@gmod/bam 2.0.3 → 3.0.0

package/dist/record.js

@@ -6,157 +6,70 @@ Object.defineProperty(exports, "__esModule", { value: true });
 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.
- */
 class BamRecord {
     constructor(args) {
-        this.data = {};
-        this._tagList = [];
-        this._allTagsParsed = false;
-        const { bytes, fileOffset } = args;
-        const { byteArray, start } = bytes;
-        this.data = {};
-        this.bytes = bytes;
-        this._id = fileOffset;
-        this._refID = byteArray.readInt32LE(start + 4);
-        this.data.start = byteArray.readInt32LE(start + 8);
-        this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
-    }
-    get(field) {
-        //@ts-ignore
-        if (this[field]) {
-            //@ts-ignore
-            if (this.data[field]) {
-                return this.data[field];
-            }
-            //@ts-ignore
-            this.data[field] = this[field]();
-            return this.data[field];
-        }
-        return this._get(field.toLowerCase());
+        this.bytes = args.bytes;
+        this.fileOffset = args.fileOffset;
     }
-    end() {
-        return this.get('start') + this.get('length_on_ref');
+    get byteArray() {
+        return this.bytes.byteArray;
     }
-    seq_id() {
-        return this._refID;
+    get flags() {
+        return ((this.byteArray.readInt32LE(this.bytes.start + 16) & 0xffff0000) >> 16);
     }
-    // same as get(), except requires lower-case arguments.  used
-    // internally to save lots of calls to field.toLowerCase()
-    _get(field) {
-        if (field in this.data) {
-            return this.data[field];
-        }
-        this.data[field] = this._parseTag(field);
-        return this.data[field];
-    }
-    _tags() {
-        this._parseAllTags();
-        let tags = ['seq'];
-        if (!this.isSegmentUnmapped()) {
-            tags.push('start', 'end', 'strand', 'score', 'qual', 'MQ', 'CIGAR', 'length_on_ref', 'template_length');
-        }
-        if (this.isPaired()) {
-            tags.push('next_segment_position', 'pair_orientation');
-        }
-        tags = tags.concat(this._tagList || []);
-        for (const k of Object.keys(this.data)) {
-            if (!k.startsWith('_') && k !== 'next_seq_id') {
-                tags.push(k);
-            }
-        }
-        const seen = {};
-        return tags.filter(t => {
-            if ((t in this.data && this.data[t] === undefined) ||
-                t === 'CG' ||
-                t === 'cg') {
-                return false;
-            }
-            const lt = t.toLowerCase();
-            const s = seen[lt];
-            seen[lt] = true;
-            return !s;
-        });
+    get ref_id() {
+        return this.byteArray.readInt32LE(this.bytes.start + 4);
     }
-    parent() {
-        return;
+    get start() {
+        return this.byteArray.readInt32LE(this.bytes.start + 8);
     }
-    children() {
-        return this.get('subfeatures');
+    get end() {
+        return this.start + this.length_on_ref;
     }
-    id() {
-        return this._id;
+    get id() {
+        return this.fileOffset;
     }
-    // special parsers
-    /**
-     * Mapping quality score.
-     */
-    mq() {
-        const mq = (this.get('_bin_mq_nl') & 0xff00) >> 8;
+    get mq() {
+        const mq = (this.bin_mq_nl & 0xff00) >> 8;
         return mq === 255 ? undefined : mq;
     }
-    score() {
-        return this.get('mq');
+    get score() {
+        return this.mq;
     }
-    qual() {
+    get qual() {
         var _a;
-        return (_a = this.qualRaw()) === null || _a === void 0 ? void 0 : _a.join(' ');
+        return (_a = this.qualRaw) === null || _a === void 0 ? void 0 : _a.join(' ');
     }
-    qualRaw() {
+    get qualRaw() {
         if (this.isSegmentUnmapped()) {
             return;
         }
-        const { start, byteArray } = this.bytes;
-        const p = start +
-            36 +
-            this.get('_l_read_name') +
-            this.get('_n_cigar_op') * 4 +
-            this.get('_seq_bytes');
-        const lseq = this.get('seq_length');
-        return byteArray.subarray(p, p + lseq);
-    }
-    strand() {
-        return this.isReverseComplemented() ? -1 : 1;
+        const p = this.b0 +
+            this.read_name_length +
+            this.num_cigar_ops * 4 +
+            this.num_seq_bytes;
+        return this.byteArray.subarray(p, p + this.seq_length);
     }
-    multi_segment_next_segment_strand() {
-        if (this.isMateUnmapped()) {
-            return;
-        }
-        return this.isMateReverseComplemented() ? -1 : 1;
+    get strand() {
+        return this.isReverseComplemented() ? -1 : 1;
     }
-    name() {
-        return this.get('_read_name');
+    get b0() {
+        return this.bytes.start + 36;
     }
-    _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 name() {
+        return this.byteArray.toString('ascii', this.b0, this.b0 + this.read_name_length - 1);
     }
-    /**
-     * Get the value of a tag, parsing the tags as far as necessary.
-     * Only called if we have not already parsed that field.
-     */
-    _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;
-        }
-        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');
+    get tags() {
+        const { byteArray } = this.bytes;
+        let p = this.b0 +
+            this.read_name_length +
+            this.num_cigar_ops * 4 +
+            this.num_seq_bytes +
+            this.seq_length;
         const blockEnd = this.bytes.end;
-        let lcTag;
-        while (p < blockEnd && lcTag !== tagName) {
+        const tags = {};
+        while (p < blockEnd) {
             const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
-            lcTag = tag.toLowerCase();
             const type = String.fromCharCode(byteArray[p + 2]);
             p += 3;
             let value;
@@ -314,29 +227,13 @@ class BamRecord {
                     p = blockEnd;
                 } // stop parsing tags
             }
-            this._tagOffset = p;
-            this._tagList.push(tag);
-            if (lcTag === tagName) {
-                return value;
-            }
-            this.data[lcTag] = value;
+            tags[tag] = value;
         }
-        this._allTagsParsed = true;
-        return;
-    }
-    _parseAllTags() {
-        this._parseTag('');
-    }
-    _parseCigar(cigar) {
-        return (
-        //@ts-ignore
-        cigar
-            .match(/\d+\D/g)
-            //@ts-ignore
-            .map(op => [op.match(/\D/)[0].toUpperCase(), Number.parseInt(op, 10)]));
+        return tags;
     }
     /**
-     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     * @returns {boolean} true if the read is paired, regardless of whether both
+     * segments are mapped
      */
     isPaired() {
         return !!(this.flags & constants_1.default.BAM_FPAIRED);
@@ -385,40 +282,43 @@ class BamRecord {
     isSupplementary() {
         return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
     }
-    cigar() {
+    get cigarAndLength() {
         if (this.isSegmentUnmapped()) {
-            return;
+            return {
+                length_on_ref: 0,
+                CIGAR: '',
+            };
         }
-        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
-        let cigop = byteArray.readInt32LE(p);
+        const numCigarOps = this.num_cigar_ops;
+        let p = this.b0 + this.read_name_length;
+        let CIGAR = '';
+        // check for CG tag by inspecting whether the CIGAR field contains a clip
+        // that consumes entire seqLen
+        let cigop = this.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
+        if (op === 'S' && lop === this.seq_length) {
+            // if there is a CG the second CIGAR field will be a N tag the represents
+            // the length on ref
             p += 4;
-            cigop = byteArray.readInt32LE(p);
+            cigop = this.byteArray.readInt32LE(p);
             lop = cigop >> 4;
             op = CIGAR_DECODER[cigop & 0xf];
             if (op !== 'N') {
                 console.warn('CG tag with no N tag');
             }
-            this.data.length_on_ref = lop;
-            return this.get('CG');
+            return {
+                CIGAR: this.tags.CG,
+                length_on_ref: lop,
+            };
         }
         else {
+            let lref = 0;
             for (let c = 0; c < numCigarOps; ++c) {
-                cigop = byteArray.readInt32LE(p);
+                cigop = this.byteArray.readInt32LE(p);
                 lop = cigop >> 4;
                 op = CIGAR_DECODER[cigop & 0xf];
-                cigar += lop + op;
+                CIGAR += lop + op;
                 // soft clip, hard clip, and insertion don't count toward
                 // the length on the reference
                 if (op !== 'H' && op !== 'S' && op !== 'I') {
@@ -426,39 +326,32 @@ class BamRecord {
                 }
                 p += 4;
             }
-            this.data.length_on_ref = lref;
-            return cigar;
+            return {
+                CIGAR,
+                length_on_ref: lref,
+            };
         }
     }
-    length_on_ref() {
-        if (this.data.length_on_ref) {
-            return this.data.length_on_ref;
-        }
-        else {
-            this.get('cigar'); // the length_on_ref is set as a side effect
-            return this.data.length_on_ref;
-        }
+    get length_on_ref() {
+        return this.cigarAndLength.length_on_ref;
     }
-    _n_cigar_op() {
-        return this.get('_flag_nc') & 0xffff;
+    get CIGAR() {
+        return this.cigarAndLength.CIGAR;
     }
-    _l_read_name() {
-        return this.get('_bin_mq_nl') & 0xff;
+    get num_cigar_ops() {
+        return this.flag_nc & 0xffff;
     }
-    /**
-     * number of bytes in the sequence field
-     */
-    _seq_bytes() {
-        return (this.get('seq_length') + 1) >> 1;
+    get read_name_length() {
+        return this.bin_mq_nl & 0xff;
     }
-    getReadBases() {
-        return this.seq();
+    get num_seq_bytes() {
+        return (this.seq_length + 1) >> 1;
     }
-    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');
+    get seq() {
+        const { byteArray } = this.bytes;
+        const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
+        const seqBytes = this.num_seq_bytes;
+        const len = this.seq_length;
         let buf = '';
         let i = 0;
         for (let j = 0; j < seqBytes; ++j) {
@@ -473,10 +366,10 @@ class BamRecord {
         return buf;
     }
     // adapted from igv.js
-    getPairOrientation() {
+    get pair_orientation() {
         if (!this.isSegmentUnmapped() &&
             !this.isMateUnmapped() &&
-            this._refID === this._next_refid()) {
+            this.ref_id === this.next_refid) {
             const s1 = this.isReverseComplemented() ? 'R' : 'F';
             const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
             let o1 = ' ';
@@ -490,7 +383,7 @@ class BamRecord {
                 o2 = '1';
             }
             const tmp = [];
-            const isize = this.template_length();
+            const isize = this.template_length;
             if (isize > 0) {
                 tmp[0] = s1;
                 tmp[1] = o1;
@@ -507,23 +400,23 @@ class BamRecord {
         }
         return '';
     }
-    _bin_mq_nl() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
+    get bin_mq_nl() {
+        return this.byteArray.readInt32LE(this.bytes.start + 12);
     }
-    _flag_nc() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
+    get flag_nc() {
+        return this.byteArray.readInt32LE(this.bytes.start + 16);
     }
-    seq_length() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
+    get seq_length() {
+        return this.byteArray.readInt32LE(this.bytes.start + 20);
     }
-    _next_refid() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
+    get next_refid() {
+        return this.byteArray.readInt32LE(this.bytes.start + 24);
     }
-    _next_pos() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
+    get next_pos() {
+        return this.byteArray.readInt32LE(this.bytes.start + 28);
     }
-    template_length() {
-        return this.bytes.byteArray.readInt32LE(this.bytes.start + 32);
+    get template_length() {
+        return this.byteArray.readInt32LE(this.bytes.start + 32);
     }
     toJSON() {
         const data = {};
@@ -538,4 +431,26 @@ class BamRecord {
     }
 }
 exports.default = BamRecord;
+function cacheGetter(ctor, prop) {
+    const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop);
+    if (!desc) {
+        throw new Error('OH NO, NO PROPERTY DESCRIPTOR');
+    }
+    // eslint-disable-next-line @typescript-eslint/unbound-method
+    const getter = desc.get;
+    if (!getter) {
+        throw new Error('OH NO, NOT A GETTER');
+    }
+    Object.defineProperty(ctor.prototype, prop, {
+        get() {
+            const ret = getter.call(this);
+            Object.defineProperty(this, prop, { value: ret });
+            return ret;
+        },
+    });
+}
+cacheGetter(BamRecord, 'tags');
+cacheGetter(BamRecord, 'cigarAndLength');
+cacheGetter(BamRecord, 'seq');
+cacheGetter(BamRecord, 'qual');
 //# sourceMappingURL=record.js.map

package/dist/record.js.map

@@ -1 +1 @@
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package/dist/util.d.ts

@@ -1,8 +1,6 @@
-import Long from 'long';
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function timeout(ms: number): Promise<unknown>;
-export declare function longToNumber(long: Long): number;
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,

package/dist/util.js

@@ -13,7 +13,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.timeout = timeout;
-exports.longToNumber = longToNumber;
 exports.checkAbortSignal = checkAbortSignal;
 exports.abortBreakPoint = abortBreakPoint;
 exports.canMergeBlocks = canMergeBlocks;
@@ -26,13 +25,6 @@ const long_1 = __importDefault(require("long"));
 function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
-function longToNumber(long) {
-    if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
-        long.lessThan(Number.MIN_SAFE_INTEGER)) {
-        throw new Error('integer overflow');
-    }
-    return long.toNumber();
-}
 /**
  * Properly check if the given AbortSignal is aborted.
  * Per the standard, if the signal reads as aborted,
@@ -112,8 +104,9 @@ function optimizeChunks(chunks, lowest) {
     return mergedChunks;
 }
 function parsePseudoBin(bytes, offset) {
-    const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
-    return { lineCount };
+    return {
+        lineCount: long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true).toNumber(),
+    };
 }
 function findFirstData(firstDataLine, virtualOffset) {
     return firstDataLine

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/bai.js

@@ -99,6 +99,7 @@ export default class BAI extends IndexFile {
         const range = start !== undefined;
         const indexData = await this.parse(opts);
         const seqIdx = indexData.indices[seqId];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!seqIdx) {
             return [];
         }
@@ -134,10 +135,12 @@ export default class BAI extends IndexFile {
             min = 0;
         }
         const indexData = await this.parse(opts);
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!indexData) {
             return [];
         }
         const ba = indexData.indices[refId];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!ba) {
             return [];
         }
@@ -147,6 +150,7 @@ export default class BAI extends IndexFile {
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (ba.binIndex[bin]) {
                     const binChunks = ba.binIndex[bin];
                     for (const binChunk of binChunks) {
@@ -163,6 +167,7 @@ export default class BAI extends IndexFile {
         const maxLin = Math.min(max >> 14, nintv - 1);
         for (let i = minLin; i <= maxLin; ++i) {
             const vp = ba.linearIndex[i];
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
                 lowest = vp;
             }
@@ -171,7 +176,7 @@ export default class BAI extends IndexFile {
     }
     async parse(opts = {}) {
         if (!this.setupP) {
-            this.setupP = this._parse(opts).catch(e => {
+            this.setupP = this._parse(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/bai.js.map

@@ -1 +1 @@
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