@jbrowse/plugin-variants 2.1.0 → 2.1.2

package/dist/VcfTabixAdapter/VcfFeature.js

@@ -1,105 +1,69 @@
 "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 vcf_1 = require("@gmod/vcf");
-var VCFFeature = /** @class */ (function () {
+const vcf_1 = require("@gmod/vcf");
+class VCFFeature {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    function VCFFeature(args) {
+    constructor(args) {
         this.variant = args.variant;
         this.parser = args.parser;
         this.data = this.dataFromVariant(this.variant);
         this._id = args.id;
     }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    VCFFeature.prototype.get = function (field) {
+    get(field) {
         return field === 'samples'
             ? this.variant.SAMPLES
             : this.data[field] || this.variant[field];
-    };
-    VCFFeature.prototype.set = function () { };
-    VCFFeature.prototype.parent = function () {
+    }
+    set() { }
+    parent() {
         return undefined;
-    };
-    VCFFeature.prototype.children = function () {
+    }
+    children() {
         return undefined;
-    };
-    VCFFeature.prototype.tags = function () {
-        var t = __spreadArray(__spreadArray(__spreadArray([], __read(Object.keys(this.data)), false), __read(Object.keys(this.variant)), false), [
+    }
+    tags() {
+        const t = [
+            ...Object.keys(this.data),
+            ...Object.keys(this.variant),
             'samples',
-        ], false);
+        ];
         return t;
-    };
-    VCFFeature.prototype.id = function () {
+    }
+    id() {
         return this._id;
-    };
-    VCFFeature.prototype.dataFromVariant = function (variant) {
-        var REF = variant.REF, ALT = variant.ALT, POS = variant.POS, CHROM = variant.CHROM, INFO = variant.INFO, ID = variant.ID;
-        var start = POS - 1;
-        var _a = __read(this._getSOTermAndDescription(REF, ALT), 2), SO_term = _a[0], description = _a[1];
-        var isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) { return f === '<TRA>'; });
-        var isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(function (f) { return f.indexOf('<') !== -1; });
+    }
+    dataFromVariant(variant) {
+        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
+        const start = POS - 1;
+        const [SO_term, description] = this._getSOTermAndDescription(REF, ALT);
+        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
+        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
         return {
             refName: CHROM,
-            start: start,
+            start,
             end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-            description: description,
+            description,
             type: SO_term,
             name: ID === null || ID === void 0 ? void 0 : ID.join(','),
             aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,
         };
-    };
+    }
     /**
      * Get a sequence ontology (SO) term that describes the variant type
      */
-    VCFFeature.prototype._getSOTermAndDescription = function (ref, alt) {
-        var _this = this;
+    _getSOTermAndDescription(ref, alt) {
         // it's just a remark if there are no alternate alleles
         if (!alt || alt.length === 0) {
             return ['remark', 'no alternative alleles'];
         }
-        var soTerms = new Set();
-        var descriptions = new Set();
-        alt.forEach(function (a) {
-            var _a;
-            var _b = __read(_this._getSOAndDescFromAltDefs(ref, a), 2), soTerm = _b[0], description = _b[1];
+        const soTerms = new Set();
+        let descriptions = new Set();
+        alt.forEach(a => {
+            let [soTerm, description] = this._getSOAndDescFromAltDefs(ref, a);
             if (!soTerm) {
                 ;
-                _a = __read(_this._getSOAndDescByExamination(ref, a), 2), soTerm = _a[0], description = _a[1];
+                [soTerm, description] = this._getSOAndDescByExamination(ref, a);
             }
             if (soTerm && description) {
                 soTerms.add(soTerm);
@@ -108,33 +72,34 @@ var VCFFeature = /** @class */ (function () {
         });
         // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
         if (descriptions.size > 1) {
-            var prefixes = new Set(__spreadArray([], __read(descriptions), false).map(function (desc) {
-                var prefix = desc.split('->');
+            const prefixes = new Set([...descriptions].map(desc => {
+                const prefix = desc.split('->');
                 return prefix[1] ? prefix[0] : desc;
             }));
-            var new_descs = __spreadArray([], __read(prefixes), false).map(function (prefix) {
-                var suffixes = __spreadArray([], __read(descriptions), false).map(function (desc) {
-                    var pref = desc.split('-> ');
+            const new_descs = [...prefixes].map(prefix => {
+                const suffixes = [...descriptions]
+                    .map(desc => {
+                    const pref = desc.split('-> ');
                     return pref[1] && pref[0] === prefix ? pref[1] : '';
                 })
-                    .filter(function (f) { return !!f; });
+                    .filter(f => !!f);
                 return suffixes.length
                     ? prefix + '-> ' + suffixes.join(',')
-                    : __spreadArray([], __read(descriptions), false).join(',');
+                    : [...descriptions].join(',');
             });
             descriptions = new Set(new_descs);
         }
         if (soTerms.size) {
-            return [__spreadArray([], __read(soTerms), false).join(','), __spreadArray([], __read(descriptions), false).join(',')];
+            return [[...soTerms].join(','), [...descriptions].join(',')];
         }
         return [undefined, undefined];
-    };
-    VCFFeature.prototype._getSOAndDescFromAltDefs = function (ref, alt) {
+    }
+    _getSOAndDescFromAltDefs(ref, alt) {
         if (typeof alt === 'string' && !alt.startsWith('<')) {
             return [undefined, undefined];
         }
         // look for a definition with an SO type for this
-        var soTerm = VCFFeature._altTypeToSO[alt];
+        let soTerm = VCFFeature._altTypeToSO[alt];
         // if no SO term but ALT is in metadata, assume sequence_variant
         if (!soTerm && this.parser.getMetadata('ALT', alt)) {
             soTerm = 'sequence_variant';
@@ -143,18 +108,18 @@ var VCFFeature = /** @class */ (function () {
             return [soTerm, alt];
         }
         // try to look for a definition for a parent term if we can
-        var modAlt = alt.split(':');
+        const modAlt = alt.split(':');
         if (modAlt.length > 1) {
-            return this._getSOAndDescFromAltDefs(ref, "<".concat(modAlt.slice(0, modAlt.length - 1).join(':'), ">"));
+            return this._getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`);
         }
         // no parent
         return [undefined, undefined];
-    };
+    }
     // note: term SNV is used instead of SNP because SO definition of SNP says
     // abundance must be at least 1% in population, and can't be sure we meet
     // that
-    VCFFeature.prototype._getSOAndDescByExamination = function (ref, alt) {
-        var bnd = (0, vcf_1.parseBreakend)(alt);
+    _getSOAndDescByExamination(ref, alt) {
+        const bnd = (0, vcf_1.parseBreakend)(alt);
         if (bnd) {
             return ['breakend', alt];
         }
@@ -192,27 +157,31 @@ var VCFFeature = /** @class */ (function () {
             return ['deletion', this._makeDescriptionString('deletion', ref, alt)];
         }
         return ['indel', this._makeDescriptionString('indel', ref, alt)];
-    };
-    VCFFeature.prototype._makeDescriptionString = function (soTerm, ref, alt) {
-        return "".concat(soTerm, " ").concat(ref, " -> ").concat(alt);
-    };
+    }
+    _makeDescriptionString(soTerm, ref, alt) {
+        return `${soTerm} ${ref} -> ${alt}`;
+    }
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    VCFFeature.prototype.toJSON = function () {
-        return __assign(__assign(__assign({ uniqueId: this._id }, this.variant), this.data), { samples: this.variant.SAMPLES });
-    };
-    VCFFeature._altTypeToSO = {
-        DEL: 'deletion',
-        INS: 'insertion',
-        DUP: 'duplication',
-        INV: 'inversion',
-        INVDUP: 'inverted duplication',
-        CNV: 'copy_number_variation',
-        TRA: 'translocation',
-        'DUP:TANDEM': 'tandem_duplication',
-        NON_REF: 'sequence_variant',
-        '*': 'sequence_variant',
-    };
-    return VCFFeature;
-}());
+    toJSON() {
+        return {
+            uniqueId: this._id,
+            ...this.variant,
+            ...this.data,
+            samples: this.variant.SAMPLES,
+        };
+    }
+}
 exports.default = VCFFeature;
+VCFFeature._altTypeToSO = {
+    DEL: 'deletion',
+    INS: 'insertion',
+    DUP: 'duplication',
+    INV: 'inversion',
+    INVDUP: 'inverted duplication',
+    CNV: 'copy_number_variation',
+    TRA: 'translocation',
+    'DUP:TANDEM': 'tandem_duplication',
+    NON_REF: 'sequence_variant',
+    '*': 'sequence_variant',
+};
 //# sourceMappingURL=VcfFeature.js.map

package/dist/VcfTabixAdapter/VcfFeature.js.map

@@ -1 +1 @@
-{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,iCAAyC;AAyBzC;IAWE,8DAA8D;IAC9D,oBAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,wBAAG,GAAH,UAAI,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,wBAAG,GAAH,cAAa,CAAC;IAEd,2BAAM,GAAN;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,6BAAQ,GAAR;QACE,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,yBAAI,GAAJ;QACE,IAAM,CAAC,wDACF,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,kBACtB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;iBACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,uBAAE,GAAF;QACE,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,oCAAe,GAAf,UAAgB,OAOf;QACS,IAAA,GAAG,GAAgC,OAAO,IAAvC,EAAE,GAAG,GAA2B,OAAO,IAAlC,EAAE,GAAG,GAAsB,OAAO,IAA7B,EAAE,KAAK,GAAe,OAAO,MAAtB,EAAE,IAAI,GAAS,OAAO,KAAhB,EAAE,EAAE,GAAK,OAAO,GAAZ,CAAY;QAClD,IAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACf,IAAA,KAAA,OAAyB,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,IAAA,EAA/D,OAAO,QAAA,EAAE,WAAW,QAA2C,CAAA;QACtE,IAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,KAAK,OAAO,EAAb,CAAa,CAAC,CAAA;QAC3C,IAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAArB,CAAqB,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK,OAAA;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW,aAAA;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,6CAAwB,GAAxB,UACE,GAAW,EACX,GAAa;QAFf,iBAmDC;QA/CC,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;SAC5C;QAED,IAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,GAAG,CAAC,OAAO,CAAC,UAAA,CAAC;;YACP,IAAA,KAAA,OAAwB,KAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,IAAA,EAA5D,MAAM,QAAA,EAAE,WAAW,QAAyC,CAAA;YAEjE,IAAI,CAAC,MAAM,EAAE;gBACX,CAAC;gBAAA,KAAA,OAAwB,KAAI,CAAC,0BAA0B,CAAC,GAAG,EAAE,CAAC,CAAC,IAAA,EAA9D,MAAM,QAAA,EAAE,WAAW,QAAA,CAA2C;aACjE;YACD,IAAI,MAAM,IAAI,WAAW,EAAE;gBACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;gBACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;aAC9B;QACH,CAAC,CAAC,CAAA;QAEF,6EAA6E;QAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;YACzB,IAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,yBAAI,YAAY,UAAE,GAAG,CAAC,UAAA,IAAI;gBACxB,IAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YACrC,CAAC,CAAC,CACH,CAAA;YAED,IAAM,SAAS,GAAG,yBAAI,QAAQ,UAAE,GAAG,CAAC,UAAA,MAAM;gBACxC,IAAM,QAAQ,GAAG,yBAAI,YAAY,UAC9B,GAAG,CAAC,UAAA,IAAI;oBACP,IAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;gBACrD,CAAC,CAAC;qBACD,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,EAAH,CAAG,CAAC,CAAA;gBAEnB,OAAO,QAAQ,CAAC,MAAM;oBACpB,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrC,CAAC,CAAC,yBAAI,YAAY,UAAE,IAAI,CAAC,GAAG,CAAC,CAAA;YACjC,CAAC,CAAC,CAAA;YAEF,YAAY,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;SAClC;QACD,IAAI,OAAO,CAAC,IAAI,EAAE;YAChB,OAAO,CAAC,yBAAI,OAAO,UAAE,IAAI,CAAC,GAAG,CAAC,EAAE,yBAAI,YAAY,UAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAeD,6CAAwB,GAAxB,UACE,GAAW,EACX,GAAW;QAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;SAC9B;QAED,iDAAiD;QACjD,IAAI,MAAM,GAAG,UAAU,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACzC,gEAAgE;QAChE,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;YAClD,MAAM,GAAG,kBAAkB,CAAA;SAC5B;QACD,IAAI,MAAM,EAAE;YACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;SACrB;QAED,2DAA2D;QAC3D,IAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,wBAAwB,CAClC,GAAG,EACH,WAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,MAAG,CACpD,CAAA;SACF;QAED,YAAY;QACZ,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAED,0EAA0E;IAC1E,yEAAyE;IACzE,OAAO;IACP,+CAA0B,GAA1B,UAA2B,GAAW,EAAE,GAAW;QACjD,IAAM,GAAG,GAAG,IAAA,mBAAa,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,GAAG,EAAE;YACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/C,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,sBAAsB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SAC7D;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;SAC1B;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;SAC9B;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;YAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;SACnB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;YACpC,IAAI,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE;gBAC5C,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;aACzE;YACD,OAAO;gBACL,cAAc;gBACd,IAAI,CAAC,sBAAsB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC;aACtD,CAAA;SACF;aAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;YACnC,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACzE;aAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;YAClC,OAAO,CAAC,UAAU,EAAE,IAAI,CAAC,sBAAsB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACvE;QAED,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,sBAAsB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAClE,CAAC;IAED,2CAAsB,GAAtB,UAAuB,MAAc,EAAE,GAAW,EAAE,GAAW;QAC7D,OAAO,UAAG,MAAM,cAAI,GAAG,iBAAO,GAAG,CAAE,CAAA;IACrC,CAAC;IAED,8DAA8D;IAC9D,2BAAM,GAAN;QACE,oCACE,QAAQ,EAAE,IAAI,CAAC,GAAG,IACf,IAAI,CAAC,OAAO,GACZ,IAAI,CAAC,IAAI,KACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO,IAC9B;IACH,CAAC;IA5FM,uBAAY,GAA0C;QAC3D,GAAG,EAAE,UAAU;QACf,GAAG,EAAE,WAAW;QAChB,GAAG,EAAE,aAAa;QAClB,GAAG,EAAE,WAAW;QAChB,MAAM,EAAE,sBAAsB;QAC9B,GAAG,EAAE,uBAAuB;QAC5B,GAAG,EAAE,eAAe;QACpB,YAAY,EAAE,oBAAoB;QAClC,OAAO,EAAE,kBAAkB;QAC3B,GAAG,EAAE,kBAAkB;KACxB,CAAA;IAkFH,iBAAC;CAAA,AA/ND,IA+NC;kBA/NoB,UAAU"}
+{"version":3,"file":"VcfFeature.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfFeature.ts"],"names":[],"mappings":";;AACA,mCAAyC;AAyBzC,MAAqB,UAAU;IAW7B,8DAA8D;IAC9D,YAAY,IAA+C;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QAC9C,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAA;IACpB,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO;YACtB,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IAC7C,CAAC;IAED,GAAG,KAAU,CAAC;IAEd,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI;QACF,MAAM,CAAC,GAAG;YACR,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;YACzB,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC;YAC5B,SAAS;SACV,CAAA;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,EAAE;QACA,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,eAAe,CAAC,OAOf;QACC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,OAAO,CAAA;QAClD,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,CAAC,OAAO,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtE,MAAM,KAAK,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,OAAO,CAAC,CAAA;QAC3C,MAAM,UAAU,GAAG,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAExD,OAAO;YACL,OAAO,EAAE,KAAK;YACd,KAAK;YACL,GAAG,EAAE,UAAU,IAAI,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,MAAM;YACzE,WAAW;YACX,IAAI,EAAE,OAAO;YACb,IAAI,EAAE,EAAE,aAAF,EAAE,uBAAF,EAAE,CAAE,IAAI,CAAC,GAAG,CAAC;YACnB,OAAO,EAAE,EAAE,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS;SAC/D,CAAA;IACH,CAAC;IAED;;OAEG;IACH,wBAAwB,CACtB,GAAW,EACX,GAAa;QAEb,uDAAuD;QACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;QACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,wBAAwB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAEjE,IAAI,CAAC,MAAM,EAAE;gBACX,CAAC;gBAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI,CAAC,0BAA0B,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;aACjE;YACD,IAAI,MAAM,IAAI,WAAW,EAAE;gBACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;gBACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;aAC9B;QACH,CAAC,CAAC,CAAA;QAEF,6EAA6E;QAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,CAAC,GAAG,YAAY,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;gBAC3B,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YACrC,CAAC,CAAC,CACH,CAAA;YAED,MAAM,SAAS,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;gBAC3C,MAAM,QAAQ,GAAG,CAAC,GAAG,YAAY,CAAC;qBAC/B,GAAG,CAAC,IAAI,CAAC,EAAE;oBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;oBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;gBACrD,CAAC,CAAC;qBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAEnB,OAAO,QAAQ,CAAC,MAAM;oBACpB,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;oBACrC,CAAC,CAAC,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACjC,CAAC,CAAC,CAAA;YAEF,YAAY,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;SAClC;QACD,IAAI,OAAO,CAAC,IAAI,EAAE;YAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAeD,wBAAwB,CACtB,GAAW,EACX,GAAW;QAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACnD,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;SAC9B;QAED,iDAAiD;QACjD,IAAI,MAAM,GAAG,UAAU,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;QACzC,gEAAgE;QAChE,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;YAClD,MAAM,GAAG,kBAAkB,CAAA;SAC5B;QACD,IAAI,MAAM,EAAE;YACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;SACrB;QAED,2DAA2D;QAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,wBAAwB,CAClC,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CACpD,CAAA;SACF;QAED,YAAY;QACZ,OAAO,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;IAC/B,CAAC;IAED,0EAA0E;IAC1E,yEAAyE;IACzE,OAAO;IACP,0BAA0B,CAAC,GAAW,EAAE,GAAW;QACjD,MAAM,GAAG,GAAG,IAAA,mBAAa,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,GAAG,EAAE;YACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;YAC/C,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,sBAAsB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SAC7D;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;SAC1B;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;SACzB;aAAM,IAAI,GAAG,KAAK,OAAO,EAAE;YAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;SAC9B;aAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;YAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;SACnB;aAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;YACpC,IAAI,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE;gBAC5C,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;aACzE;YACD,OAAO;gBACL,cAAc;gBACd,IAAI,CAAC,sBAAsB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC;aACtD,CAAA;SACF;aAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;YACnC,OAAO,CAAC,WAAW,EAAE,IAAI,CAAC,sBAAsB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACzE;aAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;YAClC,OAAO,CAAC,UAAU,EAAE,IAAI,CAAC,sBAAsB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;SACvE;QAED,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,sBAAsB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;IAClE,CAAC;IAED,sBAAsB,CAAC,MAAc,EAAE,GAAW,EAAE,GAAW;QAC7D,OAAO,GAAG,MAAM,IAAI,GAAG,OAAO,GAAG,EAAE,CAAA;IACrC,CAAC;IAED,8DAA8D;IAC9D,MAAM;QACJ,OAAO;YACL,QAAQ,EAAE,IAAI,CAAC,GAAG;YAClB,GAAG,IAAI,CAAC,OAAO;YACf,GAAG,IAAI,CAAC,IAAI;YACZ,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO;SAC9B,CAAA;IACH,CAAC;;AA9NH,6BA+NC;AA7FQ,uBAAY,GAA0C;IAC3D,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA"}

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,199 +1,79 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-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 __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var util_1 = require("@jbrowse/core/util");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var tabix_1 = require("@gmod/tabix");
-var vcf_1 = __importDefault(require("@gmod/vcf"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var VcfFeature_1 = __importDefault(require("./VcfFeature"));
-var default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    default_1.prototype.configurePre = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var vcfGzLocation, location, indexType, filehandle, isCSI, vcf, header;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        vcfGzLocation = (0, configuration_1.readConfObject)(this.config, 'vcfGzLocation');
-                        location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
-                        indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
-                        filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
-                        isCSI = indexType === 'CSI';
-                        vcf = new tabix_1.TabixIndexedFile({
-                            filehandle: filehandle,
-                            csiFilehandle: isCSI
-                                ? (0, io_1.openLocation)(location, this.pluginManager)
-                                : undefined,
-                            tbiFilehandle: !isCSI
-                                ? (0, io_1.openLocation)(location, this.pluginManager)
-                                : undefined,
-                            chunkCacheSize: 50 * Math.pow(2, 20),
-                            chunkSizeLimit: 1000000000,
-                        });
-                        return [4 /*yield*/, vcf.getHeader()];
-                    case 1:
-                        header = _a.sent();
-                        return [2 /*return*/, {
-                                filehandle: filehandle,
-                                vcf: vcf,
-                                parser: new vcf_1.default({ header: header }),
-                            }];
-                }
-            });
-        });
-    };
-    default_1.prototype.configure = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.configured) {
-                    this.configured = this.configurePre().catch(function (e) {
-                        _this.configured = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.configured];
-            });
-        });
-    };
-    default_1.prototype.getRefNames = function (opts) {
-        if (opts === void 0) { opts = {}; }
-        return __awaiter(this, void 0, void 0, function () {
-            var vcf;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        vcf = (_a.sent()).vcf;
-                        return [2 /*return*/, vcf.getReferenceSequenceNames(opts)];
-                }
-            });
-        });
-    };
-    default_1.prototype.getHeader = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var vcf;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        vcf = (_a.sent()).vcf;
-                        return [2 /*return*/, vcf.getHeader()];
-                }
-            });
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const util_1 = require("@jbrowse/core/util");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const tabix_1 = require("@gmod/tabix");
+const vcf_1 = __importDefault(require("@gmod/vcf"));
+const configuration_1 = require("@jbrowse/core/configuration");
+const VcfFeature_1 = __importDefault(require("./VcfFeature"));
+class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+    async configurePre() {
+        const vcfGzLocation = (0, configuration_1.readConfObject)(this.config, 'vcfGzLocation');
+        const location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
+        const indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
+        const filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
+        const isCSI = indexType === 'CSI';
+        const vcf = new tabix_1.TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+            chunkSizeLimit: 1000000000,
         });
-    };
-    default_1.prototype.getMetadata = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var parser;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        parser = (_a.sent()).parser;
-                        return [2 /*return*/, parser.getMetadata()];
-                }
+        const header = await vcf.getHeader();
+        return {
+            filehandle,
+            vcf,
+            parser: new vcf_1.default({ header }),
+        };
+    }
+    async configure() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch(e => {
+                this.configured = undefined;
+                throw e;
             });
-        });
-    };
-    default_1.prototype.getFeatures = function (query, opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var refName, start, end, _a, vcf, parser;
-            var _this = this;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        refName = query.refName, start = query.start, end = query.end;
-                        return [4 /*yield*/, this.configure()];
-                    case 1:
-                        _a = _b.sent(), vcf = _a.vcf, parser = _a.parser;
-                        return [4 /*yield*/, vcf.getLines(refName, start, end, __assign({ lineCallback: function (line, fileOffset) {
-                                    observer.next(new VcfFeature_1.default({
-                                        variant: parser.parseLine(line),
-                                        parser: parser,
-                                        id: "".concat(_this.id, "-vcf-").concat(fileOffset),
-                                    }));
-                                } }, opts))];
-                    case 2:
-                        _b.sent();
-                        observer.complete();
-                        return [2 /*return*/];
-                }
+        }
+        return this.configured;
+    }
+    async getRefNames(opts = {}) {
+        const { vcf } = await this.configure();
+        return vcf.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        const { vcf } = await this.configure();
+        return vcf.getHeader();
+    }
+    async getMetadata() {
+        const { parser } = await this.configure();
+        return parser.getMetadata();
+    }
+    getFeatures(query, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { refName, start, end } = query;
+            const { vcf, parser } = await this.configure();
+            await vcf.getLines(refName, start, end, {
+                lineCallback: (line, fileOffset) => {
+                    observer.next(new VcfFeature_1.default({
+                        variant: parser.parseLine(line),
+                        parser,
+                        id: `${this.id}-vcf-${fileOffset}`,
+                    }));
+                },
+                ...opts,
             });
-        }); }, opts.signal);
-    };
+            observer.complete();
+        }, opts.signal);
+    }
     /**
      * Checks if the data source has data for the given reference sequence,
      * and then gets the features in the region if it does
@@ -208,43 +88,25 @@ var default_1 = /** @class */ (function (_super) {
      * @param opts - Feature adapter options
      * @returns Observable of Feature objects in the regions
      */
-    default_1.prototype.getFeaturesInMultipleRegions = function (regions, opts) {
-        var _this = this;
-        if (opts === void 0) { opts = {}; }
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var vcf, bytes, filehandle, stat, pct;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()
-                        // @ts-ignore
-                    ];
-                    case 1:
-                        vcf = (_a.sent()).vcf;
-                        return [4 /*yield*/, (0, util_1.bytesForRegions)(regions, vcf.index)];
-                    case 2:
-                        bytes = _a.sent();
-                        return [4 /*yield*/, this.configure()];
-                    case 3:
-                        filehandle = (_a.sent()).filehandle;
-                        return [4 /*yield*/, filehandle.stat()];
-                    case 4:
-                        stat = _a.sent();
-                        pct = Math.round((bytes / stat.size) * 100);
-                        if (pct > 100) {
-                            // this is just a bad estimate, make 100% if it goes over
-                            pct = 100;
-                        }
-                        if (pct > 60) {
-                            console.warn("getFeaturesInMultipleRegions fetching ".concat(pct, "% of VCF file, but whole-file streaming not yet implemented"));
-                        }
-                        _super.prototype.getFeaturesInMultipleRegions.call(this, regions, opts).subscribe(observer);
-                        return [2 /*return*/];
-                }
-            });
-        }); });
-    };
-    default_1.prototype.freeResources = function ( /* { region } */) { };
-    return default_1;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+    getFeaturesInMultipleRegions(regions, opts = {}) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const { vcf } = await this.configure();
+            // @ts-ignore
+            const bytes = await (0, util_1.bytesForRegions)(regions, vcf.index);
+            const { filehandle } = await this.configure();
+            const stat = await filehandle.stat();
+            let pct = Math.round((bytes / stat.size) * 100);
+            if (pct > 100) {
+                // this is just a bad estimate, make 100% if it goes over
+                pct = 100;
+            }
+            if (pct > 60) {
+                console.warn(`getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`);
+            }
+            super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer);
+        });
+    }
+    freeResources( /* { region } */) { }
+}
 exports.default = default_1;
 //# sourceMappingURL=VcfTabixAdapter.js.map