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;
}
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::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;
}
_mainBuf = new bufType[MAIN_BUF_READ_SIZE +1];
memset(_mainBuf, 0, MAIN_BUF_READ_SIZE +1);
return true;
}
