@gmod/cram 6.0.0 → 7.0.0

package/dist/rans/index.js

@@ -1,198 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = uncompress;
-// @ts-nocheck
-const errors_ts_1 = require("../errors.js");
-const d04_ts_1 = __importDefault(require("./d04.js"));
-const d14_ts_1 = __importDefault(require("./d14.js"));
-const decoding_ts_1 = __importDefault(require("./decoding.js"));
-const frequencies_ts_1 = require("./frequencies.js");
-// const /* int */ ORDER_BYTE_LENGTH = 1
-// const /* int */ COMPRESSED_BYTE_LENGTH = 4
-const /* int */ RAW_BYTE_LENGTH = 4;
-// const /* int */ PREFIX_BYTE_LENGTH =
-//   ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH + RAW_BYTE_LENGTH
-// enum ORDER {
-//     ZERO, ONE;
-//     static ORDER fromInt(const /* int */ value) {
-//         try {
-//             return ORDER.values()[value];
-//         } catch (const ArrayIndexOutOfBoundsException e) {
-//             throw new RuntimeException("Unknown rANS order: " + value);
-//         }
-//     }
-// }
-// static ByteBuffer compress(const ByteBuffer input, const ORDER order, const ByteBuffer out) {
-//     if (input.remaining() == 0)
-//         return EMPTY_BUFFER;
-//     if (input.remaining() < 4)
-//         return encode_order0_way4(input, out);
-//     switch (order) {
-//         case ZERO:
-//             return encode_order0_way4(input, out);
-//         case ONE:
-//             return encode_order1_way4(input, out);
-//         default:
-//             throw new RuntimeException("Unknown rANS order: " + order);
-//     }
-// }
-// static /* ByteBuffer */ allocateIfNeeded(/* const int */ in_size,
-//                                            /* const ByteBuffer */ out_buf) {
-//     const /* int */ compressedSize = (/* int */) (1.05 * in_size + 257 * 257 * 3 + 4);
-//     if (out_buf == null)
-//         return ByteBuffer.allocate(compressedSize);
-//     if (out_buf.remaining() < compressedSize)
-//         throw new RuntimeException("Insufficient buffer size.");
-//     out_buf.order(ByteOrder.LITTLE_ENDIAN);
-//     return out_buf;
-// }
-// static ByteBuffer encode_order0_way4(const ByteBuffer input,
-//                                              ByteBuffer out_buf) {
-//     const /* int */ in_size = input.remaining();
-//     out_buf = allocateIfNeeded(in_size, out_buf);
-//     const /* int */ freqTableStart = PREFIX_BYTE_LENGTH;
-//     out_buf.position(freqTableStart);
-//     const /* int */[] F = Frequencies.calcFrequencies_o0(in);
-//     const RansEncSymbol[] syms = Frequencies.buildSyms_o0(F);
-//     const ByteBuffer cp = out_buf.slice();
-//     const /* int */ frequencyTable_size = Frequencies.writeFrequencies_o0(cp, F);
-//     input.rewind();
-//     const /* int */ compressedBlob_size = E04.compress(input, syms, cp);
-//     finalizeCompressed(0, out_buf, in_size, frequencyTable_size,
-//             compressedBlob_size);
-//     return out_buf;
-// }
-// static ByteBuffer encode_order1_way4(const ByteBuffer input,
-//                                              ByteBuffer out_buf) {
-//     const /* int */ in_size = input.remaining();
-//     out_buf = allocateIfNeeded(in_size, out_buf);
-//     const /* int */ freqTableStart = PREFIX_BYTE_LENGTH;
-//     out_buf.position(freqTableStart);
-//     const /* int */[][] F = Frequencies.calcFrequencies_o1(in);
-//     const RansEncSymbol[][] syms = Frequencies.buildSyms_o1(F);
-//     const ByteBuffer cp = out_buf.slice();
-//     const /* int */ frequencyTable_size = Frequencies.writeFrequencies_o1(cp, F);
-//     input.rewind();
-//     const /* int */ compressedBlob_size = E14.compress(input, syms, cp);
-//     finalizeCompressed(1, out_buf, in_size, frequencyTable_size,
-//             compressedBlob_size);
-//     return out_buf;
-// }
-// static void finalizeCompressed(const /* int */ order, const ByteBuffer out_buf,
-//                                        const /* int */ in_size, const /* int */ frequencyTable_size, const /* int */ compressedBlob_size) {
-//     out_buf.limit(PREFIX_BYTE_LENGTH + frequencyTable_size
-//             + compressedBlob_size);
-//     out_buf.put(0, (byte) order);
-//     out_buf.order(ByteOrder.LITTLE_ENDIAN);
-//     const /* int */ compressedSizeOffset = ORDER_BYTE_LENGTH;
-//     out_buf.putInt(compressedSizeOffset, frequencyTable_size
-//             + compressedBlob_size);
-//     const /* int */ rawSizeOffset = ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH;
-//     out_buf.putInt(rawSizeOffset, in_size);
-//     out_buf.rewind();
-// }
-function uncompressOrder0Way4(
-/* const ByteBuffer  */ input, 
-/* const ByteBuffer  */ out) {
-    // input.order(ByteOrder.LITTLE_ENDIAN);
-    const D = new decoding_ts_1.default.AriDecoder();
-    const syms = new Array(256);
-    for (let i = 0; i < 256; i += 1) {
-        syms[i] = new decoding_ts_1.default.DecodingSymbol();
-    }
-    (0, frequencies_ts_1.readStatsO0)(input, D, syms);
-    (0, d04_ts_1.default)(input, D, syms, out);
-    return out;
-}
-function uncompressOrder1Way4(
-/* const ByteBuffer */ input, 
-/* const ByteBuffer */ output) {
-    const D = new Array(256);
-    for (let i = 0; i < 256; i += 1) {
-        D[i] = new decoding_ts_1.default.AriDecoder();
-    }
-    const syms = new Array(256);
-    for (let i = 0; i < 256; i += 1) {
-        syms[i] = new Array(256);
-        for (let j = 0; j < 256; j += 1) {
-            syms[i][j] = new decoding_ts_1.default.DecodingSymbol();
-        }
-    }
-    (0, frequencies_ts_1.readStatsO1)(input, D, syms);
-    (0, d14_ts_1.default)(input, output, D, syms);
-    return output;
-}
-/* compat layer to make a node buffer act like a java ByteBuffer */
-class ByteBuffer {
-    constructor(nodeBuffer, initialInputPosition = 0) {
-        this._buffer = nodeBuffer;
-        this._dataView = new DataView(nodeBuffer.buffer);
-        this._position = initialInputPosition;
-        this.length = nodeBuffer.length;
-    }
-    get() {
-        return this._buffer[this._position++];
-    }
-    getByte() {
-        return this._buffer[this._position++];
-    }
-    getByteAt(position) {
-        return this._buffer[position];
-    }
-    position() {
-        return this._position;
-    }
-    put(val) {
-        this._buffer[this._position++] = val;
-    }
-    putAt(position, val) {
-        this._buffer[position] = val;
-    }
-    setPosition(pos) {
-        this._position = pos;
-        return pos;
-    }
-    getInt() {
-        const i = this._dataView.getInt32(this._position, true);
-        this._position += 4;
-        return i;
-    }
-    remaining() {
-        return this.length - this._position;
-    }
-}
-// static /* const */ ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
-function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
-    if (inputBuffer.length === 0) {
-        outputBuffer.fill(0);
-        return outputBuffer;
-    }
-    const input = new ByteBuffer(inputBuffer, initialInputPosition);
-    // input.order(ByteOrder.LITTLE_ENDIAN);
-    const order = input.get();
-    if (order !== 0 && order !== 1) {
-        throw new errors_ts_1.CramMalformedError(`Invalid rANS order ${order}`);
-    }
-    const /* int */ inputSize = input.getInt();
-    if (inputSize !== input.remaining() - RAW_BYTE_LENGTH) {
-        throw new errors_ts_1.CramMalformedError('Incorrect input length.');
-    }
-    const /* int */ outputSize = input.getInt();
-    const output = new ByteBuffer(outputBuffer || new Uint8Array(outputSize));
-    // TODO output.limit(outputSize)
-    if (output.length < outputSize) {
-        throw new errors_ts_1.CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);
-    }
-    switch (order) {
-        case 0:
-            return uncompressOrder0Way4(input, output);
-        case 1:
-            return uncompressOrder1Way4(input, output);
-        default:
-            throw new errors_ts_1.CramMalformedError(`Invalid rANS order: ${order}`);
-    }
-}
-//# sourceMappingURL=index.js.map

package/dist/rans/index.js.map

@@ -1 +0,0 @@
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package/dist/seek-bzip/bitreader.d.ts

@@ -1,27 +0,0 @@
-interface Stream {
-    readByte(): number;
-    seek(pos: number): void;
-}
-export default class BitReader {
-    private stream;
-    private bitOffset;
-    private curByte;
-    private hasByte;
-    constructor(stream: Stream);
-    private _ensureByte;
-    /**
-     * Reads bits from the buffer
-     * @param bits Number of bits to read
-     */
-    read(bits: number): number;
-    /**
-     * Seek to an arbitrary point in the buffer (expressed in bits)
-     * @param pos Position in bits
-     */
-    seek(pos: number): void;
-    /**
-     * Reads 6 bytes worth of data using the read method
-     */
-    pi(): string;
-}
-export {};

package/dist/seek-bzip/bitreader.js

@@ -1,101 +0,0 @@
-"use strict";
-/*
-node-bzip - a pure-javascript Node.JS module for decoding bzip2 data
-
-Copyright (C) 2012 Eli Skeggs
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-Adapted from bzip2.js, copyright 2011 antimatter15 (antimatter15@gmail.com).
-
-Based on micro-bunzip by Rob Landley (rob@landley.net).
-
-Based on bzip2 decompression code by Julian R Seward (jseward@acm.org),
-which also acknowledges contributions by Mike Burrows, David Wheeler,
-Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
-Robert Sedgewick, and Jon L. Bentley.
-*/
-Object.defineProperty(exports, "__esModule", { value: true });
-const toHex_ts_1 = require("./toHex.js");
-const BITMASK = [0x00, 0x01, 0x03, 0x07, 0x0f, 0x1f, 0x3f, 0x7f, 0xff];
-class BitReader {
-    constructor(stream) {
-        this.stream = stream;
-        this.bitOffset = 0;
-        this.curByte = 0;
-        this.hasByte = false;
-    }
-    _ensureByte() {
-        if (!this.hasByte) {
-            this.curByte = this.stream.readByte();
-            this.hasByte = true;
-        }
-    }
-    /**
-     * Reads bits from the buffer
-     * @param bits Number of bits to read
-     */
-    read(bits) {
-        let result = 0;
-        while (bits > 0) {
-            this._ensureByte();
-            const remaining = 8 - this.bitOffset;
-            // if we're in a byte
-            if (bits >= remaining) {
-                result <<= remaining;
-                result |= BITMASK[remaining] & this.curByte;
-                this.hasByte = false;
-                this.bitOffset = 0;
-                bits -= remaining;
-            }
-            else {
-                result <<= bits;
-                const shift = remaining - bits;
-                result |= (this.curByte & (BITMASK[bits] << shift)) >> shift;
-                this.bitOffset += bits;
-                bits = 0;
-            }
-        }
-        return result;
-    }
-    /**
-     * Seek to an arbitrary point in the buffer (expressed in bits)
-     * @param pos Position in bits
-     */
-    seek(pos) {
-        const n_bit = pos % 8;
-        const n_byte = (pos - n_bit) / 8;
-        this.bitOffset = n_bit;
-        this.stream.seek(n_byte);
-        this.hasByte = false;
-    }
-    /**
-     * Reads 6 bytes worth of data using the read method
-     */
-    pi() {
-        const buf = new Uint8Array(6);
-        for (let i = 0; i < buf.length; i++) {
-            buf[i] = this.read(8);
-        }
-        return (0, toHex_ts_1.toHex)(buf);
-    }
-}
-exports.default = BitReader;
-//# sourceMappingURL=bitreader.js.map

package/dist/seek-bzip/bitreader.js.map

@@ -1 +0,0 @@
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package/dist/seek-bzip/crc32.d.ts

@@ -1,26 +0,0 @@
-export default class CRC32 {
-    /**
-     * The current CRC
-     * @private
-     */
-    private crc;
-    /**
-     * Constructor initializes the CRC value
-     */
-    constructor();
-    /**
-     * @return The current CRC
-     */
-    getCRC(): number;
-    /**
-     * Update the CRC with a single byte
-     * @param value The value to update the CRC with
-     */
-    updateCRC(value: number): void;
-    /**
-     * Update the CRC with a sequence of identical bytes
-     * @param value The value to update the CRC with
-     * @param count The number of bytes
-     */
-    updateCRCRun(value: number, count: number): void;
-}

package/dist/seek-bzip/crc32.js

@@ -1,115 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-/* CRC32, used in Bzip2 implementation.
- * This is a port of CRC32.java from the jbzip2 implementation at
- *   https://code.google.com/p/jbzip2
- * which is:
- *   Copyright (c) 2011 Matthew Francis
- *
- *   Permission is hereby granted, free of charge, to any person
- *   obtaining a copy of this software and associated documentation
- *   files (the "Software"), to deal in the Software without
- *   restriction, including without limitation the rights to use,
- *   copy, modify, merge, publish, distribute, sublicense, and/or sell
- *   copies of the Software, and to permit persons to whom the
- *   Software is furnished to do so, subject to the following
- *   conditions:
- *
- *   The above copyright notice and this permission notice shall be
- *   included in all copies or substantial portions of the Software.
- *
- *   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- *   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- *   OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- *   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- *   HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- *   WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- *   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- *   OTHER DEALINGS IN THE SOFTWARE.
- * This JavaScript implementation is:
- *   Copyright (c) 2013 C. Scott Ananian
- * with the same licensing terms as Matthew Francis' original implementation.
- */
-/**
- * A static CRC lookup table
- */
-const crc32Lookup = new Uint32Array([
-    0x00000000, 0x04c11db7, 0x09823b6e, 0x0d4326d9, 0x130476dc, 0x17c56b6b,
-    0x1a864db2, 0x1e475005, 0x2608edb8, 0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61,
-    0x350c9b64, 0x31cd86d3, 0x3c8ea00a, 0x384fbdbd, 0x4c11db70, 0x48d0c6c7,
-    0x4593e01e, 0x4152fda9, 0x5f15adac, 0x5bd4b01b, 0x569796c2, 0x52568b75,
-    0x6a1936c8, 0x6ed82b7f, 0x639b0da6, 0x675a1011, 0x791d4014, 0x7ddc5da3,
-    0x709f7b7a, 0x745e66cd, 0x9823b6e0, 0x9ce2ab57, 0x91a18d8e, 0x95609039,
-    0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52, 0x8664e6e5, 0xbe2b5b58, 0xbaea46ef,
-    0xb7a96036, 0xb3687d81, 0xad2f2d84, 0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d,
-    0xd4326d90, 0xd0f37027, 0xddb056fe, 0xd9714b49, 0xc7361b4c, 0xc3f706fb,
-    0xceb42022, 0xca753d95, 0xf23a8028, 0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1,
-    0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a, 0xec7dd02d, 0x34867077, 0x30476dc0,
-    0x3d044b19, 0x39c556ae, 0x278206ab, 0x23431b1c, 0x2e003dc5, 0x2ac12072,
-    0x128e9dcf, 0x164f8078, 0x1b0ca6a1, 0x1fcdbb16, 0x018aeb13, 0x054bf6a4,
-    0x0808d07d, 0x0cc9cdca, 0x7897ab07, 0x7c56b6b0, 0x71159069, 0x75d48dde,
-    0x6b93dddb, 0x6f52c06c, 0x6211e6b5, 0x66d0fb02, 0x5e9f46bf, 0x5a5e5b08,
-    0x571d7dd1, 0x53dc6066, 0x4d9b3063, 0x495a2dd4, 0x44190b0d, 0x40d816ba,
-    0xaca5c697, 0xa864db20, 0xa527fdf9, 0xa1e6e04e, 0xbfa1b04b, 0xbb60adfc,
-    0xb6238b25, 0xb2e29692, 0x8aad2b2f, 0x8e6c3698, 0x832f1041, 0x87ee0df6,
-    0x99a95df3, 0x9d684044, 0x902b669d, 0x94ea7b2a, 0xe0b41de7, 0xe4750050,
-    0xe9362689, 0xedf73b3e, 0xf3b06b3b, 0xf771768c, 0xfa325055, 0xfef34de2,
-    0xc6bcf05f, 0xc27dede8, 0xcf3ecb31, 0xcbffd686, 0xd5b88683, 0xd1799b34,
-    0xdc3abded, 0xd8fba05a, 0x690ce0ee, 0x6dcdfd59, 0x608edb80, 0x644fc637,
-    0x7a089632, 0x7ec98b85, 0x738aad5c, 0x774bb0eb, 0x4f040d56, 0x4bc510e1,
-    0x46863638, 0x42472b8f, 0x5c007b8a, 0x58c1663d, 0x558240e4, 0x51435d53,
-    0x251d3b9e, 0x21dc2629, 0x2c9f00f0, 0x285e1d47, 0x36194d42, 0x32d850f5,
-    0x3f9b762c, 0x3b5a6b9b, 0x0315d626, 0x07d4cb91, 0x0a97ed48, 0x0e56f0ff,
-    0x1011a0fa, 0x14d0bd4d, 0x19939b94, 0x1d528623, 0xf12f560e, 0xf5ee4bb9,
-    0xf8ad6d60, 0xfc6c70d7, 0xe22b20d2, 0xe6ea3d65, 0xeba91bbc, 0xef68060b,
-    0xd727bbb6, 0xd3e6a601, 0xdea580d8, 0xda649d6f, 0xc423cd6a, 0xc0e2d0dd,
-    0xcda1f604, 0xc960ebb3, 0xbd3e8d7e, 0xb9ff90c9, 0xb4bcb610, 0xb07daba7,
-    0xae3afba2, 0xaafbe615, 0xa7b8c0cc, 0xa379dd7b, 0x9b3660c6, 0x9ff77d71,
-    0x92b45ba8, 0x9675461f, 0x8832161a, 0x8cf30bad, 0x81b02d74, 0x857130c3,
-    0x5d8a9099, 0x594b8d2e, 0x5408abf7, 0x50c9b640, 0x4e8ee645, 0x4a4ffbf2,
-    0x470cdd2b, 0x43cdc09c, 0x7b827d21, 0x7f436096, 0x7200464f, 0x76c15bf8,
-    0x68860bfd, 0x6c47164a, 0x61043093, 0x65c52d24, 0x119b4be9, 0x155a565e,
-    0x18197087, 0x1cd86d30, 0x029f3d35, 0x065e2082, 0x0b1d065b, 0x0fdc1bec,
-    0x3793a651, 0x3352bbe6, 0x3e119d3f, 0x3ad08088, 0x2497d08d, 0x2056cd3a,
-    0x2d15ebe3, 0x29d4f654, 0xc5a92679, 0xc1683bce, 0xcc2b1d17, 0xc8ea00a0,
-    0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb, 0xdbee767c, 0xe3a1cbc1, 0xe760d676,
-    0xea23f0af, 0xeee2ed18, 0xf0a5bd1d, 0xf464a0aa, 0xf9278673, 0xfde69bc4,
-    0x89b8fd09, 0x8d79e0be, 0x803ac667, 0x84fbdbd0, 0x9abc8bd5, 0x9e7d9662,
-    0x933eb0bb, 0x97ffad0c, 0xafb010b1, 0xab710d06, 0xa6322bdf, 0xa2f33668,
-    0xbcb4666d, 0xb8757bda, 0xb5365d03, 0xb1f740b4,
-]);
-class CRC32 {
-    /**
-     * Constructor initializes the CRC value
-     */
-    constructor() {
-        this.crc = 0xffffffff;
-    }
-    /**
-     * @return The current CRC
-     */
-    getCRC() {
-        return ~this.crc >>> 0; // return an unsigned value
-    }
-    /**
-     * Update the CRC with a single byte
-     * @param value The value to update the CRC with
-     */
-    updateCRC(value) {
-        this.crc =
-            (this.crc << 8) ^ crc32Lookup[((this.crc >>> 24) ^ value) & 0xff];
-    }
-    /**
-     * Update the CRC with a sequence of identical bytes
-     * @param value The value to update the CRC with
-     * @param count The number of bytes
-     */
-    updateCRCRun(value, count) {
-        while (count-- > 0) {
-            this.crc =
-                (this.crc << 8) ^ crc32Lookup[((this.crc >>> 24) ^ value) & 0xff];
-        }
-    }
-}
-exports.default = CRC32;
-//# sourceMappingURL=crc32.js.map

package/dist/seek-bzip/crc32.js.map

@@ -1 +0,0 @@
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package/dist/seek-bzip/index.d.ts

@@ -1,9 +0,0 @@
-declare class Bunzip {
-    constructor(inputStream: any, outputStream: any);
-    _init_block(): boolean;
-    _start_bunzip(inputStream: any, outputStream: any): void;
-    _get_next_block(): boolean;
-    _read_bunzip(outputBuffer: any, len: any): any;
-}
-export declare function decode(input: Uint8Array, output?: any, multistream?: any): any;
-export default Bunzip;