@gmod/cram 1.5.6 → 1.6.0

package/dist/cramFile/record.js

@@ -1,310 +1,260 @@
 "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 _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var Constants = require('./constants');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var constants_1 = __importDefault(require("./constants"));
 function decodeReadSequence(cramRecord, refRegion) {
-  // if it has no length, it has no sequence
-  if (!cramRecord.lengthOnRef && !cramRecord.readLength) return undefined;
-  if (cramRecord.isUnknownBases()) return undefined; // remember: all coordinates are 1-based closed
-
-  var regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
-  if (!cramRecord.readFeatures) return refRegion.seq.substr(regionSeqOffset, cramRecord.lengthOnRef).toUpperCase();
-  var bases = '';
-  var regionPos = regionSeqOffset;
-  var currentReadFeature = 0;
-
-  while (bases.length < cramRecord.readLength) {
-    if (currentReadFeature < cramRecord.readFeatures.length) {
-      var feature = cramRecord.readFeatures[currentReadFeature];
-
-      if (feature.code === 'Q' || feature.code === 'q') {
-        currentReadFeature += 1;
-      } else if (feature.pos === bases.length + 1) {
-        // process the read feature
-        currentReadFeature += 1;
-
-        if (feature.code === 'b') {
-          // specify a base pair for some reason
-          var ret = feature.data.split(',');
-          var added = String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(ret));
-          bases += added;
-          regionPos += added.length;
-        } else if (feature.code === 'B') {
-          // base pair and associated quality
-          // TODO: do we need to set the quality in the qual scores?
-          bases += feature.data[0];
-          regionPos += 1;
-        } else if (feature.code === 'X') {
-          // base substitution
-          bases += feature.sub;
-          regionPos += 1;
-        } else if (feature.code === 'I') {
-          // insertion
-          bases += feature.data;
-        } else if (feature.code === 'D') {
-          // deletion
-          regionPos += feature.data;
-        } else if (feature.code === 'i') {
-          // insert single base
-          bases += feature.data;
-        } else if (feature.code === 'N') {
-          // reference skip. delete some bases
-          // do nothing
-          // seqBases.splice(feature.pos - 1, feature.data)
-          regionPos += feature.data;
-        } else if (feature.code === 'S') {
-          // soft clipped bases that should be present in the read seq
-          // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
-          bases += feature.data;
-        } else if (feature.code === 'P') {// padding, do nothing
-        } else if (feature.code === 'H') {// hard clip, do nothing
+    // if it has no length, it has no sequence
+    if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
+        return undefined;
+    }
+    if (cramRecord.isUnknownBases()) {
+        return undefined;
+    }
+    // remember: all coordinates are 1-based closed
+    var regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
+    if (!cramRecord.readFeatures) {
+        return refRegion.seq
+            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .toUpperCase();
+    }
+    var bases = '';
+    var regionPos = regionSeqOffset;
+    var currentReadFeature = 0;
+    while (bases.length < cramRecord.readLength) {
+        if (currentReadFeature < cramRecord.readFeatures.length) {
+            var feature = cramRecord.readFeatures[currentReadFeature];
+            if (feature.code === 'Q' || feature.code === 'q') {
+                currentReadFeature += 1;
+            }
+            else if (feature.pos === bases.length + 1) {
+                // process the read feature
+                currentReadFeature += 1;
+                if (feature.code === 'b') {
+                    // specify a base pair for some reason
+                    var ret = feature.data.split(',');
+                    var added = String.fromCharCode.apply(String, ret);
+                    bases += added;
+                    regionPos += added.length;
+                }
+                else if (feature.code === 'B') {
+                    // base pair and associated quality
+                    // TODO: do we need to set the quality in the qual scores?
+                    bases += feature.data[0];
+                    regionPos += 1;
+                }
+                else if (feature.code === 'X') {
+                    // base substitution
+                    bases += feature.sub;
+                    regionPos += 1;
+                }
+                else if (feature.code === 'I') {
+                    // insertion
+                    bases += feature.data;
+                }
+                else if (feature.code === 'D') {
+                    // deletion
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'i') {
+                    // insert single base
+                    bases += feature.data;
+                }
+                else if (feature.code === 'N') {
+                    // reference skip. delete some bases
+                    // do nothing
+                    // seqBases.splice(feature.pos - 1, feature.data)
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'S') {
+                    // soft clipped bases that should be present in the read seq
+                    // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
+                    bases += feature.data;
+                }
+                else if (feature.code === 'P') {
+                    // padding, do nothing
+                }
+                else if (feature.code === 'H') {
+                    // hard clip, do nothing
+                }
+            }
+            else if (currentReadFeature < cramRecord.readFeatures.length) {
+                // put down a chunk of sequence up to the next read feature
+                var chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                bases += chunk;
+                regionPos += chunk.length;
+            }
+        }
+        else {
+            // put down a chunk of reference up to the full read length
+            var chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            bases += chunk;
+            regionPos += chunk.length;
         }
-      } else if (currentReadFeature < cramRecord.readFeatures.length) {
-        // put down a chunk of sequence up to the next read feature
-        var chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
-        bases += chunk;
-        regionPos += chunk.length;
-      }
-    } else {
-      // put down a chunk of reference up to the full read length
-      var _chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
-
-      bases += _chunk;
-      regionPos += _chunk.length;
     }
-  }
-
-  return bases.toUpperCase();
+    return bases.toUpperCase();
 }
-
 var baseNumbers = {
-  a: 0,
-  A: 0,
-  c: 1,
-  C: 1,
-  g: 2,
-  G: 2,
-  t: 3,
-  T: 3,
-  n: 4,
-  N: 4
+    a: 0,
+    A: 0,
+    c: 1,
+    C: 1,
+    g: 2,
+    G: 2,
+    t: 3,
+    T: 3,
+    n: 4,
+    N: 4,
 };
-
 function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
-  if (!refRegion) return; // decode base substitution code using the substitution matrix
-
-  var refCoord = readFeature.refPos - refRegion.start;
-  var refBase = refRegion.seq.charAt(refCoord);
-  if (refBase) readFeature.ref = refBase;
-  var baseNumber = baseNumbers[refBase];
-  if (baseNumber === undefined) baseNumber = 4;
-  var substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
-  var base = substitutionScheme[readFeature.data];
-  if (base) readFeature.sub = base;
+    if (!refRegion) {
+        return;
+    }
+    // decode base substitution code using the substitution matrix
+    var refCoord = readFeature.refPos - refRegion.start;
+    var refBase = refRegion.seq.charAt(refCoord);
+    if (refBase) {
+        readFeature.ref = refBase;
+    }
+    var baseNumber = baseNumbers[refBase];
+    if (baseNumber === undefined) {
+        baseNumber = 4;
+    }
+    var substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
+    var base = substitutionScheme[readFeature.data];
+    if (base) {
+        readFeature.sub = base;
+    }
 }
 /**
  * Class of each CRAM record returned by this API.
  */
-
-
-var CramRecord =
-/*#__PURE__*/
-function () {
-  function CramRecord() {
-    (0, _classCallCheck2.default)(this, CramRecord);
-    this.tags = {};
-  }
-  /**
-   * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
-   */
-
-
-  (0, _createClass2.default)(CramRecord, [{
-    key: "isPaired",
-    value: function isPaired() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FPAIRED);
+var CramRecord = /** @class */ (function () {
+    function CramRecord() {
+        this.tags = {};
     }
+    /**
+     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     */
+    CramRecord.prototype.isPaired = function () {
+        return !!(this.flags & constants_1.default.BAM_FPAIRED);
+    };
     /** @returns {boolean} true if the read is paired, and both segments are mapped */
-
-  }, {
-    key: "isProperlyPaired",
-    value: function isProperlyPaired() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FPROPER_PAIR);
-    }
+    CramRecord.prototype.isProperlyPaired = function () {
+        return !!(this.flags & constants_1.default.BAM_FPROPER_PAIR);
+    };
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: "isSegmentUnmapped",
-    value: function isSegmentUnmapped() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FUNMAP);
-    }
+    CramRecord.prototype.isSegmentUnmapped = function () {
+        return !!(this.flags & constants_1.default.BAM_FUNMAP);
+    };
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: "isMateUnmapped",
-    value: function isMateUnmapped() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FMUNMAP);
-    }
+    CramRecord.prototype.isMateUnmapped = function () {
+        return !!(this.flags & constants_1.default.BAM_FMUNMAP);
+    };
     /** @returns {boolean} true if the read is mapped to the reverse strand */
-
-  }, {
-    key: "isReverseComplemented",
-    value: function isReverseComplemented() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREVERSE);
-    }
+    CramRecord.prototype.isReverseComplemented = function () {
+        return !!(this.flags & constants_1.default.BAM_FREVERSE);
+    };
     /** @returns {boolean} true if the mate is mapped to the reverse strand */
-
-  }, {
-    key: "isMateReverseComplemented",
-    value: function isMateReverseComplemented() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FMREVERSE);
-    }
+    CramRecord.prototype.isMateReverseComplemented = function () {
+        return !!(this.flags & constants_1.default.BAM_FMREVERSE);
+    };
     /** @returns {boolean} true if this is read number 1 in a pair */
-
-  }, {
-    key: "isRead1",
-    value: function isRead1() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREAD1);
-    }
+    CramRecord.prototype.isRead1 = function () {
+        return !!(this.flags & constants_1.default.BAM_FREAD1);
+    };
     /** @returns {boolean} true if this is read number 2 in a pair */
-
-  }, {
-    key: "isRead2",
-    value: function isRead2() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREAD2);
-    }
+    CramRecord.prototype.isRead2 = function () {
+        return !!(this.flags & constants_1.default.BAM_FREAD2);
+    };
     /** @returns {boolean} true if this is a secondary alignment */
-
-  }, {
-    key: "isSecondary",
-    value: function isSecondary() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FSECONDARY);
-    }
+    CramRecord.prototype.isSecondary = function () {
+        return !!(this.flags & constants_1.default.BAM_FSECONDARY);
+    };
     /** @returns {boolean} true if this read has failed QC checks */
-
-  }, {
-    key: "isFailedQc",
-    value: function isFailedQc() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FQCFAIL);
-    }
+    CramRecord.prototype.isFailedQc = function () {
+        return !!(this.flags & constants_1.default.BAM_FQCFAIL);
+    };
     /** @returns {boolean} true if the read is an optical or PCR duplicate */
-
-  }, {
-    key: "isDuplicate",
-    value: function isDuplicate() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FDUP);
-    }
+    CramRecord.prototype.isDuplicate = function () {
+        return !!(this.flags & constants_1.default.BAM_FDUP);
+    };
     /** @returns {boolean} true if this is a supplementary alignment */
-
-  }, {
-    key: "isSupplementary",
-    value: function isSupplementary() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FSUPPLEMENTARY);
-    }
+    CramRecord.prototype.isSupplementary = function () {
+        return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
+    };
     /**
      * @returns {boolean} true if the read is detached
      */
-
-  }, {
-    key: "isDetached",
-    value: function isDetached() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_DETACHED);
-    }
+    CramRecord.prototype.isDetached = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_DETACHED);
+    };
     /** @returns {boolean} true if the read has a mate in this same CRAM segment */
-
-  }, {
-    key: "hasMateDownStream",
-    value: function hasMateDownStream() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_MATE_DOWNSTREAM);
-    }
+    CramRecord.prototype.hasMateDownStream = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_MATE_DOWNSTREAM);
+    };
     /** @returns {boolean} true if the read contains qual scores */
-
-  }, {
-    key: "isPreservingQualityScores",
-    value: function isPreservingQualityScores() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_PRESERVE_QUAL_SCORES);
-    }
+    CramRecord.prototype.isPreservingQualityScores = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_PRESERVE_QUAL_SCORES);
+    };
     /** @returns {boolean} true if the read has no sequence bases */
-
-  }, {
-    key: "isUnknownBases",
-    value: function isUnknownBases() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_NO_SEQ);
-    }
+    CramRecord.prototype.isUnknownBases = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_NO_SEQ);
+    };
     /**
      * Get the original sequence of this read.
      * @returns {String} sequence basepairs
      */
-
-  }, {
-    key: "getReadBases",
-    value: function getReadBases() {
-      if (!this.readBases && this._refRegion) {
-        this.readBases = decodeReadSequence(this, this._refRegion);
-      }
-
-      return this.readBases;
-    }
+    CramRecord.prototype.getReadBases = function () {
+        if (!this.readBases && this._refRegion) {
+            this.readBases = decodeReadSequence(this, this._refRegion);
+        }
+        return this.readBases;
+    };
     /**
      * Get the pair orientation of a paired read. Adapted from igv.js
      * @returns {String} of paired orientatin
      */
-
-  }, {
-    key: "getPairOrientation",
-    value: function getPairOrientation() {
-      if (!this.isSegmentUnmapped() && this.isPaired() && !this.isMateUnmapped() && this.mate && this.sequenceId === this.mate.sequenceId) {
-        var s1 = this.isReverseComplemented() ? 'R' : 'F';
-        var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-        var o1 = ' ';
-        var o2 = ' ';
-
-        if (this.isRead1()) {
-          o1 = '1';
-          o2 = '2';
-        } else if (this.isRead2()) {
-          o1 = '2';
-          o2 = '1';
-        }
-
-        var tmp = [];
-        var isize = this.templateLength || this.templateSize;
-
-        if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-          isize = -isize;
+    CramRecord.prototype.getPairOrientation = function () {
+        if (!this.isSegmentUnmapped() &&
+            this.isPaired() &&
+            !this.isMateUnmapped() &&
+            this.mate &&
+            this.sequenceId === this.mate.sequenceId) {
+            var s1 = this.isReverseComplemented() ? 'R' : 'F';
+            var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
+            var o1 = ' ';
+            var o2 = ' ';
+            if (this.isRead1()) {
+                o1 = '1';
+                o2 = '2';
+            }
+            else if (this.isRead2()) {
+                o1 = '2';
+                o2 = '1';
+            }
+            var tmp = [];
+            var isize = this.templateLength || this.templateSize;
+            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
+                isize = -isize;
+            }
+            if (isize > 0) {
+                tmp[0] = s1;
+                tmp[1] = o1;
+                tmp[2] = s2;
+                tmp[3] = o2;
+            }
+            else {
+                tmp[2] = s1;
+                tmp[3] = o1;
+                tmp[0] = s2;
+                tmp[1] = o2;
+            }
+            return tmp.join('');
         }
-
-        if (isize > 0) {
-          tmp[0] = s1;
-          tmp[1] = o1;
-          tmp[2] = s2;
-          tmp[3] = o2;
-        } else {
-          tmp[2] = s1;
-          tmp[3] = o1;
-          tmp[0] = s2;
-          tmp[1] = o2;
-        }
-
-        return tmp.join('');
-      }
-
-      return null;
-    }
+        return null;
+    };
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
@@ -318,44 +268,39 @@ function () {
      * @param {CramContainerCompressionScheme} compressionScheme
      * @returns {undefined} nothing
      */
-
-  }, {
-    key: "addReferenceSequence",
-    value: function addReferenceSequence(refRegion, compressionScheme) {
-      var _this = this;
-
-      if (this.readFeatures) {
-        var _context;
-
-        // use the reference bases to decode the bases
-        // substituted in each base substitution
-        (0, _forEach.default)(_context = this.readFeatures).call(_context, function (readFeature) {
-          if (readFeature.code === 'X') decodeBaseSubstitution(_this, refRegion, compressionScheme, readFeature);
+    CramRecord.prototype.addReferenceSequence = function (refRegion, compressionScheme) {
+        var _this = this;
+        if (this.readFeatures) {
+            // use the reference bases to decode the bases
+            // substituted in each base substitution
+            this.readFeatures.forEach(function (readFeature) {
+                if (readFeature.code === 'X') {
+                    decodeBaseSubstitution(_this, refRegion, compressionScheme, readFeature);
+                }
+            });
+        }
+        // if this region completely covers this read,
+        // keep a reference to it
+        if (!this.readBases &&
+            refRegion.start <= this.alignmentStart &&
+            refRegion.end >=
+                this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
+            this._refRegion = refRegion;
+        }
+    };
+    CramRecord.prototype.toJSON = function () {
+        var _this = this;
+        var data = {};
+        Object.keys(this).forEach(function (k) {
+            if (k.charAt(0) === '_') {
+                return;
+            }
+            data[k] = _this[k];
         });
-      } // if this region completely covers this read,
-      // keep a reference to it
-
-
-      if (!this.readBases && refRegion.start <= this.alignmentStart && refRegion.end >= this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
-        this._refRegion = refRegion;
-      }
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _context2,
-          _this2 = this;
-
-      var data = {};
-      (0, _forEach.default)(_context2 = (0, _keys.default)(this)).call(_context2, function (k) {
-        if (k.charAt(0) === '_') return;
-        data[k] = _this2[k];
-      });
-      data.readBases = this.getReadBases();
-      return data;
-    }
-  }]);
-  return CramRecord;
-}();
-
-module.exports = CramRecord;
+        data.readBases = this.getReadBases();
+        return data;
+    };
+    return CramRecord;
+}());
+exports.default = CramRecord;
+//# sourceMappingURL=record.js.map

package/dist/cramFile/record.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/cramFile/record.js"],"names":[],"mappings":";;;;;AAAA,0DAAmC;AAEnC,SAAS,kBAAkB,CAAC,UAAU,EAAE,SAAS;IAC/C,0CAA0C;IAC1C,IAAI,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,UAAU,CAAC,UAAU,EAAE;QACrD,OAAO,SAAS,CAAA;KACjB;IAED,IAAI,UAAU,CAAC,cAAc,EAAE,EAAE;QAC/B,OAAO,SAAS,CAAA;KACjB;IAED,+CAA+C;IAC/C,IAAM,eAAe,GAAG,UAAU,CAAC,cAAc,GAAG,SAAS,CAAC,KAAK,CAAA;IAEnE,IAAI,CAAC,UAAU,CAAC,YAAY,EAAE;QAC5B,OAAO,SAAS,CAAC,GAAG;aACjB,MAAM,CAAC,eAAe,EAAE,UAAU,CAAC,WAAW,CAAC;aAC/C,WAAW,EAAE,CAAA;KACjB;IAED,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,SAAS,GAAG,eAAe,CAAA;IAC/B,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,OAAO,KAAK,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE;QAC3C,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE;YACvD,IAAM,OAAO,GAAG,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAC,CAAA;YAC3D,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;gBAChD,kBAAkB,IAAI,CAAC,CAAA;aACxB;iBAAM,IAAI,OAAO,CAAC,GAAG,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE;gBAC3C,2BAA2B;gBAC3B,kBAAkB,IAAI,CAAC,CAAA;gBAEvB,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBACxB,sCAAsC;oBACtC,IAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACnC,IAAM,KAAK,GAAG,MAAM,CAAC,YAAY,OAAnB,MAAM,EAAiB,GAAG,CAAC,CAAA;oBACzC,KAAK,IAAI,KAAK,CAAA;oBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;iBAC1B;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,mCAAmC;oBACnC,0DAA0D;oBAC1D,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBACxB,SAAS,IAAI,CAAC,CAAA;iBACf;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,oBAAoB;oBACpB,KAAK,IAAI,OAAO,CAAC,GAAG,CAAA;oBACpB,SAAS,IAAI,CAAC,CAAA;iBACf;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,YAAY;oBACZ,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;iBACtB;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,WAAW;oBACX,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;iBAC1B;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,qBAAqB;oBACrB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;iBACtB;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,oCAAoC;oBACpC,aAAa;oBACb,iDAAiD;oBACjD,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;iBAC1B;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,4DAA4D;oBAC5D,iEAAiE;oBACjE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;iBACtB;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,sBAAsB;iBACvB;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE;oBAC/B,wBAAwB;iBACzB;aACF;iBAAM,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE;gBAC9D,2DAA2D;gBAC3D,IAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAChC,SAAS,EACT,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CACnE,CAAA;gBACD,KAAK,IAAI,KAAK,CAAA;gBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;aAC1B;SACF;aAAM;YACL,2DAA2D;YAC3D,IAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAChC,SAAS,EACT,UAAU,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,CACrC,CAAA;YACD,KAAK,IAAI,KAAK,CAAA;YACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;SAC1B;KACF;IAED,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;AAC5B,CAAC;AAED,IAAM,WAAW,GAAG;IAClB,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;CACL,CAAA;AAED,SAAS,sBAAsB,CAC7B,UAAU,EACV,SAAS,EACT,iBAAiB,EACjB,WAAW;IAEX,IAAI,CAAC,SAAS,EAAE;QACd,OAAM;KACP;IAED,8DAA8D;IAC9D,IAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,GAAG,SAAS,CAAC,KAAK,CAAA;IACrD,IAAM,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC9C,IAAI,OAAO,EAAE;QACX,WAAW,CAAC,GAAG,GAAG,OAAO,CAAA;KAC1B;IACD,IAAI,UAAU,GAAG,WAAW,CAAC,OAAO,CAAC,CAAA;IACrC,IAAI,UAAU,KAAK,SAAS,EAAE;QAC5B,UAAU,GAAG,CAAC,CAAA;KACf;IACD,IAAM,kBAAkB,GAAG,iBAAiB,CAAC,kBAAkB,CAAC,UAAU,CAAC,CAAA;IAC3E,IAAM,IAAI,GAAG,kBAAkB,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACjD,IAAI,IAAI,EAAE;QACR,WAAW,CAAC,GAAG,GAAG,IAAI,CAAA;KACvB;AACH,CAAC;AAED;;GAEG;AACH;IACE;QACE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAA;IAChB,CAAC;IAED;;OAEG;IACH,6BAAQ,GAAR;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,WAAW,CAAC,CAAA;IAC/C,CAAC;IAED,kFAAkF;IAClF,qCAAgB,GAAhB;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,gBAAgB,CAAC,CAAA;IACpD,CAAC;IAED,gGAAgG;IAChG,sCAAiB,GAAjB;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,UAAU,CAAC,CAAA;IAC9C,CAAC;IAED,gGAAgG;IAChG,mCAAc,GAAd;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,WAAW,CAAC,CAAA;IAC/C,CAAC;IAED,0EAA0E;IAC1E,0CAAqB,GAArB;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,YAAY,CAAC,CAAA;IAChD,CAAC;IAED,0EAA0E;IAC1E,8CAAyB,GAAzB;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,aAAa,CAAC,CAAA;IACjD,CAAC;IAED,iEAAiE;IACjE,4BAAO,GAAP;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,UAAU,CAAC,CAAA;IAC9C,CAAC;IAED,iEAAiE;IACjE,4BAAO,GAAP;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,UAAU,CAAC,CAAA;IAC9C,CAAC;IAED,+DAA+D;IAC/D,gCAAW,GAAX;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,cAAc,CAAC,CAAA;IAClD,CAAC;IAED,gEAAgE;IAChE,+BAAU,GAAV;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,WAAW,CAAC,CAAA;IAC/C,CAAC;IAED,yEAAyE;IACzE,gCAAW,GAAX;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,QAAQ,CAAC,CAAA;IAC5C,CAAC;IAED,mEAAmE;IACnE,oCAAe,GAAf;QACE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,mBAAS,CAAC,kBAAkB,CAAC,CAAA;IACtD,CAAC;IAED;;OAEG;IACH,+BAAU,GAAV;Q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package/dist/cramFile/sectionParsers.d.ts

@@ -0,0 +1,18 @@
+export namespace cramFileDefinition {
+    const parser: any;
+    const maxLength: number;
+}
+export function getSectionParsers(majorVersion: any): {
+    cramFileDefinition: {
+        parser: any;
+        maxLength: number;
+    };
+    cramBlockHeader: {
+        parser: any;
+        maxLength: number;
+    };
+    cramBlockCrc32: {
+        parser: any;
+        maxLength: number;
+    };
+};