@gmod/cram 1.5.9 → 1.6.2

package/esm/cramFile/file.d.ts

@@ -0,0 +1,63 @@
+export default class CramFile {
+    /**
+     * @param {object} args
+     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
+     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
+     * @param {object} [args.path] - path to the cram file
+     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
+     * @param {function} [args.seqFetch] - a function with signature
+     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
+     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
+     */
+    constructor(args: {
+        filehandle?: object | undefined;
+        path?: object | undefined;
+        url?: object | undefined;
+        seqFetch?: Function | undefined;
+        cacheSize?: number | undefined;
+        checkSequenceMD5?: boolean | undefined;
+    });
+    file: any;
+    validateChecksums: boolean;
+    fetchReferenceSequenceCallback: Function | undefined;
+    options: {
+        checkSequenceMD5: boolean;
+        cacheSize: number;
+    };
+    featureCache: any;
+    toString(): any;
+    read(buffer: any, offset: any, length: any, position: any): any;
+    stat(): any;
+    getDefinition(): Promise<any>;
+    getSamHeader(): Promise<any[]>;
+    header: any;
+    getHeaderText(): Promise<any>;
+    getSectionParsers(): Promise<{
+        cramFileDefinition: {
+            parser: any;
+            maxLength: number;
+        };
+        cramBlockHeader: {
+            parser: any;
+            maxLength: number;
+        };
+        cramBlockCrc32: {
+            parser: any;
+            maxLength: number;
+        };
+    }>;
+    getContainerById(containerNumber: any): Promise<CramContainer | undefined>;
+    checkCrc32(position: any, length: any, recordedCrc32: any, description: any): Promise<void>;
+    /**
+     * @returns {Promise[number]} the number of containers in the file
+     */
+    containerCount(): any;
+    getContainerAtPosition(position: any): CramContainer;
+    readBlockHeader(position: any): Promise<any>;
+    _parseSection(section: any, position: any, size: any, preReadBuffer: any): Promise<any>;
+    _uncompress(compressionMethod: any, inputBuffer: any, outputBuffer: any): void;
+    readBlock(position: any): Promise<any>;
+}
+import CramContainer from "./container";

package/esm/cramFile/file.js

@@ -0,0 +1,281 @@
+import { unzip } from '../unzip';
+import crc32 from 'buffer-crc32';
+import LRU from 'quick-lru';
+import { CramUnimplementedError, CramMalformedError } from '../errors';
+import ransuncompress from '../rans';
+import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';
+import htscodecs from '@jkbonfield/htscodecs';
+import CramContainer from './container';
+import { open } from '../io';
+import { parseItem, tinyMemoize } from './util';
+import { parseHeaderText } from '../sam';
+export default class CramFile {
+    /**
+     * @param {object} args
+     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
+     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
+     * @param {object} [args.path] - path to the cram file
+     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
+     * @param {function} [args.seqFetch] - a function with signature
+     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
+     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
+     */
+    constructor(args) {
+        this.file = open(args.url, args.path, args.filehandle);
+        this.validateChecksums = true;
+        this.fetchReferenceSequenceCallback = args.seqFetch;
+        this.options = {
+            checkSequenceMD5: args.checkSequenceMD5 !== false,
+            cacheSize: args.cacheSize !== undefined ? args.cacheSize : 20000,
+        };
+        // cache of features in a slice, keyed by the
+        // slice offset. caches all of the features in a slice, or none.
+        // the cache is actually used by the slice object, it's just
+        // kept here at the level of the file
+        this.featureCache = new LRU({
+            maxSize: this.options.cacheSize,
+        });
+    }
+    toString() {
+        if (this.file.filename) {
+            return this.file.filename;
+        }
+        if (this.file.url) {
+            return this.file.url;
+        }
+        return '(cram file)';
+    }
+    // can just read this object like a filehandle
+    read(buffer, offset, length, position) {
+        return this.file.read(buffer, offset, length, position);
+    }
+    // can just stat this object like a filehandle
+    stat() {
+        return this.file.stat();
+    }
+    // memoized
+    async getDefinition() {
+        const headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength);
+        await this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0);
+        const definition = cramFileDefinitionParser.parser.parse(headbytes).result;
+        if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
+            throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
+        }
+        return definition;
+    }
+    // memoize
+    async getSamHeader() {
+        const firstContainer = await this.getContainerById(0);
+        if (!firstContainer) {
+            throw new CramMalformedError('file contains no containers');
+        }
+        const { content } = await firstContainer.getFirstBlock();
+        // find the end of the trailing zeros in the header text
+        const headerLength = content.readInt32LE(0);
+        const textStart = 4;
+        // let textEnd = content.length - 1
+        // while (textEnd >= textStart && !content[textEnd]) textEnd -= 1
+        // trim off the trailing zeros
+        const text = content.toString('utf8', textStart, textStart + headerLength);
+        this.header = text;
+        return parseHeaderText(text);
+    }
+    async getHeaderText() {
+        await this.getSamHeader();
+        return this.header;
+    }
+    // memoize
+    async getSectionParsers() {
+        const { majorVersion } = await this.getDefinition();
+        return getSectionParsers(majorVersion);
+    }
+    async getContainerById(containerNumber) {
+        const sectionParsers = await this.getSectionParsers();
+        let position = sectionParsers.cramFileDefinition.maxLength;
+        const { size: fileSize } = await this.file.stat();
+        const { cramContainerHeader1 } = sectionParsers;
+        // skip with a series of reads to the proper container
+        let currentContainer;
+        for (let i = 0; i <= containerNumber; i += 1) {
+            // if we are about to go off the end of the file
+            // and have not found that container, it does not exist
+            if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
+                return undefined;
+            }
+            currentContainer = this.getContainerAtPosition(position);
+            const currentHeader = await currentContainer.getHeader();
+            if (!currentHeader) {
+                throw new CramMalformedError(`container ${containerNumber} not found in file`);
+            }
+            // if this is the first container, read all the blocks in the
+            // container to determine its length, because we cannot trust
+            // the container header's given length due to a bug somewhere
+            // in htslib
+            if (i === 0) {
+                position = currentHeader._endPosition;
+                for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    const block = await this.readBlock(position);
+                    position = block._endPosition;
+                }
+            }
+            else {
+                // otherwise, just traverse to the next container using the container's length
+                position += currentHeader._size + currentHeader.length;
+            }
+        }
+        return currentContainer;
+    }
+    async checkCrc32(position, length, recordedCrc32, description) {
+        const b = Buffer.allocUnsafe(length);
+        await this.file.read(b, 0, length, position);
+        const calculatedCrc32 = crc32.unsigned(b);
+        if (calculatedCrc32 !== recordedCrc32) {
+            throw new CramMalformedError(`crc mismatch in ${description}: recorded CRC32 = ${recordedCrc32}, but calculated CRC32 = ${calculatedCrc32}`);
+        }
+    }
+    /**
+     * @returns {Promise[number]} the number of containers in the file
+     */
+    async containerCount() {
+        const sectionParsers = await this.getSectionParsers();
+        const { size: fileSize } = await this.file.stat();
+        const { cramContainerHeader1 } = sectionParsers;
+        let containerCount = 0;
+        let position = sectionParsers.cramFileDefinition.maxLength;
+        while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
+            const currentHeader = await this.getContainerAtPosition(position).getHeader();
+            if (!currentHeader) {
+                break;
+            }
+            // if this is the first container, read all the blocks in the
+            // container, because we cannot trust the container
+            // header's given length due to a bug somewhere in htslib
+            if (containerCount === 0) {
+                position = currentHeader._endPosition;
+                for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    const block = await this.readBlock(position);
+                    position = block._endPosition;
+                }
+            }
+            else {
+                // otherwise, just traverse to the next container using the container's length
+                position += currentHeader._size + currentHeader.length;
+            }
+            containerCount += 1;
+        }
+        return containerCount;
+    }
+    getContainerAtPosition(position) {
+        return new CramContainer(this, position);
+    }
+    async readBlockHeader(position) {
+        const sectionParsers = await this.getSectionParsers();
+        const { cramBlockHeader } = sectionParsers;
+        const { size: fileSize } = await this.file.stat();
+        if (position + cramBlockHeader.maxLength >= fileSize) {
+            return undefined;
+        }
+        const buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
+        await this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
+        return parseItem(buffer, cramBlockHeader.parser, 0, position);
+    }
+    async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
+        let buffer;
+        if (preReadBuffer) {
+            buffer = preReadBuffer;
+        }
+        else {
+            const { size: fileSize } = await this.file.stat();
+            if (position + size >= fileSize) {
+                return undefined;
+            }
+            buffer = Buffer.allocUnsafe(size);
+            await this.file.read(buffer, 0, size, position);
+        }
+        const data = parseItem(buffer, section.parser, 0, position);
+        if (data._size !== size) {
+            throw new CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
+        }
+        return data;
+    }
+    _uncompress(compressionMethod, inputBuffer, outputBuffer) {
+        if (compressionMethod === 'gzip') {
+            const result = unzip(inputBuffer);
+            result.copy(outputBuffer);
+        }
+        else if (compressionMethod === 'bzip2') {
+            var bits = bzip2.array(inputBuffer);
+            var size = bzip2.header(bits);
+            var j = 0;
+            do {
+                var chunk = bzip2.decompress(bits, size);
+                if (chunk != -1) {
+                    Buffer.from(chunk).copy(outputBuffer, j);
+                    j += chunk.length;
+                    size -= chunk.length;
+                }
+            } while (chunk != -1);
+        }
+        else if (compressionMethod === 'rans') {
+            ransuncompress(inputBuffer, outputBuffer);
+            //htscodecs r4x8 is slower, but compatible.
+            //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'rans4x16') {
+            htscodecs.r4x16_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'arith') {
+            htscodecs.arith_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'fqzcomp') {
+            htscodecs.fqzcomp_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'tok3') {
+            htscodecs.tok3_uncompress(inputBuffer, outputBuffer);
+        }
+        else {
+            throw new CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
+        }
+    }
+    async readBlock(position) {
+        const { majorVersion } = await this.getDefinition();
+        const sectionParsers = await this.getSectionParsers();
+        const block = await this.readBlockHeader(position);
+        const blockContentPosition = block._endPosition;
+        block.contentPosition = block._endPosition;
+        const uncompressedData = Buffer.allocUnsafe(block.uncompressedSize);
+        if (block.compressionMethod !== 'raw') {
+            const compressedData = Buffer.allocUnsafe(block.compressedSize);
+            await this.read(compressedData, 0, block.compressedSize, blockContentPosition);
+            this._uncompress(block.compressionMethod, compressedData, uncompressedData);
+        }
+        else {
+            await this.read(uncompressedData, 0, block.uncompressedSize, blockContentPosition);
+        }
+        block.content = uncompressedData;
+        if (majorVersion >= 3) {
+            // parse the crc32
+            const crc = await this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + block.compressedSize);
+            block.crc32 = crc.crc32;
+            // check the block data crc32
+            if (this.validateChecksums) {
+                await this.checkCrc32(position, block._size + block.compressedSize, block.crc32, 'block data');
+            }
+            // make the endposition and size reflect the whole block
+            block._endPosition = crc._endPosition;
+            block._size =
+                block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
+        }
+        else {
+            block._endPosition = blockContentPosition + block.compressedSize;
+            block._size = block.compressedSize;
+        }
+        return block;
+    }
+}
+'getDefinition getSectionParsers getSamHeader'
+    .split(' ')
+    .forEach(method => tinyMemoize(CramFile, method));
+//# sourceMappingURL=file.js.map

package/esm/cramFile/file.js.map

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

@@ -0,0 +1,2 @@
+export default CramFile;
+import CramFile from "./file";

package/esm/cramFile/index.js

@@ -0,0 +1,3 @@
+import CramFile from './file';
+export default CramFile;
+//# sourceMappingURL=index.js.map

package/esm/cramFile/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.js"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,QAAQ,CAAA;AAE7B,eAAe,QAAQ,CAAA"}

package/esm/cramFile/record.d.ts

@@ -0,0 +1,79 @@
+/**
+ * Class of each CRAM record returned by this API.
+ */
+export default class CramRecord {
+    tags: {};
+    /**
+     * @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;
+    /**
+     * @returns {boolean} true if the read is detached
+     */
+    isDetached(): boolean;
+    /** @returns {boolean} true if the read has a mate in this same CRAM segment */
+    hasMateDownStream(): boolean;
+    /** @returns {boolean} true if the read contains qual scores */
+    isPreservingQualityScores(): boolean;
+    /** @returns {boolean} true if the read has no sequence bases */
+    isUnknownBases(): boolean;
+    /**
+     * Get the original sequence of this read.
+     * @returns {String} sequence basepairs
+     */
+    getReadBases(): string;
+    readBases: any;
+    /**
+     * Get the pair orientation of a paired read. Adapted from igv.js
+     * @returns {String} of paired orientatin
+     */
+    getPairOrientation(): string;
+    /**
+     * Annotates this feature with the given reference sequence basepair
+     * information. This will add a `sub` and a `ref` item to base
+     * subsitution read features given the actual substituted and reference
+     * base pairs, and will make the `getReadSequence()` method work.
+     *
+     * @param {object} refRegion
+     * @param {number} refRegion.start
+     * @param {number} refRegion.end
+     * @param {string} refRegion.seq
+     * @param {CramContainerCompressionScheme} compressionScheme
+     * @returns {undefined} nothing
+     */
+    addReferenceSequence(refRegion: {
+        start: number;
+        end: number;
+        seq: string;
+    }, compressionScheme: CramContainerCompressionScheme): undefined;
+    _refRegion: {
+        start: number;
+        end: number;
+        seq: string;
+    } | undefined;
+    toJSON(): {
+        readBases: string;
+    };
+}