@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/slice/index.js.map

@@ -0,0 +1 @@
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package/dist/cramFile/util.d.ts

@@ -0,0 +1,5 @@
+export function itf8Size(v: any): 1 | 2 | 3 | 4 | 5;
+export function parseItf8(buffer: any, initialOffset: any): any[];
+export function parseItem(buffer: any, parser: any, startBufferPosition?: number, startFilePosition?: number): any;
+export function tinyMemoize(_class: any, methodName: any): void;
+export function sequenceMD5(seq: any): any;

package/dist/cramFile/util.js

@@ -1,161 +1,175 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var md5 = require('md5');
-
-var _require = require('../errors'),
-    CramBufferOverrunError = _require.CramBufferOverrunError;
-
-module.exports = {
-  itf8Size: function itf8Size(v) {
-    if (!(v & ~0x7f)) return 1;
-    if (!(v & ~0x3fff)) return 2;
-    if (!(v & ~0x1fffff)) return 3;
-    if (!(v & ~0xfffffff)) return 4;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.sequenceMD5 = exports.tinyMemoize = exports.parseItem = exports.parseItf8 = exports.itf8Size = void 0;
+var md5_1 = __importDefault(require("md5"));
+var errors_1 = require("../errors");
+function itf8Size(v) {
+    if (!(v & ~0x7f)) {
+        return 1;
+    }
+    if (!(v & ~0x3fff)) {
+        return 2;
+    }
+    if (!(v & ~0x1fffff)) {
+        return 3;
+    }
+    if (!(v & ~0xfffffff)) {
+        return 4;
+    }
     return 5;
-  },
-  parseItf8: function parseItf8(buffer, initialOffset) {
+}
+exports.itf8Size = itf8Size;
+function parseItf8(buffer, initialOffset) {
     var offset = initialOffset;
     var countFlags = buffer[offset];
     var result;
-
     if (countFlags < 0x80) {
-      result = countFlags;
-      offset += 1;
-    } else if (countFlags < 0xc0) {
-      result = (countFlags << 8 | buffer[offset + 1]) & 0x3fff;
-      offset += 2;
-    } else if (countFlags < 0xe0) {
-      result = (countFlags << 16 | buffer[offset + 1] << 8 | buffer[offset + 2]) & 0x1fffff;
-      offset += 3;
-    } else if (countFlags < 0xf0) {
-      result = (countFlags << 24 | buffer[offset + 1] << 16 | buffer[offset + 2] << 8 | buffer[offset + 3]) & 0x0fffffff;
-      offset += 4;
-    } else {
-      result = (countFlags & 0x0f) << 28 | buffer[offset + 1] << 20 | buffer[offset + 2] << 12 | buffer[offset + 3] << 4 | buffer[offset + 4] & 0x0f; // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
-      // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-
-      offset += 5;
+        result = countFlags;
+        offset += 1;
+    }
+    else if (countFlags < 0xc0) {
+        result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
+        offset += 2;
+    }
+    else if (countFlags < 0xe0) {
+        result =
+            ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
+                0x1fffff;
+        offset += 3;
+    }
+    else if (countFlags < 0xf0) {
+        result =
+            ((countFlags << 24) |
+                (buffer[offset + 1] << 16) |
+                (buffer[offset + 2] << 8) |
+                buffer[offset + 3]) &
+                0x0fffffff;
+        offset += 4;
+    }
+    else {
+        result =
+            ((countFlags & 0x0f) << 28) |
+                (buffer[offset + 1] << 20) |
+                (buffer[offset + 2] << 12) |
+                (buffer[offset + 3] << 4) |
+                (buffer[offset + 4] & 0x0f);
+        // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
+        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+        offset += 5;
     }
-
     if (offset > buffer.length) {
-      throw new CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
+        throw new errors_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
     }
-
     return [result, offset - initialOffset];
-  },
-  // parseLtf8(buffer, initialOffset) {
-  //   let offset = initialOffset
-  //   const countFlags = buffer[offset]
-  //   let result
-  //   if (countFlags < 0x80) {
-  //     result = countFlags
-  //     offset += 1
-  //   } else if (countFlags < 0xc0) {
-  //     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
-  //     offset += 2
-  //   } else if (countFlags < 0xe0) {
-  //     result =
-  //       ((buffer[offset] << 16) |
-  //         (buffer[offset + 1] << 8) |
-  //         buffer[offset + 2]) &
-  //       0x1fffff
-  //     offset += 3
-  //   } else if (countFlags < 0xf0) {
-  //     result =
-  //       ((buffer[offset] << 24) |
-  //         (buffer[offset + 1] << 16) |
-  //         (buffer[offset + 2] << 8) |
-  //         buffer[offset + 3]) &
-  //       0x0fffffff
-  //     offset += 4
-  //   } else if (countFlags < 0xf8) {
-  //     result =
-  //       ((buffer[offset] & 15) * Math.pow(2,32) + (buffer[offset + 1] << 24)) |
-  //       ((buffer[offset + 2] << 16) |
-  //         (buffer[offset + 3] << 8) |
-  //         buffer[offset + 4])
-  //     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-  //     offset += 5
-  //   } else if (countFlags < 0xfc) {
-  //     result =
-  //       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
-  //         (buffer[offset + 2] << 24)) |
-  //       ((buffer[offset + 3] << 16) |
-  //         (buffer[offset + 4] << 8) |
-  //         buffer[offset + 5])
-  //     offset += 6
-  //   } else if (countFlags < 0xfe) {
-  //     result =
-  //       ((((buffer[offset] & 3) << 16) |
-  //         (buffer[offset + 1] << 8) |
-  //         buffer[offset + 2]) *
-  //         Math.pow(2,32) +
-  //         (buffer[offset + 3] << 24)) |
-  //       ((buffer[offset + 4] << 16) |
-  //         (buffer[offset + 5] << 8) |
-  //         buffer[offset + 6])
-  //     offset += 7
-  //   } else if (countFlags < 0xff) {
-  //     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
-  //     if (
-  //       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-  //       result.lessThan(Number.MIN_SAFE_INTEGER)
-  //     )
-  //       throw new CramUnimplementedError('integer overflow')
-  //     result = result.toNumber()
-  //     offset += 8
-  //   } else {
-  //     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
-  //     if (
-  //       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-  //       result.lessThan(Number.MIN_SAFE_INTEGER)
-  //     )
-  //       throw new CramUnimplementedError('integer overflow')
-  //     result = result.toNumber()
-  //     offset += 9
-  //   }
-  //   return [result, offset - initialOffset]
-  // },
-  parseItem: function parseItem(buffer, parser) {
-    var startBufferPosition = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 0;
-    var startFilePosition = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : 0;
-
-    var _parser$parse = parser.parse(buffer),
-        offset = _parser$parse.offset,
-        result = _parser$parse.result;
-
+}
+exports.parseItf8 = parseItf8;
+// parseLtf8(buffer, initialOffset) {
+//   let offset = initialOffset
+//   const countFlags = buffer[offset]
+//   let result
+//   if (countFlags < 0x80) {
+//     result = countFlags
+//     offset += 1
+//   } else if (countFlags < 0xc0) {
+//     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
+//     offset += 2
+//   } else if (countFlags < 0xe0) {
+//     result =
+//       ((buffer[offset] << 16) |
+//         (buffer[offset + 1] << 8) |
+//         buffer[offset + 2]) &
+//       0x1fffff
+//     offset += 3
+//   } else if (countFlags < 0xf0) {
+//     result =
+//       ((buffer[offset] << 24) |
+//         (buffer[offset + 1] << 16) |
+//         (buffer[offset + 2] << 8) |
+//         buffer[offset + 3]) &
+//       0x0fffffff
+//     offset += 4
+//   } else if (countFlags < 0xf8) {
+//     result =
+//       ((buffer[offset] & 15) * Math.pow(2,32) + (buffer[offset + 1] << 24)) |
+//       ((buffer[offset + 2] << 16) |
+//         (buffer[offset + 3] << 8) |
+//         buffer[offset + 4])
+//     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+//     offset += 5
+//   } else if (countFlags < 0xfc) {
+//     result =
+//       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
+//         (buffer[offset + 2] << 24)) |
+//       ((buffer[offset + 3] << 16) |
+//         (buffer[offset + 4] << 8) |
+//         buffer[offset + 5])
+//     offset += 6
+//   } else if (countFlags < 0xfe) {
+//     result =
+//       ((((buffer[offset] & 3) << 16) |
+//         (buffer[offset + 1] << 8) |
+//         buffer[offset + 2]) *
+//         Math.pow(2,32) +
+//         (buffer[offset + 3] << 24)) |
+//       ((buffer[offset + 4] << 16) |
+//         (buffer[offset + 5] << 8) |
+//         buffer[offset + 6])
+//     offset += 7
+//   } else if (countFlags < 0xff) {
+//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
+//     if (
+//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
+//       result.lessThan(Number.MIN_SAFE_INTEGER)
+//     )
+//       throw new CramUnimplementedError('integer overflow')
+//     result = result.toNumber()
+//     offset += 8
+//   } else {
+//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
+//     if (
+//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
+//       result.lessThan(Number.MIN_SAFE_INTEGER)
+//     )
+//       throw new CramUnimplementedError('integer overflow')
+//     result = result.toNumber()
+//     offset += 9
+//   }
+//   return [result, offset - initialOffset]
+// },
+function parseItem(buffer, parser, startBufferPosition, startFilePosition) {
+    if (startBufferPosition === void 0) { startBufferPosition = 0; }
+    if (startFilePosition === void 0) { startFilePosition = 0; }
+    var _a = parser.parse(buffer), offset = _a.offset, result = _a.result;
     result._endPosition = offset + startFilePosition;
     result._size = offset - startBufferPosition;
     return result;
-  },
-  // this would be nice as a decorator, but i'm a little worried about
-  // babel support for it going away or changing.
-  // memoizes a method in the stupidest possible way, with no regard for the
-  // arguments.  actually, this only works on methods that take no arguments
-  tinyMemoize: function tinyMemoize(_class, methodName) {
+}
+exports.parseItem = parseItem;
+// this would be nice as a decorator, but i'm a little worried about
+// babel support for it going away or changing.
+// memoizes a method in the stupidest possible way, with no regard for the
+// arguments.  actually, this only works on methods that take no arguments
+function tinyMemoize(_class, methodName) {
     var method = _class.prototype[methodName];
     var memoAttrName = "_memo_".concat(methodName);
-
     _class.prototype[methodName] = function _tinyMemoized() {
-      var _this = this;
-
-      if (!(memoAttrName in this)) {
-        var res = method.call(this);
-        this[memoAttrName] = res;
-
-        _promise.default.resolve(res).catch(function () {
-          delete _this[memoAttrName];
-        });
-      }
-
-      return this[memoAttrName];
+        var _this = this;
+        if (!(memoAttrName in this)) {
+            var res = method.call(this);
+            this[memoAttrName] = res;
+            Promise.resolve(res).catch(function () {
+                delete _this[memoAttrName];
+            });
+        }
+        return this[memoAttrName];
     };
-  },
-  sequenceMD5: function sequenceMD5(seq) {
-    return md5(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
-  }
-};
+}
+exports.tinyMemoize = tinyMemoize;
+function sequenceMD5(seq) {
+    return (0, md5_1.default)(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
+}
+exports.sequenceMD5 = sequenceMD5;
+//# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map

@@ -0,0 +1 @@
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package/dist/errors.d.ts

@@ -0,0 +1,23 @@
+export class CramError extends Error {
+}
+/** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
+export class CramUnimplementedError extends Error {
+}
+/** An error caused by malformed data.  */
+export class CramMalformedError extends CramError {
+}
+/**
+ * An error caused by attempting to read beyond the end of the defined data.
+ */
+export class CramBufferOverrunError extends CramMalformedError {
+}
+/**
+ * An error caused by data being too big, exceeding a size limit.
+ */
+export class CramSizeLimitError extends CramError {
+}
+/**
+ * An invalid argument was supplied to a cram-js method or object.
+ */
+export class CramArgumentError extends CramError {
+}

package/dist/errors.js

@@ -1,115 +1,78 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/getPrototypeOf"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/inherits"));
-
-var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/wrapNativeSuper"));
-
-var CramError =
-/*#__PURE__*/
-function (_Error) {
-  (0, _inherits2.default)(CramError, _Error);
-
-  function CramError() {
-    (0, _classCallCheck2.default)(this, CramError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramError).apply(this, arguments));
-  }
-
-  return CramError;
-}((0, _wrapNativeSuper2.default)(Error));
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CramArgumentError = exports.CramSizeLimitError = exports.CramBufferOverrunError = exports.CramMalformedError = exports.CramUnimplementedError = exports.CramError = void 0;
+var CramError = /** @class */ (function (_super) {
+    __extends(CramError, _super);
+    function CramError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramError;
+}(Error));
+exports.CramError = CramError;
 /** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
-
-
-var CramUnimplementedError =
-/*#__PURE__*/
-function (_Error2) {
-  (0, _inherits2.default)(CramUnimplementedError, _Error2);
-
-  function CramUnimplementedError() {
-    (0, _classCallCheck2.default)(this, CramUnimplementedError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramUnimplementedError).apply(this, arguments));
-  }
-
-  return CramUnimplementedError;
-}((0, _wrapNativeSuper2.default)(Error));
+var CramUnimplementedError = /** @class */ (function (_super) {
+    __extends(CramUnimplementedError, _super);
+    function CramUnimplementedError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramUnimplementedError;
+}(Error));
+exports.CramUnimplementedError = CramUnimplementedError;
 /** An error caused by malformed data.  */
-
-
-var CramMalformedError =
-/*#__PURE__*/
-function (_CramError) {
-  (0, _inherits2.default)(CramMalformedError, _CramError);
-
-  function CramMalformedError() {
-    (0, _classCallCheck2.default)(this, CramMalformedError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramMalformedError).apply(this, arguments));
-  }
-
-  return CramMalformedError;
-}(CramError);
+var CramMalformedError = /** @class */ (function (_super) {
+    __extends(CramMalformedError, _super);
+    function CramMalformedError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramMalformedError;
+}(CramError));
+exports.CramMalformedError = CramMalformedError;
 /**
  * An error caused by attempting to read beyond the end of the defined data.
  */
-
-
-var CramBufferOverrunError =
-/*#__PURE__*/
-function (_CramMalformedError) {
-  (0, _inherits2.default)(CramBufferOverrunError, _CramMalformedError);
-
-  function CramBufferOverrunError() {
-    (0, _classCallCheck2.default)(this, CramBufferOverrunError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramBufferOverrunError).apply(this, arguments));
-  }
-
-  return CramBufferOverrunError;
-}(CramMalformedError);
+var CramBufferOverrunError = /** @class */ (function (_super) {
+    __extends(CramBufferOverrunError, _super);
+    function CramBufferOverrunError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramBufferOverrunError;
+}(CramMalformedError));
+exports.CramBufferOverrunError = CramBufferOverrunError;
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-
-
-var CramSizeLimitError =
-/*#__PURE__*/
-function (_CramError2) {
-  (0, _inherits2.default)(CramSizeLimitError, _CramError2);
-
-  function CramSizeLimitError() {
-    (0, _classCallCheck2.default)(this, CramSizeLimitError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramSizeLimitError).apply(this, arguments));
-  }
-
-  return CramSizeLimitError;
-}(CramError);
+var CramSizeLimitError = /** @class */ (function (_super) {
+    __extends(CramSizeLimitError, _super);
+    function CramSizeLimitError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramSizeLimitError;
+}(CramError));
+exports.CramSizeLimitError = CramSizeLimitError;
 /**
  * An invalid argument was supplied to a cram-js method or object.
  */
-
-
-var CramArgumentError =
-/*#__PURE__*/
-function (_CramError3) {
-  (0, _inherits2.default)(CramArgumentError, _CramError3);
-
-  function CramArgumentError() {
-    (0, _classCallCheck2.default)(this, CramArgumentError);
-    return (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(CramArgumentError).apply(this, arguments));
-  }
-
-  return CramArgumentError;
-}(CramError);
-
-module.exports = {
-  CramBufferOverrunError: CramBufferOverrunError,
-  CramMalformedError: CramMalformedError,
-  CramUnimplementedError: CramUnimplementedError,
-  CramSizeLimitError: CramSizeLimitError,
-  CramArgumentError: CramArgumentError
-};
+var CramArgumentError = /** @class */ (function (_super) {
+    __extends(CramArgumentError, _super);
+    function CramArgumentError() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    return CramArgumentError;
+}(CramError));
+exports.CramArgumentError = CramArgumentError;
+//# sourceMappingURL=errors.js.map

package/dist/errors.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,4 @@
+import CramFile from "./cramFile";
+import IndexedCramFile from "./indexedCramFile";
+import CraiIndex from "./craiIndex";
+export { CramFile, IndexedCramFile, CraiIndex };

package/dist/index.js

@@ -1,13 +1,13 @@
 "use strict";
-
-var CramFile = require('./cramFile');
-
-var IndexedCramFile = require('./indexedCramFile');
-
-var CraiIndex = require('./craiIndex');
-
-module.exports = {
-  CramFile: CramFile,
-  IndexedCramFile: IndexedCramFile,
-  CraiIndex: CraiIndex
-};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CraiIndex = exports.IndexedCramFile = exports.CramFile = void 0;
+var cramFile_1 = __importDefault(require("./cramFile"));
+exports.CramFile = cramFile_1.default;
+var indexedCramFile_1 = __importDefault(require("./indexedCramFile"));
+exports.IndexedCramFile = indexedCramFile_1.default;
+var craiIndex_1 = __importDefault(require("./craiIndex"));
+exports.CraiIndex = craiIndex_1.default;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":";;;;;;AAAA,wDAAiC;AAIxB,mBAJF,kBAAQ,CAIE;AAHjB,sEAA+C;AAG5B,0BAHZ,yBAAe,CAGY;AAFlC,0DAAmC;AAEC,oBAF7B,mBAAS,CAE6B"}