@gmod/cram 1.5.9 → 1.6.2

package/esm/cramFile/record.js

@@ -0,0 +1,297 @@
+import Constants from './constants';
+function decodeReadSequence(cramRecord, refRegion) {
+    // if it has no length, it has no sequence
+    if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
+        return undefined;
+    }
+    if (cramRecord.isUnknownBases()) {
+        return undefined;
+    }
+    // remember: all coordinates are 1-based closed
+    const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
+    if (!cramRecord.readFeatures) {
+        return refRegion.seq
+            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .toUpperCase();
+    }
+    let bases = '';
+    let regionPos = regionSeqOffset;
+    let currentReadFeature = 0;
+    while (bases.length < cramRecord.readLength) {
+        if (currentReadFeature < cramRecord.readFeatures.length) {
+            const feature = cramRecord.readFeatures[currentReadFeature];
+            if (feature.code === 'Q' || feature.code === 'q') {
+                currentReadFeature += 1;
+            }
+            else if (feature.pos === bases.length + 1) {
+                // process the read feature
+                currentReadFeature += 1;
+                if (feature.code === 'b') {
+                    // specify a base pair for some reason
+                    const ret = feature.data.split(',');
+                    const added = String.fromCharCode(...ret);
+                    bases += added;
+                    regionPos += added.length;
+                }
+                else if (feature.code === 'B') {
+                    // base pair and associated quality
+                    // TODO: do we need to set the quality in the qual scores?
+                    bases += feature.data[0];
+                    regionPos += 1;
+                }
+                else if (feature.code === 'X') {
+                    // base substitution
+                    bases += feature.sub;
+                    regionPos += 1;
+                }
+                else if (feature.code === 'I') {
+                    // insertion
+                    bases += feature.data;
+                }
+                else if (feature.code === 'D') {
+                    // deletion
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'i') {
+                    // insert single base
+                    bases += feature.data;
+                }
+                else if (feature.code === 'N') {
+                    // reference skip. delete some bases
+                    // do nothing
+                    // seqBases.splice(feature.pos - 1, feature.data)
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'S') {
+                    // soft clipped bases that should be present in the read seq
+                    // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
+                    bases += feature.data;
+                }
+                else if (feature.code === 'P') {
+                    // padding, do nothing
+                }
+                else if (feature.code === 'H') {
+                    // hard clip, do nothing
+                }
+            }
+            else if (currentReadFeature < cramRecord.readFeatures.length) {
+                // put down a chunk of sequence up to the next read feature
+                const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                bases += chunk;
+                regionPos += chunk.length;
+            }
+        }
+        else {
+            // put down a chunk of reference up to the full read length
+            const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            bases += chunk;
+            regionPos += chunk.length;
+        }
+    }
+    return bases.toUpperCase();
+}
+const baseNumbers = {
+    a: 0,
+    A: 0,
+    c: 1,
+    C: 1,
+    g: 2,
+    G: 2,
+    t: 3,
+    T: 3,
+    n: 4,
+    N: 4,
+};
+function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
+    if (!refRegion) {
+        return;
+    }
+    // decode base substitution code using the substitution matrix
+    const refCoord = readFeature.refPos - refRegion.start;
+    const refBase = refRegion.seq.charAt(refCoord);
+    if (refBase) {
+        readFeature.ref = refBase;
+    }
+    let baseNumber = baseNumbers[refBase];
+    if (baseNumber === undefined) {
+        baseNumber = 4;
+    }
+    const substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
+    const base = substitutionScheme[readFeature.data];
+    if (base) {
+        readFeature.sub = base;
+    }
+}
+/**
+ * Class of each CRAM record returned by this API.
+ */
+export default class CramRecord {
+    constructor() {
+        this.tags = {};
+    }
+    /**
+     * @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);
+    }
+    /**
+     * @returns {boolean} true if the read is detached
+     */
+    isDetached() {
+        return !!(this.cramFlags & Constants.CRAM_FLAG_DETACHED);
+    }
+    /** @returns {boolean} true if the read has a mate in this same CRAM segment */
+    hasMateDownStream() {
+        return !!(this.cramFlags & Constants.CRAM_FLAG_MATE_DOWNSTREAM);
+    }
+    /** @returns {boolean} true if the read contains qual scores */
+    isPreservingQualityScores() {
+        return !!(this.cramFlags & Constants.CRAM_FLAG_PRESERVE_QUAL_SCORES);
+    }
+    /** @returns {boolean} true if the read has no sequence bases */
+    isUnknownBases() {
+        return !!(this.cramFlags & Constants.CRAM_FLAG_NO_SEQ);
+    }
+    /**
+     * Get the original sequence of this read.
+     * @returns {String} sequence basepairs
+     */
+    getReadBases() {
+        if (!this.readBases && this._refRegion) {
+            this.readBases = decodeReadSequence(this, this._refRegion);
+        }
+        return this.readBases;
+    }
+    /**
+     * Get the pair orientation of a paired read. Adapted from igv.js
+     * @returns {String} of paired orientatin
+     */
+    getPairOrientation() {
+        if (!this.isSegmentUnmapped() &&
+            this.isPaired() &&
+            !this.isMateUnmapped() &&
+            this.mate &&
+            this.sequenceId === this.mate.sequenceId) {
+            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 = [];
+            let isize = this.templateLength || this.templateSize;
+            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
+                isize = -isize;
+            }
+            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;
+    }
+    /**
+     * 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, compressionScheme) {
+        if (this.readFeatures) {
+            // use the reference bases to decode the bases
+            // substituted in each base substitution
+            this.readFeatures.forEach(readFeature => {
+                if (readFeature.code === 'X') {
+                    decodeBaseSubstitution(this, refRegion, compressionScheme, readFeature);
+                }
+            });
+        }
+        // if this region completely covers this read,
+        // keep a reference to it
+        if (!this.readBases &&
+            refRegion.start <= this.alignmentStart &&
+            refRegion.end >=
+                this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
+            this._refRegion = refRegion;
+        }
+    }
+    toJSON() {
+        const data = {};
+        Object.keys(this).forEach(k => {
+            if (k.charAt(0) === '_') {
+                return;
+            }
+            data[k] = this[k];
+        });
+        data.readBases = this.getReadBases();
+        return data;
+    }
+}
+//# sourceMappingURL=record.js.map

package/esm/cramFile/record.js.map

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

@@ -0,0 +1,18 @@
+export namespace cramFileDefinition {
+    const parser: any;
+    const maxLength: number;
+}
+export function getSectionParsers(majorVersion: any): {
+    cramFileDefinition: {
+        parser: any;
+        maxLength: number;
+    };
+    cramBlockHeader: {
+        parser: any;
+        maxLength: number;
+    };
+    cramBlockCrc32: {
+        parser: any;
+        maxLength: number;
+    };
+};

package/esm/cramFile/sectionParsers.js

@@ -0,0 +1,347 @@
+import { Parser } from '@gmod/binary-parser';
+const singleItf8 = new Parser().itf8();
+const cramFileDefinition = {
+    parser: new Parser()
+        .string('magic', { length: 4 })
+        .uint8('majorVersion')
+        .uint8('minorVersion')
+        .string('fileId', { length: 20, stripNull: true }),
+    maxLength: 26,
+};
+const cramBlockHeader = {
+    parser: new Parser()
+        .uint8('compressionMethod', {
+        formatter: /* istanbul ignore next */ /* istanbul ignore next */ b => {
+            const method = [
+                'raw',
+                'gzip',
+                'bzip2',
+                'lzma',
+                'rans',
+                'rans4x16',
+                'arith',
+                'fqzcomp',
+                'tok3',
+            ][b];
+            if (!method) {
+                throw new Error(`compression method number ${b} not implemented`);
+            }
+            return method;
+        },
+    })
+        .uint8('contentType', {
+        formatter: /* istanbul ignore next */ /* istanbul ignore next */ b => {
+            const type = [
+                'FILE_HEADER',
+                'COMPRESSION_HEADER',
+                'MAPPED_SLICE_HEADER',
+                'UNMAPPED_SLICE_HEADER',
+                'EXTERNAL_DATA',
+                'CORE_DATA',
+            ][b];
+            if (!type) {
+                throw new Error(`invalid block content type id ${b}`);
+            }
+            return type;
+        },
+    })
+        .itf8('contentId')
+        .itf8('compressedSize')
+        .itf8('uncompressedSize'),
+    maxLength: 17,
+};
+const cramBlockCrc32 = {
+    parser: new Parser().uint32('crc32'),
+    maxLength: 4,
+};
+// const ENCODING_NAMES = [
+//   'NULL', // 0
+//   'EXTERNAL', // 1
+//   'GOLOMB', // 2
+//   'HUFFMAN_INT', // 3
+//   'BYTE_ARRAY_LEN', // 4
+//   'BYTE_ARRAY_STOP', // 5
+//   'BETA', // 6
+//   'SUBEXP', // 7
+//   'GOLOMB_RICE', // 8
+//   'GAMMA', // 9
+// ]
+const cramTagDictionary = new Parser().itf8('size').buffer('ents', {
+    length: 'size',
+    formatter: /* istanbul ignore next */ /* istanbul ignore next */ buffer => {
+        function makeTagSet(stringStart, stringEnd) {
+            const str = buffer.toString('utf8', stringStart, stringEnd);
+            const tags = [];
+            for (let i = 0; i < str.length; i += 3) {
+                tags.push(str.substr(i, 3));
+            }
+            return tags;
+        }
+        /* eslint-disable */
+        var tagSets = [];
+        var stringStart = 0;
+        var i;
+        /* eslint-enable */
+        for (i = 0; i < buffer.length; i += 1) {
+            if (!buffer[i]) {
+                tagSets.push(makeTagSet(stringStart, i));
+                stringStart = i + 1;
+            }
+        }
+        if (i > stringStart) {
+            tagSets.push(makeTagSet(stringStart, i));
+        }
+        return tagSets;
+    },
+});
+// const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
+const parseByteAsBool = new Parser().uint8(null, {
+    formatter: /* istanbul ignore next */ /* istanbul ignore next */ val => !!val,
+});
+const cramPreservationMap = new Parser()
+    .itf8('mapSize')
+    .itf8('mapCount')
+    .array('ents', {
+    length: 'mapCount',
+    type: new Parser()
+        .string('key', {
+        length: 2,
+        stripNull: false,
+        // formatter: val => cramPreservationMapKeys[val] || 0,
+    })
+        .choice('value', {
+        tag: 'key',
+        choices: {
+            MI: parseByteAsBool,
+            UI: parseByteAsBool,
+            PI: parseByteAsBool,
+            RN: parseByteAsBool,
+            AP: parseByteAsBool,
+            RR: parseByteAsBool,
+            SM: new Parser().array(null, { type: 'uint8', length: 5 }),
+            TD: new Parser().nest(null, {
+                type: cramTagDictionary,
+                formatter: /* istanbul ignore next */ /* istanbul ignore next */ data => data.ents,
+            }),
+        },
+    }),
+});
+/* istanbul ignore next */
+function formatMap(data) {
+    const map = {};
+    for (let i = 0; i < data.ents.length; i += 1) {
+        const { key, value } = data.ents[i];
+        if (map[key]) {
+            console.warn(`duplicate key ${key} in map`);
+        }
+        map[key] = value;
+    }
+    return map;
+}
+const unversionedParsers = {
+    cramFileDefinition,
+    cramBlockHeader,
+    cramBlockCrc32,
+};
+// each of these is a function of the major and minor version
+const versionedParsers = {
+    // assemble a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramUnmappedSliceHeader(majorVersion) {
+        let maxLength = 0;
+        let parser = new Parser().itf8('numRecords');
+        maxLength += 5;
+        // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        });
+        maxLength += 5 * 2; // + numContentIds*5
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        const maxLengthFunc = numContentIds => maxLength + numContentIds * 5;
+        return { parser, maxLength: maxLengthFunc }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
+    },
+    // assembles a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramMappedSliceHeader(majorVersion) {
+        let parser = new Parser()
+            .itf8('refSeqId')
+            .itf8('refSeqStart')
+            .itf8('refSeqSpan')
+            .itf8('numRecords');
+        let maxLength = 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        })
+            .itf8('refBaseBlockId');
+        maxLength += 5 * 3;
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        const maxLengthFunc = numContentIds => maxLength + numContentIds * 5;
+        return { parser, maxLength: maxLengthFunc };
+    },
+    cramEncoding(majorVersion) {
+        const parser = new Parser()
+            .namely('cramEncoding')
+            .itf8('codecId')
+            .itf8('parametersBytes')
+            .choice('parameters', {
+            tag: 'codecId',
+            choices: {
+                0: new Parser(),
+                1: new Parser().itf8('blockContentId'),
+                2: new Parser().itf8('offset').itf8('M'),
+                // HUFFMAN_INT
+                3: Parser.start()
+                    .itf8('numCodes')
+                    .array('symbols', { length: 'numCodes', type: singleItf8 })
+                    .itf8('numLengths')
+                    .array('bitLengths', { length: 'numLengths', type: singleItf8 }),
+                4: Parser.start() // BYTE_ARRAY_LEN
+                    .nest('lengthsEncoding', { type: 'cramEncoding' })
+                    .nest('valuesEncoding', { type: 'cramEncoding' }),
+                // BYTE_ARRAY_STOP is a little different for CRAM v1
+                5: new Parser()
+                    .uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
+                6: new Parser().itf8('offset').itf8('length'),
+                7: new Parser().itf8('offset').itf8('K'),
+                8: new Parser().itf8('offset').itf8('log2m'),
+                9: new Parser().itf8('offset'), // GAMMA
+            },
+        });
+        return { parser };
+    },
+    cramDataSeriesEncodingMap(majorVersion) {
+        return new Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new Parser()
+                .string('key', { length: 2, stripNull: false })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramTagEncodingMap(majorVersion) {
+        return new Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new Parser()
+                .itf8('key', {
+                formatter: /* istanbul ignore next */ /* istanbul ignore next */ integerRepresentation => 
+                /* istanbul ignore next */
+                String.fromCharCode((integerRepresentation >> 16) & 0xff) +
+                    String.fromCharCode((integerRepresentation >> 8) & 0xff) +
+                    String.fromCharCode(integerRepresentation & 0xff),
+            })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramCompressionHeader(majorVersion) {
+        let parser = new Parser();
+        // TODO: if we want to support CRAM v1, we will need to refactor
+        // compression header into 2 parts to parse the landmarks,
+        // like the container header
+        parser = parser
+            .nest('preservation', {
+            type: cramPreservationMap,
+            formatter: formatMap,
+        })
+            .nest('dataSeriesEncoding', {
+            type: this.cramDataSeriesEncodingMap(majorVersion),
+            formatter: formatMap,
+        })
+            .nest('tagEncoding', {
+            type: this.cramTagEncodingMap(majorVersion),
+            formatter: formatMap,
+        });
+        return { parser };
+    },
+    cramContainerHeader1(majorVersion) {
+        let parser = new Parser()
+            .int32('length') // byte size of the container data (blocks)
+            .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
+            .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
+            .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
+            .itf8('numRecords'); // number of records in the container
+        let maxLength = 4 + 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        if (majorVersion > 1) {
+            parser = parser.ltf8('numBases'); // number of read bases
+            maxLength += 9;
+        }
+        parser = parser
+            .itf8('numBlocks') // the number of blocks
+            .itf8('numLandmarks'); // the number of landmarks
+        maxLength += 5 + 5;
+        return { parser, maxLength };
+    },
+    cramContainerHeader2(majorVersion) {
+        let parser = new Parser()
+            .itf8('numLandmarks') // the number of blocks
+            // Each integer value of this array is a byte offset
+            // into the blocks byte array. Landmarks are used for
+            // random access indexing.
+            .array('landmarks', {
+            type: new Parser().itf8(),
+            length: 'numLandmarks',
+        });
+        let crcLength = 0;
+        if (majorVersion >= 3) {
+            parser = parser.uint32('crc32');
+            crcLength = 4;
+        }
+        return {
+            parser,
+            maxLength: numLandmarks => 5 + numLandmarks * 5 + crcLength,
+        };
+    },
+};
+function getSectionParsers(majorVersion) {
+    const parsers = Object.assign({}, unversionedParsers);
+    Object.keys(versionedParsers).forEach(parserName => {
+        parsers[parserName] = versionedParsers[parserName](majorVersion);
+    });
+    return parsers;
+}
+export { cramFileDefinition, getSectionParsers };
+//# sourceMappingURL=sectionParsers.js.map