@gmod/bam - npm Package Compare versions

Comparing version 1.0.15 to 1.0.16

CHANGELOG.md

@@ -0,1 +1,9 @@
+## [1.0.16](https://github.com/GMOD/bam-js/compare/v1.0.15...v1.0.16) (2019-04-28)
+
+
+
+- Added indexCov algorithm to retrieve approximate coverage of the BAM inferred from the size of the BAI linear index bins
+- Fixed abortSignal on read() calls
+- Updated API to allow bamUrl/baiUrl/csiUrl
+
 ## [1.0.15](https://github.com/GMOD/bam-js/compare/v1.0.14...v1.0.15) (2019-04-04)
@@ -2,0 +10,0 @@

dist/bai.js

@@ -1,9 +0,17 @@
-"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');
+"use strict";var _interopRequireWildcard = require("@babel/runtime/helpers/interopRequireWildcard");var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.default = void 0;var _objectSpread2 = _interopRequireDefault(require("@babel/runtime/helpers/objectSpread"));var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));var Long = _interopRequireWildcard(require("long"));
+var _virtualOffset = require("./virtualOffset");
+var _chunk = _interopRequireDefault(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,abortBreakPoint = _require.abortBreakPoint;
 
+function roundDown(n, multiple) {
+  return n - n % multiple;
+}
+function roundUp(n, multiple) {
+  return n - n % multiple + multiple;
+}var
+
 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(
@@ -27,5 +35,5 @@ bytes, offset) {
     // 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$(_context2) {while (1) {switch (_context2.prev = _context2.next) {case 0:
+  }, { key: "_parse", value: function () {var _parse2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(abortSignal) {var data, bytes, depth, binLimit, currOffset, i, binCount, stats, binIndex, j, bin, chunkCount, chunks, k, u, v, linearCount, linearIndex, _k;return _regenerator.default.wrap(function _callee2$(_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 (!(
+                  this.filehandle.readFile({ signal: abortSignal }));case 3:bytes = _context2.sent;if (!(
 
@@ -67,7 +75,7 @@
                 for (k = 0; k < chunkCount; k += 1) {
-                  u = VirtualOffset.fromBytes(bytes, currOffset);
-                  v = VirtualOffset.fromBytes(bytes, currOffset + 8);
+                  u = (0, _virtualOffset.fromBytes)(bytes, currOffset);
+                  v = (0, _virtualOffset.fromBytes)(bytes, currOffset + 8);
                   currOffset += 16;
                   this._findFirstData(data, u);
-                  chunks[k] = new Chunk(u, v, bin);
+                  chunks[k] = new _chunk.default(u, v, bin);
                 }
@@ -78,3 +86,3 @@ binIndex[bin] = chunks;case 38:j += 1;_context2.next = 20;break;case 41:
 
-                nintv = bytes.readInt32LE(currOffset);
+                linearCount = bytes.readInt32LE(currOffset);
                 currOffset += 4;
@@ -84,21 +92,79 @@ // as we're going through the linear index, figure out
                 // tells us where the BAM header ends
-                if (nintv) {
-                  this._findFirstData(bytes, VirtualOffset.fromBytes(bytes, currOffset));
+                linearIndex = new Array(linearCount);
+                for (_k = 0; _k < linearCount; _k += 1) {
+                  linearIndex[_k] = (0, _virtualOffset.fromBytes)(bytes, currOffset);
+                  currOffset += 8;
+                  this._findFirstData(data, linearIndex[_k]);
                 }
 
-                currOffset += nintv * 8;
+                data.indices[i] = { binIndex: binIndex, linearIndex: linearIndex, stats: stats };case 46:i += 1;_context2.next = 12;break;case 49:return _context2.abrupt("return",
 
-                data.indices[i] = { binIndex: binIndex, stats: stats };case 46:i += 1;_context2.next = 12;break;case 49:return _context2.abrupt("return",
 
+                data);case 50:case "end":return _context2.stop();}}}, _callee2, this);}));function _parse(_x2) {return _parse2.apply(this, arguments);}return _parse;}() }, { key: "indexCov", value: function () {var _indexCov = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(
 
-                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(
 
+      seqId, start, end) {var v, range, indexData, seqIdx, _seqIdx$linearIndex, linearIndex, stats, e, s, depths, totalSize, currentPos, i, j;return _regenerator.default.wrap(function _callee3$(_context3) {while (1) {switch (_context3.prev = _context3.next) {case 0:
+                v = 16384;
+                range = start !== undefined;_context3.next = 4;return (
+                  this.parse());case 4:indexData = _context3.sent;
+                seqIdx = indexData.indices[seqId];if (
+                seqIdx) {_context3.next = 8;break;}return _context3.abrupt("return", []);case 8:_seqIdx$linearIndex =
+                seqIdx.linearIndex, linearIndex = _seqIdx$linearIndex === void 0 ? [] : _seqIdx$linearIndex, stats = seqIdx.stats;if (
+                linearIndex.length) {_context3.next = 11;break;}return _context3.abrupt("return", []);case 11:
+                e = range ? roundUp(end, v) : (linearIndex.length - 1) * v;
+                s = range ? roundDown(start, v) : 0;
 
-      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 (
+                if (range) {
+                  depths = new Array(Math.floor((e - s) / v));
+                } else {
+                  depths = new Array(linearIndex.length - 1);
+                }
+                totalSize = linearIndex[linearIndex.length - 1].blockPosition;if (!(
+                e > (linearIndex.length - 1) * v)) {_context3.next = 17;break;}throw (
+                  new Error('query outside of range of linear index'));case 17:
 
-                  this.parse());case 3:indexData = _context3.sent;if (
-                indexData) {_context3.next = 6;break;}return _context3.abrupt("return", []);case 6:
+                currentPos = linearIndex[s / v].blockPosition;
+                for (i = s / v, j = 0; i + 1 < e / v; i++, j++) {
+                  depths[j] = {
+                    score: linearIndex[i + 1].blockPosition - currentPos,
+                    start: i * v,
+                    end: i * v + v };
+
+                  currentPos = linearIndex[i + 1].blockPosition;
+                }return _context3.abrupt("return",
+                depths.map(function (d) {
+                  return (0, _objectSpread2.default)({}, d, { score: d.score * stats.lineCount / totalSize });
+                }));case 20:case "end":return _context3.stop();}}}, _callee3, this);}));function indexCov(_x3, _x4, _x5) {return _indexCov.apply(this, arguments);}return indexCov;}() }, { key: "indexCovTotal", value: function () {var _indexCovTotal = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(
+
+
+      seqId) {var v, indexData, seqIdx, _seqIdx$linearIndex2, linearIndex, stats, currentPos, depths, totalSize, i, j;return _regenerator.default.wrap(function _callee4$(_context4) {while (1) {switch (_context4.prev = _context4.next) {case 0:
+                v = 16384;_context4.next = 3;return (
+                  this.parse());case 3:indexData = _context4.sent;
+                seqIdx = indexData.indices[seqId];if (
+                seqIdx) {_context4.next = 7;break;}return _context4.abrupt("return", []);case 7:_seqIdx$linearIndex2 =
+                seqIdx.linearIndex, linearIndex = _seqIdx$linearIndex2 === void 0 ? [] : _seqIdx$linearIndex2, stats = seqIdx.stats;if (
+                linearIndex.length) {_context4.next = 10;break;}return _context4.abrupt("return", []);case 10:
+                currentPos = linearIndex[0].blockPosition;
+                depths = new Array(linearIndex.length - 1);
+                totalSize = linearIndex.slice(-1)[0].blockPosition;
+                for (i = 1, j = 0; i < linearIndex.length; i++, j++) {
+                  depths[j] = linearIndex[i].blockPosition - currentPos;
+                  currentPos = linearIndex[i].blockPosition;
+                }return _context4.abrupt("return",
+                depths.map(function (d, i) {
+                  return {
+                    score: d * stats.lineCount / totalSize,
+                    start: i * v,
+                    end: i * v + v };
+
+                }));case 15:case "end":return _context4.stop();}}}, _callee4, this);}));function indexCovTotal(_x6) {return _indexCovTotal.apply(this, arguments);}return indexCovTotal;}() }, { key: "blocksForRange", value: function () {var _blocksForRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(
+
+
+      refId, beg, end) {var indexData, indexes, binIndex, bins, l, numOffsets, i, off, _i, chunks, j, _i2, _i3, _i4;return _regenerator.default.wrap(function _callee5$(_context5) {while (1) {switch (_context5.prev = _context5.next) {case 0:
+                if (beg < 0) beg = 0;_context5.next = 3;return (
+
+                  this.parse());case 3:indexData = _context5.sent;if (
+                indexData) {_context5.next = 6;break;}return _context5.abrupt("return", []);case 6:
                 indexes = indexData.indices[refId];if (
-                indexes) {_context3.next = 9;break;}return _context3.abrupt("return", []);case 9:
+                indexes) {_context5.next = 9;break;}return _context5.abrupt("return", []);case 9:
 
@@ -117,3 +183,3 @@ binIndex = indexes.binIndex;
 
-                numOffsets === 0)) {_context3.next = 15;break;}return _context3.abrupt("return", []);case 15:
+                numOffsets === 0)) {_context5.next = 15;break;}return _context5.abrupt("return", []);case 15:
 
@@ -126,3 +192,3 @@ off = [];
                   for (j = 0; j < chunks.length; j += 1) {
-                    off[numOffsets] = new Chunk(
+                    off[numOffsets] = new _chunk.default(
                     chunks[j].minv,
@@ -136,3 +202,3 @@ chunks[j].maxv,
 
-                off.length) {_context3.next = 20;break;}return _context3.abrupt("return", []);case 20:
+                off.length) {_context5.next = 20;break;}return _context5.abrupt("return", []);case 20:
 
@@ -167,11 +233,21 @@ off = off.sort(function (a, b) {return a.compareTo(b);});
                 }
-                numOffsets = l + 1;return _context3.abrupt("return",
+                numOffsets = l + 1;return _context5.abrupt("return",
 
-                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;}()
+                off.slice(0, numOffsets));case 29:case "end":return _context5.stop();}}}, _callee5, this);}));function blocksForRange(_x7, _x8, _x9) {return _blocksForRange.apply(this, arguments);}return blocksForRange;}()
 
 
     /**
-                                                                                                                                                                                                                                * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-                                                                                                                                                                                                                                * @returns {Array[number]}
-                                                                                                                                                                                                                                */ }, { key: "reg2bins", value: function reg2bins(
+                                                                                                                                                                                                                                * @param {number} seqId
+                                                                                                                                                                                                                                * @param {AbortSignal} [abortSignal]
+                                                                                                                                                                                                                                * @returns {Promise} true if the index contains entries for
+                                                                                                                                                                                                                                * the given reference sequence ID, false otherwise
+                                                                                                                                                                                                                                */ }, { key: "hasRefSeq", value: function () {var _hasRefSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(
+      seqId, abortSignal) {return _regenerator.default.wrap(function _callee6$(_context6) {while (1) {switch (_context6.prev = _context6.next) {case 0:_context6.next = 2;return (
+                  this.parse(abortSignal));case 2:_context6.t1 = seqId;_context6.t0 = _context6.sent.indices[_context6.t1];if (_context6.t0) {_context6.next = 6;break;}_context6.t0 = {};case 6:return _context6.abrupt("return", !!_context6.t0.binIndex);case 7:case "end":return _context6.stop();}}}, _callee6, this);}));function hasRefSeq(_x10, _x11) {return _hasRefSeq.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) {
@@ -181,11 +257,8 @@ var list = [0];
       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);}
+      for (var _k2 = 9 + (beg >> 23); _k2 <= 9 + (end >> 23); _k2 += 1) {list.push(_k2);}
+      for (var _k3 = 73 + (beg >> 20); _k3 <= 73 + (end >> 20); _k3 += 1) {list.push(_k3);}
+      for (var _k4 = 585 + (beg >> 17); _k4 <= 585 + (end >> 17); _k4 += 1) {list.push(_k4);}
+      for (var _k5 = 4681 + (beg >> 14); _k5 <= 4681 + (end >> 14); _k5 += 1) {
+        list.push(_k5);}
       return list;
-    } }]);return BAI;}(IndexFile);
-
-
-module.exports = BAI;
+    } }]);return BAI;}(IndexFile);exports.default = BAI;

dist/bamFile.js

@@ -1,11 +0,13 @@
-"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 =
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.default = void 0;var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
+var _bai = _interopRequireDefault(require("./bai"));
+var _csi = _interopRequireDefault(require("./csi"));
 
+var entries = require('object.entries-ponyfill');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 _require3 =
-require('./util'),abortBreakPoint = _require3.abortBreakPoint,checkAbortSignal = _require3.checkAbortSignal;
+var LRU = require('quick-lru');var _require2 =
+require('generic-filehandle'),LocalFile = _require2.LocalFile,RemoteFile = _require2.RemoteFile;
+var BAMFeature = require('./record');var _require3 =
+require('./sam'),parseHeaderText = _require3.parseHeaderText;var _require4 =
+require('./util'),abortBreakPoint = _require4.abortBreakPoint,checkAbortSignal = _require4.checkAbortSignal;
 
@@ -35,3 +37,6 @@ var BAM_MAGIC = 21840194;
 
-  {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$renameRefSeqs;(0, _classCallCheck2.default)(this, BamFile);
+
+
+
+  {var bamFilehandle = _ref.bamFilehandle,bamPath = _ref.bamPath,bamUrl = _ref.bamUrl,baiPath = _ref.baiPath,baiFilehandle = _ref.baiFilehandle,baiUrl = _ref.baiUrl,csiPath = _ref.csiPath,csiFilehandle = _ref.csiFilehandle,csiUrl = _ref.csiUrl,cacheSize = _ref.cacheSize,fetchSizeLimit = _ref.fetchSizeLimit,chunkSizeLimit = _ref.chunkSizeLimit,_ref$renameRefSeqs = _ref.renameRefSeqs,renameRefSeqs = _ref$renameRefSeqs === void 0 ? function (n) {return n;} : _ref$renameRefSeqs;(0, _classCallCheck2.default)(this, BamFile);
     this.renameRefSeq = renameRefSeqs;
@@ -43,18 +48,24 @@
       this.bam = new LocalFile(bamPath);
+    } else if (bamUrl) {
+      this.bam = new RemoteFile(bamUrl);
     }
-
     if (csiFilehandle) {
-      this.index = new CSI({ filehandle: csiFilehandle });
+      this.index = new _csi.default({ filehandle: csiFilehandle });
     } else if (csiPath) {
-      this.index = new CSI({
-        filehandle: new LocalFile(csiPath) });
-
+      this.index = new _csi.default({ filehandle: new LocalFile(csiPath) });
+    } else if (csiUrl) {
+      this.index = new _csi.default({ filehandle: new RemoteFile(csiUrl) });
     } else if (baiFilehandle) {
-      this.index = new BAI({ filehandle: baiFilehandle });
+      this.index = new _bai.default({ filehandle: baiFilehandle });
     } else if (baiPath) {
-      this.index = new BAI({ filehandle: new LocalFile(baiPath) });
+      this.index = new _bai.default({ filehandle: new LocalFile(baiPath) });
+    } else if (baiUrl) {
+      this.index = new _bai.default({ filehandle: new RemoteFile(baiUrl) });
+    } else if (bamPath) {
+      this.index = new _bai.default({ filehandle: new LocalFile("".concat(bamPath, ".bai")) });
+    } else if (bamUrl) {
+      this.index = new _bai.default({ filehandle: new RemoteFile("".concat(bamUrl, ".bai")) });
     } else {
-      this.index = new BAI({ filehandle: new LocalFile("".concat(bamPath, ".bai")) });
+      throw new Error('unable to infer index format');
     }
-
     this.featureCache = new _abortablePromiseCache.default({
@@ -79,8 +90,4 @@ cache: new LRU({
                 buf = Buffer.alloc(ret + blockLen);_context.next = 8;return (
-                  this.bam.read(
-                  buf,
-                  0,
-                  ret + blockLen,
-                  0,
-                  abortSignal));case 8:bytesRead = _context.sent;if (
+                  this.bam.read(buf, 0, ret + blockLen, 0, {
+                    signal: abortSignal }));case 8:bytesRead = _context.sent;if (
 
@@ -96,3 +103,3 @@ bytesRead) {_context.next = 11;break;}throw (
 
-                  this.bam.readFile(abortSignal));case 16:buf = _context.sent;case 17:_context.next = 19;return (
+                  this.bam.readFile({ signal: abortSignal }));case 16:buf = _context.sent;case 17:_context.next = 19;return (
 
@@ -124,7 +131,4 @@
 
-                  this.bam.read(
-                  buf,
-                  0,
-                  refSeqBytes + blockLen,
-                  abortSignal));case 5:bytesRead = _context2.sent;if (
+                  this.bam.read(buf, 0, refSeqBytes + blockLen, {
+                    signal: abortSignal }));case 5:bytesRead = _context2.sent;if (
 
@@ -231,3 +235,3 @@ bytesRead) {_context2.next = 8;break;}return _context2.abrupt("return",
                 });_context4.next = 6;return (
-                  _promise.default.all(featPromises));case 6:recs = _context4.sent;
+                  Promise.all(featPromises));case 6:recs = _context4.sent;
                 checkAbortSignal(opts.signal);
@@ -246,3 +250,3 @@ ret = (_ref3 = []).concat.apply(_ref3, (0, _toConsumableArray2.default)(recs));if (!
                 unmatedPairs = {};
-                (0, _entries.default)(readNames).forEach(function (_ref4) {var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),k = _ref5[0],v = _ref5[1];
+                entries(readNames).forEach(function (_ref4) {var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),k = _ref5[0],v = _ref5[1];
                   if (v === 1) unmatedPairs[k] = true;
@@ -269,3 +273,3 @@ });
                 }_context4.next = 19;return (
-                  _promise.default.all(matePromises));case 19:mateBlocks = _context4.sent;
+                  Promise.all(matePromises));case 19:mateBlocks = _context4.sent;
                 mateChunks = [];
@@ -316,3 +320,3 @@ for (_i2 = 0; _i2 < mateBlocks.length; _i2++) {
                 });_context4.next = 31;return (
-                  _promise.default.all(mateFeatPromises));case 31:newMateFeats = _context4.sent;
+                  Promise.all(mateFeatPromises));case 31:newMateFeats = _context4.sent;
                 if (newMateFeats.length) {
@@ -337,3 +341,3 @@ newMates = newMateFeats.reduce(function (result, current) {return (
                   chunk.minv.blockPosition,
-                  abortSignal));case 4:bytesRead = _context5.sent;
+                  { signal: abortSignal }));case 4:bytesRead = _context5.sent;
 
@@ -378,5 +382,10 @@ checkAbortSignal(abortSignal);if (
       return this.index.hasRefSeq(seqId);
-    } }]);return BamFile;}();
+    } }, { key: "indexCov", value: function () {var _indexCov = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(
 
-
-module.exports = BamFile;
+      seqName, start, end) {var range, seqId;return _regenerator.default.wrap(function _callee6$(_context6) {while (1) {switch (_context6.prev = _context6.next) {case 0:_context6.next = 2;return (
+                  this.index.parse());case 2:
+                range = start !== undefined;
+                seqId = this.chrToIndex && this.chrToIndex[seqName];return _context6.abrupt("return",
+                range ?
+                this.index.indexCov(seqId, start, end) :
+                this.index.indexCovTotal(seqId));case 5:case "end":return _context6.stop();}}}, _callee6, this);}));function indexCov(_x14, _x15, _x16) {return _indexCov.apply(this, arguments);}return indexCov;}() }]);return BamFile;}();exports.default = BamFile;

dist/chunk.js

@@ -1,2 +0,2 @@
-"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
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass")); // little class representing a chunk in the index
 var Chunk = /*#__PURE__*/function () {
@@ -3,0 +3,0 @@ /**

dist/csi.js

@@ -1,9 +0,9 @@
-"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;
+"use strict";var _interopRequireWildcard = require("@babel/runtime/helpers/interopRequireWildcard");var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.default = void 0;var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));var Long = _interopRequireWildcard(require("long"));
+var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
 
-var VirtualOffset = require('./virtualOffset');
-var Chunk = require('./chunk');
-var IndexFile = require('./indexFile');var _require2 =
+var _virtualOffset = require("./virtualOffset");
+var _chunk = _interopRequireDefault(require("./chunk"));
+var _util = require("./util");
 
-require('./util'),longToNumber = _require2.longToNumber,abortBreakPoint = _require2.abortBreakPoint;
+var IndexFile = require('./indexFile');
 
@@ -51,3 +51,3 @@ var CSI1_MAGIC = 21582659; // CSI\1
 
-      (0, _assign.default)(
+      Object.assign(
       data,
@@ -84,5 +84,7 @@ this._parseNameBytes(
                 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 (!(
+                _bgzfFilehandle.unzip;_context2.next = 4;return (
+                  this.filehandle.readFile({ signal: abortSignal }));case 4:_context2.t1 = _context2.sent;_context2.next = 7;return (0, _context2.t0)(_context2.t1);case 7:bytes = _context2.sent;if (!(
 
 
+
                 bytes.readUInt32LE(0) === CSI1_MAGIC)) {_context2.next = 12;break;}
@@ -102,3 +104,3 @@ data.csiVersion = 1;_context2.next = 17;break;case 12:if (!(
                 if (auxLength) {
-                  (0, _assign.default)(data, this.parseAuxData(bytes, 16, auxLength));
+                  Object.assign(data, this.parseAuxData(bytes, 16, auxLength));
                 }
@@ -111,3 +113,3 @@ data.refCount = bytes.readInt32LE(16 + auxLength);
                 i = 0;case 26:if (!(i < data.refCount)) {_context2.next = 38;break;}_context2.next = 29;return (
-                  abortBreakPoint(abortSignal));case 29:
+                  (0, _util.abortBreakPoint)(abortSignal));case 29:
                 // the binning index
@@ -126,3 +128,3 @@ binCount = bytes.readInt32LE(currOffset);
                   } else {
-                    loffset = VirtualOffset.fromBytes(bytes, currOffset + 4);
+                    loffset = (0, _virtualOffset.fromBytes)(bytes, currOffset + 4);
                     this._findFirstData(data, loffset);
@@ -133,7 +135,7 @@ chunkCount = bytes.readInt32LE(currOffset + 12);
                     for (k = 0; k < chunkCount; k += 1) {
-                      u = VirtualOffset.fromBytes(bytes, currOffset);
-                      v = VirtualOffset.fromBytes(bytes, currOffset + 8);
+                      u = (0, _virtualOffset.fromBytes)(bytes, currOffset);
+                      v = (0, _virtualOffset.fromBytes)(bytes, currOffset + 8);
                       currOffset += 16;
                       // this._findFirstData(data, u)
-                      chunks[k] = new Chunk(u, v, bin);
+                      chunks[k] = new _chunk.default(u, v, bin);
                     }
@@ -156,3 +158,3 @@ binIndex[bin] = chunks;
       // )
-      var lineCount = longToNumber(
+      var lineCount = (0, _util.longToNumber)(
       Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
@@ -189,3 +191,3 @@
                   for (j = 0; j < chunks.length; j += 1) {
-                    off[numOffsets] = new Chunk(
+                    off[numOffsets] = new _chunk.default(
                     chunks[j].minv,
@@ -235,5 +237,15 @@ chunks[j].maxv,
     /**
-                                                                                                                                                                                                                                     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-                                                                                                                                                                                                                                     * @returns {Array[number]}
-                                                                                                                                                                                                                                     */ }, { key: "reg2bins", value: function reg2bins(
+                                                                                                                                                                                                                                     * @param {number} seqId
+                                                                                                                                                                                                                                     * @param {AbortSignal} [abortSignal]
+                                                                                                                                                                                                                                     * @returns {Promise} true if the index contains entries for
+                                                                                                                                                                                                                                     * the given reference sequence ID, false otherwise
+                                                                                                                                                                                                                                     */ }, { key: "hasRefSeq", value: function () {var _hasRefSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(
+      seqId, abortSignal) {return _regenerator.default.wrap(function _callee4$(_context4) {while (1) {switch (_context4.prev = _context4.next) {case 0:_context4.next = 2;return (
+                  this.parse(abortSignal));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(_x7, _x8) {return _hasRefSeq.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) {
@@ -262,5 +274,2 @@ beg -= 1; // < convert to 1-based closed
       return bins;
-    } }]);return CSI;}(IndexFile);
-
-
-module.exports = CSI;
+    } }]);return CSI;}(IndexFile);exports.default = CSI;

dist/errors.js

@@ -1,2 +0,2 @@
-"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));
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime/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));
 
@@ -3,0 +3,0 @@ /** Error caused by encountering a part of the BAM spec that has not yet been implemented */var

dist/index.js

@@ -1,2 +0,2 @@
-"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"));
+"use strict";var _interopRequireDefault = require("@babel/runtime/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/indexFile.js

@@ -1,2 +0,2 @@
-"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 _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
 var _quickLru = _interopRequireDefault(require("quick-lru"));var
@@ -3,0 +3,0 @@

dist/record.js

@@ -1,2 +0,2 @@
-"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');
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var crc32 = require('buffer-crc32');
 var Constants = require('./constants');
@@ -99,3 +99,3 @@
 
-      (0, _keys.default)(this.data).forEach(function (k) {
+      Object.keys(this.data).forEach(function (k) {
         if (
@@ -322,3 +322,3 @@ k[0] !== '_' &&
       match(/\d+\D/g).
-      map(function (op) {return [op.match(/\D/)[0].toUpperCase(), (0, _parseInt2.default)(op, 10)];});
+      map(function (op) {return [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)];});
     }
@@ -516,3 +516,3 @@
       var data = {};
-      (0, _keys.default)(this).forEach(function (k) {
+      Object.keys(this).forEach(function (k) {
         if (k.charAt(0) === '_' || k === 'bytes') return;
@@ -519,0 +519,0 @@ data[k] = _this2[k];

dist/sam.js

@@ -1,2 +0,2 @@
-"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) {
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.parseHeaderText = parseHeaderText;var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));var _toArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toArray"));function parseHeaderText(text) {
   var lines = text.split(/\r?\n/);
@@ -13,4 +13,2 @@ var data = [];
   return data;
-}
-
-module.exports = { parseHeaderText: parseHeaderText };
+}

dist/util.js

@@ -1,5 +0,5 @@
-"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) {
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));function longToNumber(long) {
   if (
-  long.greaterThan(_maxSafeInteger.default) ||
-  long.lessThan(_minSafeInteger.default))
+  long.greaterThan(Number.MAX_SAFE_INTEGER) ||
+  long.lessThan(Number.MIN_SAFE_INTEGER))
   {
@@ -45,3 +45,3 @@ throw new Error('integer overflow');
 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:
+              Promise.resolve());case 2:
             checkAbortSignal(signal);case 3:case "end":return _context.stop();}}}, _callee);}));return _abortBreakPoint.apply(this, arguments);}
@@ -48,0 +48,0 @@

dist/virtualOffset.js

@@ -1,2 +0,2 @@
-"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 () {
+"use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.fromBytes = fromBytes;exports.VirtualOffset = void 0;var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var VirtualOffset = /*#__PURE__*/function () {
   function VirtualOffset(blockPosition, dataPosition) {(0, _classCallCheck2.default)(this, VirtualOffset);
@@ -7,17 +7,2 @@ this.blockPosition = blockPosition; // < offset of the compressed data block
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
     {
@@ -31,3 +16,3 @@ return "".concat(this.blockPosition, ":").concat(this.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()
+    } }], [{ key: "min", value: function min()
 
@@ -42,5 +27,17 @@ {
       return min;
-    } }]);return VirtualOffset;}();
+    } }]);return VirtualOffset;}();exports.VirtualOffset = VirtualOffset;
 
+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');
 
-module.exports = VirtualOffset;
+  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]);
+
+}

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.0.15",
+  "version": "1.0.16",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -40,8 +40,11 @@ "license": "MIT",
   "dependencies": {
-    "@babel/runtime-corejs2": "^7.3.4",
+    "@babel/runtime": "^7.4.3",
     "@gmod/bgzf-filehandle": "^1.2.3",
     "abortable-promise-cache": "^1.0.0",
     "buffer-crc32": "^0.2.13",
+    "cross-fetch": "^3.0.2",
     "es6-promisify": "^6.0.1",
+    "generic-filehandle": "^1.0.7",
     "long": "^4.0.0",
+    "object.entries-ponyfill": "^1.0.1",
     "quick-lru": "^2.0.0"
@@ -48,0 +51,0 @@ },

README.md

@@ -5,3 +5,2 @@ [![Generated with nod](https://img.shields.io/badge/generator-nod-2196F3.svg?style=flat-square)](https://github.com/diegohaz/nod)
 [![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/)
 
@@ -19,3 +18,3 @@
 const t = new BamFile({
-		bamPath: 'test.bam',
+    bamPath: 'test.bam',
 });
@@ -32,33 +31,73 @@
 
-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" })
+### BAM constructor
 
-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 BAM class constructor accepts arguments
 
+* bamPath/baiUrl/bamFilehandle - a string file path to a local file or a class object with a read method
+* csiPath/csiUrl/csiFilehandle - a CSI index for the BAM file, required for long chromosomes greater than 2^29 in length
+* baiPath/baiUrl/baiFilehandle - a BAI index for the BAM file
+* fetchSizeLimit - total size of the number of chunks being fetched at once. default: ~50MB
+* chunkSizeLimit - size limit on any individual chunk. default: ~10MB
+* cacheSize - limit on number of chunks to cache. default: 50
 
+Note: filehandles implement the Filehandle interface from https://www.npmjs.com/package/generic-filehandle. This module offers the path and url arguments as convenience methods for supplying the LocalFile and RemoteFile
 
-The method getRecordsForRange(refName, start, end, opts) has the opts blob that can contain
+### Documentation
 
+#### getRecordsForRange(refName, start, end, opts)
 
+* refName - a string for the chrom to fetch from
+* start - a 0 based half open start coordinate
+* end - a 0 based half open end coordinate
 * 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
+* opts.viewAsPairs - re-dispatches requests to find mate pairs. default: false
+* opts.pairAcrossChr - control the viewAsPairs option behavior to pair across chromosomes. default: false
+* opts.maxInsertSize - control the viewAsPairs option behavior to limit distance within a chromosome to fetch. default: 200kb
 
-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
+### indexCov(refName, start, end)
 
+* refName - a string for the chrom to fetch from
+* start - a 0 based half open start coordinate (optional, will fetch whole chromosome without)
+* end - a 0 based half open end coordinate (optional, will fetch whole chromosome without even if start is specified)
+
+Returns features of the form {start, end, score} containing estimated feature density across 16kb windows in the genome
+
+### Returned features
+
+The returned features from BAM are lazy features meaning that it delays processing of all the feature tags until necessary.
+
+You can access data 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
+    feature.get('seq_id') // numerical sequence id corresponding to position in the sam header
+    feature.get('start') // 0 based half open start coordinate
+    feature.get('end') // 0 based half open end coordinate
 
-This may change in future versions to make it raw records but will be a major version bump
+## Fields
 
+    feature.get('name') // QNAME
+    feature.get('seq') // feature sequence
+    feature.get('qual') // qualities
+    feature.get('cigar') // cigar string
+    feature.get('MD') // MD string
+    feature.get('SA') // supplementary alignments
+    feature.get('template_length') // TLEN
+    feature.get('length_on_ref') // derived from CIGAR using standard algorithm
+
+### Flags
+
+    feature.get('seq_reverse_complemented')
+    feature.get('unmapped')
+    feature.get('qc_failed')
+    feature.get('duplicate')
+    feature.get('secondary_alignment')
+    feature.get('supplementary_alignment')
+
+The feature format may change in future versions to be more raw records but will be a major version bump
+
 ## License
 
 MIT © [Colin Diesh](https://github.com/cmdcolin)

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