@gmod/bam 1.1.17 → 2.0.0

package/dist/record.js

@@ -4,19 +4,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-empty-function */
-var constants_1 = __importDefault(require("./constants"));
-var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
-var CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
+const constants_1 = __importDefault(require("./constants"));
+const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
+const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
 /**
  * Class of each BAM record returned by this API.
  */
-var BamRecord = /** @class */ (function () {
-    function BamRecord(args) {
+class BamRecord {
+    constructor(args) {
         this.data = {};
         this._tagList = [];
         this._allTagsParsed = false;
-        var bytes = args.bytes, fileOffset = args.fileOffset;
-        var byteArray = bytes.byteArray, start = bytes.start;
+        const { bytes, fileOffset } = args;
+        const { byteArray, start } = bytes;
         this.data = {};
         this.bytes = bytes;
         this._id = fileOffset;
@@ -24,7 +24,7 @@ var BamRecord = /** @class */ (function () {
         this.data.start = byteArray.readInt32LE(start + 8);
         this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
     }
-    BamRecord.prototype.get = function (field) {
+    get(field) {
         //@ts-ignore
         if (this[field]) {
             //@ts-ignore
@@ -36,26 +36,25 @@ var BamRecord = /** @class */ (function () {
             return this.data[field];
         }
         return this._get(field.toLowerCase());
-    };
-    BamRecord.prototype.end = function () {
+    }
+    end() {
         return this.get('start') + this.get('length_on_ref');
-    };
-    BamRecord.prototype.seq_id = function () {
+    }
+    seq_id() {
         return this._refID;
-    };
+    }
     // same as get(), except requires lower-case arguments.  used
     // internally to save lots of calls to field.toLowerCase()
-    BamRecord.prototype._get = function (field) {
+    _get(field) {
         if (field in this.data) {
             return this.data[field];
         }
         this.data[field] = this._parseTag(field);
         return this.data[field];
-    };
-    BamRecord.prototype._tags = function () {
-        var _this = this;
+    }
+    _tags() {
         this._parseAllTags();
-        var tags = ['seq'];
+        let tags = ['seq'];
         if (!this.isSegmentUnmapped()) {
             tags.push('start', 'end', 'strand', 'score', 'qual', 'MQ', 'CIGAR', 'length_on_ref', 'template_length');
         }
@@ -63,143 +62,151 @@ var BamRecord = /** @class */ (function () {
             tags.push('next_segment_position', 'pair_orientation');
         }
         tags = tags.concat(this._tagList || []);
-        Object.keys(this.data).forEach(function (k) {
+        for (const k of Object.keys(this.data)) {
             if (k[0] !== '_' && k !== 'next_seq_id') {
                 tags.push(k);
             }
-        });
-        var seen = {};
-        return tags.filter(function (t) {
-            if ((t in _this.data && _this.data[t] === undefined) ||
+        }
+        const seen = {};
+        return tags.filter(t => {
+            if ((t in this.data && this.data[t] === undefined) ||
                 t === 'CG' ||
                 t === 'cg') {
                 return false;
             }
-            var lt = t.toLowerCase();
-            var s = seen[lt];
+            const lt = t.toLowerCase();
+            const s = seen[lt];
             seen[lt] = true;
             return !s;
         });
-    };
-    BamRecord.prototype.parent = function () {
-        return undefined;
-    };
-    BamRecord.prototype.children = function () {
+    }
+    parent() {
+        return;
+    }
+    children() {
         return this.get('subfeatures');
-    };
-    BamRecord.prototype.id = function () {
+    }
+    id() {
         return this._id;
-    };
+    }
     // special parsers
     /**
      * Mapping quality score.
      */
-    BamRecord.prototype.mq = function () {
-        var mq = (this.get('_bin_mq_nl') & 0xff00) >> 8;
+    mq() {
+        const mq = (this.get('_bin_mq_nl') & 0xff00) >> 8;
         return mq === 255 ? undefined : mq;
-    };
-    BamRecord.prototype.score = function () {
+    }
+    score() {
         return this.get('mq');
-    };
-    BamRecord.prototype.qual = function () {
+    }
+    qual() {
         var _a;
         return (_a = this.qualRaw()) === null || _a === void 0 ? void 0 : _a.join(' ');
-    };
-    BamRecord.prototype.qualRaw = function () {
+    }
+    qualRaw() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
-        var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
-        var p = start +
+        const { start, byteArray } = this.bytes;
+        const p = start +
             36 +
             this.get('_l_read_name') +
             this.get('_n_cigar_op') * 4 +
             this.get('_seq_bytes');
-        var lseq = this.get('seq_length');
+        const lseq = this.get('seq_length');
         return byteArray.subarray(p, p + lseq);
-    };
-    BamRecord.prototype.strand = function () {
+    }
+    strand() {
         return this.isReverseComplemented() ? -1 : 1;
-    };
-    BamRecord.prototype.multi_segment_next_segment_strand = function () {
+    }
+    multi_segment_next_segment_strand() {
         if (this.isMateUnmapped()) {
-            return undefined;
+            return;
         }
         return this.isMateReverseComplemented() ? -1 : 1;
-    };
-    BamRecord.prototype.name = function () {
+    }
+    name() {
         return this.get('_read_name');
-    };
-    BamRecord.prototype._read_name = function () {
-        var nl = this.get('_l_read_name');
-        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
+    }
+    _read_name() {
+        const nl = this.get('_l_read_name');
+        const { byteArray, start } = this.bytes;
         return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
-    };
+    }
     /**
      * Get the value of a tag, parsing the tags as far as necessary.
      * Only called if we have not already parsed that field.
      */
-    BamRecord.prototype._parseTag = function (tagName) {
+    _parseTag(tagName) {
         // if all of the tags have been parsed and we're still being
         // called, we already know that we have no such tag, because
         // it would already have been cached.
         if (this._allTagsParsed) {
-            return undefined;
+            return;
         }
-        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
-        var p = this._tagOffset ||
+        const { byteArray, start } = this.bytes;
+        let p = this._tagOffset ||
             start +
                 36 +
                 this.get('_l_read_name') +
                 this.get('_n_cigar_op') * 4 +
                 this.get('_seq_bytes') +
                 this.get('seq_length');
-        var blockEnd = this.bytes.end;
-        var lcTag;
+        const blockEnd = this.bytes.end;
+        let lcTag;
         while (p < blockEnd && lcTag !== tagName) {
-            var tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
+            const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
             lcTag = tag.toLowerCase();
-            var type = String.fromCharCode(byteArray[p + 2]);
+            const type = String.fromCharCode(byteArray[p + 2]);
             p += 3;
-            var value = void 0;
+            let value;
             switch (type) {
-                case 'A':
+                case 'A': {
                     value = String.fromCharCode(byteArray[p]);
                     p += 1;
                     break;
-                case 'i':
+                }
+                case 'i': {
                     value = byteArray.readInt32LE(p);
                     p += 4;
                     break;
-                case 'I':
+                }
+                case 'I': {
                     value = byteArray.readUInt32LE(p);
                     p += 4;
                     break;
-                case 'c':
+                }
+                case 'c': {
                     value = byteArray.readInt8(p);
                     p += 1;
                     break;
-                case 'C':
+                }
+                case 'C': {
                     value = byteArray.readUInt8(p);
                     p += 1;
                     break;
-                case 's':
+                }
+                case 's': {
                     value = byteArray.readInt16LE(p);
                     p += 2;
                     break;
-                case 'S':
+                }
+                case 'S': {
                     value = byteArray.readUInt16LE(p);
                     p += 2;
                     break;
-                case 'f':
+                }
+                case 'f': {
                     value = byteArray.readFloatLE(p);
                     p += 4;
                     break;
+                }
                 case 'Z':
-                case 'H':
+                case 'H': {
                     value = '';
                     while (p <= blockEnd) {
-                        var cc = byteArray[p++];
+                        const cc = byteArray[p++];
                         if (cc === 0) {
                             break;
                         }
@@ -208,24 +215,25 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     break;
+                }
                 case 'B': {
                     value = '';
-                    var cc = byteArray[p++];
-                    var Btype = String.fromCharCode(cc);
-                    var limit = byteArray.readInt32LE(p);
+                    const cc = byteArray[p++];
+                    const Btype = String.fromCharCode(cc);
+                    const limit = byteArray.readInt32LE(p);
                     p += 4;
                     if (Btype === 'i') {
                         if (tag === 'CG') {
-                            for (var k = 0; k < limit; k++) {
-                                var cigop = byteArray.readInt32LE(p);
-                                var lop = cigop >> 4;
-                                var op = CIGAR_DECODER[cigop & 0xf];
+                            for (let k = 0; k < limit; k++) {
+                                const cigop = byteArray.readInt32LE(p);
+                                const lop = cigop >> 4;
+                                const op = CIGAR_DECODER[cigop & 0xf];
                                 value += lop + op;
                                 p += 4;
                             }
                         }
                         else {
-                            for (var k = 0; k < limit; k++) {
+                            for (let k = 0; k < limit; k++) {
                                 value += byteArray.readInt32LE(p);
                                 if (k + 1 < limit) {
                                     value += ',';
@@ -236,16 +244,16 @@ var BamRecord = /** @class */ (function () {
                     }
                     if (Btype === 'I') {
                         if (tag === 'CG') {
-                            for (var k = 0; k < limit; k++) {
-                                var cigop = byteArray.readUInt32LE(p);
-                                var lop = cigop >> 4;
-                                var op = CIGAR_DECODER[cigop & 0xf];
+                            for (let k = 0; k < limit; k++) {
+                                const cigop = byteArray.readUInt32LE(p);
+                                const lop = cigop >> 4;
+                                const op = CIGAR_DECODER[cigop & 0xf];
                                 value += lop + op;
                                 p += 4;
                             }
                         }
                         else {
-                            for (var k = 0; k < limit; k++) {
+                            for (let k = 0; k < limit; k++) {
                                 value += byteArray.readUInt32LE(p);
                                 if (k + 1 < limit) {
                                     value += ',';
@@ -255,7 +263,7 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     if (Btype === 's') {
-                        for (var k = 0; k < limit; k++) {
+                        for (let k = 0; k < limit; k++) {
                             value += byteArray.readInt16LE(p);
                             if (k + 1 < limit) {
                                 value += ',';
@@ -264,7 +272,7 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     if (Btype === 'S') {
-                        for (var k = 0; k < limit; k++) {
+                        for (let k = 0; k < limit; k++) {
                             value += byteArray.readUInt16LE(p);
                             if (k + 1 < limit) {
                                 value += ',';
@@ -273,7 +281,7 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     if (Btype === 'c') {
-                        for (var k = 0; k < limit; k++) {
+                        for (let k = 0; k < limit; k++) {
                             value += byteArray.readInt8(p);
                             if (k + 1 < limit) {
                                 value += ',';
@@ -282,7 +290,7 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     if (Btype === 'C') {
-                        for (var k = 0; k < limit; k++) {
+                        for (let k = 0; k < limit; k++) {
                             value += byteArray.readUInt8(p);
                             if (k + 1 < limit) {
                                 value += ',';
@@ -291,7 +299,7 @@ var BamRecord = /** @class */ (function () {
                         }
                     }
                     if (Btype === 'f') {
-                        for (var k = 0; k < limit; k++) {
+                        for (let k = 0; k < limit; k++) {
                             value += byteArray.readFloatLE(p);
                             if (k + 1 < limit) {
                                 value += ',';
@@ -301,10 +309,11 @@ var BamRecord = /** @class */ (function () {
                     }
                     break;
                 }
-                default:
-                    console.warn("Unknown BAM tag type '".concat(type, "', tags may be incomplete"));
+                default: {
+                    console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
                     value = undefined;
-                    p = blockEnd; // stop parsing tags
+                    p = blockEnd;
+                } // stop parsing tags
             }
             this._tagOffset = p;
             this._tagList.push(tag);
@@ -314,84 +323,84 @@ var BamRecord = /** @class */ (function () {
             this.data[lcTag] = value;
         }
         this._allTagsParsed = true;
-        return undefined;
-    };
-    BamRecord.prototype._parseAllTags = function () {
+        return;
+    }
+    _parseAllTags() {
         this._parseTag('');
-    };
-    BamRecord.prototype._parseCigar = function (cigar) {
+    }
+    _parseCigar(cigar) {
         return (
         //@ts-ignore
         cigar
             .match(/\d+\D/g)
             //@ts-ignore
-            .map(function (op) { return [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)]; }));
-    };
+            .map(op => [op.match(/\D/)[0].toUpperCase(), Number.parseInt(op, 10)]));
+    }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
-    BamRecord.prototype.isPaired = function () {
+    isPaired() {
         return !!(this.flags & constants_1.default.BAM_FPAIRED);
-    };
+    }
     /** @returns {boolean} true if the read is paired, and both segments are mapped */
-    BamRecord.prototype.isProperlyPaired = function () {
+    isProperlyPaired() {
         return !!(this.flags & constants_1.default.BAM_FPROPER_PAIR);
-    };
+    }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-    BamRecord.prototype.isSegmentUnmapped = function () {
+    isSegmentUnmapped() {
         return !!(this.flags & constants_1.default.BAM_FUNMAP);
-    };
+    }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-    BamRecord.prototype.isMateUnmapped = function () {
+    isMateUnmapped() {
         return !!(this.flags & constants_1.default.BAM_FMUNMAP);
-    };
+    }
     /** @returns {boolean} true if the read is mapped to the reverse strand */
-    BamRecord.prototype.isReverseComplemented = function () {
+    isReverseComplemented() {
         return !!(this.flags & constants_1.default.BAM_FREVERSE);
-    };
+    }
     /** @returns {boolean} true if the mate is mapped to the reverse strand */
-    BamRecord.prototype.isMateReverseComplemented = function () {
+    isMateReverseComplemented() {
         return !!(this.flags & constants_1.default.BAM_FMREVERSE);
-    };
+    }
     /** @returns {boolean} true if this is read number 1 in a pair */
-    BamRecord.prototype.isRead1 = function () {
+    isRead1() {
         return !!(this.flags & constants_1.default.BAM_FREAD1);
-    };
+    }
     /** @returns {boolean} true if this is read number 2 in a pair */
-    BamRecord.prototype.isRead2 = function () {
+    isRead2() {
         return !!(this.flags & constants_1.default.BAM_FREAD2);
-    };
+    }
     /** @returns {boolean} true if this is a secondary alignment */
-    BamRecord.prototype.isSecondary = function () {
+    isSecondary() {
         return !!(this.flags & constants_1.default.BAM_FSECONDARY);
-    };
+    }
     /** @returns {boolean} true if this read has failed QC checks */
-    BamRecord.prototype.isFailedQc = function () {
+    isFailedQc() {
         return !!(this.flags & constants_1.default.BAM_FQCFAIL);
-    };
+    }
     /** @returns {boolean} true if the read is an optical or PCR duplicate */
-    BamRecord.prototype.isDuplicate = function () {
+    isDuplicate() {
         return !!(this.flags & constants_1.default.BAM_FDUP);
-    };
+    }
     /** @returns {boolean} true if this is a supplementary alignment */
-    BamRecord.prototype.isSupplementary = function () {
+    isSupplementary() {
         return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
-    };
-    BamRecord.prototype.cigar = function () {
+    }
+    cigar() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
-        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
-        var numCigarOps = this.get('_n_cigar_op');
-        var p = start + 36 + this.get('_l_read_name');
-        var seqLen = this.get('seq_length');
-        var cigar = '';
-        var lref = 0;
+        const { byteArray, start } = this.bytes;
+        const numCigarOps = this.get('_n_cigar_op');
+        let p = start + 36 + this.get('_l_read_name');
+        const seqLen = this.get('seq_length');
+        let cigar = '';
+        let lref = 0;
         // check for CG tag by inspecting whether the CIGAR field
         // contains a clip that consumes entire seqLen
-        var cigop = byteArray.readInt32LE(p);
-        var lop = cigop >> 4;
-        var op = CIGAR_DECODER[cigop & 0xf];
+        let cigop = byteArray.readInt32LE(p);
+        let lop = cigop >> 4;
+        let op = CIGAR_DECODER[cigop & 0xf];
         if (op === 'S' && lop === seqLen) {
             // if there is a CG the second CIGAR field will
             // be a N tag the represents the length on ref
@@ -406,7 +415,7 @@ var BamRecord = /** @class */ (function () {
             return this.get('CG');
         }
         else {
-            for (var c = 0; c < numCigarOps; ++c) {
+            for (let c = 0; c < numCigarOps; ++c) {
                 cigop = byteArray.readInt32LE(p);
                 lop = cigop >> 4;
                 op = CIGAR_DECODER[cigop & 0xf];
@@ -421,9 +430,9 @@ var BamRecord = /** @class */ (function () {
             this.data.length_on_ref = lref;
             return cigar;
         }
-    };
-    BamRecord.prototype._flags = function () { };
-    BamRecord.prototype.length_on_ref = function () {
+    }
+    _flags() { }
+    length_on_ref() {
         if (this.data.length_on_ref) {
             return this.data.length_on_ref;
         }
@@ -431,31 +440,31 @@ var BamRecord = /** @class */ (function () {
             this.get('cigar'); // the length_on_ref is set as a side effect
             return this.data.length_on_ref;
         }
-    };
-    BamRecord.prototype._n_cigar_op = function () {
+    }
+    _n_cigar_op() {
         return this.get('_flag_nc') & 0xffff;
-    };
-    BamRecord.prototype._l_read_name = function () {
+    }
+    _l_read_name() {
         return this.get('_bin_mq_nl') & 0xff;
-    };
+    }
     /**
      * number of bytes in the sequence field
      */
-    BamRecord.prototype._seq_bytes = function () {
+    _seq_bytes() {
         return (this.get('seq_length') + 1) >> 1;
-    };
-    BamRecord.prototype.getReadBases = function () {
+    }
+    getReadBases() {
         return this.seq();
-    };
-    BamRecord.prototype.seq = function () {
-        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
-        var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
-        var seqBytes = this.get('_seq_bytes');
-        var len = this.get('seq_length');
-        var buf = '';
-        var i = 0;
-        for (var j = 0; j < seqBytes; ++j) {
-            var sb = byteArray[p + j];
+    }
+    seq() {
+        const { byteArray, start } = this.bytes;
+        const p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
+        const seqBytes = this.get('_seq_bytes');
+        const len = this.get('seq_length');
+        let buf = '';
+        let i = 0;
+        for (let j = 0; j < seqBytes; ++j) {
+            const sb = byteArray[p + j];
             buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
             i++;
             if (i < len) {
@@ -464,16 +473,16 @@ var BamRecord = /** @class */ (function () {
             }
         }
         return buf;
-    };
+    }
     // adapted from igv.js
-    BamRecord.prototype.getPairOrientation = function () {
+    getPairOrientation() {
         if (!this.isSegmentUnmapped() &&
             !this.isMateUnmapped() &&
             this._refID === this._next_refid()) {
-            var s1 = this.isReverseComplemented() ? 'R' : 'F';
-            var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            var o1 = ' ';
-            var o2 = ' ';
+            const s1 = this.isReverseComplemented() ? 'R' : 'F';
+            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
+            let o1 = ' ';
+            let o2 = ' ';
             if (this.isRead1()) {
                 o1 = '1';
                 o2 = '2';
@@ -482,8 +491,8 @@ var BamRecord = /** @class */ (function () {
                 o1 = '2';
                 o2 = '1';
             }
-            var tmp = [];
-            var isize = this.template_length();
+            const tmp = [];
+            const isize = this.template_length();
             if (isize > 0) {
                 tmp[0] = s1;
                 tmp[1] = o1;
@@ -498,39 +507,37 @@ var BamRecord = /** @class */ (function () {
             }
             return tmp.join('');
         }
-        return null;
-    };
-    BamRecord.prototype._bin_mq_nl = function () {
+        return '';
+    }
+    _bin_mq_nl() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
-    };
-    BamRecord.prototype._flag_nc = function () {
+    }
+    _flag_nc() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
-    };
-    BamRecord.prototype.seq_length = function () {
+    }
+    seq_length() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
-    };
-    BamRecord.prototype._next_refid = function () {
+    }
+    _next_refid() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
-    };
-    BamRecord.prototype._next_pos = function () {
+    }
+    _next_pos() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
-    };
-    BamRecord.prototype.template_length = function () {
+    }
+    template_length() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 32);
-    };
-    BamRecord.prototype.toJSON = function () {
-        var _this = this;
-        var data = {};
-        Object.keys(this).forEach(function (k) {
+    }
+    toJSON() {
+        const data = {};
+        for (const k of Object.keys(this)) {
             if (k.charAt(0) === '_' || k === 'bytes') {
-                return;
+                continue;
             }
             //@ts-ignore
-            data[k] = _this[k];
-        });
+            data[k] = this[k];
+        }
         return data;
-    };
-    return BamRecord;
-}());
+    }
+}
 exports.default = BamRecord;
 //# sourceMappingURL=record.js.map