@gmod/bam 2.0.4 → 3.0.1

package/esm/record.js

@@ -1,156 +1,70 @@
 import Constants from './constants';
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
-/**
- * Class of each BAM record returned by this API.
- */
 export default class BamRecord {
     constructor(args) {
-        this.data = {};
-        this._tagList = [];
-        this._allTagsParsed = false;
-        const { bytes, fileOffset } = args;
-        const { byteArray, start } = bytes;
-        this.data = { start: byteArray.readInt32LE(start + 8) };
-        this.bytes = bytes;
-        this._id = fileOffset;
-        this._refID = byteArray.readInt32LE(start + 4);
-        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;
@@ -308,26 +222,9 @@ export default 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 => [/\D/.exec(op)[0].toUpperCase(), Number.parseInt(op, 10)]));
+        return tags;
     }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both
@@ -380,40 +277,43 @@ export default class BamRecord {
     isSupplementary() {
         return !!(this.flags & Constants.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') {
@@ -421,39 +321,32 @@ export default 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) {
@@ -468,10 +361,10 @@ export default 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 = ' ';
@@ -485,7 +378,7 @@ export default 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;
@@ -502,23 +395,23 @@ export default 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 = {};
@@ -532,4 +425,26 @@ export default class BamRecord {
         return data;
     }
 }
+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/esm/record.js.map

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

@@ -2,13 +2,6 @@ import Long from 'long';
 export function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
-export 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,
@@ -86,8 +79,9 @@ export function optimizeChunks(chunks, lowest) {
     return mergedChunks;
 }
 export function parsePseudoBin(bytes, offset) {
-    const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
-    return { lineCount };
+    return {
+        lineCount: Long.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true).toNumber(),
+    };
 }
 export function findFirstData(firstDataLine, virtualOffset) {
     return firstDataLine

package/esm/util.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "2.0.4",
+  "version": "3.0.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -20,15 +20,14 @@
     "src"
   ],
   "scripts": {
-    "test": "jest",
-    "coverage": "npm test -- --coverage",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
+    "test": "vitest",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "clean": "rimraf dist esm",
     "build:esm": "tsc --target es2018 --outDir esm",
     "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
     "build": "npm run build:esm && npm run build:es5",
     "prebuild": "npm run clean && npm run lint",
-    "preversion": "npm run lint && npm test && npm run build",
+    "preversion": "npm run lint && npm test run && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
@@ -41,28 +40,28 @@
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
     "@gmod/bgzf-filehandle": "^1.4.4",
+    "buffer": "^6.0.3",
     "crc": "^4.3.2",
     "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^29.5.1",
     "@types/long": "^4.0.0",
     "@types/node": "^20.11.19",
-    "@typescript-eslint/eslint-plugin": "^8.0.1",
-    "@typescript-eslint/parser": "^8.0.1",
-    "eslint": "^9.8.0",
+    "@typescript-eslint/eslint-plugin": "^8.1.0",
+    "@typescript-eslint/parser": "^8.1.0",
+    "@vitest/coverage-v8": "^2.0.5",
+    "eslint": "^9.9.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^55.0.0",
-    "jest": "^29.5.0",
-    "jest-fetch-mock": "^3.0.3",
-    "prettier": "^3.2.5",
+    "eslint-plugin-unicorn": "^56.0.0",
+    "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
-    "ts-jest": "^29.2.4",
-    "typescript": "^5.0.4"
+    "typescript": "^5.0.4",
+    "typescript-eslint": "^8.1.0",
+    "vitest": "^2.0.5"
   },
   "publishConfig": {
     "access": "public"