@gmod/cram 1.5.9 → 1.6.2

package/esm/cramFile/codecs/gamma.d.ts

@@ -0,0 +1,4 @@
+export default class GammaCodec extends CramCodec {
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/gamma.js

@@ -0,0 +1,20 @@
+import { CramUnimplementedError } from '../../errors';
+import CramCodec from './_base';
+export default class GammaCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        let length = 1;
+        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
+            length += 1;
+        }
+        const readBits = this._getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
+        const value = readBits | (1 << (length - 1));
+        return value - this.parameters.offset;
+    }
+}
+//# sourceMappingURL=gamma.js.map

package/esm/cramFile/codecs/gamma.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;SACF;IACH,CAAC;IAED,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE;YACvE,MAAM,IAAI,CAAC,CAAA;SACZ;QAED,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAC5B,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF"}

package/esm/cramFile/codecs/huffman.d.ts

@@ -0,0 +1,17 @@
+export default class HuffmanIntCodec extends CramCodec {
+    _decode(slice: any, coreDataBlock: any, coreCursor: any): any;
+    buildCodeBook(): void;
+    codeBook: {} | undefined;
+    buildCodes(): void;
+    codes: {} | undefined;
+    buildCaches(): void;
+    sortedCodes: any[] | undefined;
+    sortedByValue: any[] | undefined;
+    sortedValuesByBitCode: any[] | undefined;
+    sortedBitCodes: any[] | undefined;
+    sortedBitLengthsByBitCode: any[] | undefined;
+    bitCodeToValue: any[] | undefined;
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
+    _decodeZeroLengthCode(): any;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/huffman.js

@@ -0,0 +1,107 @@
+import { CramMalformedError } from '../../errors';
+import CramCodec from './_base';
+function numberOfSetBits(ii) {
+    let i = (ii - (ii >> 1)) & 0x55555555;
+    i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
+    return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24;
+}
+export default class HuffmanIntCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (!['byte', 'int'].includes(this.dataType)) {
+            throw new TypeError(`${this.dataType} decoding not yet implemented by HUFFMAN_INT codec`);
+        }
+        this.buildCodeBook();
+        this.buildCodes();
+        this.buildCaches();
+        // if this is a degenerate zero-length huffman code, special-case the decoding
+        if (this.sortedCodes[0].bitLength === 0) {
+            this._decode = this._decodeZeroLengthCode;
+        }
+    }
+    buildCodeBook() {
+        // parse the parameters together into a `codes` data structure
+        let codes = new Array(this.parameters.numCodes);
+        for (let i = 0; i < this.parameters.numCodes; i += 1) {
+            codes[i] = {
+                symbol: this.parameters.symbols[i],
+                bitLength: this.parameters.bitLengths[i],
+            };
+        }
+        // sort the codes by bit length and symbol value
+        codes = codes.sort((a, b) => a.bitLength - b.bitLength || a.symbol - b.symbol);
+        this.codeBook = {};
+        codes.forEach(code => {
+            if (!this.codeBook[code.bitLength]) {
+                this.codeBook[code.bitLength] = [];
+            }
+            this.codeBook[code.bitLength].push(code.symbol);
+        });
+    }
+    buildCodes() {
+        this.codes = {}; /*  new TreeMap<Integer, HuffmanBitCode>(); */
+        let codeLength = 0;
+        let codeValue = -1;
+        Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
+            bitLength = parseInt(bitLength, 10);
+            symbols.forEach(symbol => {
+                const code = { bitLength, value: symbol };
+                codeValue += 1;
+                const delta = bitLength - codeLength; // new length?
+                codeValue <<= delta; // pad with 0's
+                code.bitCode = codeValue; // calculated: huffman code
+                codeLength += delta; // adjust current code length
+                if (numberOfSetBits(codeValue) > bitLength) {
+                    throw new CramMalformedError('Symbol out of range');
+                }
+                this.codes[symbol] = code;
+            });
+        });
+    }
+    buildCaches() {
+        this.sortedCodes = Object.values(this.codes).sort((a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode);
+        // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
+        this.sortedByValue = Object.values(this.codes).sort((a, b) => a.value - b.value);
+        this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value);
+        this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode);
+        this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength);
+        const maxBitCode = Math.max(...this.sortedBitCodes);
+        this.bitCodeToValue = new Array(maxBitCode + 1).fill(-1);
+        for (let i = 0; i < this.sortedBitCodes.length; i += 1) {
+            this.bitCodeToValue[this.sortedCodes[i].bitCode] = i;
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        return this._decode(slice, coreDataBlock, cursors.coreBlock);
+    }
+    // _decodeNull() {
+    //   return -1
+    // }
+    // the special case for zero-length codes
+    _decodeZeroLengthCode() {
+        return this.sortedCodes[0].value;
+    }
+    _decode(slice, coreDataBlock, coreCursor) {
+        const input = coreDataBlock.content;
+        let prevLen = 0;
+        let bits = 0;
+        for (let i = 0; i < this.sortedCodes.length; i += 1) {
+            const length = this.sortedCodes[i].bitLength;
+            bits <<= length - prevLen;
+            bits |= this._getBits(input, coreCursor, length - prevLen);
+            prevLen = length;
+            {
+                const index = this.bitCodeToValue[bits];
+                if (index > -1 && this.sortedBitLengthsByBitCode[index] === length) {
+                    return this.sortedValuesByBitCode[index];
+                }
+                for (let j = i; this.sortedCodes[j + 1].bitLength === length &&
+                    j < this.sortedCodes.length; j += 1) {
+                    i += 1;
+                }
+            }
+        }
+        throw new CramMalformedError('Huffman symbol not found.');
+    }
+}
+//# sourceMappingURL=huffman.js.map

package/esm/cramFile/codecs/huffman.js.map

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

@@ -0,0 +1,2 @@
+export function getCodecClassWithId(id: any): any;
+export function instantiateCodec(encodingData: any, dataType: any): any;

package/esm/cramFile/codecs/index.js

@@ -0,0 +1,30 @@
+import { CramUnimplementedError } from '../../errors';
+import HuffmanIntCodec from './huffman';
+import ExternalCodec from './external';
+import ByteArrayStopCodec from './byteArrayStop';
+import ByteArrayLengthCodec from './byteArrayLength';
+import BetaCodec from './beta';
+import GammaCodec from './gamma';
+import SubexpCodec from './subexp';
+const codecClasses = {
+    1: ExternalCodec,
+    // 2: GolombCodec,
+    3: HuffmanIntCodec,
+    4: ByteArrayLengthCodec,
+    5: ByteArrayStopCodec,
+    6: BetaCodec,
+    7: SubexpCodec,
+    // 8: GolombRiceCodec,
+    9: GammaCodec,
+};
+export function getCodecClassWithId(id) {
+    return codecClasses[id];
+}
+export function instantiateCodec(encodingData, dataType) {
+    const CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
+    if (!CodecClass) {
+        throw new CramUnimplementedError(`no codec implemented for codec ID ${encodingData.codecId}`);
+    }
+    return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
+}
+//# sourceMappingURL=index.js.map

package/esm/cramFile/codecs/index.js.map

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

@@ -0,0 +1,4 @@
+export default class SubexpCodec extends CramCodec {
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+}
+import CramCodec from "./_base";

package/esm/cramFile/codecs/subexp.js

@@ -0,0 +1,28 @@
+import { CramUnimplementedError } from '../../errors';
+import CramCodec from './_base';
+export default class SubexpCodec extends CramCodec {
+    constructor(parameters = {}, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by SUBEXP codec`);
+        }
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        let numLeadingOnes = 0;
+        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
+            numLeadingOnes += 1;
+        }
+        let b;
+        let n;
+        if (numLeadingOnes === 0) {
+            b = this.parameters.K;
+            n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        else {
+            b = numLeadingOnes + this.parameters.K - 1;
+            n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        return n - this.parameters.offset;
+    }
+}
+//# sourceMappingURL=subexp.js.map

package/esm/cramFile/codecs/subexp.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAAS;IAChD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;SACF;IACH,CAAC;IAED,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE;YACjE,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE;YACxB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SAC/D;aAAM;YACL,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SAC1E;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}

package/esm/cramFile/constants.d.ts

@@ -0,0 +1,36 @@
+export default Constants;
+declare namespace Constants {
+    const CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
+    const CRAM_FLAG_DETACHED: number;
+    const CRAM_FLAG_MATE_DOWNSTREAM: number;
+    const CRAM_FLAG_NO_SEQ: number;
+    const CRAM_FLAG_MASK: number;
+    const CRAM_M_REVERSE: number;
+    const CRAM_M_UNMAP: number;
+    const BAM_FPAIRED: number;
+    const BAM_FPROPER_PAIR: number;
+    const BAM_FUNMAP: number;
+    const BAM_FMUNMAP: number;
+    const BAM_FREVERSE: number;
+    const BAM_FMREVERSE: number;
+    const BAM_FREAD1: number;
+    const BAM_FREAD2: number;
+    const BAM_FSECONDARY: number;
+    const BAM_FQCFAIL: number;
+    const BAM_FDUP: number;
+    const BAM_FSUPPLEMENTARY: number;
+    const BAM_CMATCH: number;
+    const BAM_CINS: number;
+    const BAM_CDEL: number;
+    const BAM_CREF_SKIP: number;
+    const BAM_CSOFT_CLIP: number;
+    const BAM_CHARD_CLIP: number;
+    const BAM_CPAD: number;
+    const BAM_CEQUAL: number;
+    const BAM_CDIFF: number;
+    const BAM_CBACK: number;
+    const BAM_CIGAR_STR: string;
+    const BAM_CIGAR_SHIFT: number;
+    const BAM_CIGAR_MASK: number;
+    const BAM_CIGAR_TYPE: number;
+}

package/esm/cramFile/constants.js

@@ -0,0 +1,51 @@
+const Constants = {
+    CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
+    CRAM_FLAG_DETACHED: 1 << 1,
+    CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
+    CRAM_FLAG_NO_SEQ: 1 << 3,
+    CRAM_FLAG_MASK: (1 << 4) - 1,
+    // mate read is reversed
+    CRAM_M_REVERSE: 1,
+    // mated read is unmapped
+    CRAM_M_UNMAP: 2,
+    //  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,
+    BAM_CMATCH: 0,
+    BAM_CINS: 1,
+    BAM_CDEL: 2,
+    BAM_CREF_SKIP: 3,
+    BAM_CSOFT_CLIP: 4,
+    BAM_CHARD_CLIP: 5,
+    BAM_CPAD: 6,
+    BAM_CEQUAL: 7,
+    BAM_CDIFF: 8,
+    BAM_CBACK: 9,
+    BAM_CIGAR_STR: 'MIDNSHP:XB',
+    BAM_CIGAR_SHIFT: 4,
+    BAM_CIGAR_MASK: 0xf,
+    BAM_CIGAR_TYPE: 0x3c1a7,
+};
+export default Constants;
+//# sourceMappingURL=constants.js.map

package/esm/cramFile/constants.js.map

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

@@ -0,0 +1,23 @@
+export default class CramContainerCompressionScheme {
+    constructor(content: any);
+    readNamesIncluded: any;
+    APdelta: any;
+    referenceRequired: boolean;
+    tagIdsDictionary: any;
+    substitutionMatrix: any[];
+    dataSeriesCodecCache: {};
+    tagCodecCache: {};
+    /**
+     * @param {string} tagName three-character tag name
+     * @private
+     */
+    private getCodecForTag;
+    /**
+     *
+     * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
+     * @private
+     */
+    private getTagNames;
+    getCodecForDataSeries(dataSeriesName: any): any;
+    toJSON(): {};
+}

package/esm/cramFile/container/compressionScheme.js

@@ -0,0 +1,123 @@
+import { CramMalformedError } from '../../errors';
+import { instantiateCodec } from '../codecs';
+// the hardcoded data type to be decoded for each core
+// data field
+const dataSeriesTypes = {
+    BF: 'int',
+    CF: 'int',
+    RI: 'int',
+    RL: 'int',
+    AP: 'int',
+    RG: 'int',
+    MF: 'int',
+    NS: 'int',
+    NP: 'int',
+    TS: 'int',
+    NF: 'int',
+    TC: 'byte',
+    TN: 'int',
+    FN: 'int',
+    FC: 'byte',
+    FP: 'int',
+    BS: 'byte',
+    IN: 'byteArray',
+    SC: 'byteArray',
+    DL: 'int',
+    BA: 'byte',
+    BB: 'byteArray',
+    RS: 'int',
+    PD: 'int',
+    HC: 'int',
+    MQ: 'int',
+    RN: 'byteArray',
+    QS: 'byte',
+    QQ: 'byteArray',
+    TL: 'int',
+    TM: 'ignore',
+    TV: 'ignore',
+};
+function parseSubstitutionMatrix(byteArray) {
+    const matrix = new Array(5);
+    for (let i = 0; i < 5; i += 1) {
+        matrix[i] = new Array(4);
+    }
+    matrix[0][(byteArray[0] >> 6) & 3] = 'C';
+    matrix[0][(byteArray[0] >> 4) & 3] = 'G';
+    matrix[0][(byteArray[0] >> 2) & 3] = 'T';
+    matrix[0][(byteArray[0] >> 0) & 3] = 'N';
+    matrix[1][(byteArray[1] >> 6) & 3] = 'A';
+    matrix[1][(byteArray[1] >> 4) & 3] = 'G';
+    matrix[1][(byteArray[1] >> 2) & 3] = 'T';
+    matrix[1][(byteArray[1] >> 0) & 3] = 'N';
+    matrix[2][(byteArray[2] >> 6) & 3] = 'A';
+    matrix[2][(byteArray[2] >> 4) & 3] = 'C';
+    matrix[2][(byteArray[2] >> 2) & 3] = 'T';
+    matrix[2][(byteArray[2] >> 0) & 3] = 'N';
+    matrix[3][(byteArray[3] >> 6) & 3] = 'A';
+    matrix[3][(byteArray[3] >> 4) & 3] = 'C';
+    matrix[3][(byteArray[3] >> 2) & 3] = 'G';
+    matrix[3][(byteArray[3] >> 0) & 3] = 'N';
+    matrix[4][(byteArray[4] >> 6) & 3] = 'A';
+    matrix[4][(byteArray[4] >> 4) & 3] = 'C';
+    matrix[4][(byteArray[4] >> 2) & 3] = 'G';
+    matrix[4][(byteArray[4] >> 0) & 3] = 'T';
+    return matrix;
+}
+export default class CramContainerCompressionScheme {
+    constructor(content) {
+        Object.assign(this, content);
+        // interpret some of the preservation map tags for convenient use
+        this.readNamesIncluded = content.preservation.RN;
+        this.APdelta = content.preservation.AP;
+        this.referenceRequired = !!content.preservation.RR;
+        this.tagIdsDictionary = content.preservation.TD;
+        this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
+        this.dataSeriesCodecCache = {};
+        this.tagCodecCache = {};
+    }
+    /**
+     * @param {string} tagName three-character tag name
+     * @private
+     */
+    getCodecForTag(tagName) {
+        if (!this.tagCodecCache[tagName]) {
+            const encodingData = this.tagEncoding[tagName];
+            if (encodingData) {
+                this.tagCodecCache[tagName] = instantiateCodec(encodingData, 'byteArray');
+            }
+        }
+        return this.tagCodecCache[tagName];
+    }
+    /**
+     *
+     * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
+     * @private
+     */
+    getTagNames(tagListId) {
+        return this.tagIdsDictionary[tagListId];
+    }
+    getCodecForDataSeries(dataSeriesName) {
+        if (!this.dataSeriesCodecCache[dataSeriesName]) {
+            const encodingData = this.dataSeriesEncoding[dataSeriesName];
+            if (encodingData) {
+                const dataType = dataSeriesTypes[dataSeriesName];
+                if (!dataType) {
+                    throw new CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);
+                }
+                this.dataSeriesCodecCache[dataSeriesName] = instantiateCodec(encodingData, dataType);
+            }
+        }
+        return this.dataSeriesCodecCache[dataSeriesName];
+    }
+    toJSON() {
+        const data = {};
+        Object.keys(this).forEach(k => {
+            if (/Cache$/.test(k)) {
+                return;
+            }
+            data[k] = this[k];
+        });
+        return data;
+    }
+}
+//# sourceMappingURL=compressionScheme.js.map

package/esm/cramFile/container/compressionScheme.js.map

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package/esm/cramFile/container/index.d.ts

@@ -0,0 +1,13 @@
+export default class CramContainer {
+    constructor(cramFile: any, position: any);
+    file: any;
+    filePosition: any;
+    getHeader(): Promise<any>;
+    getCompressionHeaderBlock(): Promise<any>;
+    getFirstBlock(): Promise<any>;
+    getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
+    getSlice(slicePosition: any, sliceSize: any): CramSlice;
+    _readContainerHeader(position: any): Promise<any>;
+}
+import CramContainerCompressionScheme from "./compressionScheme";
+import CramSlice from "../slice";

package/esm/cramFile/container/index.js

@@ -0,0 +1,84 @@
+import { CramMalformedError } from '../../errors';
+import { itf8Size, parseItem, tinyMemoize } from '../util';
+import CramSlice from '../slice';
+import CramContainerCompressionScheme from './compressionScheme';
+export default class CramContainer {
+    constructor(cramFile, position) {
+        // cram file this container comes from
+        this.file = cramFile;
+        // position of this container in the file
+        this.filePosition = position;
+        // console.log(`container: ${this.filePosition}`)
+    }
+    // memoize
+    getHeader() {
+        return this._readContainerHeader(this.filePosition);
+    }
+    // memoize
+    async getCompressionHeaderBlock() {
+        const containerHeader = await this.getHeader();
+        // if there are no records in the container, there will be no compression header
+        if (!containerHeader.numRecords) {
+            return null;
+        }
+        const sectionParsers = await this.file.getSectionParsers();
+        const block = await this.getFirstBlock();
+        if (block.contentType !== 'COMPRESSION_HEADER') {
+            throw new CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
+        }
+        const content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+        block.content = content;
+        return block;
+    }
+    async getFirstBlock() {
+        const containerHeader = await this.getHeader();
+        return this.file.readBlock(containerHeader._endPosition);
+    }
+    // parses the compression header data into a CramContainerCompressionScheme object
+    // memoize
+    async getCompressionScheme() {
+        const header = await this.getCompressionHeaderBlock();
+        if (!header) {
+            return undefined;
+        }
+        return new CramContainerCompressionScheme(header.content);
+    }
+    getSlice(slicePosition, sliceSize) {
+        // note: slicePosition is relative to the end of the container header
+        // TODO: perhaps we should cache slices?
+        return new CramSlice(this, slicePosition, sliceSize);
+    }
+    async _readContainerHeader(position) {
+        const sectionParsers = await this.file.getSectionParsers();
+        const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
+        const { size: fileSize } = await this.file.stat();
+        if (position >= fileSize) {
+            return undefined;
+        }
+        // parse the container header. do it in 2 pieces because you cannot tell
+        // how much to buffer until you read numLandmarks
+        const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+        await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
+        const header1 = parseItem(bytes1, cramContainerHeader1.parser);
+        const numLandmarksSize = itf8Size(header1.numLandmarks);
+        if (position + header1.length >= fileSize) {
+            console.warn(`${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
+            return undefined;
+        }
+        const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+        await this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
+        const header2 = parseItem(bytes2, cramContainerHeader2.parser);
+        if (this.file.validateChecksums && header2.crc32 !== undefined) {
+            await this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
+        }
+        const completeHeader = Object.assign(header1, header2, {
+            _size: header1._size + header2._size - numLandmarksSize,
+            _endPosition: header1._size + header2._size - numLandmarksSize + position,
+        });
+        return completeHeader;
+    }
+}
+'getHeader getCompressionHeaderBlock getCompressionScheme'
+    .split(' ')
+    .forEach(method => tinyMemoize(CramContainer, method));
+//# sourceMappingURL=index.js.map

package/esm/cramFile/container/index.js.map

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