@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,452 +1,387 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-/* eslint-disable no-underscore-dangle */
-var CramSlightlyLazyFeature = /*#__PURE__*/function () {
-  // uses parameter properties to automatically create fields on the class
-  // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  function CramSlightlyLazyFeature(record, _store) {
-    (0, _classCallCheck2.default)(this, CramSlightlyLazyFeature);
-    this.record = record;
-    this._store = _store;
-  }
-
-  (0, _createClass2.default)(CramSlightlyLazyFeature, [{
-    key: "_get_name",
-    value: function _get_name() {
-      return this.record.readName;
-    }
-  }, {
-    key: "_get_start",
-    value: function _get_start() {
-      return this.record.alignmentStart - 1;
-    }
-  }, {
-    key: "_get_end",
-    value: function _get_end() {
-      return this.record.alignmentStart + this.record.lengthOnRef - 1;
-    }
-  }, {
-    key: "_get_cram_read_features",
-    value: function _get_cram_read_features() {
-      return this.record.readFeatures;
-    }
-  }, {
-    key: "_get_type",
-    value: function _get_type() {
-      return 'match';
-    }
-  }, {
-    key: "_get_score",
-    value: function _get_score() {
-      return this.record.mappingQuality;
-    }
-  }, {
-    key: "_get_flags",
-    value: function _get_flags() {
-      return this.record.flags;
-    }
-  }, {
-    key: "_get_strand",
-    value: function _get_strand() {
-      return this.record.isReverseComplemented() ? -1 : 1;
-    }
-  }, {
-    key: "_read_group_id",
-    value: function _read_group_id() {
-      var rg = this._store.samHeader.readGroups;
-      return rg ? rg[this.record.readGroupId] : undefined;
-    }
-  }, {
-    key: "_get_qual",
-    value: function _get_qual() {
-      return (this.record.qualityScores || []).join(' ');
-    }
-  }, {
-    key: "qualRaw",
-    value: function qualRaw() {
-      return this.record.qualityScores;
-    }
-  }, {
-    key: "_get_seq_id",
-    value: function _get_seq_id() {
-      return this._store.refIdToName(this.record.sequenceId);
-    }
-  }, {
-    key: "_get_refName",
-    value: function _get_refName() {
-      return this._get_seq_id();
-    }
-  }, {
-    key: "_get_is_paired",
-    value: function _get_is_paired() {
-      return !!this.record.mate;
-    }
-  }, {
-    key: "_get_pair_orientation",
-    value: function _get_pair_orientation() {
-      return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    }
-  }, {
-    key: "_get_template_length",
-    value: function _get_template_length() {
-      return this.record.templateLength || this.record.templateSize;
-    }
-  }, {
-    key: "_get_next_seq_id",
-    value: function _get_next_seq_id() {
-      return this.record.mate ? this._store.refIdToName(this.record.mate.sequenceId) : undefined;
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
     }
-  }, {
-    key: "_get_next_pos",
-    value: function _get_next_pos() {
-      return this.record.mate ? this.record.mate.alignmentStart : undefined;
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
     }
-  }, {
-    key: "_get_next_segment_position",
-    value: function _get_next_segment_position() {
-      return this.record.mate ? "".concat(this._store.refIdToName(this.record.mate.sequenceId), ":").concat(this.record.mate.alignmentStart) : undefined;
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
     }
-  }, {
-    key: "_get_tags",
-    value: function _get_tags() {
-      var RG = this._read_group_id();
-
-      var tags = this.record.tags; // avoids a tag copy if no RG, but just copy if there is one
-
-      return RG !== undefined ? _objectSpread(_objectSpread({}, tags), {}, {
-        RG: RG
-      }) : tags;
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var CramSlightlyLazyFeature = /** @class */ (function () {
+    // uses parameter properties to automatically create fields on the class
+    // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    function CramSlightlyLazyFeature(record, _store) {
+        this.record = record;
+        this._store = _store;
     }
-  }, {
-    key: "_get_seq",
-    value: function _get_seq() {
-      return this.record.getReadBases();
-    } // generate a CIGAR, based on code from jkbonfield
-
-  }, {
-    key: "_get_CIGAR",
-    value: function _get_CIGAR() {
-      var seq = '';
-      var cigar = '';
-      var op = 'M';
-      var oplen = 0; // not sure I should access these, but...
-
-      var ref = this.record._refRegion.seq;
-      var refStart = this.record._refRegion.start;
-      var last_pos = this.record.alignmentStart;
-      var sublen = 0;
-
-      if (typeof this.record.readFeatures !== 'undefined') {
-        // @ts-ignore
-        for (var i = 0; i < this.record.readFeatures.length; i++) {
-          var _this$record$readFeat = this.record.readFeatures[i],
-              code = _this$record$readFeat.code,
-              refPos = _this$record$readFeat.refPos,
-              sub = _this$record$readFeat.sub,
-              data = _this$record$readFeat.data;
-          sublen = refPos - last_pos;
-          seq += ref.substring(last_pos - refStart, refPos - refStart);
-          last_pos = refPos;
-
-          if (oplen && op !== 'M') {
-            cigar += oplen + op;
-            oplen = 0;
-          }
-
-          if (sublen) {
-            op = 'M';
-            oplen += sublen;
-          }
-
-          if (code === 'b') {
-            // An array of bases stored verbatim
-            var ret = data.split(',');
-            var added = String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(ret));
-            seq += added;
-            last_pos += added.length;
-            oplen += added.length;
-          } else if (code === 'B') {
-            // Single base (+ qual score)
-            seq += sub;
-            last_pos++;
-            oplen++;
-          } else if (code === 'X') {
-            // Substitution
-            seq += sub;
-            last_pos++;
-            oplen++;
-          } else if (code === 'D' || code === 'N') {
-            // Deletion or Ref Skip
-            last_pos += data;
-
-            if (oplen) {
-              cigar += oplen + op;
-            }
-
-            cigar += data + code;
-            oplen = 0;
-          } else if (code === 'I' || code === 'S') {
-            // Insertion or soft-clip
-            seq += data;
-
-            if (oplen) {
-              cigar += oplen + op;
-            }
-
-            cigar += data.length + code;
-            oplen = 0;
-          } else if (code === 'i') {
-            // Single base insertion
-            seq += data;
-
-            if (oplen) {
-              cigar += oplen + op;
+    CramSlightlyLazyFeature.prototype._get_name = function () {
+        return this.record.readName;
+    };
+    CramSlightlyLazyFeature.prototype._get_start = function () {
+        return this.record.alignmentStart - 1;
+    };
+    CramSlightlyLazyFeature.prototype._get_end = function () {
+        return this.record.alignmentStart + this.record.lengthOnRef - 1;
+    };
+    CramSlightlyLazyFeature.prototype._get_cram_read_features = function () {
+        return this.record.readFeatures;
+    };
+    CramSlightlyLazyFeature.prototype._get_type = function () {
+        return 'match';
+    };
+    CramSlightlyLazyFeature.prototype._get_score = function () {
+        return this.record.mappingQuality;
+    };
+    CramSlightlyLazyFeature.prototype._get_flags = function () {
+        return this.record.flags;
+    };
+    CramSlightlyLazyFeature.prototype._get_strand = function () {
+        return this.record.isReverseComplemented() ? -1 : 1;
+    };
+    CramSlightlyLazyFeature.prototype._read_group_id = function () {
+        var rg = this._store.samHeader.readGroups;
+        return rg ? rg[this.record.readGroupId] : undefined;
+    };
+    CramSlightlyLazyFeature.prototype._get_qual = function () {
+        return (this.record.qualityScores || []).join(' ');
+    };
+    CramSlightlyLazyFeature.prototype.qualRaw = function () {
+        return this.record.qualityScores;
+    };
+    CramSlightlyLazyFeature.prototype._get_seq_id = function () {
+        return this._store.refIdToName(this.record.sequenceId);
+    };
+    CramSlightlyLazyFeature.prototype._get_refName = function () {
+        return this._get_seq_id();
+    };
+    CramSlightlyLazyFeature.prototype._get_is_paired = function () {
+        return !!this.record.mate;
+    };
+    CramSlightlyLazyFeature.prototype._get_pair_orientation = function () {
+        return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
+    };
+    CramSlightlyLazyFeature.prototype._get_template_length = function () {
+        return this.record.templateLength || this.record.templateSize;
+    };
+    CramSlightlyLazyFeature.prototype._get_next_seq_id = function () {
+        return this.record.mate
+            ? this._store.refIdToName(this.record.mate.sequenceId)
+            : undefined;
+    };
+    CramSlightlyLazyFeature.prototype._get_next_pos = function () {
+        return this.record.mate ? this.record.mate.alignmentStart : undefined;
+    };
+    CramSlightlyLazyFeature.prototype._get_next_segment_position = function () {
+        return this.record.mate
+            ? "".concat(this._store.refIdToName(this.record.mate.sequenceId), ":").concat(this.record.mate.alignmentStart)
+            : undefined;
+    };
+    CramSlightlyLazyFeature.prototype._get_tags = function () {
+        var RG = this._read_group_id();
+        var tags = this.record.tags;
+        // avoids a tag copy if no RG, but just copy if there is one
+        return RG !== undefined ? __assign(__assign({}, tags), { RG: RG }) : tags;
+    };
+    CramSlightlyLazyFeature.prototype._get_seq = function () {
+        return this.record.getReadBases();
+    };
+    // generate a CIGAR, based on code from jkbonfield
+    CramSlightlyLazyFeature.prototype._get_CIGAR = function () {
+        var seq = '';
+        var cigar = '';
+        var op = 'M';
+        var oplen = 0;
+        // not sure I should access these, but...
+        var ref = this.record._refRegion.seq;
+        var refStart = this.record._refRegion.start;
+        var last_pos = this.record.alignmentStart;
+        var sublen = 0;
+        if (typeof this.record.readFeatures !== 'undefined') {
+            // @ts-ignore
+            for (var i = 0; i < this.record.readFeatures.length; i++) {
+                var _a = this.record.readFeatures[i], code = _a.code, refPos = _a.refPos, sub = _a.sub, data = _a.data;
+                sublen = refPos - last_pos;
+                seq += ref.substring(last_pos - refStart, refPos - refStart);
+                last_pos = refPos;
+                if (oplen && op !== 'M') {
+                    cigar += oplen + op;
+                    oplen = 0;
+                }
+                if (sublen) {
+                    op = 'M';
+                    oplen += sublen;
+                }
+                if (code === 'b') {
+                    // An array of bases stored verbatim
+                    var ret = data.split(',');
+                    var added = String.fromCharCode.apply(String, __spreadArray([], __read(ret), false));
+                    seq += added;
+                    last_pos += added.length;
+                    oplen += added.length;
+                }
+                else if (code === 'B') {
+                    // Single base (+ qual score)
+                    seq += sub;
+                    last_pos++;
+                    oplen++;
+                }
+                else if (code === 'X') {
+                    // Substitution
+                    seq += sub;
+                    last_pos++;
+                    oplen++;
+                }
+                else if (code === 'D' || code === 'N') {
+                    // Deletion or Ref Skip
+                    last_pos += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += data + code;
+                    oplen = 0;
+                }
+                else if (code === 'I' || code === 'S') {
+                    // Insertion or soft-clip
+                    seq += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += data.length + code;
+                    oplen = 0;
+                }
+                else if (code === 'i') {
+                    // Single base insertion
+                    seq += data;
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += "".concat(1, "I");
+                    oplen = 0;
+                }
+                else if (code === 'P') {
+                    // Padding
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += "".concat(data, "P");
+                }
+                else if (code === 'H') {
+                    // Hard clip
+                    if (oplen) {
+                        cigar += oplen + op;
+                    }
+                    cigar += "".concat(data, "H");
+                    oplen = 0;
+                } // else q or Q
             }
-
-            cigar += "".concat(1, "I");
-            oplen = 0;
-          } else if (code === 'P') {
-            // Padding
-            if (oplen) {
-              cigar += oplen + op;
-            }
-
-            cigar += "".concat(data, "P");
-          } else if (code === 'H') {
-            // Hard clip
-            if (oplen) {
-              cigar += oplen + op;
+        }
+        else {
+            sublen = this.record.readLength - seq.length;
+        }
+        if (seq.length !== this.record.readLength) {
+            sublen = this.record.readLength - seq.length;
+            seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen);
+            if (oplen && op !== 'M') {
+                cigar += oplen + op;
+                oplen = 0;
             }
-
-            cigar += "".concat(data, "H");
-            oplen = 0;
-          } // else q or Q
-
+            op = 'M';
+            oplen += sublen;
         }
-      } else {
-        sublen = this.record.readLength - seq.length;
-      }
-
-      if (seq.length !== this.record.readLength) {
-        sublen = this.record.readLength - seq.length;
-        seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen);
-
-        if (oplen && op !== 'M') {
-          cigar += oplen + op;
-          oplen = 0;
+        if (oplen) {
+            cigar += oplen + op;
         }
-
-        op = 'M';
-        oplen += sublen;
-      }
-
-      if (oplen) {
-        cigar += oplen + op;
-      }
-
-      return cigar;
-    }
-  }, {
-    key: "tags",
-    value: function tags() {
-      var properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
-      return properties.filter(function (prop) {
-        return prop.startsWith('_get_') && prop !== '_get_mismatches' && prop !== '_get_cram_read_features';
-      }).map(function (methodName) {
-        return methodName.replace('_get_', '');
-      });
-    }
-  }, {
-    key: "id",
-    value: function id() {
-      return "".concat(this._store.id, "-").concat(this.record.uniqueId);
-    }
-  }, {
-    key: "get",
-    value: function get(field) {
-      var methodName = "_get_".concat(field); // @ts-ignore
-
-      if (this[methodName]) {
+        return cigar;
+    };
+    CramSlightlyLazyFeature.prototype.tags = function () {
+        var properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
+        return properties
+            .filter(function (prop) {
+            return prop.startsWith('_get_') &&
+                prop !== '_get_mismatches' &&
+                prop !== '_get_cram_read_features';
+        })
+            .map(function (methodName) { return methodName.replace('_get_', ''); });
+    };
+    CramSlightlyLazyFeature.prototype.id = function () {
+        return "".concat(this._store.id, "-").concat(this.record.uniqueId);
+    };
+    CramSlightlyLazyFeature.prototype.get = function (field) {
+        var methodName = "_get_".concat(field);
         // @ts-ignore
-        return this[methodName]();
-      }
-
-      return undefined;
-    }
-  }, {
-    key: "parent",
-    value: function parent() {
-      return undefined;
-    }
-  }, {
-    key: "children",
-    value: function children() {
-      return undefined;
-    }
-  }, {
-    key: "set",
-    value: function set() {}
-  }, {
-    key: "pairedFeature",
-    value: function pairedFeature() {
-      return false;
-    }
-  }, {
-    key: "_get_clipPos",
-    value: function _get_clipPos() {
-      var mismatches = this.get('mismatches');
-
-      if (mismatches.length) {
-        var _record = this.get('strand') === -1 ? mismatches[mismatches.length - 1] : mismatches[0];
-
-        var type = _record.type,
-            cliplen = _record.cliplen;
-
-        if (type === 'softclip' || type === 'hardclip') {
-          return cliplen;
+        if (this[methodName]) {
+            // @ts-ignore
+            return this[methodName]();
         }
-      }
-
-      return 0;
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _this = this;
-
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      var tags = {};
-      this.tags().forEach(function (t) {
-        var val = _this.get(t);
-
-        if (val !== undefined) {
-          tags[t] = val;
+        return undefined;
+    };
+    CramSlightlyLazyFeature.prototype.parent = function () {
+        return undefined;
+    };
+    CramSlightlyLazyFeature.prototype.children = function () {
+        return undefined;
+    };
+    CramSlightlyLazyFeature.prototype.set = function () { };
+    CramSlightlyLazyFeature.prototype.pairedFeature = function () {
+        return false;
+    };
+    CramSlightlyLazyFeature.prototype._get_clipPos = function () {
+        var mismatches = this.get('mismatches');
+        if (mismatches.length) {
+            var record = this.get('strand') === -1
+                ? mismatches[mismatches.length - 1]
+                : mismatches[0];
+            var type = record.type, cliplen = record.cliplen;
+            if (type === 'softclip' || type === 'hardclip') {
+                return cliplen;
+            }
         }
-      });
-      return _objectSpread(_objectSpread({}, tags), {}, {
-        name: this.get('name'),
-        type: this.get('type'),
-        uniqueId: this.id()
-      });
-    }
-  }, {
-    key: "_get_mismatches",
-    value: function _get_mismatches() {
-      var readFeatures = this.get('cram_read_features');
-      var qual = this.qualRaw();
-
-      if (!readFeatures) {
-        return [];
-      }
-
-      var start = this.get('start');
-      var mismatches = new Array(readFeatures.length);
-      var j = 0;
-
-      for (var i = 0; i < readFeatures.length; i++) {
-        var f = readFeatures[i];
-        var code = f.code,
-            pos = f.pos,
-            data = f.data,
-            sub = f.sub,
-            ref = f.ref;
-        var refPos = f.refPos - 1 - start;
-
-        if (code === 'X') {
-          // substitution
-          mismatches[j++] = {
-            start: refPos,
-            length: 1,
-            base: sub,
-            qual: qual === null || qual === void 0 ? void 0 : qual[pos],
-            altbase: ref,
-            type: 'mismatch'
-          };
-        } else if (code === 'I') {
-          // insertion
-          mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: "".concat(data.length),
-            length: 0
-          };
-        } else if (code === 'N') {
-          // reference skip
-          mismatches[j++] = {
-            type: 'skip',
-            length: data,
-            start: refPos,
-            base: 'N'
-          };
-        } else if (code === 'S') {
-          // soft clip
-          var len = data.length;
-          mismatches[j++] = {
-            start: refPos,
-            type: 'softclip',
-            base: "S".concat(len),
-            cliplen: len,
-            length: 1
-          };
-        } else if (code === 'P') {// padding
-        } else if (code === 'H') {
-          // hard clip
-          var _len = data;
-          mismatches[j++] = {
-            start: refPos,
-            type: 'hardclip',
-            base: "H".concat(_len),
-            cliplen: _len,
-            length: 1
-          };
-        } else if (code === 'D') {
-          // deletion
-          mismatches[j++] = {
-            type: 'deletion',
-            length: data,
-            start: refPos,
-            base: '*'
-          };
-        } else if (code === 'b') {// stretch of bases
-        } else if (code === 'q') {// stretch of qual scores
-        } else if (code === 'B') {// a pair of [base, qual]
-        } else if (code === 'i') {
-          // single-base insertion
-          // insertion
-          mismatches[j++] = {
-            start: refPos,
-            type: 'insertion',
-            base: data,
-            length: 1
-          };
-        } else if (code === 'Q') {// single quality value
+        return 0;
+    };
+    CramSlightlyLazyFeature.prototype.toJSON = function () {
+        var _this = this;
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        var tags = {};
+        this.tags().forEach(function (t) {
+            var val = _this.get(t);
+            if (val !== undefined) {
+                tags[t] = val;
+            }
+        });
+        return __assign(__assign({}, tags), { name: this.get('name'), type: this.get('type'), uniqueId: this.id() });
+    };
+    CramSlightlyLazyFeature.prototype._get_mismatches = function () {
+        var readFeatures = this.get('cram_read_features');
+        var qual = this.qualRaw();
+        if (!readFeatures) {
+            return [];
         }
-      }
-
-      return mismatches.slice(0, j);
-    }
-  }]);
-  return CramSlightlyLazyFeature;
-}();
-
-exports.default = CramSlightlyLazyFeature;
+        var start = this.get('start');
+        var mismatches = new Array(readFeatures.length);
+        var j = 0;
+        for (var i = 0; i < readFeatures.length; i++) {
+            var f = readFeatures[i];
+            var code = f.code, pos = f.pos, data = f.data, sub = f.sub, ref = f.ref;
+            var refPos = f.refPos - 1 - start;
+            if (code === 'X') {
+                // substitution
+                mismatches[j++] = {
+                    start: refPos,
+                    length: 1,
+                    base: sub,
+                    qual: qual === null || qual === void 0 ? void 0 : qual[pos],
+                    altbase: ref,
+                    type: 'mismatch',
+                };
+            }
+            else if (code === 'I') {
+                // insertion
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: "".concat(data.length),
+                    length: 0,
+                };
+            }
+            else if (code === 'N') {
+                // reference skip
+                mismatches[j++] = {
+                    type: 'skip',
+                    length: data,
+                    start: refPos,
+                    base: 'N',
+                };
+            }
+            else if (code === 'S') {
+                // soft clip
+                var len = data.length;
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'softclip',
+                    base: "S".concat(len),
+                    cliplen: len,
+                    length: 1,
+                };
+            }
+            else if (code === 'P') {
+                // padding
+            }
+            else if (code === 'H') {
+                // hard clip
+                var len = data;
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'hardclip',
+                    base: "H".concat(len),
+                    cliplen: len,
+                    length: 1,
+                };
+            }
+            else if (code === 'D') {
+                // deletion
+                mismatches[j++] = {
+                    type: 'deletion',
+                    length: data,
+                    start: refPos,
+                    base: '*',
+                };
+            }
+            else if (code === 'b') {
+                // stretch of bases
+            }
+            else if (code === 'q') {
+                // stretch of qual scores
+            }
+            else if (code === 'B') {
+                // a pair of [base, qual]
+            }
+            else if (code === 'i') {
+                // single-base insertion
+                // insertion
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: data,
+                    length: 1,
+                };
+            }
+            else if (code === 'Q') {
+                // single quality value
+            }
+        }
+        return mismatches.slice(0, j);
+    };
+    return CramSlightlyLazyFeature;
+}());
+exports.default = CramSlightlyLazyFeature;
+//# sourceMappingURL=CramSlightlyLazyFeature.js.map