/* Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved */

/**

* compression.cpp

* Exported: filterThroughProcess/BytePacker/ByteUnpacker

*

* @author Magnus Jedvert

* @version 1.1 april 2012

*/

#include "compression.h"

#include <cassert>

#include <string>

#include <vector>

#include <sys/stat.h>

#include <unistd.h>

using namespace std;

/**

* filterThroughProcess - Send stdin_ to command and store output in stdout_.

* Will be used for zipping/unzipping.

* Can probably be made with pipes instead to avoid I/O.

*/

void filterThroughProcess(const string &command, const vector<u8> &stdin_, vector<u8> &stdout_) {

// char buff[2038];

// Don't use this code until the temporary file creation is worked out

assert(1==2);

const string fileName = "hello"; // tmpnam(buff); // get a random temporary file name

// call command and store in temporary file:

FILE *pstdin = popen( (command + " > " + fileName).c_str(), "w" );

fwrite ( stdin_.data(), 1, stdin_.size(), pstdin );

pclose(pstdin);

// get number of bytes in file:

struct stat statbuf;

assert( stat(fileName.c_str(), &statbuf) != -1 );

const size_t nBytes = statbuf.st_size;

// read the file back:

stdout_.resize( nBytes );

FILE *fin = fopen(fileName.c_str(), "rb");

assert( fread( stdout_.data(), 1, nBytes, fin ) == nBytes );

fclose(fin);

unlink( fileName.c_str() );

remove(fileName.c_str());

}

BytePacker::BytePacker(vector<u8> &compressed_): compressed( compressed_ ), byteIdx(0) {

compressed.resize(30 * 1000000); // reserve 30MB to start with

}

void BytePacker::push(const char *data, int len) {

while ( byteIdx + len > compressed.size() ) {

compressed.resize( compressed.size() * 2 );

}

memcpy( &compressed[byteIdx], data, len );

byteIdx += len;

}

void BytePacker::finalize() {

compressed.resize( byteIdx ); // shrink to fit

}

ByteUnpacker::ByteUnpacker(const char* compressed): ptr(compressed) {}