@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,145 +1,110 @@
 "use strict";
-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);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    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];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var MismatchParser_1 = require("./MismatchParser");
-var BamSlightlyLazyFeature = /** @class */ (function () {
+const MismatchParser_1 = require("./MismatchParser");
+class BamSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-    function BamSlightlyLazyFeature(record, adapter, ref) {
+    constructor(record, adapter, ref) {
         this.record = record;
         this.adapter = adapter;
         this.ref = ref;
     }
-    BamSlightlyLazyFeature.prototype._get_name = function () {
+    _get_name() {
         return this.record.get('name');
-    };
-    BamSlightlyLazyFeature.prototype._get_type = function () {
+    }
+    _get_type() {
         return 'match';
-    };
-    BamSlightlyLazyFeature.prototype._get_score = function () {
+    }
+    _get_score() {
         return this.record.get('mq');
-    };
-    BamSlightlyLazyFeature.prototype._get_flags = function () {
+    }
+    _get_flags() {
         return this.record.flags;
-    };
-    BamSlightlyLazyFeature.prototype._get_strand = function () {
+    }
+    _get_strand() {
         return this.record.isReverseComplemented() ? -1 : 1;
-    };
-    BamSlightlyLazyFeature.prototype._get_pair_orientation = function () {
+    }
+    _get_pair_orientation() {
         return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    };
-    BamSlightlyLazyFeature.prototype._get_next_seq_id = function () {
+    }
+    _get_next_seq_id() {
         return this.record._next_refid();
-    };
-    BamSlightlyLazyFeature.prototype._get_seq_id = function () {
+    }
+    _get_seq_id() {
         // @ts-ignore
         return this.record._refID;
-    };
-    BamSlightlyLazyFeature.prototype._get_next_refName = function () {
+    }
+    _get_next_refName() {
         return this.adapter.refIdToName(this.record._next_refid());
-    };
-    BamSlightlyLazyFeature.prototype._get_next_segment_position = function () {
-        var _a = this, record = _a.record, adapter = _a.adapter;
+    }
+    _get_next_segment_position() {
+        const { record, adapter } = this;
         return record.isPaired()
-            ? "".concat(adapter.refIdToName(record._next_refid()), ":").concat(record._next_pos() + 1)
+            ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`
             : undefined;
-    };
-    BamSlightlyLazyFeature.prototype._get_seq = function () {
+    }
+    _get_seq() {
         return this.record.getReadBases();
-    };
-    BamSlightlyLazyFeature.prototype.qualRaw = function () {
+    }
+    qualRaw() {
         return this.record.qualRaw();
-    };
-    BamSlightlyLazyFeature.prototype.set = function () { };
-    BamSlightlyLazyFeature.prototype.tags = function () {
-        var properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
-        return __spreadArray([], __read(new Set(properties
-            .filter(function (prop) {
-            return prop.startsWith('_get_') &&
+    }
+    set() { }
+    tags() {
+        const properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
+        return [
+            ...new Set(properties
+                .filter(prop => prop.startsWith('_get_') &&
                 prop !== '_get_mismatches' &&
                 prop !== '_get_tags' &&
                 prop !== '_get_next_seq_id' &&
-                prop !== '_get_seq_id';
-        })
-            .map(function (methodName) { return methodName.replace('_get_', ''); })
-            .concat(this.record._tags()))), false);
-    };
-    BamSlightlyLazyFeature.prototype.id = function () {
-        return "".concat(this.adapter.id, "-").concat(this.record.id());
-    };
+                prop !== '_get_seq_id')
+                .map(methodName => methodName.replace('_get_', ''))
+                .concat(this.record._tags())),
+        ];
+    }
+    id() {
+        return `${this.adapter.id}-${this.record.id()}`;
+    }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    BamSlightlyLazyFeature.prototype.get = function (field) {
-        var methodName = "_get_".concat(field);
+    get(field) {
+        const methodName = `_get_${field}`;
         // @ts-ignore
         if (this[methodName]) {
             // @ts-ignore
             return this[methodName]();
         }
         return this.record.get(field);
-    };
-    BamSlightlyLazyFeature.prototype._get_refName = function () {
+    }
+    _get_refName() {
         return this.adapter.refIdToName(this.record.seq_id());
-    };
-    BamSlightlyLazyFeature.prototype.parent = function () {
+    }
+    parent() {
         return undefined;
-    };
-    BamSlightlyLazyFeature.prototype.children = function () {
+    }
+    children() {
         return undefined;
-    };
-    BamSlightlyLazyFeature.prototype.pairedFeature = function () {
+    }
+    pairedFeature() {
         return false;
-    };
-    BamSlightlyLazyFeature.prototype.toJSON = function () {
-        var _this = this;
-        return __assign(__assign({}, Object.fromEntries(this.tags()
-            .map(function (t) { return [t, _this.get(t)]; })
-            .filter(function (elt) { return elt[1] !== undefined; }))), { uniqueId: this.id() });
-    };
-    BamSlightlyLazyFeature.prototype._get_mismatches = function () {
+    }
+    toJSON() {
+        return {
+            ...Object.fromEntries(this.tags()
+                .map(t => [t, this.get(t)])
+                .filter(elt => elt[1] !== undefined)),
+            uniqueId: this.id(),
+        };
+    }
+    _get_mismatches() {
         return (0, MismatchParser_1.getMismatches)(this.get('CIGAR'), this.get('MD'), this.get('seq'), this.ref, this.qualRaw());
-    };
-    BamSlightlyLazyFeature.prototype._get_clipPos = function () {
-        var cigar = this.get('CIGAR') || '';
+    }
+    _get_clipPos() {
+        const cigar = this.get('CIGAR') || '';
         return this.get('strand') === -1
             ? +(cigar.match(/(\d+)[SH]$/) || [])[1] || 0
             : +(cigar.match(/^(\d+)([SH])/) || [])[1] || 0;
-    };
-    return BamSlightlyLazyFeature;
-}());
+    }
+}
 exports.default = BamSlightlyLazyFeature;
 //# sourceMappingURL=BamSlightlyLazyFeature.js.map

package/dist/BamAdapter/BamSlightlyLazyFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAMA,mDAAgD;AAIhD;IACE,wEAAwE;IACxE,iFAAiF;IACjF,gCACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,0CAAS,GAAT;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,0CAAS,GAAT;QACE,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,2CAAU,GAAV;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,2CAAU,GAAV;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,4CAAW,GAAX;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,sDAAqB,GAArB;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,iDAAgB,GAAhB;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAA;IAClC,CAAC;IAED,4CAAW,GAAX;QACE,aAAa;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,kDAAiB,GAAjB;QACE,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;IAC5D,CAAC;IAED,2DAA0B,GAA1B;QACQ,IAAA,KAAsB,IAAI,EAAxB,MAAM,YAAA,EAAE,OAAO,aAAS,CAAA;QAChC,OAAO,MAAM,CAAC,QAAQ,EAAE;YACtB,CAAC,CAAC,UAAG,OAAO,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,cAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,CAAE;YAC1E,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,yCAAQ,GAAR;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,wCAAO,GAAP;QACE,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,oCAAG,GAAH,cAAO,CAAC;IAER,qCAAI,GAAJ;QACE,IAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,gCACK,IAAI,GAAG,CACR,UAAU;aACP,MAAM,CACL,UAAA,IAAI;YACF,OAAA,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW;gBACpB,IAAI,KAAK,kBAAkB;gBAC3B,IAAI,KAAK,aAAa;QAJtB,CAIsB,CACzB;aACA,GAAG,CAAC,UAAA,UAAU,IAAI,OAAA,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,EAA/B,CAA+B,CAAC;aAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B,UACF;IACH,CAAC;IAED,mCAAE,GAAF;QACE,OAAO,UAAG,IAAI,CAAC,OAAO,CAAC,EAAE,cAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,oCAAG,GAAH,UAAI,KAAa;QACf,IAAM,UAAU,GAAG,eAAQ,KAAK,CAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,6CAAY,GAAZ;QACE,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,uCAAM,GAAN;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,yCAAQ,GAAR;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,8CAAa,GAAb;QACE,OAAO,KAAK,CAAA;IACd,CAAC;IAED,uCAAM,GAAN;QAAA,iBASC;QARC,6BACK,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;aACR,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,EAAE,KAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAhB,CAAgB,CAAC;aAC1B,MAAM,CAAC,UAAA,GAAG,IAAI,OAAA,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,EAApB,CAAoB,CAAC,CACvC,KACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE,IACpB;IACH,CAAC;IAED,gDAAe,GAAf;QACE,OAAO,IAAA,8BAAa,EAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,6CAAY,GAAZ;QACE,IAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAClD,CAAC;IACH,6BAAC;AAAD,CAAC,AA/ID,IA+IC"}
+{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":";;AAMA,qDAAgD;AAIhD,MAAqB,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,gBAAgB;QACd,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAA;IAClC,CAAC;IAED,WAAW;QACT,aAAa;QACb,OAAO,IAAI,CAAC,MAAM,CAAC,MAAM,CAAA;IAC3B,CAAC;IAED,iBAAiB;QACf,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;IAC5D,CAAC;IAED,0BAA0B;QACxB,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,MAAM,CAAC,QAAQ,EAAE;YACtB,CAAC,CAAC,GAAG,OAAO,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,EAAE;YAC1E,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW;gBACpB,IAAI,KAAK,kBAAkB;gBAC3B,IAAI,KAAK,aAAa,CACzB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,aAAa;QACb,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,aAAa;YACb,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,IAAA,8BAAa,EAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;YAC5C,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAClD,CAAC;CACF;AA/ID,yCA+IC"}

package/dist/BamAdapter/MismatchParser.d.ts

@@ -9,7 +9,7 @@ export interface Mismatch {
     seq?: string;
     cliplen?: number;
 }
-export declare function parseCigar(cigar: string): string[];
+export declare function parseCigar(cigar?: string): string[];
 export declare function cigarToMismatches(ops: string[], seq: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
  * parse a SAM MD tag to find mismatching bases of the template versus the reference

package/dist/BamAdapter/MismatchParser.js

@@ -1,67 +1,24 @@
 "use strict";
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-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);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getModificationTypes = exports.getModificationPositions = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
-var util_1 = require("@jbrowse/core/util");
-var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
-var modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
-function parseCigar(cigar) {
-    return (cigar || '').split(/([MIDNSHPX=])/);
+const util_1 = require("@jbrowse/core/util");
+const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
+const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
+function parseCigar(cigar = '') {
+    return cigar.split(/([MIDNSHPX=])/).slice(0, -1);
 }
 exports.parseCigar = parseCigar;
 function cigarToMismatches(ops, seq, ref, qual) {
-    var roffset = 0; // reference offset
-    var soffset = 0; // seq offset
-    var mismatches = [];
-    var hasRefAndSeq = ref && seq;
-    for (var i = 0; i < ops.length; i += 2) {
-        var len = +ops[i];
-        var op = ops[i + 1];
+    let roffset = 0; // reference offset
+    let soffset = 0; // seq offset
+    const mismatches = [];
+    const hasRefAndSeq = ref && seq;
+    for (let i = 0; i < ops.length; i += 2) {
+        const len = +ops[i];
+        const op = ops[i + 1];
         if (op === 'M' || op === '=' || op === 'E') {
             if (hasRefAndSeq) {
-                for (var j = 0; j < len; j++) {
+                for (let j = 0; j < len; j++) {
                     if (
                     // @ts-ignore in the full yarn build of the repo, this says that object is possibly undefined for some reason, ignored
                     seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()) {
@@ -81,7 +38,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
             mismatches.push({
                 start: roffset,
                 type: 'insertion',
-                base: "".concat(len),
+                base: `${len}`,
                 length: 0,
             });
             soffset += len;
@@ -103,9 +60,9 @@ function cigarToMismatches(ops, seq, ref, qual) {
             });
         }
         else if (op === 'X') {
-            var r = seq.slice(soffset, soffset + len);
-            var q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
-            for (var j = 0; j < len; j++) {
+            const r = seq.slice(soffset, soffset + len);
+            const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
+            for (let j = 0; j < len; j++) {
                 mismatches.push({
                     start: roffset + j,
                     type: 'mismatch',
@@ -120,7 +77,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
             mismatches.push({
                 start: roffset,
                 type: 'hardclip',
-                base: "H".concat(len),
+                base: `H${len}`,
                 cliplen: len,
                 length: 1,
             });
@@ -129,7 +86,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
             mismatches.push({
                 start: roffset,
                 type: 'softclip',
-                base: "S".concat(len),
+                base: `S${len}`,
                 cliplen: len,
                 length: 1,
             });
@@ -147,13 +104,13 @@ exports.cigarToMismatches = cigarToMismatches;
  * @returns array of mismatches and their positions
  */
 function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
-    var mismatchRecords = [];
-    var curr = { start: 0, base: '', length: 0, type: 'mismatch' };
-    var skips = cigarMismatches.filter(function (cigar) { return cigar.type === 'skip'; });
-    var lastCigar = 0;
-    var lastTemplateOffset = 0;
-    var lastRefOffset = 0;
-    var lastSkipPos = 0;
+    const mismatchRecords = [];
+    let curr = { start: 0, base: '', length: 0, type: 'mismatch' };
+    const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
+    let lastCigar = 0;
+    let lastTemplateOffset = 0;
+    let lastRefOffset = 0;
+    let lastSkipPos = 0;
     // convert a position on the reference sequence to a position
     // on the template sequence, taking into account hard and soft
     // clipping of reads
@@ -168,11 +125,11 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
         };
     }
     function getTemplateCoordLocal(refCoord) {
-        var templateOffset = lastTemplateOffset;
-        var refOffset = lastRefOffset;
-        for (var i = lastCigar; i < ops.length && refOffset <= refCoord; i += 2, lastCigar = i) {
-            var len = +ops[i];
-            var op = ops[i + 1];
+        let templateOffset = lastTemplateOffset;
+        let refOffset = lastRefOffset;
+        for (let i = lastCigar; i < ops.length && refOffset <= refCoord; i += 2, lastCigar = i) {
+            const len = +ops[i];
+            const op = ops[i + 1];
             if (op === 'S' || op === 'I') {
                 templateOffset += len;
             }
@@ -189,10 +146,10 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
         return templateOffset - (refOffset - refCoord);
     }
     // now actually parse the MD string
-    var md = mdstring.match(mdRegex) || [];
-    for (var i = 0; i < md.length; i++) {
-        var token = md[i];
-        var num = +token;
+    const md = mdstring.match(mdRegex) || [];
+    for (let i = 0; i < md.length; i++) {
+        const token = md[i];
+        const num = +token;
         if (!Number.isNaN(num)) {
             curr.start += num;
         }
@@ -201,10 +158,10 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
         }
         else {
             // mismatch
-            for (var j = 0; j < token.length; j += 1) {
+            for (let j = 0; j < token.length; j += 1) {
                 curr.length = 1;
                 while (lastSkipPos < skips.length) {
-                    var mismatch = skips[lastSkipPos];
+                    const mismatch = skips[lastSkipPos];
                     if (curr.start >= mismatch.start) {
                         curr.start += mismatch.length;
                         lastSkipPos++;
@@ -213,9 +170,9 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
                         break;
                     }
                 }
-                var s = getTemplateCoordLocal(curr.start);
+                const s = getTemplateCoordLocal(curr.start);
                 curr.base = seq[s] || 'X';
-                var qualScore = qual === null || qual === void 0 ? void 0 : qual[s];
+                const qualScore = qual === null || qual === void 0 ? void 0 : qual[s];
                 if (qualScore) {
                     curr.qual = qualScore;
                 }
@@ -228,8 +185,8 @@ function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
 }
 exports.mdToMismatches = mdToMismatches;
 function getMismatches(cigar, md, seq, ref, qual) {
-    var mismatches = [];
-    var ops = parseCigar(cigar);
+    let mismatches = [];
+    const ops = parseCigar(cigar);
     // parse the CIGAR tag if it has one
     if (cigar) {
         mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual));
@@ -243,75 +200,53 @@ function getMismatches(cigar, md, seq, ref, qual) {
 exports.getMismatches = getMismatches;
 // get relative reference sequence positions for positions given relative to
 // the read sequence
-function getNextRefPos(cigarOps, positions) {
-    var readPos, refPos, currPos, i, len, op, i_1, i_2;
-    return __generator(this, function (_a) {
-        switch (_a.label) {
-            case 0:
-                readPos = 0;
-                refPos = 0;
-                currPos = 0;
-                i = 0;
-                _a.label = 1;
-            case 1:
-                if (!(i < cigarOps.length && currPos < positions.length)) return [3 /*break*/, 9];
-                len = +cigarOps[i];
-                op = cigarOps[i + 1];
-                if (!(op === 'S' || op === 'I')) return [3 /*break*/, 2];
-                for (i_1 = 0; i_1 < len && currPos < positions.length; i_1++) {
-                    if (positions[currPos] === readPos + i_1) {
-                        currPos++;
-                    }
+function* getNextRefPos(cigarOps, positions) {
+    let readPos = 0;
+    let refPos = 0;
+    let currPos = 0;
+    for (let i = 0; i < cigarOps.length && currPos < positions.length; i += 2) {
+        const len = +cigarOps[i];
+        const op = cigarOps[i + 1];
+        if (op === 'S' || op === 'I') {
+            for (let i = 0; i < len && currPos < positions.length; i++) {
+                if (positions[currPos] === readPos + i) {
+                    currPos++;
                 }
-                readPos += len;
-                return [3 /*break*/, 8];
-            case 2:
-                if (!(op === 'D' || op === 'N')) return [3 /*break*/, 3];
-                refPos += len;
-                return [3 /*break*/, 8];
-            case 3:
-                if (!(op === 'M' || op === 'X' || op === '=')) return [3 /*break*/, 8];
-                i_2 = 0;
-                _a.label = 4;
-            case 4:
-                if (!(i_2 < len && currPos < positions.length)) return [3 /*break*/, 7];
-                if (!(positions[currPos] === readPos + i_2)) return [3 /*break*/, 6];
-                return [4 /*yield*/, refPos + i_2];
-            case 5:
-                _a.sent();
-                currPos++;
-                _a.label = 6;
-            case 6:
-                i_2++;
-                return [3 /*break*/, 4];
-            case 7:
-                readPos += len;
-                refPos += len;
-                _a.label = 8;
-            case 8:
-                i += 2;
-                return [3 /*break*/, 1];
-            case 9: return [2 /*return*/];
+            }
+            readPos += len;
+        }
+        else if (op === 'D' || op === 'N') {
+            refPos += len;
+        }
+        else if (op === 'M' || op === 'X' || op === '=') {
+            for (let i = 0; i < len && currPos < positions.length; i++) {
+                if (positions[currPos] === readPos + i) {
+                    yield refPos + i;
+                    currPos++;
+                }
+            }
+            readPos += len;
+            refPos += len;
         }
-    });
+    }
 }
 exports.getNextRefPos = getNextRefPos;
 function getModificationPositions(mm, fseq, fstrand) {
-    var seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
-    var mods = mm.split(';').filter(function (mod) { return !!mod; });
-    var result = [];
-    for (var i = 0; i < mods.length; i++) {
-        var mod = mods[i];
-        var _a = __read(mod.split(',')), basemod = _a[0], skips = _a.slice(1);
+    const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
+    const mods = mm.split(';').filter(mod => !!mod);
+    const result = [];
+    for (let i = 0; i < mods.length; i++) {
+        const mod = mods[i];
+        const [basemod, ...skips] = mod.split(',');
         // regexes based on parse_mm.pl from hts-specs
-        var matches = basemod.match(modificationRegex);
+        const matches = basemod.match(modificationRegex);
         if (!matches) {
             throw new Error('bad format for MM tag');
         }
-        var _b = __read(matches, 4), base = _b[1], strand = _b[2], typestr = _b[3];
+        const [, base, strand, typestr] = matches;
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
         // split, and they can also be chemical codes (ChEBI) e.g. C+16061
-        var types = typestr.split(/(\d+|.)/).filter(function (f) { return !!f; });
+        const types = typestr.split(/(\d+|.)/).filter(f => !!f);
         if (strand === '-') {
             console.warn('unsupported negative strand modifications');
             // make sure to return a somewhat matching type even in this case
@@ -321,27 +256,27 @@ function getModificationPositions(mm, fseq, fstrand) {
         // sequence of the read, if we have a modification type e.g. C+m;2 and a
         // sequence ACGTACGTAC we skip the two instances of C and go to the last
         // C
-        for (var j = 0; j < types.length; j++) {
-            var type = types[j];
-            var i_3 = 0;
-            var positions = [];
-            for (var k = 0; k < skips.length; k++) {
-                var delta = +skips[k];
+        for (let j = 0; j < types.length; j++) {
+            const type = types[j];
+            let i = 0;
+            const positions = [];
+            for (let k = 0; k < skips.length; k++) {
+                let delta = +skips[k];
                 do {
-                    if (base === 'N' || base === seq[i_3]) {
+                    if (base === 'N' || base === seq[i]) {
                         delta--;
                     }
-                    i_3++;
-                } while (delta >= 0 && i_3 < seq.length);
-                var temp = i_3 - 1;
+                    i++;
+                } while (delta >= 0 && i < seq.length);
+                const temp = i - 1;
                 positions.push(fstrand === -1 ? seq.length - 1 - temp : temp);
             }
             if (fstrand === -1) {
-                positions.sort(function (a, b) { return a - b; });
+                positions.sort((a, b) => a - b);
             }
             result.push({
-                type: type,
-                positions: positions,
+                type,
+                positions,
             });
         }
     }
@@ -349,19 +284,19 @@ function getModificationPositions(mm, fseq, fstrand) {
 }
 exports.getModificationPositions = getModificationPositions;
 function getModificationTypes(mm) {
-    var mods = mm.split(';');
+    const mods = mm.split(';');
     return mods
-        .filter(function (mod) { return !!mod; })
-        .map(function (mod) {
-        var _a = __read(mod.split(','), 1), basemod = _a[0];
-        var matches = basemod.match(modificationRegex);
+        .filter(mod => !!mod)
+        .map(mod => {
+        const [basemod] = mod.split(',');
+        const matches = basemod.match(modificationRegex);
         if (!matches) {
             throw new Error('bad format for MM tag');
         }
-        var _b = __read(matches, 4), typestr = _b[3];
+        const [, , , typestr] = matches;
         // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
         // split, and they can also be chemical codes (ChEBI) e.g. C+16061
-        return typestr.split(/(\d+|.)/).filter(function (f) { return !!f; });
+        return typestr.split(/(\d+|.)/).filter(f => !!f);
     })
         .flat();
 }