@gmod/bam 1.1.8 → 1.1.9

package/esm/indexFile.js

@@ -0,0 +1,27 @@
+export default class IndexFile {
+    /**
+     * @param {filehandle} filehandle
+     * @param {function} [renameRefSeqs]
+     */
+    constructor({ filehandle, renameRefSeq = (n) => n, }) {
+        this.filehandle = filehandle;
+        this.renameRefSeq = renameRefSeq;
+    }
+    _findFirstData(data, virtualOffset) {
+        const currentFdl = data.firstDataLine;
+        if (currentFdl) {
+            data.firstDataLine =
+                currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
+        }
+        else {
+            data.firstDataLine = virtualOffset;
+        }
+    }
+    async parse(opts = {}) {
+        return this._parse(opts);
+    }
+    async hasRefSeq(seqId, opts = {}) {
+        return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;
+    }
+}
+//# sourceMappingURL=indexFile.js.map

package/esm/indexFile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,cAAc,CAAC,IAAS,EAAE,aAA4B;QACpD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;IACnE,CAAC;CACF"}

package/esm/record.d.ts

@@ -0,0 +1,88 @@
+/// <reference types="node" />
+/**
+ * Class of each BAM record returned by this API.
+ */
+export default class BamRecord {
+    private data;
+    private bytes;
+    private flags;
+    private _id;
+    private _refID;
+    private _tagOffset;
+    private _tagList;
+    private _allTagsParsed;
+    constructor(args: any);
+    get(field: string): any;
+    end(): any;
+    seq_id(): number;
+    _get(field: string): any;
+    _tags(): string[];
+    parent(): undefined;
+    children(): any;
+    id(): number;
+    /**
+     * Mapping quality score.
+     */
+    mq(): number | undefined;
+    score(): any;
+    qual(): string | undefined;
+    qualRaw(): Buffer | undefined;
+    strand(): 1 | -1;
+    multi_segment_next_segment_strand(): 1 | -1 | undefined;
+    name(): any;
+    _read_name(): any;
+    /**
+     * 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?: string): any;
+    _parseAllTags(): void;
+    _parseCigar(cigar: string): (string | number)[][];
+    /**
+     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     */
+    isPaired(): boolean;
+    /** @returns {boolean} true if the read is paired, and both segments are mapped */
+    isProperlyPaired(): boolean;
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isSegmentUnmapped(): boolean;
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isMateUnmapped(): boolean;
+    /** @returns {boolean} true if the read is mapped to the reverse strand */
+    isReverseComplemented(): boolean;
+    /** @returns {boolean} true if the mate is mapped to the reverse strand */
+    isMateReverseComplemented(): boolean;
+    /** @returns {boolean} true if this is read number 1 in a pair */
+    isRead1(): boolean;
+    /** @returns {boolean} true if this is read number 2 in a pair */
+    isRead2(): boolean;
+    /** @returns {boolean} true if this is a secondary alignment */
+    isSecondary(): boolean;
+    /** @returns {boolean} true if this read has failed QC checks */
+    isFailedQc(): boolean;
+    /** @returns {boolean} true if the read is an optical or PCR duplicate */
+    isDuplicate(): boolean;
+    /** @returns {boolean} true if this is a supplementary alignment */
+    isSupplementary(): boolean;
+    cigar(): any;
+    _flags(): void;
+    length_on_ref(): any;
+    _n_cigar_op(): number;
+    _l_read_name(): number;
+    /**
+     * number of bytes in the sequence field
+     */
+    _seq_bytes(): number;
+    getReadBases(): string;
+    seq(): string;
+    getPairOrientation(): string | null;
+    _bin_mq_nl(): any;
+    _flag_nc(): any;
+    seq_length(): any;
+    _next_refid(): any;
+    _next_pos(): any;
+    template_length(): any;
+    toJSON(): {
+        [key: string]: any;
+    };
+}

package/esm/record.js

@@ -0,0 +1,534 @@
+/* eslint-disable @typescript-eslint/no-empty-function */
+import Constants from './constants';
+const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('').map(s => s.charCodeAt(0));
+const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
+/**
+ * Class of each BAM record returned by this API.
+ */
+export default class BamRecord {
+    constructor(args) {
+        this._tagOffset = undefined;
+        this._tagList = [];
+        this._allTagsParsed = false;
+        this.data = {};
+        this.bytes = {
+            start: args.bytes.start,
+            end: args.bytes.end,
+            byteArray: args.bytes.byteArray,
+        };
+        this._id = args.fileOffset;
+        const { start, byteArray } = this.bytes;
+        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());
+    }
+    end() {
+        return (this.get('start') +
+            (this.get('length_on_ref') || this.get('seq_length') || undefined));
+    }
+    seq_id() {
+        return this._refID;
+    }
+    // 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 || []);
+        Object.keys(this.data).forEach(k => {
+            if (k[0] !== '_' && k !== 'next_seq_id') {
+                tags.push(k);
+            }
+        });
+        const seen = {};
+        tags = 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;
+        });
+        return tags;
+    }
+    parent() {
+        return undefined;
+    }
+    children() {
+        return this.get('subfeatures');
+    }
+    id() {
+        return this._id;
+    }
+    // special parsers
+    /**
+     * Mapping quality score.
+     */
+    mq() {
+        const mq = (this.get('_bin_mq_nl') & 0xff00) >> 8;
+        return mq === 255 ? undefined : mq;
+    }
+    score() {
+        return this.get('mq');
+    }
+    qual() {
+        var _a;
+        return (_a = this.qualRaw()) === null || _a === void 0 ? void 0 : _a.join(' ');
+    }
+    qualRaw() {
+        if (this.isSegmentUnmapped()) {
+            return undefined;
+        }
+        const { byteArray } = this.bytes;
+        const p = this.bytes.start +
+            36 +
+            this.get('_l_read_name') +
+            this.get('_n_cigar_op') * 4 +
+            this.get('_seq_bytes');
+        const lseq = this.get('seq_length');
+        const qseq = Buffer.allocUnsafe(lseq);
+        for (let j = 0; j < lseq; ++j) {
+            qseq[j] = byteArray[p + j];
+        }
+        return qseq;
+    }
+    strand() {
+        return this.isReverseComplemented() ? -1 : 1;
+    }
+    multi_segment_next_segment_strand() {
+        if (this.isMateUnmapped()) {
+            return undefined;
+        }
+        return this.isMateReverseComplemented() ? -1 : 1;
+    }
+    name() {
+        return this.get('_read_name');
+    }
+    _read_name() {
+        const nl = this.get('_l_read_name');
+        return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.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.
+     */
+    _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;
+        }
+        const { byteArray } = this.bytes;
+        let p = this._tagOffset ||
+            this.bytes.start +
+                36 +
+                this.get('_l_read_name') +
+                this.get('_n_cigar_op') * 4 +
+                this.get('_seq_bytes') +
+                this.get('seq_length');
+        const blockEnd = this.bytes.end;
+        let lcTag;
+        while (p < blockEnd && lcTag !== tagName) {
+            const tag = String.fromCharCode(byteArray[p], byteArray[p + 1]);
+            lcTag = tag.toLowerCase();
+            const type = String.fromCharCode(byteArray[p + 2]);
+            p += 3;
+            let value;
+            switch (type) {
+                case 'A':
+                    value = String.fromCharCode(byteArray[p]);
+                    p += 1;
+                    break;
+                case 'i':
+                    value = byteArray.readInt32LE(p);
+                    p += 4;
+                    break;
+                case 'I':
+                    value = byteArray.readUInt32LE(p);
+                    p += 4;
+                    break;
+                case 'c':
+                    value = byteArray.readInt8(p);
+                    p += 1;
+                    break;
+                case 'C':
+                    value = byteArray.readUInt8(p);
+                    p += 1;
+                    break;
+                case 's':
+                    value = byteArray.readInt16LE(p);
+                    p += 2;
+                    break;
+                case 'S':
+                    value = byteArray.readUInt16LE(p);
+                    p += 2;
+                    break;
+                case 'f':
+                    value = byteArray.readFloatLE(p);
+                    p += 4;
+                    break;
+                case 'Z':
+                case 'H':
+                    value = '';
+                    while (p <= blockEnd) {
+                        const cc = byteArray[p++];
+                        if (cc === 0) {
+                            break;
+                        }
+                        else {
+                            value += String.fromCharCode(cc);
+                        }
+                    }
+                    break;
+                case 'B': {
+                    value = '';
+                    const cc = byteArray[p++];
+                    const Btype = String.fromCharCode(cc);
+                    const limit = byteArray.readInt32LE(p);
+                    p += 4;
+                    if (Btype === 'i') {
+                        if (tag === 'CG') {
+                            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 (let k = 0; k < limit; k++) {
+                                value += byteArray.readInt32LE(p);
+                                if (k + 1 < limit) {
+                                    value += ',';
+                                }
+                                p += 4;
+                            }
+                        }
+                    }
+                    if (Btype === 'I') {
+                        if (tag === 'CG') {
+                            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 (let k = 0; k < limit; k++) {
+                                value += byteArray.readUInt32LE(p);
+                                if (k + 1 < limit) {
+                                    value += ',';
+                                }
+                                p += 4;
+                            }
+                        }
+                    }
+                    if (Btype === 's') {
+                        for (let k = 0; k < limit; k++) {
+                            value += byteArray.readInt16LE(p);
+                            if (k + 1 < limit) {
+                                value += ',';
+                            }
+                            p += 2;
+                        }
+                    }
+                    if (Btype === 'S') {
+                        for (let k = 0; k < limit; k++) {
+                            value += byteArray.readUInt16LE(p);
+                            if (k + 1 < limit) {
+                                value += ',';
+                            }
+                            p += 2;
+                        }
+                    }
+                    if (Btype === 'c') {
+                        for (let k = 0; k < limit; k++) {
+                            value += byteArray.readInt8(p);
+                            if (k + 1 < limit) {
+                                value += ',';
+                            }
+                            p += 1;
+                        }
+                    }
+                    if (Btype === 'C') {
+                        for (let k = 0; k < limit; k++) {
+                            value += byteArray.readUInt8(p);
+                            if (k + 1 < limit) {
+                                value += ',';
+                            }
+                            p += 1;
+                        }
+                    }
+                    if (Btype === 'f') {
+                        for (let k = 0; k < limit; k++) {
+                            value += byteArray.readFloatLE(p);
+                            if (k + 1 < limit) {
+                                value += ',';
+                            }
+                            p += 4;
+                        }
+                    }
+                    break;
+                }
+                default:
+                    console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
+                    value = undefined;
+                    p = blockEnd; // stop parsing tags
+            }
+            this._tagOffset = p;
+            this._tagList.push(tag);
+            if (lcTag === tagName) {
+                return value;
+            }
+            this.data[lcTag] = value;
+        }
+        this._allTagsParsed = true;
+        return undefined;
+    }
+    _parseAllTags() {
+        this._parseTag('');
+    }
+    _parseCigar(cigar) {
+        return (
+        //@ts-ignore
+        cigar
+            .match(/\d+\D/g)
+            //@ts-ignore
+            .map(op => [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)]));
+    }
+    /**
+     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     */
+    isPaired() {
+        return !!(this.flags & Constants.BAM_FPAIRED);
+    }
+    /** @returns {boolean} true if the read is paired, and both segments are mapped */
+    isProperlyPaired() {
+        return !!(this.flags & Constants.BAM_FPROPER_PAIR);
+    }
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isSegmentUnmapped() {
+        return !!(this.flags & Constants.BAM_FUNMAP);
+    }
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isMateUnmapped() {
+        return !!(this.flags & Constants.BAM_FMUNMAP);
+    }
+    /** @returns {boolean} true if the read is mapped to the reverse strand */
+    isReverseComplemented() {
+        return !!(this.flags & Constants.BAM_FREVERSE);
+    }
+    /** @returns {boolean} true if the mate is mapped to the reverse strand */
+    isMateReverseComplemented() {
+        return !!(this.flags & Constants.BAM_FMREVERSE);
+    }
+    /** @returns {boolean} true if this is read number 1 in a pair */
+    isRead1() {
+        return !!(this.flags & Constants.BAM_FREAD1);
+    }
+    /** @returns {boolean} true if this is read number 2 in a pair */
+    isRead2() {
+        return !!(this.flags & Constants.BAM_FREAD2);
+    }
+    /** @returns {boolean} true if this is a secondary alignment */
+    isSecondary() {
+        return !!(this.flags & Constants.BAM_FSECONDARY);
+    }
+    /** @returns {boolean} true if this read has failed QC checks */
+    isFailedQc() {
+        return !!(this.flags & Constants.BAM_FQCFAIL);
+    }
+    /** @returns {boolean} true if the read is an optical or PCR duplicate */
+    isDuplicate() {
+        return !!(this.flags & Constants.BAM_FDUP);
+    }
+    /** @returns {boolean} true if this is a supplementary alignment */
+    isSupplementary() {
+        return !!(this.flags & Constants.BAM_FSUPPLEMENTARY);
+    }
+    cigar() {
+        if (this.isSegmentUnmapped()) {
+            return undefined;
+        }
+        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);
+        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
+            p += 4;
+            cigop = 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');
+        }
+        else {
+            for (let c = 0; c < numCigarOps; ++c) {
+                cigop = byteArray.readInt32LE(p);
+                lop = cigop >> 4;
+                op = CIGAR_DECODER[cigop & 0xf];
+                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') {
+                    lref += lop;
+                }
+                p += 4;
+            }
+            this.data.length_on_ref = lref;
+            return cigar;
+        }
+    }
+    _flags() { }
+    length_on_ref() {
+        this.get('cigar'); // the length_on_ref is set as a
+        // side effect of the CIGAR parsing
+        return this.data.length_on_ref;
+    }
+    _n_cigar_op() {
+        return this.get('_flag_nc') & 0xffff;
+    }
+    _l_read_name() {
+        return this.get('_bin_mq_nl') & 0xff;
+    }
+    /**
+     * number of bytes in the sequence field
+     */
+    _seq_bytes() {
+        return (this.get('seq_length') + 1) >> 1;
+    }
+    getReadBases() {
+        return this.seq();
+    }
+    seq() {
+        const { byteArray } = this.bytes;
+        const p = this.bytes.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 += String.fromCharCode(SEQRET_DECODER[(sb & 0xf0) >> 4]);
+            i++;
+            if (i < len) {
+                buf += String.fromCharCode(SEQRET_DECODER[sb & 0x0f]);
+                i++;
+            }
+        }
+        return buf;
+    }
+    // adapted from igv.js
+    getPairOrientation() {
+        if (!this.isSegmentUnmapped() &&
+            !this.isMateUnmapped() &&
+            this._refID === this._next_refid()) {
+            const s1 = this.isReverseComplemented() ? 'R' : 'F';
+            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
+            let o1 = ' ';
+            let o2 = ' ';
+            if (this.isRead1()) {
+                o1 = '1';
+                o2 = '2';
+            }
+            else if (this.isRead2()) {
+                o1 = '2';
+                o2 = '1';
+            }
+            const tmp = [];
+            const isize = this.template_length();
+            if (isize > 0) {
+                tmp[0] = s1;
+                tmp[1] = o1;
+                tmp[2] = s2;
+                tmp[3] = o2;
+            }
+            else {
+                tmp[2] = s1;
+                tmp[3] = o1;
+                tmp[0] = s2;
+                tmp[1] = o2;
+            }
+            return tmp.join('');
+        }
+        return null;
+    }
+    _bin_mq_nl() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
+    }
+    _flag_nc() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
+    }
+    seq_length() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
+    }
+    _next_refid() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
+    }
+    _next_pos() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
+    }
+    template_length() {
+        return this.bytes.byteArray.readInt32LE(this.bytes.start + 32);
+    }
+    toJSON() {
+        const data = {};
+        Object.keys(this).forEach(k => {
+            if (k.charAt(0) === '_' || k === 'bytes') {
+                return;
+            }
+            //@ts-ignore
+            data[k] = this[k];
+        });
+        return data;
+    }
+}
+//# sourceMappingURL=record.js.map

package/esm/record.js.map

@@ -0,0 +1 @@
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