@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/BamAdapter/BamAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"BamAdapter.js","sourceRoot":"","sources":["../../src/BamAdapter/BamAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAAmC;AACnC,uEAGgD;AAEhD,2CAAkE;AAClE,4CAAoD;AACpD,gDAA0D;AAE1D,4CAAwC;AACxC,6DAA4D;AAC5D,oFAA6D;AAO7D;IAAwC,8BAAsB;IAA9D;;IAmOA,CAAC;IAzNC,iEAAiE;IACjE,oEAAoE;IACpD,8BAAS,GAAzB;;;;gBACE,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;oBACd,WAAW,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,aAAa,CAAC,CAAA;oBACxD,aAAW,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;oBAC7D,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;oBAC/D,QAAM,IAAI,aAAO,CAAC;wBACtB,aAAa,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;wBAC5D,aAAa,EACX,SAAS,KAAK,KAAK;4BACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,UAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;4BAC5C,CAAC,CAAC,SAAS;wBACf,aAAa,EACX,SAAS,KAAK,KAAK;4BACjB,CAAC,CAAC,IAAA,iBAAY,EAAC,UAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;4BAC5C,CAAC,CAAC,SAAS;wBAEf,8DAA8D;wBAC9D,gEAAgE;wBAChE,mEAAmE;wBACnE,cAAc,EAAE,QAAQ;wBACxB,cAAc,EAAE,QAAQ;wBACxB,eAAe,EAAE,QAAQ;qBAC1B,CAAC,CAAA;oBAEI,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;oBACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;wBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,UAAC,EAAe;gCAAb,WAAW,iBAAA;4BAAO,OAAA,CAAC;gCACpB,GAAG,OAAA;gCACH,eAAe,EAAE,WAAqC;6BACvD,CAAC;wBAHmB,CAGnB,CACH,CAAA;qBACF;yBAAM;wBACL,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,OAAA,EAAE,CAAC,CAAA;qBAC3C;iBACF;gBACD,sBAAO,IAAI,CAAC,UAAU,EAAA;;;KACvB;IAEK,8BAAS,GAAf,UAAgB,IAAkB;;;;;4BAChB,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBACX,sBAAO,GAAG,CAAC,aAAa,CAAC,IAAI,CAAC,EAAA;;;;KAC/B;IAEa,6BAAQ,GAAtB,UAAuB,IAAkB;;;;;;;wBAC/B,KAA8B,CAAA,IAAI,IAAI,EAAE,CAAA,eAAf,EAAzB,cAAc,mBAAG,cAAO,CAAC,KAAA,CAAe;wBAChC,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBACX,KAAA,IAAI,CAAA;wBAAa,qBAAM,IAAA,mBAAY,EACjC,mBAAmB,EACnB,cAAc,EACd;;;;gDACoB,qBAAM,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC;4CAE3C,oDAAoD;4CACpD,+CAA+C;0CAHJ;;4CAArC,SAAS,GAAG,SAAyB;4CAIrC,QAAQ,GAAa,EAAE,CAAA;4CACvB,QAAQ,GAA2B,EAAE,CAAA;4CAC3C,SAAS;iDACN,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,GAAG,KAAK,IAAI,EAAd,CAAc,CAAC;iDAC3B,OAAO,CAAC,UAAC,MAAM,EAAE,KAAK;gDACrB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,UAAA,IAAI;oDACtB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wDACrB,uBAAuB;wDACvB,IAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wDAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wDACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qDAC1B;gDACH,CAAC,CAAC,CAAA;4CACJ,CAAC,CAAC,CAAA;4CAEJ,sBAAO,EAAE,QAAQ,UAAA,EAAE,QAAQ,UAAA,EAAE,EAAA;;;iCAC9B,CACF,EAAA;;wBAzBD,GAAK,SAAS,GAAG,SAyBhB,CAAA;wBACD,sBAAO,IAAI,CAAC,SAAS,EAAA;;;;KACtB;IAEa,0BAAK,GAAnB,UAAoB,IAAkB;;;;gBACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;oBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,UAAA,CAAC;wBACvC,KAAI,CAAC,MAAM,GAAG,SAAS,CAAA;wBACvB,MAAM,CAAC,CAAA;oBACT,CAAC,CAAC,CAAA;iBACH;gBACD,sBAAO,IAAI,CAAC,MAAM,EAAA;;;KACnB;IAEK,gCAAW,GAAjB,UAAkB,IAAkB;;;;;4BACb,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAnC,QAAQ,GAAK,CAAA,SAAsB,CAAA,SAA3B;wBAChB,sBAAO,QAAQ,EAAA;;;;KAChB;IAEa,6BAAQ,GAAtB,UAAuB,OAAe,EAAE,KAAa,EAAE,GAAW;;;;;4BACpC,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA1C,eAAe,GAAK,CAAA,SAAsB,CAAA,gBAA3B;wBACjB,WAAW,GAAG,eAAe,CAAA;wBACnC,IAAI,CAAC,WAAW,EAAE;4BAChB,sBAAO,SAAS,EAAA;yBACjB;wBACD,IAAI,CAAC,OAAO,EAAE;4BACZ,sBAAO,SAAS,EAAA;yBACjB;wBAEK,QAAQ,GAAG,WAAW,CAAC,WAAW,CAAC;4BACvC,OAAO,SAAA;4BACP,KAAK,OAAA;4BACL,GAAG,KAAA;4BACH,YAAY,EAAE,EAAE;yBACjB,CAAC,CAAA;wBAEgB,qBAAM,QAAQ,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,SAAS,EAAE,EAAA;;wBAAtD,SAAS,GAAG,SAA0C;wBAExD,QAAQ,GAAG,EAAE,CAAA;wBACjB,SAAS;6BACN,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC,IAAK,OAAA,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAA/B,CAA+B,CAAC;6BAC/C,OAAO,CAAC,UAAA,KAAK;4BACZ,IAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;4BACrC,IAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;4BACjC,IAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;4BACjD,IAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;4BACjE,IAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;4BACtC,IAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;4BAC1D,QAAQ,IAAI,QAAQ,CAAC,MAAM,CAAC,SAAS,EAAE,UAAU,CAAC,CAAA;wBACpD,CAAC,CAAC,CAAA;wBAEJ,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;4BACnC,MAAM,IAAI,KAAK,CACb,0CAAmC,OAAO,cAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,cAAI,GAAG,CAAC,cAAc,EAAE,uBAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,8CAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,CAAE,CACrB,CAAA;yBACF;wBACD,sBAAO,QAAQ,EAAA;;;;KAChB;IAED,gCAAW,GAAX,UACE,MAA6C,EAC7C,IAOC;QATH,iBA2DC;QAhDS,IAAA,OAAO,GAAkC,MAAM,QAAxC,EAAE,KAAK,GAA2B,MAAM,MAAjC,EAAE,GAAG,GAAsB,MAAM,IAA5B,EAAE,eAAe,GAAK,MAAM,gBAAX,CAAW;QACjD,IAAA,KAAkD,IAAI,IAAI,EAAE,EAA1D,MAAM,YAAA,EAAE,QAAQ,cAAA,EAAE,sBAAyB,EAAzB,cAAc,mBAAG,cAAO,CAAC,KAAe,CAAA;QAClE,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;;;4BAC7B,qBAAM,IAAI,CAAC,SAAS,EAAE,EAAA;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;wBACX,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAtB,SAAsB,CAAA;wBACtB,cAAc,CAAC,wBAAwB,CAAC,CAAA;wBACxB,qBAAM,GAAG,CAAC,kBAAkB,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,EAAA;;wBAAjE,OAAO,GAAG,SAAuD;wBAEjE,KAKF,QAAQ,IAAI,EAAE,EAJhB,mBAAe,EAAf,WAAW,mBAAG,CAAC,KAAA,EACf,mBAAe,EAAf,WAAW,mBAAG,CAAC,KAAA,EACf,SAAS,eAAA,EACT,QAAQ,cAAA,CACQ;;;;wBAEG,YAAA,SAAA,OAAO,CAAA;;;;wBAAjB,MAAM;wBACX,GAAG,SAAoB,CAAA;6BACvB,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,EAAjB,wBAAiB;wBACb,qBAAM,IAAI,CAAC,QAAQ,CACvB,eAAe,IAAI,OAAO,EAC1B,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,EACnB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAClB,EAAA;;wBAJD,GAAG,GAAG,SAIL,CAAA;;;wBAGG,KAAK,GAAG,MAAM,CAAC,KAAK,CAAA;wBAC1B,IACE,CAAC,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,KAAK,WAAW,IAAI,CAAC,CAAC,KAAK,GAAG,WAAW,CAAC,CAAC,EAClE;4BACA,wBAAQ;yBACT;wBAED,IAAI,SAAS,EAAE;4BACP,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAA;4BACrC,IAAI,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,CAAC,KAAK,CAAC,EAAE;gCAChE,wBAAQ;6BACT;yBACF;wBAED,IAAI,QAAQ,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ,EAAE;4BAC/C,wBAAQ;yBACT;wBAED,QAAQ,CAAC,IAAI,CAAC,IAAI,gCAAsB,CAAC,MAAM,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAA;;;;;;;;;;;;;;;;;wBAE9D,cAAc,CAAC,EAAE,CAAC,CAAA;wBAClB,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;;aACpB,EAAE,MAAM,CAAC,CAAA;IACZ,CAAC;IAEK,yCAAoB,GAA1B,UAA2B,OAAiB,EAAE,IAAkB;;;;;4BAC9C,qBAAM,IAAI,CAAC,SAAS,EAAE;wBACtC,uDAAuD;wBACvD,aAAa;sBAFyB;;wBAA9B,GAAG,GAAK,CAAA,SAAsB,CAAA,IAA3B;6BAGP,CAAA,GAAG,CAAC,KAAK,CAAC,UAAU,KAAK,GAAG,CAAA,EAA5B,wBAA4B;wBAChB,qBAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,EAAA;;wBAA3C,KAAK,GAAG,SAAmC;wBAC3C,cAAc,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;wBACpE,sBAAO,EAAE,KAAK,OAAA,EAAE,cAAc,gBAAA,EAAE,EAAA;4BAEhC,sBAAO,iBAAM,oBAAoB,YAAC,OAAO,EAAE,IAAI,CAAC,EAAA;;;;KAEnD;IAED,kCAAa,GAAb,WAAc,gBAAgB,IAAS,CAAC;IAExC,2DAA2D;IAC3D,gCAAW,GAAX,UAAY,KAAa;;QACvB,OAAO,MAAA,IAAI,CAAC,SAAS,0CAAE,QAAQ,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;IACH,iBAAC;AAAD,CAAC,AAnOD,CAAwC,oCAAsB,GAmO7D"}

package/dist/BamAdapter/BamSlightlyLazyFeature.js

@@ -1,176 +1,145 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _MismatchParser = require("./MismatchParser");
-
-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; }
-
-var BamSlightlyLazyFeature = /*#__PURE__*/function () {
-  // 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) {
-    (0, _classCallCheck2.default)(this, BamSlightlyLazyFeature);
-    this.record = record;
-    this.adapter = adapter;
-    this.ref = ref;
-  }
-
-  (0, _createClass2.default)(BamSlightlyLazyFeature, [{
-    key: "_get_name",
-    value: function _get_name() {
-      return this.record.get('name');
-    }
-  }, {
-    key: "_get_type",
-    value: function _get_type() {
-      return 'match';
-    }
-  }, {
-    key: "_get_score",
-    value: function _get_score() {
-      return this.record.get('mq');
-    }
-  }, {
-    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: "_get_pair_orientation",
-    value: function _get_pair_orientation() {
-      return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    }
-  }, {
-    key: "_get_next_seq_id",
-    value: function _get_next_seq_id() {
-      return this.record._next_refid();
-    }
-  }, {
-    key: "_get_seq_id",
-    value: function _get_seq_id() {
-      // @ts-ignore
-      return this.record._refID;
-    }
-  }, {
-    key: "_get_next_refName",
-    value: function _get_next_refName() {
-      return this.adapter.refIdToName(this.record._next_refid());
-    }
-  }, {
-    key: "_get_next_segment_position",
-    value: function _get_next_segment_position() {
-      var record = this.record,
-          adapter = this.adapter;
-      return record.isPaired() ? "".concat(adapter.refIdToName(record._next_refid()), ":").concat(record._next_pos() + 1) : undefined;
-    }
-  }, {
-    key: "_get_seq",
-    value: function _get_seq() {
-      return this.record.getReadBases();
-    }
-  }, {
-    key: "qualRaw",
-    value: function qualRaw() {
-      return this.record.qualRaw();
-    }
-  }, {
-    key: "set",
-    value: function set() {}
-  }, {
-    key: "tags",
-    value: function tags() {
-      var properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
-      return (0, _toConsumableArray2.default)(new Set(properties.filter(function (prop) {
-        return 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())));
-    }
-  }, {
-    key: "id",
-    value: function id() {
-      return "".concat(this.adapter.id, "-").concat(this.record.id());
-    } // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  }, {
-    key: "get",
-    value: function get(field) {
-      var methodName = "_get_".concat(field); // @ts-ignore
-
-      if (this[methodName]) {
+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 () {
+    // 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) {
+        this.record = record;
+        this.adapter = adapter;
+        this.ref = ref;
+    }
+    BamSlightlyLazyFeature.prototype._get_name = function () {
+        return this.record.get('name');
+    };
+    BamSlightlyLazyFeature.prototype._get_type = function () {
+        return 'match';
+    };
+    BamSlightlyLazyFeature.prototype._get_score = function () {
+        return this.record.get('mq');
+    };
+    BamSlightlyLazyFeature.prototype._get_flags = function () {
+        return this.record.flags;
+    };
+    BamSlightlyLazyFeature.prototype._get_strand = function () {
+        return this.record.isReverseComplemented() ? -1 : 1;
+    };
+    BamSlightlyLazyFeature.prototype._get_pair_orientation = function () {
+        return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
+    };
+    BamSlightlyLazyFeature.prototype._get_next_seq_id = function () {
+        return this.record._next_refid();
+    };
+    BamSlightlyLazyFeature.prototype._get_seq_id = function () {
         // @ts-ignore
-        return this[methodName]();
-      }
-
-      return this.record.get(field);
-    }
-  }, {
-    key: "_get_refName",
-    value: function _get_refName() {
-      return this.adapter.refIdToName(this.record.seq_id());
-    }
-  }, {
-    key: "parent",
-    value: function parent() {
-      return undefined;
-    }
-  }, {
-    key: "children",
-    value: function children() {
-      return undefined;
-    }
-  }, {
-    key: "pairedFeature",
-    value: function pairedFeature() {
-      return false;
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _this = this;
-
-      return _objectSpread(_objectSpread({}, Object.fromEntries(this.tags().map(function (t) {
-        return [t, _this.get(t)];
-      }).filter(function (elt) {
-        return elt[1] !== undefined;
-      }))), {}, {
-        uniqueId: this.id()
-      });
-    }
-  }, {
-    key: "_get_mismatches",
-    value: function _get_mismatches() {
-      return (0, _MismatchParser.getMismatches)(this.get('CIGAR'), this.get('MD'), this.get('seq'), this.ref, this.qualRaw());
-    }
-  }, {
-    key: "_get_clipPos",
-    value: function _get_clipPos() {
-      var 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;
+        return this.record._refID;
+    };
+    BamSlightlyLazyFeature.prototype._get_next_refName = function () {
+        return this.adapter.refIdToName(this.record._next_refid());
+    };
+    BamSlightlyLazyFeature.prototype._get_next_segment_position = function () {
+        var _a = this, record = _a.record, adapter = _a.adapter;
+        return record.isPaired()
+            ? "".concat(adapter.refIdToName(record._next_refid()), ":").concat(record._next_pos() + 1)
+            : undefined;
+    };
+    BamSlightlyLazyFeature.prototype._get_seq = function () {
+        return this.record.getReadBases();
+    };
+    BamSlightlyLazyFeature.prototype.qualRaw = function () {
+        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_') &&
+                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());
+    };
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    BamSlightlyLazyFeature.prototype.get = function (field) {
+        var methodName = "_get_".concat(field);
+        // @ts-ignore
+        if (this[methodName]) {
+            // @ts-ignore
+            return this[methodName]();
+        }
+        return this.record.get(field);
+    };
+    BamSlightlyLazyFeature.prototype._get_refName = function () {
+        return this.adapter.refIdToName(this.record.seq_id());
+    };
+    BamSlightlyLazyFeature.prototype.parent = function () {
+        return undefined;
+    };
+    BamSlightlyLazyFeature.prototype.children = function () {
+        return undefined;
+    };
+    BamSlightlyLazyFeature.prototype.pairedFeature = function () {
+        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 () {
+        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') || '';
+        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

@@ -0,0 +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"}