@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/dist/CramAdapter/CramAdapter.js.map

@@ -1 +1 @@
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package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -1,135 +1,99 @@
 "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 CramSlightlyLazyFeature = /** @class */ (function () {
+class CramSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    function CramSlightlyLazyFeature(record, _store) {
+    constructor(record, _store) {
         this.record = record;
         this._store = _store;
     }
-    CramSlightlyLazyFeature.prototype._get_name = function () {
+    _get_name() {
         return this.record.readName;
-    };
-    CramSlightlyLazyFeature.prototype._get_start = function () {
+    }
+    _get_start() {
         return this.record.alignmentStart - 1;
-    };
-    CramSlightlyLazyFeature.prototype._get_end = function () {
+    }
+    _get_end() {
         return this.record.alignmentStart + this.record.lengthOnRef - 1;
-    };
-    CramSlightlyLazyFeature.prototype._get_cram_read_features = function () {
+    }
+    _get_cram_read_features() {
         return this.record.readFeatures;
-    };
-    CramSlightlyLazyFeature.prototype._get_type = function () {
+    }
+    _get_type() {
         return 'match';
-    };
-    CramSlightlyLazyFeature.prototype._get_score = function () {
+    }
+    _get_score() {
         return this.record.mappingQuality;
-    };
-    CramSlightlyLazyFeature.prototype._get_flags = function () {
+    }
+    _get_flags() {
         return this.record.flags;
-    };
-    CramSlightlyLazyFeature.prototype._get_strand = function () {
+    }
+    _get_strand() {
         return this.record.isReverseComplemented() ? -1 : 1;
-    };
-    CramSlightlyLazyFeature.prototype._read_group_id = function () {
-        var rg = this._store.samHeader.readGroups;
+    }
+    _read_group_id() {
+        const rg = this._store.samHeader.readGroups;
         return rg ? rg[this.record.readGroupId] : undefined;
-    };
-    CramSlightlyLazyFeature.prototype._get_qual = function () {
+    }
+    _get_qual() {
         return (this.record.qualityScores || []).join(' ');
-    };
-    CramSlightlyLazyFeature.prototype.qualRaw = function () {
+    }
+    qualRaw() {
         return this.record.qualityScores;
-    };
-    CramSlightlyLazyFeature.prototype._get_seq_id = function () {
+    }
+    _get_seq_id() {
         return this._store.refIdToName(this.record.sequenceId);
-    };
-    CramSlightlyLazyFeature.prototype._get_refName = function () {
+    }
+    _get_refName() {
         return this._get_seq_id();
-    };
-    CramSlightlyLazyFeature.prototype._get_is_paired = function () {
+    }
+    _get_is_paired() {
         return !!this.record.mate;
-    };
-    CramSlightlyLazyFeature.prototype._get_pair_orientation = function () {
+    }
+    _get_pair_orientation() {
         return this.record.isPaired() ? this.record.getPairOrientation() : undefined;
-    };
-    CramSlightlyLazyFeature.prototype._get_template_length = function () {
+    }
+    _get_template_length() {
         return this.record.templateLength || this.record.templateSize;
-    };
-    CramSlightlyLazyFeature.prototype._get_next_seq_id = function () {
+    }
+    _get_next_seq_id() {
         return this.record.mate
             ? this._store.refIdToName(this.record.mate.sequenceId)
             : undefined;
-    };
-    CramSlightlyLazyFeature.prototype._get_next_pos = function () {
+    }
+    _get_next_pos() {
         return this.record.mate ? this.record.mate.alignmentStart : undefined;
-    };
-    CramSlightlyLazyFeature.prototype._get_next_segment_position = function () {
+    }
+    _get_next_segment_position() {
         return this.record.mate
-            ? "".concat(this._store.refIdToName(this.record.mate.sequenceId), ":").concat(this.record.mate.alignmentStart)
+            ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${this.record.mate.alignmentStart}`
             : undefined;
-    };
-    CramSlightlyLazyFeature.prototype._get_tags = function () {
-        var RG = this._read_group_id();
-        var tags = this.record.tags;
+    }
+    _get_tags() {
+        const RG = this._read_group_id();
+        const { tags } = this.record;
         // avoids a tag copy if no RG, but just copy if there is one
-        return RG !== undefined ? __assign(__assign({}, tags), { RG: RG }) : tags;
-    };
-    CramSlightlyLazyFeature.prototype._get_seq = function () {
+        return RG !== undefined ? { ...tags, RG } : tags;
+    }
+    _get_seq() {
         return this.record.getReadBases();
-    };
+    }
     // generate a CIGAR, based on code from jkbonfield
-    CramSlightlyLazyFeature.prototype._get_CIGAR = function () {
-        var seq = '';
-        var cigar = '';
-        var op = 'M';
-        var oplen = 0;
+    _get_CIGAR() {
+        let seq = '';
+        let cigar = '';
+        let op = 'M';
+        let oplen = 0;
         // not sure I should access these, but...
-        var ref = this.record._refRegion.seq;
-        var refStart = this.record._refRegion.start;
-        var last_pos = this.record.alignmentStart;
-        var sublen = 0;
+        const ref = this.record._refRegion.seq;
+        const refStart = this.record._refRegion.start;
+        let last_pos = this.record.alignmentStart;
+        let sublen = 0;
         if (typeof this.record.readFeatures !== 'undefined') {
             // @ts-ignore
-            for (var i = 0; i < this.record.readFeatures.length; i++) {
-                var _a = this.record.readFeatures[i], code = _a.code, refPos = _a.refPos, sub = _a.sub, data = _a.data;
+            for (let i = 0; i < this.record.readFeatures.length; i++) {
+                const { code, refPos, sub, data } = this.record.readFeatures[i];
                 sublen = refPos - last_pos;
                 seq += ref.substring(last_pos - refStart, refPos - refStart);
                 last_pos = refPos;
@@ -143,8 +107,8 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
                 }
                 if (code === 'b') {
                     // An array of bases stored verbatim
-                    var ret = data.split(',');
-                    var added = String.fromCharCode.apply(String, __spreadArray([], __read(ret), false));
+                    const ret = data.split(',');
+                    const added = String.fromCharCode(...ret);
                     seq += added;
                     last_pos += added.length;
                     oplen += added.length;
@@ -185,7 +149,7 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
                     if (oplen) {
                         cigar += oplen + op;
                     }
-                    cigar += "".concat(1, "I");
+                    cigar += `${1}I`;
                     oplen = 0;
                 }
                 else if (code === 'P') {
@@ -193,14 +157,14 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
                     if (oplen) {
                         cigar += oplen + op;
                     }
-                    cigar += "".concat(data, "P");
+                    cigar += `${data}P`;
                 }
                 else if (code === 'H') {
                     // Hard clip
                     if (oplen) {
                         cigar += oplen + op;
                     }
-                    cigar += "".concat(data, "H");
+                    cigar += `${data}H`;
                     oplen = 0;
                 } // else q or Q
             }
@@ -222,77 +186,79 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
             cigar += oplen + op;
         }
         return cigar;
-    };
-    CramSlightlyLazyFeature.prototype.tags = function () {
-        var properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
+    }
+    tags() {
+        const properties = Object.getOwnPropertyNames(CramSlightlyLazyFeature.prototype);
         return properties
-            .filter(function (prop) {
-            return prop.startsWith('_get_') &&
-                prop !== '_get_mismatches' &&
-                prop !== '_get_cram_read_features';
-        })
-            .map(function (methodName) { return methodName.replace('_get_', ''); });
-    };
-    CramSlightlyLazyFeature.prototype.id = function () {
-        return "".concat(this._store.id, "-").concat(this.record.uniqueId);
-    };
-    CramSlightlyLazyFeature.prototype.get = function (field) {
-        var methodName = "_get_".concat(field);
+            .filter(prop => prop.startsWith('_get_') &&
+            prop !== '_get_mismatches' &&
+            prop !== '_get_cram_read_features')
+            .map(methodName => methodName.replace('_get_', ''));
+    }
+    id() {
+        return `${this._store.id}-${this.record.uniqueId}`;
+    }
+    get(field) {
+        const methodName = `_get_${field}`;
         // @ts-ignore
         if (this[methodName]) {
             // @ts-ignore
             return this[methodName]();
         }
         return undefined;
-    };
-    CramSlightlyLazyFeature.prototype.parent = function () {
+    }
+    parent() {
         return undefined;
-    };
-    CramSlightlyLazyFeature.prototype.children = function () {
+    }
+    children() {
         return undefined;
-    };
-    CramSlightlyLazyFeature.prototype.set = function () { };
-    CramSlightlyLazyFeature.prototype.pairedFeature = function () {
+    }
+    set() { }
+    pairedFeature() {
         return false;
-    };
-    CramSlightlyLazyFeature.prototype._get_clipPos = function () {
-        var mismatches = this.get('mismatches');
+    }
+    _get_clipPos() {
+        const mismatches = this.get('mismatches');
         if (mismatches.length) {
-            var record = this.get('strand') === -1
+            const record = this.get('strand') === -1
                 ? mismatches[mismatches.length - 1]
                 : mismatches[0];
-            var type = record.type, cliplen = record.cliplen;
+            const { type, cliplen } = record;
             if (type === 'softclip' || type === 'hardclip') {
                 return cliplen;
             }
         }
         return 0;
-    };
-    CramSlightlyLazyFeature.prototype.toJSON = function () {
-        var _this = this;
+    }
+    toJSON() {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        var tags = {};
-        this.tags().forEach(function (t) {
-            var val = _this.get(t);
+        const tags = {};
+        this.tags().forEach((t) => {
+            const val = this.get(t);
             if (val !== undefined) {
                 tags[t] = val;
             }
         });
-        return __assign(__assign({}, tags), { name: this.get('name'), type: this.get('type'), uniqueId: this.id() });
-    };
-    CramSlightlyLazyFeature.prototype._get_mismatches = function () {
-        var readFeatures = this.get('cram_read_features');
-        var qual = this.qualRaw();
+        return {
+            ...tags,
+            name: this.get('name'),
+            type: this.get('type'),
+            uniqueId: this.id(),
+        };
+    }
+    _get_mismatches() {
+        const readFeatures = this.get('cram_read_features');
+        const qual = this.qualRaw();
         if (!readFeatures) {
             return [];
         }
-        var start = this.get('start');
-        var mismatches = new Array(readFeatures.length);
-        var j = 0;
-        for (var i = 0; i < readFeatures.length; i++) {
-            var f = readFeatures[i];
-            var code = f.code, pos = f.pos, data = f.data, sub = f.sub, ref = f.ref;
-            var refPos = f.refPos - 1 - start;
+        const start = this.get('start');
+        const mismatches = new Array(readFeatures.length);
+        let j = 0;
+        for (let i = 0; i < readFeatures.length; i++) {
+            const f = readFeatures[i];
+            const { code, pos, data, sub, ref } = f;
+            const refPos = f.refPos - 1 - start;
             if (code === 'X') {
                 // substitution
                 mismatches[j++] = {
@@ -309,7 +275,7 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
                 mismatches[j++] = {
                     start: refPos,
                     type: 'insertion',
-                    base: "".concat(data.length),
+                    base: `${data.length}`,
                     length: 0,
                 };
             }
@@ -324,11 +290,11 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
             }
             else if (code === 'S') {
                 // soft clip
-                var len = data.length;
+                const len = data.length;
                 mismatches[j++] = {
                     start: refPos,
                     type: 'softclip',
-                    base: "S".concat(len),
+                    base: `S${len}`,
                     cliplen: len,
                     length: 1,
                 };
@@ -338,11 +304,11 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
             }
             else if (code === 'H') {
                 // hard clip
-                var len = data;
+                const len = data;
                 mismatches[j++] = {
                     start: refPos,
                     type: 'hardclip',
-                    base: "H".concat(len),
+                    base: `H${len}`,
                     cliplen: len,
                     length: 1,
                 };
@@ -380,8 +346,7 @@ var CramSlightlyLazyFeature = /** @class */ (function () {
             }
         }
         return mismatches.slice(0, j);
-    };
-    return CramSlightlyLazyFeature;
-}());
+    }
+}
 exports.default = CramSlightlyLazyFeature;
 //# sourceMappingURL=CramSlightlyLazyFeature.js.map

package/dist/CramAdapter/CramSlightlyLazyFeature.js.map

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