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BufferedStreamMgr.cpp 2.99 KiB
/*
* 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()