@gmod/cram 1.5.7 → 1.6.1

package/dist/craiIndex.js

@@ -1,254 +1,176 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _slice = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/slice"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _sort = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/sort"));
-
-var _entries = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/entries"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _parseInt = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/parse-int"));
-
-var _bind = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/bind"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _some = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/some"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var AbortablePromiseCache = require('abortable-promise-cache').default;
-
-var QuickLRU = require('quick-lru');
-
-var _require = require('es6-promisify'),
-    promisify = _require.promisify;
-
-var zlib = require('zlib');
-
-var gunzip = promisify(zlib.gunzip);
-
-var _require2 = require('./io'),
-    open = _require2.open;
-
-var _require3 = require('./errors'),
-    CramMalformedError = _require3.CramMalformedError;
-
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+var quick_lru_1 = __importDefault(require("quick-lru"));
+var unzip_1 = require("./unzip");
+var io_1 = require("./io");
+var errors_1 = require("./errors");
 var BAI_MAGIC = 21578050; // BAI\1
-
-var Slice =
-/*#__PURE__*/
-function () {
-  function Slice(args) {
-    (0, _classCallCheck2.default)(this, Slice);
-    (0, _assign.default)(this, args);
-  }
-
-  (0, _createClass2.default)(Slice, [{
-    key: "toString",
-    value: function toString() {
-      var _context, _context2, _context3, _context4;
-
-      return (0, _concat.default)(_context = (0, _concat.default)(_context2 = (0, _concat.default)(_context3 = (0, _concat.default)(_context4 = "".concat(this.start, ":")).call(_context4, this.span, ":")).call(_context3, this.containerStart, ":")).call(_context2, this.sliceStart, ":")).call(_context, this.sliceBytes);
+var Slice = /** @class */ (function () {
+    function Slice(args) {
+        Object.assign(this, args);
     }
-  }]);
-  return Slice;
-}();
-
+    Slice.prototype.toString = function () {
+        return "".concat(this.start, ":").concat(this.span, ":").concat(this.containerStart, ":").concat(this.sliceStart, ":").concat(this.sliceBytes);
+    };
+    return Slice;
+}());
 function addRecordToIndex(index, record) {
-  if ((0, _some.default)(record).call(record, function (el) {
-    return el === undefined;
-  })) {
-    throw new CramMalformedError('invalid .crai index file');
-  }
-
-  var _record = (0, _slicedToArray2.default)(record, 6),
-      seqId = _record[0],
-      start = _record[1],
-      span = _record[2],
-      containerStart = _record[3],
-      sliceStart = _record[4],
-      sliceBytes = _record[5];
-
-  if (!index[seqId]) index[seqId] = [];
-  index[seqId].push(new Slice({
-    start: start,
-    span: span,
-    containerStart: containerStart,
-    sliceStart: sliceStart,
-    sliceBytes: sliceBytes
-  }));
+    if (record.some(function (el) { return el === undefined; })) {
+        throw new errors_1.CramMalformedError('invalid .crai index file');
+    }
+    var seqId = record[0], start = record[1], span = record[2], containerStart = record[3], sliceStart = record[4], sliceBytes = record[5];
+    if (!index[seqId]) {
+        index[seqId] = [];
+    }
+    index[seqId].push(new Slice({
+        start: start,
+        span: span,
+        containerStart: containerStart,
+        sliceStart: sliceStart,
+        sliceBytes: sliceBytes,
+    }));
 }
-
-var CraiIndex =
-/*#__PURE__*/
-function () {
-  // A CRAM index (.crai) is a gzipped tab delimited file containing the following columns:
-  // 1. Sequence id
-  // 2. Alignment start
-  // 3. Alignment span
-  // 4. Container start byte position in the file
-  // 5. Slice start byte position in the container data (‘blocks’)
-  // 6. Slice size in bytes
-  // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
-
-  /**
-   *
-   * @param {object} args
-   * @param {string} [args.path]
-   * @param {string} [args.url]
-   * @param {FileHandle} [args.filehandle]
-   */
-  function CraiIndex(args) {
-    var _this = this,
-        _context5;
-
-    (0, _classCallCheck2.default)(this, CraiIndex);
-    var filehandle = open(args.url, args.path, args.filehandle);
-    this._parseCache = new AbortablePromiseCache({
-      cache: new QuickLRU({
-        maxSize: 1
-      }),
-      fill: function fill(data, signal) {
-        return _this.parseIndex({
-          signal: signal
+var CraiIndex = /** @class */ (function () {
+    // A CRAM index (.crai) is a gzipped tab delimited file containing the following columns:
+    // 1. Sequence id
+    // 2. Alignment start
+    // 3. Alignment span
+    // 4. Container start byte position in the file
+    // 5. Slice start byte position in the container data (‘blocks’)
+    // 6. Slice size in bytes
+    // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
+    /**
+     *
+     * @param {object} args
+     * @param {string} [args.path]
+     * @param {string} [args.url]
+     * @param {FileHandle} [args.filehandle]
+     */
+    function CraiIndex(args) {
+        var _this = this;
+        var filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
+        this._parseCache = new abortable_promise_cache_1.default({
+            cache: new quick_lru_1.default({ maxSize: 1 }),
+            fill: function (data, signal) { return _this.parseIndex({ signal: signal }); },
         });
-      }
-    });
-    this.readFile = (0, _bind.default)(_context5 = filehandle.readFile).call(_context5, filehandle);
-  }
-
-  (0, _createClass2.default)(CraiIndex, [{
-    key: "parseIndex",
-    value: function parseIndex() {
-      var index = {};
-      return this.readFile().then(function (data) {
-        if (data[0] === 31 && data[1] === 139) return gunzip(data);
-        return data;
-      }).then(function (uncompressedBuffer) {
-        var _context6;
-
-        if (uncompressedBuffer.length > 4 && uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
-          throw new CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
-        } // interpret the text as regular ascii, since it is
-        // supposed to be only digits and whitespace characters
-        // this is written in a deliberately low-level fashion for performance,
-        // because some .crai files can be pretty large.
-
-
-        var currentRecord = [];
-        var currentString = '';
-
-        for (var i = 0; i < uncompressedBuffer.length; i += 1) {
-          var charCode = uncompressedBuffer[i];
-
-          if (charCode >= 48 && charCode <= 57 ||
-          /* 0-9 */
-          !currentString && charCode === 45
-          /* leading - */
-          ) {
-              currentString += String.fromCharCode(charCode);
-            } else if (charCode === 9
-          /* \t */
-          ) {
-              currentRecord.push((0, _parseInt.default)(currentString, 10));
-              currentString = '';
-            } else if (charCode === 10
-          /* \n */
-          ) {
-              currentRecord.push((0, _parseInt.default)(currentString, 10));
-              currentString = '';
-              addRecordToIndex(index, currentRecord);
-              currentRecord = [];
-            } else if (charCode !== 13
-          /* \r */
-          && charCode !== 32
-          /* space */
-          ) {
-              // if there are other characters in the file besides
-              // space and \r, something is wrong.
-              throw new CramMalformedError('invalid .crai index file');
+        this.readFile = filehandle.readFile.bind(filehandle);
+    }
+    CraiIndex.prototype.parseIndex = function () {
+        var index = {};
+        return this.readFile()
+            .then(function (data) {
+            if (data[0] === 31 && data[1] === 139) {
+                return (0, unzip_1.unzip)(data);
+            }
+            return data;
+        })
+            .then(function (uncompressedBuffer) {
+            if (uncompressedBuffer.length > 4 &&
+                uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
+                throw new errors_1.CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
+            }
+            // interpret the text as regular ascii, since it is
+            // supposed to be only digits and whitespace characters
+            // this is written in a deliberately low-level fashion for performance,
+            // because some .crai files can be pretty large.
+            var currentRecord = [];
+            var currentString = '';
+            for (var i = 0; i < uncompressedBuffer.length; i += 1) {
+                var charCode = uncompressedBuffer[i];
+                if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
+                    (!currentString && charCode === 45) /* leading - */) {
+                    currentString += String.fromCharCode(charCode);
+                }
+                else if (charCode === 9 /* \t */) {
+                    currentRecord.push(Number.parseInt(currentString, 10));
+                    currentString = '';
+                }
+                else if (charCode === 10 /* \n */) {
+                    currentRecord.push(Number.parseInt(currentString, 10));
+                    currentString = '';
+                    addRecordToIndex(index, currentRecord);
+                    currentRecord = [];
+                }
+                else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
+                    // if there are other characters in the file besides
+                    // space and \r, something is wrong.
+                    throw new errors_1.CramMalformedError('invalid .crai index file');
+                }
+            }
+            // if the file ends without a \n, we need to flush our buffers
+            if (currentString) {
+                currentRecord.push(Number.parseInt(currentString, 10));
             }
-        } // if the file ends without a \n, we need to flush our buffers
-
-
-        if (currentString) {
-          currentRecord.push((0, _parseInt.default)(currentString, 10));
-        }
-
-        if (currentRecord.length === 6) {
-          addRecordToIndex(index, currentRecord);
-        } // sort each of them by start
-
-
-        (0, _forEach.default)(_context6 = (0, _entries.default)(index)).call(_context6, function (_ref) {
-          var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-              seqId = _ref2[0],
-              ent = _ref2[1];
-
-          index[seqId] = (0, _sort.default)(ent).call(ent, function (a, b) {
-            return a.start - b.start || a.span - b.span;
-          });
+            if (currentRecord.length === 6) {
+                addRecordToIndex(index, currentRecord);
+            }
+            // sort each of them by start
+            Object.entries(index).forEach(function (_a) {
+                var seqId = _a[0], ent = _a[1];
+                index[seqId] = ent.sort(function (a, b) { return a.start - b.start || a.span - b.span; });
+            });
+            return index;
         });
-        return index;
-      });
-    }
-  }, {
-    key: "getIndex",
-    value: function getIndex() {
-      var opts = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-      return this._parseCache.get('index', null, opts.signal);
-    }
+    };
+    CraiIndex.prototype.getIndex = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return this._parseCache.get('index', null, opts.signal);
+    };
     /**
      * @param {number} seqId
      * @returns {Promise} true if the index contains entries for
      * the given reference sequence ID, false otherwise
      */
-
-  }, {
-    key: "hasDataForReferenceSequence",
-    value: function () {
-      var _hasDataForReferenceSequence = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(seqId) {
-        return _regenerator.default.wrap(function _callee$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
-                _context7.next = 2;
-                return this.getIndex();
-
-              case 2:
-                _context7.t0 = seqId;
-                return _context7.abrupt("return", !!_context7.sent[_context7.t0]);
-
-              case 4:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function hasDataForReferenceSequence(_x) {
-        return _hasDataForReferenceSequence.apply(this, arguments);
-      }
-
-      return hasDataForReferenceSequence;
-    }()
+    CraiIndex.prototype.hasDataForReferenceSequence = function (seqId) {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getIndex()];
+                    case 1: return [2 /*return*/, !!(_a.sent())[seqId]];
+                }
+            });
+        });
+    };
     /**
      * fetch index entries for the given range
      *
@@ -260,131 +182,40 @@ function () {
      * an array of objects of the form
      * `{start, span, containerStart, sliceStart, sliceBytes }`
      */
-
-  }, {
-    key: "getEntriesForRange",
-    value: function () {
-      var _getEntriesForRange = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2(seqId, queryStart, queryEnd) {
-        var seqEntries, len, compare, lowerBound, upperBound, searchPosition, nextSearchDirection, overlapStart, overlapEnd, x1, x2, y1, y2;
-        return _regenerator.default.wrap(function _callee2$(_context8) {
-          while (1) {
-            switch (_context8.prev = _context8.next) {
-              case 0:
-                _context8.next = 2;
-                return this.getIndex();
-
-              case 2:
-                _context8.t0 = seqId;
-                seqEntries = _context8.sent[_context8.t0];
-
-                if (seqEntries) {
-                  _context8.next = 6;
-                  break;
+    CraiIndex.prototype.getEntriesForRange = function (seqId, queryStart, queryEnd) {
+        return __awaiter(this, void 0, void 0, function () {
+            var seqEntries, compare, bins, i;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getIndex()];
+                    case 1:
+                        seqEntries = (_a.sent())[seqId];
+                        if (!seqEntries) {
+                            return [2 /*return*/, []];
+                        }
+                        compare = function (entry) {
+                            var entryStart = entry.start;
+                            var entryEnd = entry.start + entry.span;
+                            if (entryStart >= queryEnd) {
+                                return -1;
+                            } // entry is ahead of query
+                            if (entryEnd <= queryStart) {
+                                return 1;
+                            } // entry is behind query
+                            return 0; // entry overlaps query
+                        };
+                        bins = [];
+                        for (i = 0; i < seqEntries.length; i += 1) {
+                            if (compare(seqEntries[i]) === 0) {
+                                bins.push(seqEntries[i]);
+                            }
+                        }
+                        return [2 /*return*/, bins];
                 }
-
-                return _context8.abrupt("return", []);
-
-              case 6:
-                len = seqEntries.length; // binary search to find an entry that
-                // overlaps the range, then extend backward
-                // and forward from that
-
-                compare = function compare(entry) {
-                  var entryStart = entry.start;
-                  var entryEnd = entry.start + entry.span;
-                  if (entryStart >= queryEnd) return -1; // entry is ahead of query
-
-                  if (entryEnd <= queryStart) return 1; // entry is behind query
-
-                  return 0; // entry overlaps query
-                };
-
-                lowerBound = 0;
-                upperBound = len - 1;
-
-              case 10:
-                if (!(lowerBound <= upperBound)) {
-                  _context8.next = 24;
-                  break;
-                }
-
-                searchPosition = Math.round((upperBound + lowerBound) / 2);
-                nextSearchDirection = compare(seqEntries[searchPosition]);
-
-                if (!(nextSearchDirection > 0)) {
-                  _context8.next = 17;
-                  break;
-                }
-
-                lowerBound = searchPosition + 1;
-                _context8.next = 22;
-                break;
-
-              case 17:
-                if (!(nextSearchDirection < 0)) {
-                  _context8.next = 21;
-                  break;
-                }
-
-                upperBound = searchPosition - 1;
-                _context8.next = 22;
-                break;
-
-              case 21:
-                return _context8.abrupt("break", 24);
-
-              case 22:
-                _context8.next = 10;
-                break;
-
-              case 24:
-                // now extend backward
-                overlapStart = searchPosition;
-
-                while (overlapStart && !compare(seqEntries[overlapStart - 1])) {
-                  overlapStart -= 1;
-                } // and then extend forward
-
-
-                overlapEnd = searchPosition;
-
-                while (overlapEnd < len - 1 && !compare(seqEntries[overlapEnd + 1])) {
-                  overlapEnd += 1;
-                }
-
-                x1 = seqEntries[overlapStart].start;
-                x2 = seqEntries[overlapEnd].start + seqEntries[overlapEnd].span;
-                y1 = queryStart;
-                y2 = queryEnd;
-
-                if (!(x2 >= y1 && y2 >= x1)) {
-                  _context8.next = 34;
-                  break;
-                }
-
-                return _context8.abrupt("return", (0, _slice.default)(seqEntries).call(seqEntries, overlapStart, overlapEnd + 1));
-
-              case 34:
-                return _context8.abrupt("return", []);
-
-              case 35:
-              case "end":
-                return _context8.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getEntriesForRange(_x2, _x3, _x4) {
-        return _getEntriesForRange.apply(this, arguments);
-      }
-
-      return getEntriesForRange;
-    }()
-  }]);
-  return CraiIndex;
-}();
-
-module.exports = CraiIndex;
+            });
+        });
+    };
+    return CraiIndex;
+}());
+exports.default = CraiIndex;
+//# sourceMappingURL=craiIndex.js.map

package/dist/craiIndex.js.map

@@ -0,0 +1 @@
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