@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/container/compressionScheme.js

@@ -1,166 +1,128 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-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 _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var _require2 = require('../codecs'),
-    instantiateCodec = _require2.instantiateCodec; // the hardcoded data type to be decoded for each core
+Object.defineProperty(exports, "__esModule", { value: true });
+var errors_1 = require("../../errors");
+var codecs_1 = require("../codecs");
+// the hardcoded data type to be decoded for each core
 // data field
-
-
 var dataSeriesTypes = {
-  BF: 'int',
-  CF: 'int',
-  RI: 'int',
-  RL: 'int',
-  AP: 'int',
-  RG: 'int',
-  MF: 'int',
-  NS: 'int',
-  NP: 'int',
-  TS: 'int',
-  NF: 'int',
-  TC: 'byte',
-  TN: 'int',
-  FN: 'int',
-  FC: 'byte',
-  FP: 'int',
-  BS: 'byte',
-  IN: 'byteArray',
-  SC: 'byteArray',
-  DL: 'int',
-  BA: 'byte',
-  BB: 'byteArray',
-  RS: 'int',
-  PD: 'int',
-  HC: 'int',
-  MQ: 'int',
-  RN: 'byteArray',
-  QS: 'byte',
-  QQ: 'byteArray',
-  TL: 'int',
-  TM: 'ignore',
-  TV: 'ignore'
+    BF: 'int',
+    CF: 'int',
+    RI: 'int',
+    RL: 'int',
+    AP: 'int',
+    RG: 'int',
+    MF: 'int',
+    NS: 'int',
+    NP: 'int',
+    TS: 'int',
+    NF: 'int',
+    TC: 'byte',
+    TN: 'int',
+    FN: 'int',
+    FC: 'byte',
+    FP: 'int',
+    BS: 'byte',
+    IN: 'byteArray',
+    SC: 'byteArray',
+    DL: 'int',
+    BA: 'byte',
+    BB: 'byteArray',
+    RS: 'int',
+    PD: 'int',
+    HC: 'int',
+    MQ: 'int',
+    RN: 'byteArray',
+    QS: 'byte',
+    QQ: 'byteArray',
+    TL: 'int',
+    TM: 'ignore',
+    TV: 'ignore',
 };
-
 function parseSubstitutionMatrix(byteArray) {
-  var matrix = new Array(5);
-
-  for (var i = 0; i < 5; i += 1) {
-    matrix[i] = new Array(4);
-  }
-
-  matrix[0][byteArray[0] >> 6 & 3] = 'C';
-  matrix[0][byteArray[0] >> 4 & 3] = 'G';
-  matrix[0][byteArray[0] >> 2 & 3] = 'T';
-  matrix[0][byteArray[0] >> 0 & 3] = 'N';
-  matrix[1][byteArray[1] >> 6 & 3] = 'A';
-  matrix[1][byteArray[1] >> 4 & 3] = 'G';
-  matrix[1][byteArray[1] >> 2 & 3] = 'T';
-  matrix[1][byteArray[1] >> 0 & 3] = 'N';
-  matrix[2][byteArray[2] >> 6 & 3] = 'A';
-  matrix[2][byteArray[2] >> 4 & 3] = 'C';
-  matrix[2][byteArray[2] >> 2 & 3] = 'T';
-  matrix[2][byteArray[2] >> 0 & 3] = 'N';
-  matrix[3][byteArray[3] >> 6 & 3] = 'A';
-  matrix[3][byteArray[3] >> 4 & 3] = 'C';
-  matrix[3][byteArray[3] >> 2 & 3] = 'G';
-  matrix[3][byteArray[3] >> 0 & 3] = 'N';
-  matrix[4][byteArray[4] >> 6 & 3] = 'A';
-  matrix[4][byteArray[4] >> 4 & 3] = 'C';
-  matrix[4][byteArray[4] >> 2 & 3] = 'G';
-  matrix[4][byteArray[4] >> 0 & 3] = 'T';
-  return matrix;
+    var matrix = new Array(5);
+    for (var i = 0; i < 5; i += 1) {
+        matrix[i] = new Array(4);
+    }
+    matrix[0][(byteArray[0] >> 6) & 3] = 'C';
+    matrix[0][(byteArray[0] >> 4) & 3] = 'G';
+    matrix[0][(byteArray[0] >> 2) & 3] = 'T';
+    matrix[0][(byteArray[0] >> 0) & 3] = 'N';
+    matrix[1][(byteArray[1] >> 6) & 3] = 'A';
+    matrix[1][(byteArray[1] >> 4) & 3] = 'G';
+    matrix[1][(byteArray[1] >> 2) & 3] = 'T';
+    matrix[1][(byteArray[1] >> 0) & 3] = 'N';
+    matrix[2][(byteArray[2] >> 6) & 3] = 'A';
+    matrix[2][(byteArray[2] >> 4) & 3] = 'C';
+    matrix[2][(byteArray[2] >> 2) & 3] = 'T';
+    matrix[2][(byteArray[2] >> 0) & 3] = 'N';
+    matrix[3][(byteArray[3] >> 6) & 3] = 'A';
+    matrix[3][(byteArray[3] >> 4) & 3] = 'C';
+    matrix[3][(byteArray[3] >> 2) & 3] = 'G';
+    matrix[3][(byteArray[3] >> 0) & 3] = 'N';
+    matrix[4][(byteArray[4] >> 6) & 3] = 'A';
+    matrix[4][(byteArray[4] >> 4) & 3] = 'C';
+    matrix[4][(byteArray[4] >> 2) & 3] = 'G';
+    matrix[4][(byteArray[4] >> 0) & 3] = 'T';
+    return matrix;
 }
-
-var CramContainerCompressionScheme =
-/*#__PURE__*/
-function () {
-  function CramContainerCompressionScheme(content) {
-    (0, _classCallCheck2.default)(this, CramContainerCompressionScheme);
-    (0, _assign.default)(this, content); // interpret some of the preservation map tags for convenient use
-
-    this.readNamesIncluded = content.preservation.RN;
-    this.APdelta = content.preservation.AP;
-    this.referenceRequired = !!content.preservation.RR;
-    this.tagIdsDictionary = content.preservation.TD;
-    this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-    this.dataSeriesCodecCache = {};
-    this.tagCodecCache = {};
-  }
-  /**
-   * @param {string} tagName three-character tag name
-   * @private
-   */
-
-
-  (0, _createClass2.default)(CramContainerCompressionScheme, [{
-    key: "getCodecForTag",
-    value: function getCodecForTag(tagName) {
-      if (!this.tagCodecCache[tagName]) {
-        var encodingData = this.tagEncoding[tagName];
-
-        if (encodingData) {
-          this.tagCodecCache[tagName] = instantiateCodec(encodingData, 'byteArray' // all tags are byte array data
-          );
-        }
-      }
-
-      return this.tagCodecCache[tagName];
+var CramContainerCompressionScheme = /** @class */ (function () {
+    function CramContainerCompressionScheme(content) {
+        Object.assign(this, content);
+        // interpret some of the preservation map tags for convenient use
+        this.readNamesIncluded = content.preservation.RN;
+        this.APdelta = content.preservation.AP;
+        this.referenceRequired = !!content.preservation.RR;
+        this.tagIdsDictionary = content.preservation.TD;
+        this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
+        this.dataSeriesCodecCache = {};
+        this.tagCodecCache = {};
     }
+    /**
+     * @param {string} tagName three-character tag name
+     * @private
+     */
+    CramContainerCompressionScheme.prototype.getCodecForTag = function (tagName) {
+        if (!this.tagCodecCache[tagName]) {
+            var encodingData = this.tagEncoding[tagName];
+            if (encodingData) {
+                this.tagCodecCache[tagName] = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            }
+        }
+        return this.tagCodecCache[tagName];
+    };
     /**
      *
      * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      * @private
      */
-
-  }, {
-    key: "getTagNames",
-    value: function getTagNames(tagListId) {
-      return this.tagIdsDictionary[tagListId];
-    }
-  }, {
-    key: "getCodecForDataSeries",
-    value: function getCodecForDataSeries(dataSeriesName) {
-      if (!this.dataSeriesCodecCache[dataSeriesName]) {
-        var encodingData = this.dataSeriesEncoding[dataSeriesName];
-
-        if (encodingData) {
-          var dataType = dataSeriesTypes[dataSeriesName];
-          if (!dataType) throw new CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
-          this.dataSeriesCodecCache[dataSeriesName] = instantiateCodec(encodingData, dataType);
+    CramContainerCompressionScheme.prototype.getTagNames = function (tagListId) {
+        return this.tagIdsDictionary[tagListId];
+    };
+    CramContainerCompressionScheme.prototype.getCodecForDataSeries = function (dataSeriesName) {
+        if (!this.dataSeriesCodecCache[dataSeriesName]) {
+            var encodingData = this.dataSeriesEncoding[dataSeriesName];
+            if (encodingData) {
+                var dataType = dataSeriesTypes[dataSeriesName];
+                if (!dataType) {
+                    throw new errors_1.CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
+                }
+                this.dataSeriesCodecCache[dataSeriesName] = (0, codecs_1.instantiateCodec)(encodingData, dataType);
+            }
         }
-      }
-
-      return this.dataSeriesCodecCache[dataSeriesName];
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _context,
-          _this = this;
-
-      var data = {};
-      (0, _forEach.default)(_context = (0, _keys.default)(this)).call(_context, function (k) {
-        if (/Cache$/.test(k)) return;
-        data[k] = _this[k];
-      });
-      return data;
-    }
-  }]);
-  return CramContainerCompressionScheme;
-}();
-
-module.exports = CramContainerCompressionScheme;
+        return this.dataSeriesCodecCache[dataSeriesName];
+    };
+    CramContainerCompressionScheme.prototype.toJSON = function () {
+        var _this = this;
+        var data = {};
+        Object.keys(this).forEach(function (k) {
+            if (/Cache$/.test(k)) {
+                return;
+            }
+            data[k] = _this[k];
+        });
+        return data;
+    };
+    return CramContainerCompressionScheme;
+}());
+exports.default = CramContainerCompressionScheme;
+//# sourceMappingURL=compressionScheme.js.map

package/dist/cramFile/container/compressionScheme.js.map

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

@@ -0,0 +1,13 @@
+export default class CramContainer {
+    constructor(cramFile: any, position: any);
+    file: any;
+    filePosition: any;
+    getHeader(): Promise<any>;
+    getCompressionHeaderBlock(): Promise<any>;
+    getFirstBlock(): Promise<any>;
+    getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
+    getSlice(slicePosition: any, sliceSize: any): CramSlice;
+    _readContainerHeader(position: any): Promise<any>;
+}
+import CramContainerCompressionScheme from "./compressionScheme";
+import CramSlice from "../slice";