@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/codecs/huffman.js.map

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

@@ -0,0 +1,2 @@
+export function getCodecClassWithId(id: any): any;
+export function instantiateCodec(encodingData: any, dataType: any): any;

package/dist/cramFile/codecs/index.js

@@ -1,45 +1,38 @@
 "use strict";
-
-var _require = require('../../errors'),
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var HuffmanIntCodec = require('./huffman');
-
-var ExternalCodec = require('./external');
-
-var ByteArrayStopCodec = require('./byteArrayStop');
-
-var ByteArrayLengthCodec = require('./byteArrayLength');
-
-var BetaCodec = require('./beta');
-
-var GammaCodec = require('./gamma');
-
-var SubexpCodec = require('./subexp');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.instantiateCodec = exports.getCodecClassWithId = void 0;
+var errors_1 = require("../../errors");
+var huffman_1 = __importDefault(require("./huffman"));
+var external_1 = __importDefault(require("./external"));
+var byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
+var byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
+var beta_1 = __importDefault(require("./beta"));
+var gamma_1 = __importDefault(require("./gamma"));
+var subexp_1 = __importDefault(require("./subexp"));
 var codecClasses = {
-  1: ExternalCodec,
-  // 2: GolombCodec,
-  3: HuffmanIntCodec,
-  4: ByteArrayLengthCodec,
-  5: ByteArrayStopCodec,
-  6: BetaCodec,
-  7: SubexpCodec,
-  // 8: GolombRiceCodec,
-  9: GammaCodec
+    1: external_1.default,
+    // 2: GolombCodec,
+    3: huffman_1.default,
+    4: byteArrayLength_1.default,
+    5: byteArrayStop_1.default,
+    6: beta_1.default,
+    7: subexp_1.default,
+    // 8: GolombRiceCodec,
+    9: gamma_1.default,
 };
-
 function getCodecClassWithId(id) {
-  return codecClasses[id];
+    return codecClasses[id];
 }
-
+exports.getCodecClassWithId = getCodecClassWithId;
 function instantiateCodec(encodingData, dataType) {
-  var CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
-  if (!CodecClass) throw new CramUnimplementedError("no codec implemented for codec ID ".concat(encodingData.codecId));
-  return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
+    var CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
+    if (!CodecClass) {
+        throw new errors_1.CramUnimplementedError("no codec implemented for codec ID ".concat(encodingData.codecId));
+    }
+    return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
 }
-
-module.exports = {
-  getCodecClassWithId: getCodecClassWithId,
-  instantiateCodec: instantiateCodec
-};
+exports.instantiateCodec = instantiateCodec;
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.js"],"names":[],"mappings":";;;;;;AAAA,uCAAqD;AAErD,sDAAuC;AACvC,wDAAsC;AACtC,kEAAgD;AAChD,sEAAoD;AACpD,gDAA8B;AAC9B,kDAAgC;AAChC,oDAAkC;AAElC,IAAM,YAAY,GAAG;IACnB,CAAC,EAAE,kBAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,iBAAe;IAClB,CAAC,EAAE,yBAAoB;IACvB,CAAC,EAAE,uBAAkB;IACrB,CAAC,EAAE,cAAS;IACZ,CAAC,EAAE,gBAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,eAAU;CACd,CAAA;AAED,SAAgB,mBAAmB,CAAC,EAAE;IACpC,OAAO,YAAY,CAAC,EAAE,CAAC,CAAA;AACzB,CAAC;AAFD,kDAEC;AAED,SAAgB,gBAAgB,CAAC,YAAY,EAAE,QAAQ;IACrD,IAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE;QACf,MAAM,IAAI,+BAAsB,CAC9B,4CAAqC,YAAY,CAAC,OAAO,CAAE,CAC5D,CAAA;KACF;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC;AAXD,4CAWC"}

package/dist/cramFile/codecs/subexp.d.ts

@@ -0,0 +1,4 @@
+export default class SubexpCodec extends CramCodec {
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+}
+import CramCodec from "./_base";

package/dist/cramFile/codecs/subexp.js

@@ -1,66 +1,53 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-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 _require = require('../../errors'),
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var CramCodec = require('./_base');
-
-var SubexpCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(SubexpCodec, _CramCodec);
-
-  function SubexpCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, SubexpCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(SubexpCodec).call(this, parameters, dataType));
-
-    if (_this.dataType !== 'int') {
-      throw new CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by SUBEXP codec"));
+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 __());
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var errors_1 = require("../../errors");
+var _base_1 = __importDefault(require("./_base"));
+var SubexpCodec = /** @class */ (function (_super) {
+    __extends(SubexpCodec, _super);
+    function SubexpCodec(parameters, dataType) {
+        if (parameters === void 0) { parameters = {}; }
+        var _this = _super.call(this, parameters, dataType) || this;
+        if (_this.dataType !== 'int') {
+            throw new errors_1.CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by SUBEXP codec"));
+        }
+        return _this;
     }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(SubexpCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var numLeadingOnes = 0;
-
-      while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-        numLeadingOnes += 1;
-      }
-
-      var b;
-      var n;
-
-      if (numLeadingOnes === 0) {
-        b = this.parameters.K;
-        n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
-      } else {
-        b = numLeadingOnes + this.parameters.K - 1;
-        n = 1 << b | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
-      }
-
-      return n - this.parameters.offset;
-    }
-  }]);
-  return SubexpCodec;
-}(CramCodec);
-
-module.exports = SubexpCodec;
+    SubexpCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+        var numLeadingOnes = 0;
+        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
+            numLeadingOnes += 1;
+        }
+        var b;
+        var n;
+        if (numLeadingOnes === 0) {
+            b = this.parameters.K;
+            n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        else {
+            b = numLeadingOnes + this.parameters.K - 1;
+            n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        return n - this.parameters.offset;
+    };
+    return SubexpCodec;
+}(_base_1.default));
+exports.default = SubexpCodec;
+//# sourceMappingURL=subexp.js.map

package/dist/cramFile/codecs/subexp.js.map

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

@@ -0,0 +1,36 @@
+export default Constants;
+declare namespace Constants {
+    const CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
+    const CRAM_FLAG_DETACHED: number;
+    const CRAM_FLAG_MATE_DOWNSTREAM: number;
+    const CRAM_FLAG_NO_SEQ: number;
+    const CRAM_FLAG_MASK: number;
+    const CRAM_M_REVERSE: number;
+    const CRAM_M_UNMAP: number;
+    const BAM_FPAIRED: number;
+    const BAM_FPROPER_PAIR: number;
+    const BAM_FUNMAP: number;
+    const BAM_FMUNMAP: number;
+    const BAM_FREVERSE: number;
+    const BAM_FMREVERSE: number;
+    const BAM_FREAD1: number;
+    const BAM_FREAD2: number;
+    const BAM_FSECONDARY: number;
+    const BAM_FQCFAIL: number;
+    const BAM_FDUP: number;
+    const BAM_FSUPPLEMENTARY: number;
+    const BAM_CMATCH: number;
+    const BAM_CINS: number;
+    const BAM_CDEL: number;
+    const BAM_CREF_SKIP: number;
+    const BAM_CSOFT_CLIP: number;
+    const BAM_CHARD_CLIP: number;
+    const BAM_CPAD: number;
+    const BAM_CEQUAL: number;
+    const BAM_CDIFF: number;
+    const BAM_CBACK: number;
+    const BAM_CIGAR_STR: string;
+    const BAM_CIGAR_SHIFT: number;
+    const BAM_CIGAR_MASK: number;
+    const BAM_CIGAR_TYPE: number;
+}

package/dist/cramFile/constants.js

@@ -1,51 +1,53 @@
 "use strict";
-
-module.exports = {
-  CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
-  CRAM_FLAG_DETACHED: 1 << 1,
-  CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
-  CRAM_FLAG_NO_SEQ: 1 << 3,
-  CRAM_FLAG_MASK: (1 << 4) - 1,
-  // mate read is reversed
-  CRAM_M_REVERSE: 1,
-  // mated read is unmapped
-  CRAM_M_UNMAP: 2,
-  //  the read is paired in sequencing, no matter whether it is mapped in a pair
-  BAM_FPAIRED: 1,
-  //  the read is mapped in a proper pair
-  BAM_FPROPER_PAIR: 2,
-  //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
-  BAM_FUNMAP: 4,
-  //  the mate is unmapped
-  BAM_FMUNMAP: 8,
-  //  the read is mapped to the reverse strand
-  BAM_FREVERSE: 16,
-  //  the mate is mapped to the reverse strand
-  BAM_FMREVERSE: 32,
-  //  this is read1
-  BAM_FREAD1: 64,
-  //  this is read2
-  BAM_FREAD2: 128,
-  //  not primary alignment
-  BAM_FSECONDARY: 256,
-  //  QC failure
-  BAM_FQCFAIL: 512,
-  //  optical or PCR duplicate
-  BAM_FDUP: 1024,
-  //  supplementary alignment
-  BAM_FSUPPLEMENTARY: 2048,
-  BAM_CMATCH: 0,
-  BAM_CINS: 1,
-  BAM_CDEL: 2,
-  BAM_CREF_SKIP: 3,
-  BAM_CSOFT_CLIP: 4,
-  BAM_CHARD_CLIP: 5,
-  BAM_CPAD: 6,
-  BAM_CEQUAL: 7,
-  BAM_CDIFF: 8,
-  BAM_CBACK: 9,
-  BAM_CIGAR_STR: 'MIDNSHP:XB',
-  BAM_CIGAR_SHIFT: 4,
-  BAM_CIGAR_MASK: 0xf,
-  BAM_CIGAR_TYPE: 0x3c1a7
-};
+Object.defineProperty(exports, "__esModule", { value: true });
+var Constants = {
+    CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
+    CRAM_FLAG_DETACHED: 1 << 1,
+    CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
+    CRAM_FLAG_NO_SEQ: 1 << 3,
+    CRAM_FLAG_MASK: (1 << 4) - 1,
+    // mate read is reversed
+    CRAM_M_REVERSE: 1,
+    // mated read is unmapped
+    CRAM_M_UNMAP: 2,
+    //  the read is paired in sequencing, no matter whether it is mapped in a pair
+    BAM_FPAIRED: 1,
+    //  the read is mapped in a proper pair
+    BAM_FPROPER_PAIR: 2,
+    //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+    BAM_FUNMAP: 4,
+    //  the mate is unmapped
+    BAM_FMUNMAP: 8,
+    //  the read is mapped to the reverse strand
+    BAM_FREVERSE: 16,
+    //  the mate is mapped to the reverse strand
+    BAM_FMREVERSE: 32,
+    //  this is read1
+    BAM_FREAD1: 64,
+    //  this is read2
+    BAM_FREAD2: 128,
+    //  not primary alignment
+    BAM_FSECONDARY: 256,
+    //  QC failure
+    BAM_FQCFAIL: 512,
+    //  optical or PCR duplicate
+    BAM_FDUP: 1024,
+    //  supplementary alignment
+    BAM_FSUPPLEMENTARY: 2048,
+    BAM_CMATCH: 0,
+    BAM_CINS: 1,
+    BAM_CDEL: 2,
+    BAM_CREF_SKIP: 3,
+    BAM_CSOFT_CLIP: 4,
+    BAM_CHARD_CLIP: 5,
+    BAM_CPAD: 6,
+    BAM_CEQUAL: 7,
+    BAM_CDIFF: 8,
+    BAM_CBACK: 9,
+    BAM_CIGAR_STR: 'MIDNSHP:XB',
+    BAM_CIGAR_SHIFT: 4,
+    BAM_CIGAR_MASK: 0xf,
+    BAM_CIGAR_TYPE: 0x3c1a7,
+};
+exports.default = Constants;
+//# sourceMappingURL=constants.js.map

package/dist/cramFile/constants.js.map

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

@@ -0,0 +1,23 @@
+export default class CramContainerCompressionScheme {
+    constructor(content: any);
+    readNamesIncluded: any;
+    APdelta: any;
+    referenceRequired: boolean;
+    tagIdsDictionary: any;
+    substitutionMatrix: any[];
+    dataSeriesCodecCache: {};
+    tagCodecCache: {};
+    /**
+     * @param {string} tagName three-character tag name
+     * @private
+     */
+    private getCodecForTag;
+    /**
+     *
+     * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
+     * @private
+     */
+    private getTagNames;
+    getCodecForDataSeries(dataSeriesName: any): any;
+    toJSON(): {};
+}