@gmod/bam 1.1.8 → 1.1.9

package/esm/bamFile.js.map

@@ -0,0 +1 @@
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package/esm/chunk.d.ts

@@ -0,0 +1,18 @@
+import VirtualOffset from './virtualOffset';
+export default class Chunk {
+    minv: VirtualOffset;
+    maxv: VirtualOffset;
+    bin: number;
+    _fetchedSize?: number;
+    /**
+     * @param {VirtualOffset} minv
+     * @param {VirtualOffset} maxv
+     * @param {number} bin
+     * @param {number} [fetchedSize]
+     */
+    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
+    toUniqueString(): string;
+    toString(): string;
+    compareTo(b: Chunk): number;
+    fetchedSize(): number;
+}

package/esm/chunk.js

@@ -0,0 +1,33 @@
+// little class representing a chunk in the index
+export default class Chunk {
+    /**
+     * @param {VirtualOffset} minv
+     * @param {VirtualOffset} maxv
+     * @param {number} bin
+     * @param {number} [fetchedSize]
+     */
+    constructor(minv, maxv, bin, fetchedSize = undefined) {
+        this.minv = minv;
+        this.maxv = maxv;
+        this.bin = bin;
+        this._fetchedSize = fetchedSize;
+    }
+    toUniqueString() {
+        return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+    }
+    toString() {
+        return this.toUniqueString();
+    }
+    compareTo(b) {
+        return (this.minv.compareTo(b.minv) ||
+            this.maxv.compareTo(b.maxv) ||
+            this.bin - b.bin);
+    }
+    fetchedSize() {
+        if (this._fetchedSize !== undefined) {
+            return this._fetchedSize;
+        }
+        return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
+    }
+}
+//# sourceMappingURL=chunk.js.map

package/esm/chunk.js.map

@@ -0,0 +1 @@
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package/esm/constants.d.ts

@@ -0,0 +1,15 @@
+declare const _default: {
+    BAM_FPAIRED: number;
+    BAM_FPROPER_PAIR: number;
+    BAM_FUNMAP: number;
+    BAM_FMUNMAP: number;
+    BAM_FREVERSE: number;
+    BAM_FMREVERSE: number;
+    BAM_FREAD1: number;
+    BAM_FREAD2: number;
+    BAM_FSECONDARY: number;
+    BAM_FQCFAIL: number;
+    BAM_FDUP: number;
+    BAM_FSUPPLEMENTARY: number;
+};
+export default _default;

package/esm/constants.js

@@ -0,0 +1,27 @@
+export default {
+    //  the read is paired in sequencing, no matter whether it is mapped in a pair
+    BAM_FPAIRED: 1,
+    //  the read is mapped in a proper pair
+    BAM_FPROPER_PAIR: 2,
+    //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+    BAM_FUNMAP: 4,
+    //  the mate is unmapped
+    BAM_FMUNMAP: 8,
+    //  the read is mapped to the reverse strand
+    BAM_FREVERSE: 16,
+    //  the mate is mapped to the reverse strand
+    BAM_FMREVERSE: 32,
+    //  this is read1
+    BAM_FREAD1: 64,
+    //  this is read2
+    BAM_FREAD2: 128,
+    //  not primary alignment
+    BAM_FSECONDARY: 256,
+    //  QC failure
+    BAM_FQCFAIL: 512,
+    //  optical or PCR duplicate
+    BAM_FDUP: 1024,
+    //  supplementary alignment
+    BAM_FSUPPLEMENTARY: 2048,
+};
+//# sourceMappingURL=constants.js.map

package/esm/constants.js.map

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package/esm/csi.d.ts

@@ -0,0 +1,35 @@
+/// <reference types="node" />
+import Chunk from './chunk';
+import { BaseOpts } from './util';
+import IndexFile from './indexFile';
+export default class CSI extends IndexFile {
+    private maxBinNumber;
+    private depth;
+    private minShift;
+    constructor(args: any);
+    lineCount(refId: number): Promise<number>;
+    indexCov(): Promise<never[]>;
+    parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
+        [key: string]: any;
+    };
+    _parseNameBytes(namesBytes: Buffer): {
+        refNameToId: {
+            [key: string]: number;
+        };
+        refIdToName: string[];
+    };
+    _parse(opts: {
+        signal?: AbortSignal;
+    }): Promise<{
+        [key: string]: any;
+    }>;
+    parsePseudoBin(bytes: Buffer, offset: number): {
+        lineCount: number;
+    };
+    blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
+    /**
+     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+     * @returns {Array[number]}
+     */
+    reg2bins(beg: number, end: number): number[][];
+}

package/esm/csi.js

@@ -0,0 +1,209 @@
+import Long from 'long';
+import { unzip } from '@gmod/bgzf-filehandle';
+import VirtualOffset, { fromBytes } from './virtualOffset';
+import Chunk from './chunk';
+import { longToNumber, abortBreakPoint, optimizeChunks } from './util';
+import IndexFile from './indexFile';
+const CSI1_MAGIC = 21582659; // CSI\1
+const CSI2_MAGIC = 38359875; // CSI\2
+function lshift(num, bits) {
+    return num * 2 ** bits;
+}
+function rshift(num, bits) {
+    return Math.floor(num / 2 ** bits);
+}
+export default class CSI extends IndexFile {
+    constructor(args) {
+        super(args);
+        this.maxBinNumber = 0;
+        this.depth = 0;
+        this.minShift = 0;
+    }
+    async lineCount(refId) {
+        const indexData = await this.parse();
+        if (!indexData) {
+            return -1;
+        }
+        const idx = indexData.indices[refId];
+        if (!idx) {
+            return -1;
+        }
+        const { stats } = indexData.indices[refId];
+        if (stats) {
+            return stats.lineCount;
+        }
+        return -1;
+    }
+    async indexCov() {
+        return [];
+    }
+    parseAuxData(bytes, offset, auxLength) {
+        if (auxLength < 30) {
+            return {};
+        }
+        const data = {};
+        data.formatFlags = bytes.readInt32LE(offset);
+        data.coordinateType =
+            data.formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
+        data.format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[data.formatFlags & 0xf];
+        if (!data.format) {
+            throw new Error(`invalid Tabix preset format flags ${data.formatFlags}`);
+        }
+        data.columnNumbers = {
+            ref: bytes.readInt32LE(offset + 4),
+            start: bytes.readInt32LE(offset + 8),
+            end: bytes.readInt32LE(offset + 12),
+        };
+        data.metaValue = bytes.readInt32LE(offset + 16);
+        data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
+        data.skipLines = bytes.readInt32LE(offset + 20);
+        const nameSectionLength = bytes.readInt32LE(offset + 24);
+        Object.assign(data, this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
+        return data;
+    }
+    _parseNameBytes(namesBytes) {
+        let currRefId = 0;
+        let currNameStart = 0;
+        const refIdToName = [];
+        const refNameToId = {};
+        for (let i = 0; i < namesBytes.length; i += 1) {
+            if (!namesBytes[i]) {
+                if (currNameStart < i) {
+                    let refName = namesBytes.toString('utf8', currNameStart, i);
+                    refName = this.renameRefSeq(refName);
+                    refIdToName[currRefId] = refName;
+                    refNameToId[refName] = currRefId;
+                }
+                currNameStart = i + 1;
+                currRefId += 1;
+            }
+        }
+        return { refNameToId, refIdToName };
+    }
+    // fetch and parse the index
+    async _parse(opts) {
+        const data = { csi: true, maxBlockSize: 1 << 16 };
+        const buffer = (await this.filehandle.readFile(opts));
+        const bytes = await unzip(buffer);
+        // check TBI magic numbers
+        if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+            data.csiVersion = 1;
+        }
+        else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+            data.csiVersion = 2;
+        }
+        else {
+            throw new Error('Not a CSI file');
+            // TODO: do we need to support big-endian CSI files?
+        }
+        this.minShift = bytes.readInt32LE(4);
+        this.depth = bytes.readInt32LE(8);
+        this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+        const auxLength = bytes.readInt32LE(12);
+        if (auxLength) {
+            Object.assign(data, this.parseAuxData(bytes, 16, auxLength));
+        }
+        data.refCount = bytes.readInt32LE(16 + auxLength);
+        // read the indexes for each reference sequence
+        data.indices = new Array(data.refCount);
+        let currOffset = 16 + auxLength + 4;
+        for (let i = 0; i < data.refCount; i += 1) {
+            await abortBreakPoint(opts.signal);
+            // the binning index
+            const binCount = bytes.readInt32LE(currOffset);
+            currOffset += 4;
+            const binIndex = {};
+            let stats; // < provided by parsing a pseudo-bin, if present
+            for (let j = 0; j < binCount; j += 1) {
+                const bin = bytes.readUInt32LE(currOffset);
+                if (bin > this.maxBinNumber) {
+                    // this is a fake bin that actually has stats information
+                    // about the reference sequence in it
+                    stats = this.parsePseudoBin(bytes, currOffset + 4);
+                    currOffset += 4 + 8 + 4 + 16 + 16;
+                }
+                else {
+                    const loffset = fromBytes(bytes, currOffset + 4);
+                    this._findFirstData(data, loffset);
+                    const chunkCount = bytes.readInt32LE(currOffset + 12);
+                    currOffset += 16;
+                    const chunks = new Array(chunkCount);
+                    for (let k = 0; k < chunkCount; k += 1) {
+                        const u = fromBytes(bytes, currOffset);
+                        const v = fromBytes(bytes, currOffset + 8);
+                        currOffset += 16;
+                        // this._findFirstData(data, u)
+                        chunks[k] = new Chunk(u, v, bin);
+                    }
+                    binIndex[bin] = chunks;
+                }
+            }
+            data.indices[i] = { binIndex, stats };
+        }
+        return data;
+    }
+    parsePseudoBin(bytes, offset) {
+        // const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
+        // const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
+        // const three = longToNumber(
+        //   Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
+        // )
+        const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
+        return { lineCount };
+    }
+    async blocksForRange(refId, min, max, opts = {}) {
+        if (min < 0) {
+            min = 0;
+        }
+        const indexData = await this.parse(opts);
+        if (!indexData) {
+            return [];
+        }
+        const ba = indexData.indices[refId];
+        if (!ba) {
+            return [];
+        }
+        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        const chunks = [];
+        // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        for (const [start, end] of overlappingBins) {
+            for (let bin = start; bin <= end; bin++) {
+                if (ba.binIndex[bin]) {
+                    const binChunks = ba.binIndex[bin];
+                    for (let c = 0; c < binChunks.length; ++c) {
+                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
+                    }
+                }
+            }
+        }
+        return optimizeChunks(chunks, new VirtualOffset(0, 0));
+    }
+    /**
+     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+     * @returns {Array[number]}
+     */
+    reg2bins(beg, end) {
+        beg -= 1; // < convert to 1-based closed
+        if (beg < 1) {
+            beg = 1;
+        }
+        if (end > 2 ** 50) {
+            end = 2 ** 34;
+        } // 17 GiB ought to be enough for anybody
+        end -= 1;
+        let l = 0;
+        let t = 0;
+        let s = this.minShift + this.depth * 3;
+        const bins = [];
+        for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
+            const b = t + rshift(beg, s);
+            const e = t + rshift(end, s);
+            if (e - b + bins.length > this.maxBinNumber) {
+                throw new Error(`query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
+            }
+            bins.push([b, e]);
+        }
+        return bins;
+    }
+}
+//# sourceMappingURL=csi.js.map

package/esm/csi.js.map

@@ -0,0 +1 @@
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package/esm/errors.d.ts

@@ -0,0 +1,23 @@
+export declare class BamError extends Error {
+}
+/** Error caused by encountering a part of the BAM spec that has not yet been implemented */
+export declare class BamUnimplementedError extends Error {
+}
+/** An error caused by malformed data.  */
+export declare class BamMalformedError extends BamError {
+}
+/**
+ * An error caused by attempting to read beyond the end of the defined data.
+ */
+export declare class BamBufferOverrunError extends BamMalformedError {
+}
+/**
+ * An error caused by data being too big, exceeding a size limit.
+ */
+export declare class BamSizeLimitError extends BamError {
+}
+/**
+ * An invalid argument was supplied to a bam-js method or object.
+ */
+export declare class BamArgumentError extends BamError {
+}

package/esm/errors.js

@@ -0,0 +1,24 @@
+export class BamError extends Error {
+}
+/** Error caused by encountering a part of the BAM spec that has not yet been implemented */
+export class BamUnimplementedError extends Error {
+}
+/** An error caused by malformed data.  */
+export class BamMalformedError extends BamError {
+}
+/**
+ * An error caused by attempting to read beyond the end of the defined data.
+ */
+export class BamBufferOverrunError extends BamMalformedError {
+}
+/**
+ * An error caused by data being too big, exceeding a size limit.
+ */
+export class BamSizeLimitError extends BamError {
+}
+/**
+ * An invalid argument was supplied to a bam-js method or object.
+ */
+export class BamArgumentError extends BamError {
+}
+//# sourceMappingURL=errors.js.map

package/esm/errors.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,QAAS,SAAQ,KAAK;CAAG;AAEtC,4FAA4F;AAC5F,MAAM,OAAO,qBAAsB,SAAQ,KAAK;CAAG;AAEnD,0CAA0C;AAC1C,MAAM,OAAO,iBAAkB,SAAQ,QAAQ;CAAG;AAElD;;GAEG;AACH,MAAM,OAAO,qBAAsB,SAAQ,iBAAiB;CAAG;AAE/D;;GAEG;AACH,MAAM,OAAO,iBAAkB,SAAQ,QAAQ;CAAG;AAElD;;GAEG;AACH,MAAM,OAAO,gBAAiB,SAAQ,QAAQ;CAAG"}

package/esm/htsget.d.ts

@@ -0,0 +1,33 @@
+/// <reference types="node" />
+import { BaseOpts, BamOpts } from './util';
+import BamFile from './bamFile';
+import 'cross-fetch/polyfill';
+import Chunk from './chunk';
+export default class HtsgetFile extends BamFile {
+    private baseUrl;
+    private trackId;
+    constructor(args: {
+        trackId: string;
+        baseUrl: string;
+    });
+    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record").default[], void, unknown>;
+    _readChunk(params: {
+        chunk: {
+            buffer: Buffer;
+            chunk: Chunk;
+        };
+        opts: BaseOpts;
+    }): Promise<{
+        data: Buffer;
+        cpositions: null;
+        dpositions: null;
+        chunk: Chunk;
+    }>;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[]>;
+}

package/esm/htsget.js

@@ -0,0 +1,100 @@
+import BamFile, { BAM_MAGIC } from './bamFile';
+import 'cross-fetch/polyfill';
+import { unzip } from '@gmod/bgzf-filehandle';
+import { parseHeaderText } from './sam';
+async function concat(arr, opts) {
+    const res = await Promise.all(arr.map(async (chunk) => {
+        const { url, headers } = chunk;
+        if (url.startsWith('data:')) {
+            return Buffer.from(url.split(',')[1], 'base64');
+        }
+        else {
+            //remove referer header, it is not even allowed to be specified
+            //@ts-ignore
+            //eslint-disable-next-line @typescript-eslint/no-unused-vars
+            const { referer, ...rest } = headers;
+            const res = await fetch(url, {
+                ...opts,
+                headers: { ...opts.headers, ...rest },
+            });
+            if (!res.ok) {
+                throw new Error(`Failed to fetch ${res.statusText}`);
+            }
+            return Buffer.from(await res.arrayBuffer());
+        }
+    }));
+    return Buffer.concat(await Promise.all(res.map(elt => unzip(elt))));
+}
+export default class HtsgetFile extends BamFile {
+    constructor(args) {
+        // @ts-ignore override bam defaults
+        super({ bamFilehandle: '?', baiFilehandle: '?' });
+        this.baseUrl = args.baseUrl;
+        this.trackId = args.trackId;
+    }
+    async *streamRecordsForRange(chr, min, max, opts = {
+        viewAsPairs: false,
+        pairAcrossChr: false,
+        maxInsertSize: 200000,
+    }) {
+        const base = `${this.baseUrl}/${this.trackId}`;
+        const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
+        const chrId = this.chrToIndex && this.chrToIndex[chr];
+        const result = await fetch(url, { ...opts });
+        if (!result.ok) {
+            throw new Error(result.statusText);
+        }
+        const data = await result.json();
+        const uncba = await concat(data.htsget.urls.slice(1), opts);
+        const chunk = {
+            buffer: uncba,
+            chunk: { minv: { dataPosition: 0 } },
+            toString() {
+                return `${chr}_${min}_${max}`;
+            },
+        };
+        yield* this._fetchChunkFeatures(
+        // @ts-ignore
+        [chunk], chrId, min, max, opts);
+    }
+    //@ts-ignore
+    async _readChunk(params) {
+        const { chunk } = params;
+        const { buffer, chunk: c2 } = chunk;
+        return { data: buffer, cpositions: null, dpositions: null, chunk: c2 };
+    }
+    async getHeader(opts = {}) {
+        const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
+        const result = await fetch(url, opts);
+        if (!result.ok) {
+            throw new Error(`Failed to fetch ${result.statusText}`);
+        }
+        const data = await result.json();
+        const uncba = await concat(data.htsget.urls, opts);
+        if (uncba.readInt32LE(0) !== BAM_MAGIC) {
+            throw new Error('Not a BAM file');
+        }
+        const headLen = uncba.readInt32LE(4);
+        const headerText = uncba.toString('utf8', 8, 8 + headLen);
+        const samHeader = parseHeaderText(headerText);
+        // use the @SQ lines in the header to figure out the
+        // mapping between ref ref ID numbers and names
+        const idToName = [];
+        const nameToId = {};
+        const sqLines = samHeader.filter((l) => l.tag === 'SQ');
+        sqLines.forEach((sqLine, refId) => {
+            sqLine.data.forEach((item) => {
+                if (item.tag === 'SN') {
+                    // this is the ref name
+                    const refName = item.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
+            });
+        });
+        this.chrToIndex = nameToId;
+        this.indexToChr = idToName;
+        return samHeader;
+    }
+}
+//# sourceMappingURL=htsget.js.map

package/esm/htsget.js.map

@@ -0,0 +1 @@
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package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import BAI from './bai';
+import CSI from './csi';
+import BamFile from './bamFile';
+import HtsgetFile from './htsget';
+import BamRecord from './record';
+export { BAI, CSI, BamFile, BamRecord, HtsgetFile };

package/esm/index.js

@@ -0,0 +1,7 @@
+import BAI from './bai';
+import CSI from './csi';
+import BamFile from './bamFile';
+import HtsgetFile from './htsget';
+import BamRecord from './record';
+export { BAI, CSI, BamFile, BamRecord, HtsgetFile };
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,OAAO,MAAM,WAAW,CAAA;AAC/B,OAAO,UAAU,MAAM,UAAU,CAAA;AACjC,OAAO,SAAS,MAAM,UAAU,CAAA;AAEhC,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,CAAA"}

package/esm/indexFile.d.ts

@@ -0,0 +1,27 @@
+import { GenericFilehandle } from 'generic-filehandle';
+import VirtualOffset from './virtualOffset';
+import Chunk from './chunk';
+import { BaseOpts } from './util';
+export default abstract class IndexFile {
+    filehandle: GenericFilehandle;
+    renameRefSeq: (s: string) => string;
+    /**
+     * @param {filehandle} filehandle
+     * @param {function} [renameRefSeqs]
+     */
+    constructor({ filehandle, renameRefSeq, }: {
+        filehandle: GenericFilehandle;
+        renameRefSeq?: (a: string) => string;
+    });
+    abstract lineCount(refId: number): Promise<number>;
+    protected abstract _parse(opts?: BaseOpts): Promise<any>;
+    abstract indexCov(refId: number, start?: number, end?: number): Promise<{
+        start: number;
+        end: number;
+        score: number;
+    }[]>;
+    abstract blocksForRange(chrId: number, start: number, end: number, opts: BaseOpts): Promise<Chunk[]>;
+    _findFirstData(data: any, virtualOffset: VirtualOffset): void;
+    parse(opts?: BaseOpts): Promise<any>;
+    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
+}