BufferedStreamMgr.cpp

/*
 * BufferedStreamMgr.cpp
 *
 *  Created on: Jul 9, 2013
 *      Author: nek3d
 */

#include "BufferedStreamMgr.h"
#include "CompressionTools.h"
#include "InputStreamMgr.h"
#include <fstream>

BufferedStreamMgr::BufferedStreamMgr(const QuickString &filename)
: 	_inputStreamMgr(NULL),
	_mainBuf(NULL),
   	_filename(filename),
  	_mainBufCurrStartPos(0),
  	_mainBufCurrLen(0),
  	_eof(false),
  	_useBufSize(0),
  	_streamFinished(false)
{

}

BufferedStreamMgr::~BufferedStreamMgr()
{

	if (_mainBuf != NULL) {
		delete [] _mainBuf;
	}
	if (_inputStreamMgr != NULL) {
		delete _inputStreamMgr;
		_inputStreamMgr = NULL;
	}
}

bool BufferedStreamMgr::init()
{
	_inputStreamMgr = new InputStreamMgr(_filename);
	if (!_inputStreamMgr->init()) {
		return false;
	}
	if (_inputStreamMgr->isBam()) {
		//there is a special check for a BAM file's magic string inside
		//the inputStreamMgr's init method. If it is found, we can
		//stop here.
		_typeChecker.setBam();
		return true;
	}
	if (!getTypeData()) {
		return false;
	}
	if (_inputStreamMgr->isGzipped()) {
		_useBufSize = GZIP_LINE_BUF_SIZE;
	} else {
		_useBufSize =  MAIN_BUF_READ_SIZE;
	}

	size_t trueBufSize = max(_useBufSize, (int)_currScanBuffer.size());
	_useBufSize = trueBufSize;
	_mainBuf = new bufType[_useBufSize +1];
	memset(_mainBuf, 0, _useBufSize +1);
	memcpy(_mainBuf, _currScanBuffer.c_str(), _currScanBuffer.size());
	_mainBufCurrLen = _currScanBuffer.size();

	return true;
}

bool BufferedStreamMgr::getTypeData()