@gmod/cram
Version:
read CRAM files with pure Javascript
203 lines • 8.09 kB
JavaScript
"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 < syms.length; 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 < D.length; i += 1) {
D[i] = new decoding_ts_1.default.AriDecoder();
}
const /* Decoding.RansDecSymbol[][] */ syms = new Array(256);
for (let i = 0; i < syms.length; i += 1) {
syms[i] = new Array(256);
for (let j = 0; j < syms[i].length; 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() {
const b = this._buffer[this._position];
this._position += 1;
return b;
}
getByte() {
return this.get();
}
getByteAt(position) {
return this._buffer[position];
}
position() {
return this._position;
}
put(val) {
this._buffer[this._position] = val;
this._position += 1;
return val;
}
putAt(position, val) {
this._buffer[position] = val;
return 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._buffer.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