, featPromises, recs, ret, readNames, readIds, i, name, id, unmatedPairs, matePromises, _i, _name, blocks, mateBlocks, mateChunks, _i2, _mateChunks, mateRecordPromises, mateFeatPromises, mateTotalSize, newMateFeats, newMates;
-
-        return _regenerator2.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
+      chunks, chrId, min, max) {var _this = this,_ref3;var opts,recordPromises,featPromises,recs,ret,readNames,readIds,i,name,id,unmatedPairs,matePromises,_i,_name,blocks,mateBlocks,mateChunks,_i2,_mateChunks,mateRecordPromises,mateFeatPromises,mateTotalSize,newMateFeats,newMates,_args4 = arguments;return _regenerator.default.wrap(function _callee4$(_context4) {while (1) {switch (_context4.prev = _context4.next) {case 0:opts = _args4.length > 4 && _args4[4] !== undefined ? _args4[4] : {};
                 recordPromises = [];
                 featPromises = [];
-
                 chunks.forEach(function (c) {
-                  var recordPromise = _this.featureCache.get(c.toString());
-                  if (!recordPromise) {
-                    recordPromise = _this._readChunk(c);
-                    _this.featureCache.set(c.toString(), recordPromise);
-                  }
+                  var recordPromise = _this.featureCache.get(c.toString(), c, opts.signal);
                   recordPromises.push(recordPromise);
@@ -444,3 +221,4 @@ var featPromise = recordPromise.then(function (f) {
                           // past end of range, can stop iterating
-                          break;else if (feature.get('end') >= min) {
+                          break;else
+                        if (feature.get('end') >= min) {
                           // must be in range
@@ -454,22 +232,12 @@ recs.push(feature);
                   featPromises.push(featPromise);
-                });
-                _context4.next = 5;
-                return _promise2.default.all(featPromises);
-
-              case 5:
-                recs = _context4.sent;
-                ret = (_ref7 = []).concat.apply(_ref7, (0, _toConsumableArray3.default)(recs));
-
-                if (!opts.viewAsPairs) {
-                  _context4.next = 31;
-                  break;
-                }
-
+                });_context4.next = 6;return (
+                  _promise.default.all(featPromises));case 6:recs = _context4.sent;
+                checkAbortSignal(opts.signal);
+                ret = (_ref3 = []).concat.apply(_ref3, (0, _toConsumableArray2.default)(recs));if (!
+                opts.viewAsPairs) {_context4.next = 33;break;}
                 readNames = {};
                 readIds = {};
-
                 for (i = 0; i < ret.length; i++) {
                   name = ret[i].name();
                   id = ret[i].id();
-
                   if (!readNames[name]) readNames[name] = 0;
@@ -480,8 +248,3 @@ readNames[name]++;
                 unmatedPairs = {};
-
-                (0, _entries2.default)(readNames).forEach(function (_ref8) {
-                  var _ref9 = (0, _slicedToArray3.default)(_ref8, 2),
-                      k = _ref9[0],
-                      v = _ref9[1];
-
+                (0, _entries.default)(readNames).forEach(function (_ref4) {var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),k = _ref5[0],v = _ref5[1];
                   if (v === 1) unmatedPairs[k] = true;
@@ -491,49 +254,49 @@ });
                 matePromises = [];
-
                 for (_i = 0; _i < ret.length; _i++) {
                   _name = ret[_i].name();
+                  if (
+                  unmatedPairs[_name] && (
+                  ret[_i]._next_refid() === chrId || opts.pairAcrossChr) &&
+                  Math.abs(ret[_i].get('start') - ret[_i]._next_pos()) <
+                  opts.maxInsertSize)
+                  {
+                    blocks = this.index.blocksForRange(
+                    ret[_i]._next_refid(),
+                    ret[_i]._next_pos(),
+                    ret[_i]._next_pos() + 1,
+                    opts);
 
-                  if (unmatedPairs[_name] && (ret[_i]._next_refid() === chrId || opts.pairAcrossChr) && Math.abs(ret[_i].get('start') - ret[_i]._next_pos()) < opts.maxInsertSize) {
-                    blocks = this.index.blocksForRange(ret[_i]._next_refid(), ret[_i]._next_pos(), ret[_i]._next_pos() + 1);
-
                     matePromises.push(blocks);
                   }
-                }
-                _context4.next = 17;
-                return _promise2.default.all(matePromises);
-
-              case 17:
-                mateBlocks = _context4.sent;
+                }_context4.next = 19;return (
+                  _promise.default.all(matePromises));case 19:mateBlocks = _context4.sent;
                 mateChunks = [];
-
                 for (_i2 = 0; _i2 < mateBlocks.length; _i2++) {
-                  (_mateChunks = mateChunks).push.apply(_mateChunks, (0, _toConsumableArray3.default)(mateBlocks[_i2]));
+                  (_mateChunks = mateChunks).push.apply(_mateChunks, (0, _toConsumableArray2.default)(mateBlocks[_i2]));
                 }
                 // filter out duplicate chunks (the blocks are lists of chunks, blocks are concatenated, then filter dup chunks)
-                mateChunks = mateChunks.sort().filter(function (item, pos, ary) {
-                  return !pos || item.toString() !== ary[pos - 1].toString();
-                });
+                mateChunks = mateChunks.
+                sort().
+                filter(
+                function (item, pos, ary) {return (
+                    !pos || item.toString() !== ary[pos - 1].toString());});
 
+
                 mateRecordPromises = [];
                 mateFeatPromises = [];
-                mateTotalSize = mateChunks.map(function (s) {
-                  return s.fetchedSize();
-                }).reduce(function (a, b) {
-                  return a + b;
-                }, 0);
 
-                if (!(mateTotalSize > this.fetchSizeLimit)) {
-                  _context4.next = 26;
-                  break;
-                }
+                mateTotalSize = mateChunks.
+                map(function (s) {return s.fetchedSize();}).
+                reduce(function (a, b) {return a + b;}, 0);if (!(
+                mateTotalSize > this.fetchSizeLimit)) {_context4.next = 28;break;}throw (
+                  new Error("data size of ".concat(
+                  mateTotalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes")));case 28:
 
-                throw new Error('data size of ' + mateTotalSize.toLocaleString() + ' bytes exceeded fetch size limit of ' + this.fetchSizeLimit.toLocaleString() + ' bytes');
 
-              case 26:
                 mateChunks.forEach(function (c) {
-                  var recordPromise = _this.featureCache.get(c.toString());
-                  if (!recordPromise) {
-                    recordPromise = _this._readChunk(c);
-                    _this.featureCache.set(c.toString(), recordPromise);
-                  }
+                  var recordPromise = _this.featureCache.get(
+                  c.toString(),
+                  c,
+                  opts.signal);
+
                   mateRecordPromises.push(recordPromise);
@@ -544,3 +307,6 @@ var featPromise = recordPromise.then(function (feats) {
                       var feature = feats[_i3];
-                      if (unmatedPairs[feature.get('name')] && !readIds[feature.get('id')]) {
+                      if (
+                      unmatedPairs[feature.get('name')] &&
+                      !readIds[feature.get('id')])
+                      {
                         mateRecs.push(feature);
@@ -552,60 +318,30 @@ }
                   mateFeatPromises.push(featPromise);
-                });
-                _context4.next = 29;
-                return _promise2.default.all(mateFeatPromises);
+                });_context4.next = 31;return (
+                  _promise.default.all(mateFeatPromises));case 31:newMateFeats = _context4.sent;
+                if (newMateFeats.length) {
+                  newMates = newMateFeats.reduce(function (result, current) {return (
+                      result.concat(current));});
 
-              case 29:
-                newMateFeats = _context4.sent;
-
-                if (newMateFeats.length) {
-                  newMates = newMateFeats.reduce(function (result, current) {
-                    return result.concat(current);
-                  });
                   // console.log(chrId, min, max, newMates.map(m => m.get('name')).sort())
-
                   ret = ret.concat(newMates);
-                }
+                }case 33:return _context4.abrupt("return",
 
-              case 31:
-                return _context4.abrupt('return', ret);
+                ret);case 34:case "end":return _context4.stop();}}}, _callee4, this);}));function _fetchChunkFeatures(_x8, _x9, _x10, _x11) {return _fetchChunkFeatures2.apply(this, arguments);}return _fetchChunkFeatures;}() }, { key: "_readChunk", value: function () {var _readChunk2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(
 
-              case 32:
-              case 'end':
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
 
-      function _fetchChunkFeatures(_x7, _x8, _x9, _x10) {
-        return _ref6.apply(this, arguments);
-      }
-
-      return _fetchChunkFeatures;
-    }()
-  }, {
-    key: '_readChunk',
-    value: function () {
-      var _ref10 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee5(chunk) {
-        var bufsize, buf, bytesRead, data;
-        return _regenerator2.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
+      chunk, abortSignal) {var bufsize, buf, bytesRead, data;return _regenerator.default.wrap(function _callee5$(_context5) {while (1) {switch (_context5.prev = _context5.next) {case 0:
                 bufsize = chunk.fetchedSize();
-                buf = Buffer.alloc(bufsize + blockLen);
-                _context5.next = 4;
-                return this.bam.read(buf, 0, bufsize + blockLen, chunk.minv.blockPosition);
+                buf = Buffer.alloc(bufsize + blockLen);_context5.next = 4;return (
+                  this.bam.read(
+                  buf,
+                  0,
+                  bufsize + blockLen,
+                  chunk.minv.blockPosition,
+                  abortSignal));case 4:bytesRead = _context5.sent;
 
-              case 4:
-                bytesRead = _context5.sent;
+                checkAbortSignal(abortSignal);if (
 
-                if (bytesRead) {
-                  _context5.next = 7;
-                  break;
-                }
+                bytesRead) {_context5.next = 8;break;}return _context5.abrupt("return",
+                []);case 8:
 
-                return _context5.abrupt('return', []);
-
-              case 7:
                 if (bytesRead < bufsize) {
@@ -615,28 +351,10 @@ buf = buf.slice(0, bytesRead);
                   buf = buf.slice(0, bufsize);
-                }
+                }_context5.next = 11;return (
 
-                _context5.next = 10;
-                return unzip(buf);
+                  unzip(buf));case 11:data = _context5.sent;
+                checkAbortSignal(abortSignal);return _context5.abrupt("return",
+                this.readBamFeatures(data, chunk.minv.dataPosition));case 14:case "end":return _context5.stop();}}}, _callee5, this);}));function _readChunk(_x12, _x13) {return _readChunk2.apply(this, arguments);}return _readChunk;}() }, { key: "readBamFeatures", value: function readBamFeatures(
 
-              case 10:
-                data = _context5.sent;
-                return _context5.abrupt('return', this.readBamFeatures(data, chunk.minv.dataPosition));
 
-              case 12:
-              case 'end':
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function _readChunk(_x12) {
-        return _ref10.apply(this, arguments);
-      }
-
-      return _readChunk;
-    }()
-  }, {
-    key: 'readBamFeatures',
-    value: function readBamFeatures(ba, blockStart) {
+    ba, blockStart) {
       var sink = [];
@@ -651,4 +369,4 @@
           var feature = new BAMFeature({
-            bytes: { byteArray: ba, start: blockStart, end: blockEnd }
-          });
+            bytes: { byteArray: ba, start: blockStart, end: blockEnd } });
+
           sink.push(feature);
@@ -660,12 +378,9 @@ }
       return sink;
-    }
-  }, {
-    key: 'hasRefSeq',
-    value: function hasRefSeq(seqId) {
+    } }, { key: "hasRefSeq", value: function hasRefSeq(
+
+    seqId) {
       return this.index.hasRefSeq(seqId);
-    }
-  }]);
-  return BamFile;
-}();
+    } }]);return BamFile;}();
 
+
 module.exports = BamFile;

dist/chunk.js

@@ -1,24 +0,10 @@
-"use strict";
-
-var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck");
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require("babel-runtime/helpers/createClass");
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-// little class representing a chunk in the index
-var Chunk = function () {
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass")); // little class representing a chunk in the index
+var Chunk = /*#__PURE__*/function () {
   /**
-   * @param {VirtualOffset} minv
-   * @param {VirtualOffset} maxv
-   * @param {number} bin
-   * @param {number} [fetchedSize]
-   */
-  function Chunk(minv, maxv, bin, fetchedSize) {
-    (0, _classCallCheck3.default)(this, Chunk);
-
+                                       * @param {VirtualOffset} minv
+                                       * @param {VirtualOffset} maxv
+                                       * @param {number} bin
+                                       * @param {number} [fetchedSize]
+                                       */
+  function Chunk(minv, maxv, bin, fetchedSize) {(0, _classCallCheck2.default)(this, Chunk);
     this.minv = minv;
@@ -28,29 +14,28 @@ this.maxv = maxv;
     this._fetchedSize = fetchedSize;
-  }
+  }(0, _createClass2.default)(Chunk, [{ key: "toUniqueString", value: function toUniqueString()
 
-  (0, _createClass3.default)(Chunk, [{
-    key: "toUniqueString",
-    value: function toUniqueString() {
-      return this.minv + ".." + this.maxv + " (bin " + this.bin + ", fetchedSize " + this.fetchedSize() + ")";
-    }
-  }, {
-    key: "toString",
-    value: function toString() {
+    {
+      return "".concat(this.minv, "..").concat(this.maxv, " (bin ").concat(
+      this.bin, ", fetchedSize ").concat(
+      this.fetchedSize(), ")");
+    } }, { key: "toString", value: function toString()
+
+    {
       return this.toUniqueString();
-    }
-  }, {
-    key: "compareTo",
-    value: function compareTo(b) {
-      return this.minv.compareTo(b.minv) || this.maxv.compareTo(b.maxv) || this.bin - b.bin;
-    }
-  }, {
-    key: "fetchedSize",
-    value: function fetchedSize() {
+    } }, { key: "compareTo", value: function compareTo(
+
+    b) {
+      return (
+        this.minv.compareTo(b.minv) ||
+        this.maxv.compareTo(b.maxv) ||
+        this.bin - b.bin);
+
+    } }, { key: "fetchedSize", value: function fetchedSize()
+
+    {
       if (this._fetchedSize !== undefined) return this._fetchedSize;
       return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
-    }
-  }]);
-  return Chunk;
-}();
+    } }]);return Chunk;}();
 
+
 module.exports = Chunk;

dist/constants.js

@@ -1,4 +0,2 @@
-"use strict";
-
-module.exports = {
+"use strict";module.exports = {
   //  the read is paired in sequencing, no matter whether it is mapped in a pair
@@ -27,3 +25,2 @@ BAM_FPAIRED: 1,
   //  supplementary alignment
-  BAM_FSUPPLEMENTARY: 2048
-};
+  BAM_FSUPPLEMENTARY: 2048 };

dist/csi.js

@@ -1,35 +0,9 @@
-'use strict';
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _assign = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/object/assign"));var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/inherits"));var Long = require('long');var _require =
+require('@gmod/bgzf-filehandle'),unzip = _require.unzip;
 
-var _assign = require('babel-runtime/core-js/object/assign');
-
-var _assign2 = _interopRequireDefault(_assign);
-
-var _regenerator = require('babel-runtime/regenerator');
-
-var _regenerator2 = _interopRequireDefault(_regenerator);
-
-var _asyncToGenerator2 = require('babel-runtime/helpers/asyncToGenerator');
-
-var _asyncToGenerator3 = _interopRequireDefault(_asyncToGenerator2);
-
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require('babel-runtime/helpers/createClass');
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var Long = require('long');
-
-var _require = require('@gmod/bgzf-filehandle'),
-    unzip = _require.unzip;
-
 var VirtualOffset = require('./virtualOffset');
 var Chunk = require('./chunk');
+var IndexFile = require('./indexFile');var _require2 =
 
-var _require2 = require('./util'),
-    longToNumber = _require2.longToNumber;
+require('./util'),longToNumber = _require2.longToNumber,abortBreakPoint = _require2.abortBreakPoint;
 
@@ -44,93 +18,16 @@ var CSI1_MAGIC = 21582659; // CSI\1
   return Math.floor(num / Math.pow(2, bits));
-}
+}var
 
-var CSI = function () {
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
-  function CSI(_ref) {
-    var filehandle = _ref.filehandle,
-        _ref$renameRefSeqs = _ref.renameRefSeqs,
-        renameRefSeqs = _ref$renameRefSeqs === undefined ? function (n) {
-      return n;
-    } : _ref$renameRefSeqs;
-    (0, _classCallCheck3.default)(this, CSI);
+CSI = /*#__PURE__*/function (_IndexFile) {(0, _inherits2.default)(CSI, _IndexFile);function CSI() {(0, _classCallCheck2.default)(this, CSI);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CSI).apply(this, arguments));}(0, _createClass2.default)(CSI, [{ key: "lineCount", value: function () {var _lineCount = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(
+      refId) {var indexData, idx, stats;return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:_context.next = 2;return (
+                  this.parse());case 2:indexData = _context.sent;if (
+                indexData) {_context.next = 5;break;}return _context.abrupt("return", -1);case 5:
+                idx = indexData.indices[refId];if (
+                idx) {_context.next = 8;break;}return _context.abrupt("return", -1);case 8:
+                stats = indexData.indices[refId].stats;if (!
+                stats) {_context.next = 11;break;}return _context.abrupt("return", stats.lineCount);case 11:return _context.abrupt("return",
+                -1);case 12:case "end":return _context.stop();}}}, _callee, this);}));function lineCount(_x) {return _lineCount.apply(this, arguments);}return lineCount;}() }, { key: "parseAuxData", value: function parseAuxData(
 
-    this.filehandle = filehandle;
-    this.renameRefSeq = renameRefSeqs;
-  }
 
-  (0, _createClass3.default)(CSI, [{
-    key: '_findFirstData',
-    value: function _findFirstData(data, virtualOffset) {
-      var currentFdl = data.firstDataLine;
-      if (currentFdl) {
-        data.firstDataLine = currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-      } else {
-        data.firstDataLine = virtualOffset;
-      }
-    }
-  }, {
-    key: 'lineCount',
-    value: function () {
-      var _ref2 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee(refId) {
-        var indexData, idx, stats;
-        return _regenerator2.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.parse();
-
-              case 2:
-                indexData = _context.sent;
-
-                if (indexData) {
-                  _context.next = 5;
-                  break;
-                }
-
-                return _context.abrupt('return', -1);
-
-              case 5:
-                idx = indexData.indices[refId];
-
-                if (idx) {
-                  _context.next = 8;
-                  break;
-                }
-
-                return _context.abrupt('return', -1);
-
-              case 8:
-                stats = indexData.indices[refId].stats;
-
-                if (!stats) {
-                  _context.next = 11;
-                  break;
-                }
-
-                return _context.abrupt('return', stats.lineCount);
-
-              case 11:
-                return _context.abrupt('return', -1);
-
-              case 12:
-              case 'end':
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function lineCount(_x) {
-        return _ref2.apply(this, arguments);
-      }
-
-      return lineCount;
-    }()
-  }, {
-    key: 'parseAuxData',
-    value: function parseAuxData(bytes, offset, auxLength) {
+    bytes, offset, auxLength) {
       if (auxLength < 30) return {};
@@ -140,10 +37,12 @@
       data.formatFlags = bytes.readInt32LE(offset);
-      data.coordinateType = data.formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
+      data.coordinateType =
+      data.formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
       data.format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[data.formatFlags & 0xf];
-      if (!data.format) throw new Error('invalid Tabix preset format flags ' + data.formatFlags);
+      if (!data.format)
+      throw new Error("invalid Tabix preset format flags ".concat(data.formatFlags));
       data.columnNumbers = {
         ref: bytes.readInt32LE(offset + 4),
         start: bytes.readInt32LE(offset + 8),
-        end: bytes.readInt32LE(offset + 12)
-      };
+        end: bytes.readInt32LE(offset + 12) };
+
       data.metaValue = bytes.readInt32LE(offset + 16);
@@ -154,8 +53,12 @@ data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
 
-      (0, _assign2.default)(data, this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
+      (0, _assign.default)(
+      data,
+      this._parseNameBytes(
+      bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
+
+
       return data;
-    }
-  }, {
-    key: '_parseNameBytes',
-    value: function _parseNameBytes(namesBytes) {
+    } }, { key: "_parseNameBytes", value: function _parseNameBytes(
+
+    namesBytes) {
       var currRefId = 0;
@@ -180,51 +83,17 @@ var currNameStart = 0;
 
-    // memoize
     // fetch and parse the index
+  }, { key: "_parse", value: function () {var _parse2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(abortSignal) {var data, bytes, auxLength, currOffset, i, binCount, binIndex, stats, j, bin, loffset, chunkCount, chunks, k, u, v;return _regenerator.default.wrap(function _callee2$(_context2) {while (1) {switch (_context2.prev = _context2.next) {case 0:
+                data = { csi: true, maxBlockSize: 1 << 16 };_context2.t0 =
+                unzip;_context2.next = 4;return this.filehandle.readFile(abortSignal);case 4:_context2.t1 = _context2.sent;_context2.next = 7;return (0, _context2.t0)(_context2.t1);case 7:bytes = _context2.sent;if (!(
 
-  }, {
-    key: 'parse',
-    value: function () {
-      var _ref3 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee2() {
-        var data, bytes, auxLength, currOffset, i, binCount, binIndex, stats, j, bin, loffset, chunkCount, chunks, k, u, v;
-        return _regenerator2.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                data = { csi: true, maxBlockSize: 1 << 16 };
-                _context2.t0 = unzip;
-                _context2.next = 4;
-                return this.filehandle.readFile();
 
-              case 4:
-                _context2.t1 = _context2.sent;
-                _context2.next = 7;
-                return (0, _context2.t0)(_context2.t1);
+                bytes.readUInt32LE(0) === CSI1_MAGIC)) {_context2.next = 12;break;}
+                data.csiVersion = 1;_context2.next = 17;break;case 12:if (!(
+                bytes.readUInt32LE(0) === CSI2_MAGIC)) {_context2.next = 16;break;}
+                data.csiVersion = 2;_context2.next = 17;break;case 16:throw (
 
-              case 7:
-                bytes = _context2.sent;
+                  new Error('Not a CSI file'));case 17:
 
-                if (!(bytes.readUInt32LE(0) === CSI1_MAGIC)) {
-                  _context2.next = 12;
-                  break;
-                }
 
-                data.csiVersion = 1;
-                _context2.next = 17;
-                break;
 
-              case 12:
-                if (!(bytes.readUInt32LE(0) === CSI2_MAGIC)) {
-                  _context2.next = 16;
-                  break;
-                }
-
-                data.csiVersion = 2;
-                _context2.next = 17;
-                break;
-
-              case 16:
-                throw new Error('Not a CSI file');
-
-              case 17:
-
                 this.minShift = bytes.readInt32LE(4);
@@ -234,5 +103,4 @@ this.depth = bytes.readInt32LE(8);
                 auxLength = bytes.readInt32LE(12);
-
                 if (auxLength) {
-                  (0, _assign2.default)(data, this.parseAuxData(bytes, 16, auxLength));
+                  (0, _assign.default)(data, this.parseAuxData(bytes, 16, auxLength));
                 }
@@ -244,62 +112,40 @@ data.refCount = bytes.readInt32LE(16 + auxLength);
                 currOffset = 16 + auxLength + 4;
-
-                for (i = 0; i < data.refCount; i += 1) {
-                  // the binning index
-                  binCount = bytes.readInt32LE(currOffset);
-
-                  currOffset += 4;
-                  binIndex = {};
-                  stats = void 0; // < provided by parsing a pseudo-bin, if present
-
-                  for (j = 0; j < binCount; j += 1) {
-                    bin = bytes.readUInt32LE(currOffset);
-
-                    if (bin > this.maxBinNumber) {
-                      // this is a fake bin that actually has stats information
-                      // about the reference sequence in it
-                      stats = this.parsePseudoBin(bytes, currOffset + 4);
-                      currOffset += 4 + 8 + 4 + 16 + 16;
-                    } else {
-                      loffset = VirtualOffset.fromBytes(bytes, currOffset + 4);
-
-                      this._findFirstData(data, loffset);
-                      chunkCount = bytes.readInt32LE(currOffset + 12);
-
+                i = 0;case 26:if (!(i < data.refCount)) {_context2.next = 38;break;}_context2.next = 29;return (
+                  abortBreakPoint(abortSignal));case 29:
+                // the binning index
+                binCount = bytes.readInt32LE(currOffset);
+                currOffset += 4;
+                binIndex = {};
+                stats = void 0; // < provided by parsing a pseudo-bin, if present
+                for (j = 0; j < binCount; j += 1) {
+                  bin = bytes.readUInt32LE(currOffset);
+                  if (bin > this.maxBinNumber) {
+                    // this is a fake bin that actually has stats information
+                    // about the reference sequence in it
+                    stats = this.parsePseudoBin(bytes, currOffset + 4);
+                    currOffset += 4 + 8 + 4 + 16 + 16;
+                  } else {
+                    loffset = VirtualOffset.fromBytes(bytes, currOffset + 4);
+                    this._findFirstData(data, loffset);
+                    chunkCount = bytes.readInt32LE(currOffset + 12);
+                    currOffset += 16;
+                    chunks = new Array(chunkCount);
+                    for (k = 0; k < chunkCount; k += 1) {
+                      u = VirtualOffset.fromBytes(bytes, currOffset);
+                      v = VirtualOffset.fromBytes(bytes, currOffset + 8);
                       currOffset += 16;
-                      chunks = new Array(chunkCount);
-
-                      for (k = 0; k < chunkCount; k += 1) {
-                        u = VirtualOffset.fromBytes(bytes, currOffset);
-                        v = VirtualOffset.fromBytes(bytes, currOffset + 8);
-
-                        currOffset += 16;
-                        // this._findFirstData(data, u)
-                        chunks[k] = new Chunk(u, v, bin);
-                      }
-                      binIndex[bin] = chunks;
+                      // this._findFirstData(data, u)
+                      chunks[k] = new Chunk(u, v, bin);
                     }
+                    binIndex[bin] = chunks;
                   }
-
-                  data.indices[i] = { binIndex: binIndex, stats: stats };
                 }
 
-                return _context2.abrupt('return', data);
+                data.indices[i] = { binIndex: binIndex, stats: stats };case 35:i += 1;_context2.next = 26;break;case 38:return _context2.abrupt("return",
 
-              case 27:
-              case 'end':
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
 
-      function parse() {
-        return _ref3.apply(this, arguments);
-      }
+                data);case 39:case "end":return _context2.stop();}}}, _callee2, this);}));function _parse(_x2) {return _parse2.apply(this, arguments);}return _parse;}() }, { key: "parsePseudoBin", value: function parsePseudoBin(
 
-      return parse;
-    }()
-  }, {
-    key: 'parsePseudoBin',
-    value: function parsePseudoBin(bytes, offset) {
+
+    bytes, offset) {
       // const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
@@ -310,83 +156,47 @@ // const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
       // )
-      var lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
+      var lineCount = longToNumber(
+      Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
+
       return { lineCount: lineCount };
-    }
-  }, {
-    key: 'blocksForRange',
-    value: function () {
-      var _ref4 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee3(refId, beg, end) {
-        var indexData, indexes, binIndex, bins, l, numOffsets, i, off, _i, chunks, j, _i2, _i3, _i4;
+    } }, { key: "blocksForRange", value: function () {var _blocksForRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(
 
-        return _regenerator2.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                if (beg < 0) beg = 0;
+      refId, beg, end, opts) {var indexData, indexes, binIndex, bins, l, numOffsets, i, off, _i, chunks, j, _i2, _i3, _i4;return _regenerator.default.wrap(function _callee3$(_context3) {while (1) {switch (_context3.prev = _context3.next) {case 0:
+                if (beg < 0) beg = 0;_context3.next = 3;return (
 
-                _context3.next = 3;
-                return this.parse();
+                  this.parse(opts.signal));case 3:indexData = _context3.sent;if (
+                indexData) {_context3.next = 6;break;}return _context3.abrupt("return", []);case 6:
+                indexes = indexData.indices[refId];if (
+                indexes) {_context3.next = 9;break;}return _context3.abrupt("return", []);case 9:
 
-              case 3:
-                indexData = _context3.sent;
+                binIndex = indexes.binIndex;
 
-                if (indexData) {
-                  _context3.next = 6;
-                  break;
-                }
+                bins = this.reg2bins(beg, end);
 
-                return _context3.abrupt('return', []);
 
-              case 6:
-                indexes = indexData.indices[refId];
-
-                if (indexes) {
-                  _context3.next = 9;
-                  break;
-                }
-
-                return _context3.abrupt('return', []);
-
-              case 9:
-                binIndex = indexes.binIndex;
-                bins = this.reg2bins(beg, end);
-                l = void 0;
                 numOffsets = 0;
-
                 for (i = 0; i < bins.length; i += 1) {
                   if (binIndex[bins[i]]) numOffsets += binIndex[bins[i]].length;
-                }
+                }if (!(
 
-                if (!(numOffsets === 0)) {
-                  _context3.next = 16;
-                  break;
-                }
+                numOffsets === 0)) {_context3.next = 15;break;}return _context3.abrupt("return", []);case 15:
 
-                return _context3.abrupt('return', []);
-
-              case 16:
                 off = [];
-
                 numOffsets = 0;
                 for (_i = 0; _i < bins.length; _i += 1) {
                   chunks = binIndex[bins[_i]];
+                  if (chunks)
+                  for (j = 0; j < chunks.length; j += 1) {
+                    off[numOffsets] = new Chunk(
+                    chunks[j].minv,
+                    chunks[j].maxv,
+                    chunks[j].bin);
 
-                  if (chunks) for (j = 0; j < chunks.length; j += 1) {
-                    off[numOffsets] = new Chunk(chunks[j].minv, chunks[j].maxv, chunks[j].bin);
                     numOffsets += 1;
                   }
-                }
+                }if (
 
-                if (off.length) {
-                  _context3.next = 21;
-                  break;
-                }
+                off.length) {_context3.next = 20;break;}return _context3.abrupt("return", []);case 20:
 
-                return _context3.abrupt('return', []);
+                off = off.sort(function (a, b) {return a.compareTo(b);});
 
-              case 21:
-
-                off = off.sort(function (a, b) {
-                  return a.compareTo(b);
-                });
-
                 // resolve completely contained adjacent blocks
@@ -405,7 +215,10 @@ l = 0;
                 for (_i3 = 1; _i3 < numOffsets; _i3 += 1) {
-                  if (off[_i3 - 1].maxv.compareTo(off[_i3].minv) >= 0) off[_i3 - 1].maxv = off[_i3].minv;
-                } // merge adjacent blocks
+                  if (off[_i3 - 1].maxv.compareTo(off[_i3].minv) >= 0)
+                  off[_i3 - 1].maxv = off[_i3].minv;}
+                // merge adjacent blocks
                 l = 0;
                 for (_i4 = 1; _i4 < numOffsets; _i4 += 1) {
-                  if (off[l].maxv.blockPosition === off[_i4].minv.blockPosition) off[l].maxv = off[_i4].maxv;else {
+                  if (off[l].maxv.blockPosition === off[_i4].minv.blockPosition)
+                  off[l].maxv = off[_i4].maxv;else
+                  {
                     l += 1;
@@ -416,74 +229,12 @@ off[l].minv = off[_i4].minv;
                 }
-                numOffsets = l + 1;
+                numOffsets = l + 1;return _context3.abrupt("return",
 
-                return _context3.abrupt('return', off.slice(0, numOffsets));
+                off.slice(0, numOffsets));case 29:case "end":return _context3.stop();}}}, _callee3, this);}));function blocksForRange(_x3, _x4, _x5, _x6) {return _blocksForRange.apply(this, arguments);}return blocksForRange;}()
 
-              case 30:
-              case 'end':
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
 
-      function blocksForRange(_x2, _x3, _x4) {
-        return _ref4.apply(this, arguments);
-      }
-
-      return blocksForRange;
-    }()
-
     /**
-     * @param {number} seqId
-     * @returns {Promise} true if the index contains entries for
-     * the given reference sequence ID, false otherwise
-     */
-
-  }, {
-    key: 'hasRefSeq',
-    value: function () {
-      var _ref5 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee4(seqId) {
-        return _regenerator2.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.parse();
-
-              case 2:
-                _context4.t1 = seqId;
-                _context4.t0 = _context4.sent.indices[_context4.t1];
-
-                if (_context4.t0) {
-                  _context4.next = 6;
-                  break;
-                }
-
-                _context4.t0 = {};
-
-              case 6:
-                return _context4.abrupt('return', !!_context4.t0.binIndex);
-
-              case 7:
-              case 'end':
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function hasRefSeq(_x5) {
-        return _ref5.apply(this, arguments);
-      }
-
-      return hasRefSeq;
-    }()
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-
-  }, {
-    key: 'reg2bins',
-    value: function reg2bins(beg, end) {
+                                                                                                                                                                                                                                     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+                                                                                                                                                                                                                                     * @returns {Array[number]}
+                                                                                                                                                                                                                                     */ }, { key: "reg2bins", value: function reg2bins(
+    beg, end) {
       beg -= 1; // < convert to 1-based closed
@@ -500,28 +251,16 @@ if (beg < 1) beg = 1;
         var e = t + rshift(end, s);
-        if (e - b + bins.length > this.maxBinNumber) throw new Error('query ' + beg + '-' + end + ' is too large for current binning scheme (shift ' + this.minShift + ', depth ' + this.depth + '), try a smaller query or a coarser index binning scheme');
-        for (var i = b; i <= e; i += 1) {
-          bins.push(i);
-        }
+        if (e - b + bins.length > this.maxBinNumber)
+        throw new Error("query ".concat(
+        beg, "-").concat(end, " is too large for current binning scheme (shift ").concat(
+        this.minShift, ", depth ").concat(
+
+        this.depth, "), try a smaller query or a coarser index binning scheme"));
+
+
+        for (var i = b; i <= e; i += 1) {bins.push(i);}
       }
       return bins;
-    }
-  }]);
-  return CSI;
-}();
+    } }]);return CSI;}(IndexFile);
 
-// this is the stupidest possible memoization, ignores arguments.
 
-
-function tinyMemoize(_class, methodName) {
-  var method = _class.prototype[methodName];
-  if (!method) throw new Error('no method ' + methodName + ' found in class ' + _class.name);
-  var memoAttrName = '_memo_' + methodName;
-  _class.prototype[methodName] = function _tinyMemoized() {
-    if (!(memoAttrName in this)) this[memoAttrName] = method.call(this);
-    return this[memoAttrName];
-  };
-}
-// memoize index.parse()
-tinyMemoize(CSI, 'parse');
-
 module.exports = CSI;

dist/errors.js

@@ -1,108 +0,24 @@
-"use strict";
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/inherits"));var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/wrapNativeSuper"));var BamError = /*#__PURE__*/function (_Error) {(0, _inherits2.default)(BamError, _Error);function BamError() {(0, _classCallCheck2.default)(this, BamError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamError).apply(this, arguments));}return BamError;}((0, _wrapNativeSuper2.default)(Error));
 
-var _getPrototypeOf = require("babel-runtime/core-js/object/get-prototype-of");
+/** Error caused by encountering a part of the BAM spec that has not yet been implemented */var
+BamUnimplementedError = /*#__PURE__*/function (_Error2) {(0, _inherits2.default)(BamUnimplementedError, _Error2);function BamUnimplementedError() {(0, _classCallCheck2.default)(this, BamUnimplementedError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamUnimplementedError).apply(this, arguments));}return BamUnimplementedError;}((0, _wrapNativeSuper2.default)(Error));
 
-var _getPrototypeOf2 = _interopRequireDefault(_getPrototypeOf);
+/** An error caused by malformed data.  */var
+BamMalformedError = /*#__PURE__*/function (_BamError) {(0, _inherits2.default)(BamMalformedError, _BamError);function BamMalformedError() {(0, _classCallCheck2.default)(this, BamMalformedError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamMalformedError).apply(this, arguments));}return BamMalformedError;}(BamError);
 
-var _classCallCheck2 = require("babel-runtime/helpers/classCallCheck");
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _possibleConstructorReturn2 = require("babel-runtime/helpers/possibleConstructorReturn");
-
-var _possibleConstructorReturn3 = _interopRequireDefault(_possibleConstructorReturn2);
-
-var _inherits2 = require("babel-runtime/helpers/inherits");
-
-var _inherits3 = _interopRequireDefault(_inherits2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var BamError = function (_Error) {
-  (0, _inherits3.default)(BamError, _Error);
-
-  function BamError() {
-    (0, _classCallCheck3.default)(this, BamError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamError.__proto__ || (0, _getPrototypeOf2.default)(BamError)).apply(this, arguments));
-  }
-
-  return BamError;
-}(Error);
-
-/** Error caused by encountering a part of the BAM spec that has not yet been implemented */
-
-
-var BamUnimplementedError = function (_Error2) {
-  (0, _inherits3.default)(BamUnimplementedError, _Error2);
-
-  function BamUnimplementedError() {
-    (0, _classCallCheck3.default)(this, BamUnimplementedError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamUnimplementedError.__proto__ || (0, _getPrototypeOf2.default)(BamUnimplementedError)).apply(this, arguments));
-  }
-
-  return BamUnimplementedError;
-}(Error);
-
-/** An error caused by malformed data.  */
-
-
-var BamMalformedError = function (_BamError) {
-  (0, _inherits3.default)(BamMalformedError, _BamError);
-
-  function BamMalformedError() {
-    (0, _classCallCheck3.default)(this, BamMalformedError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamMalformedError.__proto__ || (0, _getPrototypeOf2.default)(BamMalformedError)).apply(this, arguments));
-  }
-
-  return BamMalformedError;
-}(BamError);
-
 /**
- * An error caused by attempting to read beyond the end of the defined data.
- */
+                                                                                                                                                                                                                                                                                                                                                                         * An error caused by attempting to read beyond the end of the defined data.
+                                                                                                                                                                                                                                                                                                                                                                         */var
+BamBufferOverrunError = /*#__PURE__*/function (_BamMalformedError) {(0, _inherits2.default)(BamBufferOverrunError, _BamMalformedError);function BamBufferOverrunError() {(0, _classCallCheck2.default)(this, BamBufferOverrunError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamBufferOverrunError).apply(this, arguments));}return BamBufferOverrunError;}(BamMalformedError);
 
-
-var BamBufferOverrunError = function (_BamMalformedError) {
-  (0, _inherits3.default)(BamBufferOverrunError, _BamMalformedError);
-
-  function BamBufferOverrunError() {
-    (0, _classCallCheck3.default)(this, BamBufferOverrunError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamBufferOverrunError.__proto__ || (0, _getPrototypeOf2.default)(BamBufferOverrunError)).apply(this, arguments));
-  }
-
-  return BamBufferOverrunError;
-}(BamMalformedError);
-
 /**
- * An error caused by data being too big, exceeding a size limit.
- */
+                                                                                                                                                                                                                                                                                                                                                                                                                            * An error caused by data being too big, exceeding a size limit.
+                                                                                                                                                                                                                                                                                                                                                                                                                            */var
+BamSizeLimitError = /*#__PURE__*/function (_BamError2) {(0, _inherits2.default)(BamSizeLimitError, _BamError2);function BamSizeLimitError() {(0, _classCallCheck2.default)(this, BamSizeLimitError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamSizeLimitError).apply(this, arguments));}return BamSizeLimitError;}(BamError);
 
-
-var BamSizeLimitError = function (_BamError2) {
-  (0, _inherits3.default)(BamSizeLimitError, _BamError2);
-
-  function BamSizeLimitError() {
-    (0, _classCallCheck3.default)(this, BamSizeLimitError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamSizeLimitError.__proto__ || (0, _getPrototypeOf2.default)(BamSizeLimitError)).apply(this, arguments));
-  }
-
-  return BamSizeLimitError;
-}(BamError);
-
 /**
- * An invalid argument was supplied to a bam-js method or object.
- */
+                                                                                                                                                                                                                                                                                                                                                                           * An invalid argument was supplied to a bam-js method or object.
+                                                                                                                                                                                                                                                                                                                                                                           */var
+BamArgumentError = /*#__PURE__*/function (_BamError3) {(0, _inherits2.default)(BamArgumentError, _BamError3);function BamArgumentError() {(0, _classCallCheck2.default)(this, BamArgumentError);return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(BamArgumentError).apply(this, arguments));}return BamArgumentError;}(BamError);
 
-
-var BamArgumentError = function (_BamError3) {
-  (0, _inherits3.default)(BamArgumentError, _BamError3);
-
-  function BamArgumentError() {
-    (0, _classCallCheck3.default)(this, BamArgumentError);
-    return (0, _possibleConstructorReturn3.default)(this, (BamArgumentError.__proto__ || (0, _getPrototypeOf2.default)(BamArgumentError)).apply(this, arguments));
-  }
-
-  return BamArgumentError;
-}(BamError);
-
 module.exports = {
@@ -113,3 +29,2 @@ BamBufferOverrunError: BamBufferOverrunError,
   BamSizeLimitError: BamSizeLimitError,
-  BamArgumentError: BamArgumentError
-};
+  BamArgumentError: BamArgumentError };

dist/index.js

@@ -1,19 +0,2 @@
-'use strict';
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.BamFile = exports.BAI = undefined;
-
-var _bai = require('./bai');
-
-var _bai2 = _interopRequireDefault(_bai);
-
-var _bamFile = require('./bamFile');
-
-var _bamFile2 = _interopRequireDefault(_bamFile);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-exports.BAI = _bai2.default;
-exports.BamFile = _bamFile2.default;
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });Object.defineProperty(exports, "BAI", { enumerable: true, get: function get() {return _bai.default;} });Object.defineProperty(exports, "BamFile", { enumerable: true, get: function get() {return _bamFile.default;} });var _bai = _interopRequireDefault(require("./bai"));
+var _bamFile = _interopRequireDefault(require("./bamFile"));

dist/localFile.js

@@ -1,31 +0,4 @@
-'use strict';
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));var _typeof2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/typeof"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var _require = require('es6-promisify'),promisify = _require.promisify;
 
-var _regenerator = require('babel-runtime/regenerator');
-
-var _regenerator2 = _interopRequireDefault(_regenerator);
-
-var _typeof2 = require('babel-runtime/helpers/typeof');
-
-var _typeof3 = _interopRequireDefault(_typeof2);
-
-var _asyncToGenerator2 = require('babel-runtime/helpers/asyncToGenerator');
-
-var _asyncToGenerator3 = _interopRequireDefault(_asyncToGenerator2);
-
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require('babel-runtime/helpers/createClass');
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-var _require = require('es6-promisify'),
-    promisify = _require.promisify;
-
 // don't load fs native module if running in webpacked code
-
-
 var fs = typeof __webpack_require__ !== 'function' ? require('fs') : null; // eslint-disable-line camelcase
@@ -36,141 +9,34 @@
 var fsFStat = fs && promisify(fs.fstat);
-var fsReadFile = fs && promisify(fs.readFile);
+var fsReadFile = fs && promisify(fs.readFile);var
 
-var LocalFile = function () {
-  function LocalFile(source) {
-    (0, _classCallCheck3.default)(this, LocalFile);
-
+LocalFile = /*#__PURE__*/function () {
+  function LocalFile(source) {(0, _classCallCheck2.default)(this, LocalFile);
     this.position = 0;
     this.filename = source;
     this.fd = fsOpen(this.filename, 'r');
-  }
+  }(0, _createClass2.default)(LocalFile, [{ key: "read", value: function () {var _read = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(
 
-  (0, _createClass3.default)(LocalFile, [{
-    key: 'read',
-    value: function () {
-      var _ref = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee(buffer) {
-        var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
-        var length = arguments[2];
-        var position = arguments[3];
-        var readPosition, ret;
-        return _regenerator2.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
+      buffer) {var offset,length,position,readPosition,ret,_args = arguments;return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:offset = _args.length > 1 && _args[1] !== undefined ? _args[1] : 0;length = _args.length > 2 ? _args[2] : undefined;position = _args.length > 3 ? _args[3] : undefined;
                 readPosition = position;
-
                 if (readPosition === null) {
                   readPosition = this.position;
                   this.position += length;
-                }
-                _context.t0 = fsRead;
-                _context.next = 5;
-                return this.fd;
+                }_context.t0 =
+                fsRead;_context.next = 8;return this.fd;case 8:_context.t1 = _context.sent;_context.t2 = buffer;_context.t3 = offset;_context.t4 = length;_context.t5 = position;_context.next = 15;return (0, _context.t0)(_context.t1, _context.t2, _context.t3, _context.t4, _context.t5);case 15:ret = _context.sent;if (!(
+                (0, _typeof2.default)(ret) === 'object')) {_context.next = 18;break;}return _context.abrupt("return", ret.bytesRead);case 18:return _context.abrupt("return",
+                ret);case 19:case "end":return _context.stop();}}}, _callee, this);}));function read(_x) {return _read.apply(this, arguments);}return read;}() }, { key: "readFile", value: function () {var _readFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {return _regenerator.default.wrap(function _callee2$(_context2) {while (1) {switch (_context2.prev = _context2.next) {case 0:return _context2.abrupt("return",
 
-              case 5:
-                _context.t1 = _context.sent;
-                _context.t2 = buffer;
-                _context.t3 = offset;
-                _context.t4 = length;
-                _context.t5 = position;
-                _context.next = 12;
-                return (0, _context.t0)(_context.t1, _context.t2, _context.t3, _context.t4, _context.t5);
 
-              case 12:
-                ret = _context.sent;
 
-                if (!((typeof ret === 'undefined' ? 'undefined' : (0, _typeof3.default)(ret)) === 'object')) {
-                  _context.next = 15;
-                  break;
-                }
+                fsReadFile(this.filename));case 1:case "end":return _context2.stop();}}}, _callee2, this);}));function readFile() {return _readFile.apply(this, arguments);}return readFile;}() }, { key: "stat", value: function () {var _stat = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {return _regenerator.default.wrap(function _callee3$(_context3) {while (1) {switch (_context3.prev = _context3.next) {case 0:if (
 
-                return _context.abrupt('return', ret.bytesRead);
 
-              case 15:
-                return _context.abrupt('return', ret);
 
-              case 16:
-              case 'end':
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
+                this._stat) {_context3.next = 8;break;}_context3.t0 =
+                fsFStat;_context3.next = 4;return this.fd;case 4:_context3.t1 = _context3.sent;_context3.next = 7;return (0, _context3.t0)(_context3.t1);case 7:this._stat = _context3.sent;case 8:return _context3.abrupt("return",
 
-      function read(_x) {
-        return _ref.apply(this, arguments);
-      }
+                this._stat);case 9:case "end":return _context3.stop();}}}, _callee3, this);}));function stat() {return _stat.apply(this, arguments);}return stat;}() }]);return LocalFile;}();
 
-      return read;
-    }()
-  }, {
-    key: 'readFile',
-    value: function () {
-      var _ref2 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee2() {
-        return _regenerator2.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                return _context2.abrupt('return', fsReadFile(this.filename));
 
-              case 1:
-              case 'end':
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
 
-      function readFile() {
-        return _ref2.apply(this, arguments);
-      }
-
-      return readFile;
-    }()
-  }, {
-    key: 'stat',
-    value: function () {
-      var _ref3 = (0, _asyncToGenerator3.default)( /*#__PURE__*/_regenerator2.default.mark(function _callee3() {
-        return _regenerator2.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                if (this._stat) {
-                  _context3.next = 8;
-                  break;
-                }
-
-                _context3.t0 = fsFStat;
-                _context3.next = 4;
-                return this.fd;
-
-              case 4:
-                _context3.t1 = _context3.sent;
-                _context3.next = 7;
-                return (0, _context3.t0)(_context3.t1);
-
-              case 7:
-                this._stat = _context3.sent;
-
-              case 8:
-                return _context3.abrupt('return', this._stat);
-
-              case 9:
-              case 'end':
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function stat() {
-        return _ref3.apply(this, arguments);
-      }
-
-      return stat;
-    }()
-  }]);
-  return LocalFile;
-}();
-
 module.exports = LocalFile;

dist/record.js

@@ -1,19 +0,3 @@
-'use strict';
-
-var _keys = require('babel-runtime/core-js/object/keys');
-
-var _keys2 = _interopRequireDefault(_keys);
-
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
-
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
-
-var _createClass2 = require('babel-runtime/helpers/createClass');
-
-var _createClass3 = _interopRequireDefault(_createClass2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _parseInt2 = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/parse-int"));var _keys = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/object/keys"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var crc32 = require('buffer-crc32');
 var Constants = require('./constants');
-var crc32 = require('buffer-crc32');
 
@@ -24,9 +8,6 @@ var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 /**
- * Class of each BAM record returned by this API.
- */
-
-var BamRecord = function () {
-  function BamRecord(args) {
-    (0, _classCallCheck3.default)(this, BamRecord);
-
+                                                   * Class of each BAM record returned by this API.
+                                                   */var
+BamRecord = /*#__PURE__*/function () {
+  function BamRecord(args) {(0, _classCallCheck2.default)(this, BamRecord);
     this.data = {};
@@ -36,5 +17,5 @@ this.bytes = {
       end: args.bytes.end,
-      byteArray: args.bytes.byteArray
-    };
+      byteArray: args.bytes.byteArray };
 
+
     this._coreParse();
@@ -44,41 +25,33 @@ }
   /**
-   * parse the core data: ref ID and start
-   */
-
-
-  (0, _createClass3.default)(BamRecord, [{
-    key: '_coreParse',
-    value: function _coreParse() {
-      var _bytes = this.bytes,
-          start = _bytes.start,
-          byteArray = _bytes.byteArray;
-
+     * parse the core data: ref ID and start
+     */(0, _createClass2.default)(BamRecord, [{ key: "_coreParse", value: function _coreParse()
+    {var _this$bytes =
+      this.bytes,start = _this$bytes.start,byteArray = _this$bytes.byteArray;
       this._refID = byteArray.readInt32LE(start + 4);
       this.data.start = byteArray.readInt32LE(start + 8);
       this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
-    }
-  }, {
-    key: 'get',
-    value: function get(field) {
+    } }, { key: "get", value: function get(
+
+    field) {
       return this._get(field.toLowerCase());
-    }
-  }, {
-    key: 'end',
-    value: function end() {
-      return this._get('start') + (this._get('length_on_ref') || this._get('seq_length') || undefined);
-    }
-  }, {
-    key: 'seq_id',
-    value: function seq_id() {
+    } }, { key: "end", value: function end()
+
+    {
+      return (
+        this._get('start') + (
+        this._get('length_on_ref') || this._get('seq_length') || undefined));
+
+    } }, { key: "seq_id", value: function seq_id()
+
+    {
       return this._refID;
     }
+
     // same as get(), except requires lower-case arguments.  used
     // internally to save lots of calls to field.toLowerCase()
-
-  }, {
-    key: '_get',
-    value: function _get(field) {
+  }, { key: "_get", value: function _get(field) {
       if (field in this.data) {
         return this.data[field];
-      } else if (this[field]) {
+      }
+      if (this[field]) {
         this.data[field] = this[field]();
@@ -89,20 +62,49 @@ } else {
       return this.data[field];
-    }
-  }, {
-    key: '_tags',
-    value: function _tags() {
-      var _this = this;
+    } }, { key: "_tags", value: function _tags()
 
+    {var _this = this;
       this._parseAllTags();
 
-      var tags = ['seq', 'seq_reverse_complemented', 'unmapped', 'qc_failed', 'duplicate', 'secondary_alignment', 'supplementary_alignment'];
+      var tags = [
+      'seq',
+      'seq_reverse_complemented',
+      'unmapped',
+      'qc_failed',
+      'duplicate',
+      'secondary_alignment',
+      'supplementary_alignment'];
 
-      if (!this.isSegmentUnmapped()) tags.push('start', 'end', 'strand', 'score', 'qual', 'MQ', 'CIGAR', 'length_on_ref', 'template_length');
+
+      if (!this.isSegmentUnmapped())
+      tags.push(
+      'start',
+      'end',
+      'strand',
+      'score',
+      'qual',
+      'MQ',
+      'CIGAR',
+      'length_on_ref',
+      'template_length');
+
       if (this.isPaired()) {
-        tags.push('multi_segment_all_correctly_aligned', 'multi_segment_next_segment_unmapped', 'multi_segment_next_segment_reversed', 'multi_segment_first', 'multi_segment_last', 'next_segment_position', 'pair_orientation');
+        tags.push(
+        'multi_segment_all_correctly_aligned',
+        'multi_segment_next_segment_unmapped',
+        'multi_segment_next_segment_reversed',
+        'multi_segment_first',
+        'multi_segment_last',
+        'next_segment_position',
+        'pair_orientation');
+
       }
       tags = tags.concat(this._tagList || []);
 
-      (0, _keys2.default)(this.data).forEach(function (k) {
-        if (k[0] !== '_' && k !== 'multi_segment_all_aligned' && k !== 'next_seq_id') tags.push(k);
+      (0, _keys.default)(this.data).forEach(function (k) {
+        if (
+        k[0] !== '_' &&
+        k !== 'multi_segment_all_aligned' &&
+        k !== 'next_seq_id')
+
+        tags.push(k);
       });
@@ -121,21 +123,19 @@
       return tags;
-    }
-  }, {
-    key: 'parent',
-    value: function parent() {
+    } }, { key: "parent", value: function parent()
+
+    {
       return undefined;
-    }
-  }, {
-    key: 'children',
-    value: function children() {
+    } }, { key: "children", value: function children()
+
+    {
       return this._get('subfeatures');
-    }
-  }, {
-    key: 'id',
-    value: function id() {
-      return crc32.signed(this.bytes.byteArray.slice(this.bytes.start, this.bytes.end));
-    }
-  }, {
-    key: 'multi_segment_all_aligned',
-    value: function multi_segment_all_aligned() {
+    } }, { key: "id", value: function id()
+
+    {
+      return crc32.signed(
+      this.bytes.byteArray.slice(this.bytes.start, this.bytes.end));
+
+    } }, { key: "multi_segment_all_aligned", value: function multi_segment_all_aligned()
+
+    {
       return this._get('multi_segment_all_correctly_aligned');
@@ -147,24 +147,23 @@ }
      * Mapping quality score.
-     */
-
-  }, {
-    key: 'mq',
-    value: function mq() {
+     */ }, { key: "mq", value: function mq()
+    {
       var mq = (this._get('_bin_mq_nl') & 0xff00) >> 8;
       return mq === 255 ? undefined : mq;
-    }
-  }, {
-    key: 'score',
-    value: function score() {
+    } }, { key: "score", value: function score()
+
+    {
       return this._get('mq');
-    }
-  }, {
-    key: 'qual',
-    value: function qual() {
+    } }, { key: "qual", value: function qual()
+
+    {
       if (this.isSegmentUnmapped()) return undefined;
 
-      var qseq = [];
-      var byteArray = this.bytes.byteArray;
-
-      var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op') * 4 + this._get('_seq_bytes');
+      var qseq = [];var
+      byteArray = this.bytes.byteArray;
+      var p =
+      this.bytes.start +
+      36 +
+      this._get('_l_read_name') +
+      this._get('_n_cigar_op') * 4 +
+      this._get('_seq_bytes');
       var lseq = this._get('seq_length');
@@ -175,34 +174,31 @@ for (var j = 0; j < lseq; ++j) {
       return qseq.join(' ');
-    }
-  }, {
-    key: 'strand',
-    value: function strand() {
+    } }, { key: "strand", value: function strand()
+
+    {
       return this.isReverseComplemented() ? -1 : 1;
-    }
-  }, {
-    key: 'multi_segment_next_segment_strand',
-    value: function multi_segment_next_segment_strand() {
+    } }, { key: "multi_segment_next_segment_strand", value: function multi_segment_next_segment_strand()
+
+    {
       if (this.isMateUnmapped()) return undefined;
       return this.isMateReverseComplemented() ? -1 : 1;
-    }
-  }, {
-    key: 'name',
-    value: function name() {
+    } }, { key: "name", value: function name()
+
+    {
       return this._get('_read_name');
-    }
-  }, {
-    key: '_read_name',
-    value: function _read_name() {
+    } }, { key: "_read_name", value: function _read_name()
+
+    {
       var nl = this._get('_l_read_name');
-      return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
+      return this.bytes.byteArray.toString(
+      'ascii',
+      this.bytes.start + 36,
+      this.bytes.start + 36 + nl - 1);
+
     }
 
     /**
-     * Get the value of a tag, parsing the tags as far as necessary.
-     * Only called if we have not already parsed that field.
-     */
-
-  }, {
-    key: '_parseTag',
-    value: function _parseTag(tagName) {
+       * Get the value of a tag, parsing the tags as far as necessary.
+       * Only called if we have not already parsed that field.
+       */ }, { key: "_parseTag", value: function _parseTag(
+    tagName) {
       // if all of the tags have been parsed and we're still being
@@ -213,9 +209,15 @@ // called, we already know that we have no such tag, because
 
-      this._tagList = this._tagList || [];
-      var byteArray = this.bytes.byteArray;
+      this._tagList = this._tagList || [];var
+      byteArray = this.bytes.byteArray;
+      var p =
+      this._tagOffset ||
+      this.bytes.start +
+      36 +
+      this._get('_l_read_name') +
+      this._get('_n_cigar_op') * 4 +
+      this._get('_seq_bytes') +
+      this._get('seq_length');
 
-      var p = this._tagOffset || this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op') * 4 + this._get('_seq_bytes') + this._get('seq_length');
-
       var blockEnd = this.bytes.end;
-      var lcTag = void 0;
+      var lcTag;
       while (p < blockEnd && lcTag !== tagName) {
@@ -261,4 +263,3 @@ var tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
             break;
-          case 'b':
-            {
+          case 'b':{
               value = '';
@@ -306,3 +307,3 @@ var _cc = byteArray[p++];
           default:
-            console.warn('Unknown BAM tag type \'' + type + '\', tags may be incomplete');
+            console.warn("Unknown BAM tag type '".concat(type, "', tags may be incomplete"));
             value = undefined;
@@ -321,121 +322,80 @@ p = blockEnd; // stop parsing tags
       return undefined;
-    }
-  }, {
-    key: '_parseAllTags',
-    value: function _parseAllTags() {
+    } }, { key: "_parseAllTags", value: function _parseAllTags()
+
+    {
       this._parseTag();
+    } }, { key: "_parseCigar", value: function _parseCigar(
+
+    cigar) {
+      return cigar.
+      match(/\d+\D/g).
+      map(function (op) {return [op.match(/\D/)[0].toUpperCase(), (0, _parseInt2.default)(op, 10)];});
     }
-  }, {
-    key: '_parseCigar',
-    value: function _parseCigar(cigar) {
-      return cigar.match(/\d+\D/g).map(function (op) {
-        return [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)];
-      });
-    }
+
     /**
-     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
-     */
-
-  }, {
-    key: 'isPaired',
-    value: function isPaired() {
+       * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+       */ }, { key: "isPaired", value: function isPaired()
+    {
       return !!(this.flags & Constants.BAM_FPAIRED);
     }
 
-    /** @returns {boolean} true if the read is paired, and both segments are mapped */
-
-  }, {
-    key: 'isProperlyPaired',
-    value: function isProperlyPaired() {
+    /** @returns {boolean} true if the read is paired, and both segments are mapped */ }, { key: "isProperlyPaired", value: function isProperlyPaired()
+    {
       return !!(this.flags & Constants.BAM_FPROPER_PAIR);
     }
 
-    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: 'isSegmentUnmapped',
-    value: function isSegmentUnmapped() {
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */ }, { key: "isSegmentUnmapped", value: function isSegmentUnmapped()
+    {
       return !!(this.flags & Constants.BAM_FUNMAP);
     }
 
-    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: 'isMateUnmapped',
-    value: function isMateUnmapped() {
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */ }, { key: "isMateUnmapped", value: function isMateUnmapped()
+    {
       return !!(this.flags & Constants.BAM_FMUNMAP);
     }
 
-    /** @returns {boolean} true if the read is mapped to the reverse strand */
-
-  }, {
-    key: 'isReverseComplemented',
-    value: function isReverseComplemented() {
+    /** @returns {boolean} true if the read is mapped to the reverse strand */ }, { key: "isReverseComplemented", value: function isReverseComplemented()
+    {
       return !!(this.flags & Constants.BAM_FREVERSE);
     }
 
-    /** @returns {boolean} true if the mate is mapped to the reverse strand */
-
-  }, {
-    key: 'isMateReverseComplemented',
-    value: function isMateReverseComplemented() {
+    /** @returns {boolean} true if the mate is mapped to the reverse strand */ }, { key: "isMateReverseComplemented", value: function isMateReverseComplemented()
+    {
       return !!(this.flags & Constants.BAM_FMREVERSE);
     }
 
-    /** @returns {boolean} true if this is read number 1 in a pair */
-
-  }, {
-    key: 'isRead1',
-    value: function isRead1() {
+    /** @returns {boolean} true if this is read number 1 in a pair */ }, { key: "isRead1", value: function isRead1()
+    {
       return !!(this.flags & Constants.BAM_FREAD1);
     }
 
-    /** @returns {boolean} true if this is read number 2 in a pair */
-
-  }, {
-    key: 'isRead2',
-    value: function isRead2() {
+    /** @returns {boolean} true if this is read number 2 in a pair */ }, { key: "isRead2", value: function isRead2()
+    {
       return !!(this.flags & Constants.BAM_FREAD2);
     }
 
-    /** @returns {boolean} true if this is a secondary alignment */
-
-  }, {
-    key: 'isSecondary',
-    value: function isSecondary() {
+    /** @returns {boolean} true if this is a secondary alignment */ }, { key: "isSecondary", value: function isSecondary()
+    {
       return !!(this.flags & Constants.BAM_FSECONDARY);
     }
 
-    /** @returns {boolean} true if this read has failed QC checks */
-
-  }, {
-    key: 'isFailedQc',
-    value: function isFailedQc() {
+    /** @returns {boolean} true if this read has failed QC checks */ }, { key: "isFailedQc", value: function isFailedQc()
+    {
       return !!(this.flags & Constants.BAM_FQCFAIL);
     }
 
-    /** @returns {boolean} true if the read is an optical or PCR duplicate */
-
-  }, {
-    key: 'isDuplicate',
-    value: function isDuplicate() {
+    /** @returns {boolean} true if the read is an optical or PCR duplicate */ }, { key: "isDuplicate", value: function isDuplicate()
+    {
       return !!(this.flags & Constants.BAM_FDUP);
     }
 
-    /** @returns {boolean} true if this is a supplementary alignment */
-
-  }, {
-    key: 'isSupplementary',
-    value: function isSupplementary() {
+    /** @returns {boolean} true if this is a supplementary alignment */ }, { key: "isSupplementary", value: function isSupplementary()
+    {
       return !!(this.flags & Constants.BAM_FSUPPLEMENTARY);
-    }
-  }, {
-    key: 'cigar',
-    value: function cigar() {
-      if (this.isSegmentUnmapped()) return undefined;
+    } }, { key: "cigar", value: function cigar()
 
-      var _bytes2 = this.bytes,
-          byteArray = _bytes2.byteArray,
-          start = _bytes2.start;
+    {
+      if (this.isSegmentUnmapped()) return undefined;var _this$bytes2 =
 
+      this.bytes,byteArray = _this$bytes2.byteArray,start = _this$bytes2.start;
       var numCigarOps = this._get('_n_cigar_op');
@@ -460,39 +420,35 @@ var p = start + 36 + this._get('_l_read_name');
       return cigar;
-    }
-  }, {
-    key: '_flags',
-    value: function _flags() {}
-  }, {
-    key: 'length_on_ref',
-    value: function length_on_ref() {
+    } }, { key: "_flags", value: function _flags()
+
+    {} }, { key: "length_on_ref", value: function length_on_ref()
+
+    {
       this._get('cigar'); // the length_on_ref is set as a
       // side effect of the CIGAR parsing
       return this.data.length_on_ref;
-    }
-  }, {
-    key: '_n_cigar_op',
-    value: function _n_cigar_op() {
+    } }, { key: "_n_cigar_op", value: function _n_cigar_op()
+
+    {
       return this._get('_flag_nc') & 0xffff;
-    }
-  }, {
-    key: '_l_read_name',
-    value: function _l_read_name() {
+    } }, { key: "_l_read_name", value: function _l_read_name()
+
+    {
       return this._get('_bin_mq_nl') & 0xff;
     }
+
     /**
-     * number of bytes in the sequence field
-     */
-
-  }, {
-    key: '_seq_bytes',
-    value: function _seq_bytes() {
+       * number of bytes in the sequence field
+       */ }, { key: "_seq_bytes", value: function _seq_bytes()
+    {
       return this._get('seq_length') + 1 >> 1;
-    }
-  }, {
-    key: 'getReadBases',
-    value: function getReadBases() {
-      var seq = '';
-      var byteArray = this.bytes.byteArray;
+    } }, { key: "getReadBases", value: function getReadBases()
 
-      var p = this.bytes.start + 36 + this._get('_l_read_name') + this._get('_n_cigar_op') * 4;
+    {
+      var seq = '';var
+      byteArray = this.bytes.byteArray;
+      var p =
+      this.bytes.start +
+      36 +
+      this._get('_l_read_name') +
+      this._get('_n_cigar_op') * 4;
       var seqBytes = this._get('_seq_bytes');
@@ -508,7 +464,8 @@ for (var j = 0; j < seqBytes; ++j) {
     // adapted from igv.js
-
-  }, {
-    key: 'getPairOrientation',
-    value: function getPairOrientation() {
-      if (!this.isSegmentUnmapped() && !this.isMateUnmapped() && this._refID === this._next_refid()) {
+  }, { key: "getPairOrientation", value: function getPairOrientation() {
+      if (
+      !this.isSegmentUnmapped() &&
+      !this.isMateUnmapped() &&
+      this._refID === this._next_refid())
+      {
         var s1 = this.isReverseComplemented() ? 'R' : 'F';
@@ -542,40 +499,31 @@ var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
       return null;
-    }
-  }, {
-    key: '_bin_mq_nl',
-    value: function _bin_mq_nl() {
+    } }, { key: "_bin_mq_nl", value: function _bin_mq_nl()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
-    }
-  }, {
-    key: '_flag_nc',
-    value: function _flag_nc() {
+    } }, { key: "_flag_nc", value: function _flag_nc()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
-    }
-  }, {
-    key: 'seq_length',
-    value: function seq_length() {
+    } }, { key: "seq_length", value: function seq_length()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
-    }
-  }, {
-    key: '_next_refid',
-    value: function _next_refid() {
+    } }, { key: "_next_refid", value: function _next_refid()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
-    }
-  }, {
-    key: '_next_pos',
-    value: function _next_pos() {
+    } }, { key: "_next_pos", value: function _next_pos()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
-    }
-  }, {
-    key: 'template_length',
-    value: function template_length() {
+    } }, { key: "template_length", value: function template_length()
+
+    {
       return this.bytes.byteArray.readInt32LE(this.bytes.start + 32);
-    }
-  }, {
-    key: 'toJSON',
-    value: function toJSON() {
-      var _this2 = this;
+    } }, { key: "toJSON", value: function toJSON()
 
+    {var _this2 = this;
       var data = {};
-      (0, _keys2.default)(this).forEach(function (k) {
+      (0, _keys.default)(this).forEach(function (k) {
         if (k.charAt(0) === '_' || k === 'bytes') return;
@@ -586,7 +534,5 @@ data[k] = _this2[k];
       return data;
-    }
-  }]);
-  return BamRecord;
-}();
+    } }]);return BamRecord;}();
 
+
 module.exports = BamRecord;

dist/sam.js

@@ -1,28 +0,8 @@
-'use strict';
-
-var _slicedToArray2 = require('babel-runtime/helpers/slicedToArray');
-
-var _slicedToArray3 = _interopRequireDefault(_slicedToArray2);
-
-var _toArray2 = require('babel-runtime/helpers/toArray');
-
-var _toArray3 = _interopRequireDefault(_toArray2);
-
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-function parseHeaderText(text) {
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/slicedToArray"));var _toArray2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/toArray"));function parseHeaderText(text) {
   var lines = text.split(/\r?\n/);
   var data = [];
-  lines.forEach(function (line) {
-    var _line$split = line.split(/\t/),
-        _line$split2 = (0, _toArray3.default)(_line$split),
-        tag = _line$split2[0],
-        fields = _line$split2.slice(1);
-
-    var parsedFields = fields.map(function (f) {
-      var _f$split = f.split(':', 2),
-          _f$split2 = (0, _slicedToArray3.default)(_f$split, 2),
-          fieldTag = _f$split2[0],
-          value = _f$split2[1];
-
+  lines.forEach(function (line) {var _line$split =
+    line.split(/\t/),_line$split2 = (0, _toArray2.default)(_line$split),tag = _line$split2[0],fields = _line$split2.slice(1);
+    var parsedFields = fields.map(function (f) {var _f$split =
+      f.split(':', 2),_f$split2 = (0, _slicedToArray2.default)(_f$split, 2),fieldTag = _f$split2[0],value = _f$split2[1];
       return { tag: fieldTag, value: value };
@@ -29,0 +9,0 @@ });

dist/util.js

@@ -1,20 +0,49 @@
-'use strict';
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs2/regenerator"));var _promise = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/promise"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/asyncToGenerator"));var _minSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/number/min-safe-integer"));var _maxSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs2/core-js/number/max-safe-integer"));function longToNumber(long) {
+  if (
+  long.greaterThan(_maxSafeInteger.default) ||
+  long.lessThan(_minSafeInteger.default))
+  {
+    throw new Error('integer overflow');
+  }
+  return long.toNumber();
+}
 
-var _minSafeInteger = require('babel-runtime/core-js/number/min-safe-integer');
+/**
+   * Properly check if the given AbortSignal is aborted.
+   * Per the standard, if the signal reads as aborted,
+   * this function throws either a DOMException AbortError, or a regular error
+   * with a `code` attribute set to `ERR_ABORTED`.
+   *
+   * For convenience, passing `undefined` is a no-op
+   *
+   * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
+   * @returns nothing
+   */
+function checkAbortSignal(signal) {
+  if (!signal) return;
 
-var _minSafeInteger2 = _interopRequireDefault(_minSafeInteger);
+  if (signal.aborted) {
+    // console.log('bam aborted!')
+    if (typeof DOMException !== 'undefined')
+      // eslint-disable-next-line  no-undef
+      throw new DOMException('aborted', 'AbortError');else
+    {
+      var e = new Error('aborted');
+      e.code = 'ERR_ABORTED';
+      throw e;
+    }
+  }
+}
 
-var _maxSafeInteger = require('babel-runtime/core-js/number/max-safe-integer');
+/**
+   * Skips to the next tick, then runs `checkAbortSignal`.
+   * Await this to inside an otherwise synchronous loop to
+   * provide a place to break when an abort signal is received.
+   * @param {AbortSignal} signal
+   */function
+abortBreakPoint(_x) {return _abortBreakPoint.apply(this, arguments);}function _abortBreakPoint() {_abortBreakPoint = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(signal) {return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:_context.next = 2;return (
+              _promise.default.resolve());case 2:
+            checkAbortSignal(signal);case 3:case "end":return _context.stop();}}}, _callee);}));return _abortBreakPoint.apply(this, arguments);}
 
-var _maxSafeInteger2 = _interopRequireDefault(_maxSafeInteger);
 
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
-
-module.exports = {
-  longToNumber: function longToNumber(long) {
-    if (long.greaterThan(_maxSafeInteger2.default) || long.lessThan(_minSafeInteger2.default)) {
-      throw new Error('integer overflow');
-    }
-    return long.toNumber();
-  }
-};
+module.exports = { longToNumber: longToNumber, checkAbortSignal: checkAbortSignal, abortBreakPoint: abortBreakPoint };

dist/virtualOffset.js

@@ -1,57 +0,43 @@
-'use strict';
+"use strict";var _interopRequireDefault = require("@babel/runtime-corejs2/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));var VirtualOffset = /*#__PURE__*/function () {
+  function VirtualOffset(blockPosition, dataPosition) {(0, _classCallCheck2.default)(this, VirtualOffset);
+    this.blockPosition = blockPosition; // < offset of the compressed data block
+    this.dataPosition = dataPosition; // < offset into the uncompressed data
+  }(0, _createClass2.default)(VirtualOffset, [{ key: "toString", value: function toString()
 
-var _classCallCheck2 = require('babel-runtime/helpers/classCallCheck');
 
-var _classCallCheck3 = _interopRequireDefault(_classCallCheck2);
 
-var _createClass2 = require('babel-runtime/helpers/createClass');
 
-var _createClass3 = _interopRequireDefault(_createClass2);
 
-function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
 
-var VirtualOffset = function () {
-  function VirtualOffset(blockPosition, dataPosition) {
-    (0, _classCallCheck3.default)(this, VirtualOffset);
 
-    this.blockPosition = blockPosition; // < offset of the compressed data block
-    this.dataPosition = dataPosition; // < offset into the uncompressed data
-  }
 
-  (0, _createClass3.default)(VirtualOffset, [{
-    key: 'toString',
-    value: function toString() {
-      return this.blockPosition + ':' + this.dataPosition;
-    }
-  }, {
-    key: 'compareTo',
-    value: function compareTo(b) {
-      return this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition;
-    }
-  }], [{
-    key: 'fromBytes',
-    value: function fromBytes(bytes) {
-      var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
-      var bigendian = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false;
 
-      if (bigendian) throw new Error('big-endian virtual file offsets not implemented');
 
-      return new VirtualOffset(bytes[offset + 7] * 0x10000000000 + bytes[offset + 6] * 0x100000000 + bytes[offset + 5] * 0x1000000 + bytes[offset + 4] * 0x10000 + bytes[offset + 3] * 0x100 + bytes[offset + 2], bytes[offset + 1] << 8 | bytes[offset]);
-    }
-  }, {
-    key: 'min',
-    value: function min() {
-      var min = void 0;
+
+
+
+
+
+
+    {
+      return "".concat(this.blockPosition, ":").concat(this.dataPosition);
+    } }, { key: "compareTo", value: function compareTo(
+
+    b) {
+      return (
+        this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
+
+    } }], [{ key: "fromBytes", value: function fromBytes(bytes) {var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;var bigendian = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : false;if (bigendian) throw new Error('big-endian virtual file offsets not implemented');return new VirtualOffset(bytes[offset + 7] * 0x10000000000 + bytes[offset + 6] * 0x100000000 + bytes[offset + 5] * 0x1000000 + bytes[offset + 4] * 0x10000 + bytes[offset + 3] * 0x100 + bytes[offset + 2], bytes[offset + 1] << 8 | bytes[offset]);} }, { key: "min", value: function min()
+
+    {
+      var min;
       var i = 0;
-      for (; !min; i += 1) {
-        min = arguments.length <= i ? undefined : arguments[i];
-      }for (; i < arguments.length; i += 1) {
-        if (min.compareTo(arguments.length <= i ? undefined : arguments[i]) > 0) min = arguments.length <= i ? undefined : arguments[i];
+      for (; !min; i += 1) {min = i < 0 || arguments.length <= i ? undefined : arguments[i];}
+      for (; i < arguments.length; i += 1) {
+        if (min.compareTo(i < 0 || arguments.length <= i ? undefined : arguments[i]) > 0) min = i < 0 || arguments.length <= i ? undefined : arguments[i];
       }
       return min;
-    }
-  }]);
-  return VirtualOffset;
-}();
+    } }]);return VirtualOffset;}();
 
+
 module.exports = VirtualOffset;

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.0.14",
+  "version": "1.0.15",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -22,9 +22,5 @@ "license": "MIT",
     "coverage": "npm test -- --coverage",
-    "postcoverage": "opn coverage/lcov-report/index.html",
     "lint": "eslint src test",
-    "flow": "flow check",
     "clean": "rimraf dist",
-    "docs": "echo nothing",
-    "flowbuild": "flow-copy-source src dist",
-    "prebuild": "npm run docs && npm run clean && npm run flowbuild",
+    "prebuild": "npm run clean && npm run lint",
     "build": "babel src -d dist",
@@ -45,3 +41,5 @@ "preversion": "npm run lint && npm test && npm run build",
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.2.2",
+    "@babel/runtime-corejs2": "^7.3.4",
+    "@gmod/bgzf-filehandle": "^1.2.3",
+    "abortable-promise-cache": "^1.0.0",
     "buffer-crc32": "^0.2.13",
@@ -53,23 +51,14 @@ "es6-promisify": "^6.0.1",
   "devDependencies": {
-    "babel-cli": "^6.26.0",
-    "babel-core": "^6.26.0",
-    "babel-eslint": "^8.2.2",
-    "babel-jest": "^23.0.1",
-    "babel-plugin-transform-runtime": "^6.23.0",
-    "babel-preset-env": "^1.6.1",
-    "babel-preset-flow": "^6.23.0",
-    "babel-preset-stage-2": "^6.24.1",
-    "cross-fetch": "^2.2.2",
-    "documentation": "^7.1.0",
-    "eslint": "^4.19.1",
-    "eslint-config-airbnb-base": "^12.1.0",
-    "eslint-config-prettier": "^2.9.0",
-    "eslint-plugin-flowtype": "^2.46.1",
-    "eslint-plugin-flowtype-errors": "^3.5.1",
+    "@babel/cli": "^7.2.3",
+    "@babel/core": "^7.3.3",
+    "@babel/plugin-transform-runtime": "^7.2.0",
+    "@babel/preset-env": "^7.3.1",
+    "babel-jest": "^24.1.0",
+    "documentation": "^9.1.1",
+    "eslint": "^5.12.0",
+    "eslint-config-airbnb-base": "^13.1.0",
+    "eslint-config-prettier": "^4.1.0",
     "eslint-plugin-import": "^2.10.0",
-    "eslint-plugin-prettier": "^2.6.0",
-    "flow-bin": "^0.73.0",
-    "flow-copy-source": "^1.3.0",
-    "jest-cli": "^23.1.0",
-    "opn-cli": "^3.1.0",
+    "eslint-plugin-prettier": "^3.0.1",
+    "jest": "^24.3.1",
     "prettier": "^1.11.1",
@@ -76,0 +65,0 @@ "rimraf": "^2.6.2",

README.md

 [![Generated with nod](https://img.shields.io/badge/generator-nod-2196F3.svg?style=flat-square)](https://github.com/diegohaz/nod)
 [![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
-[![Build Status](https://img.shields.io/travis/GMOD/bam-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/bam-js) [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bam-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bam-js/branch/master)
+[![Build Status](https://img.shields.io/travis/GMOD/bam-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/bam-js)
+[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bam-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bam-js/branch/master)
+[![Greenkeeper badge](https://badges.greenkeeper.io/GMOD/bam-js.svg)](https://greenkeeper.io/)
 
@@ -26,5 +28,35 @@
 
+## Documentation
 
+BAM class constructor infers BAI by default as bamPath+'.bai', or you can specify it explicitely via baiPath (also accepts csiPath)
+
+    BAM({ bamPath: "yourfile.bam", baiPath: "yourfile.bai" })
+
+Or accepts filehandles, this is an abstract filehandle concept that can represent remote files. The remote file concept is not built into this repository, but see @gmod/cram for example of the remoteFile.js class
+
+    BAM({ bamFilehandle: new FileHandle("http://localhost/file.bam", baiFilehandle: new FileHandle("yourfile.bai") })
+
+
+
+The method getRecordsForRange(refName, start, end, opts) has the opts blob that can contain
+
+
+* opts.signal - an AbortSignal to indicate stop processing
+* opts.viewAsPairs - re-dispatches requests to find mate pairs
+* opts.pairAcrossChr - control the viewAsPairs option behavior to pair across chromosomes
+* opts.maxInsertSize - control the viewAsPairs option behavior to limit distance within a chromosome to fetch
+
+The returned features from BAM are lazy features meaning that it delays processing of all the feature tags until necessary. You can perform feature.get('field') to get the value of a feature attribute
+
+Example
+
+		feature.get('seq_id')
+		feature.get('start')
+		feature.get('name') // QNAME
+		feature.get('seq') // get feature sequence
+
+This may change in future versions to make it raw records but will be a major version bump
+
 ## License
 
 MIT © [Colin Diesh](https://github.com/cmdcolin)

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Dev dependency count

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decreased by-37.5%

Number of lines in readme file

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increased by106.67%

Worsened metrics

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Dependency changes

• + Added@babel/runtime-corejs2@^7.3.4

• + Addedabortable-promise-cache@^1.0.0

• + Added@babel/runtime-corejs2@7.26.0(transitive)

• + Addedabortable-promise-cache@1.5.0(transitive)

• + Addedabortcontroller-polyfill@1.7.8(transitive)

• + Addedcore-js@2.6.12(transitive)

• + Addedregenerator-runtime@0.14.1(transitive)

• Updated@gmod/bgzf-filehandle@^1.2.3