bool FileRecordMgr::open(){
_bufStreamMgr = new BufferedStreamMgr(_filename);
if (_ioBufSize > 0) _bufStreamMgr->setIoBufSize(_ioBufSize);
if (!_bufStreamMgr->init()) {
cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
_fileType = _bufStreamMgr->getTypeChecker().getFileType();
_recordType = _bufStreamMgr->getTypeChecker().getRecordType();
if (_fileType == FileRecordTypeChecker::UNKNOWN_FILE_TYPE || _recordType == FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
cerr << "Error: Unable to determine type for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
allocateFileReader();
_recordMgr = new RecordMgr(_recordType, _freeListBlockSize);
_fileReader->setFileName(_filename.c_str());
_fileReader->setInputStream(_bufStreamMgr);
if (!_fileReader->open()) {
cerr << "Error: Types determined but can't open file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
return true;
}
bool FileRecordMgr::open(){
_filename = _context->getInputFileName(_contextFileIdx);
_bufStreamMgr = new BufferedStreamMgr(_filename);
if (!_bufStreamMgr->init()) {
cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
_fileType = _bufStreamMgr->getTypeChecker().getFileType();
_recordType = _bufStreamMgr->getTypeChecker().getRecordType();
if (_fileType == FileRecordTypeChecker::UNKNOWN_FILE_TYPE || _recordType == FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
cerr << "Error: Unable to determine type for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
allocateFileReader();
_recordMgr = new RecordMgr(_recordType, _freeListBlockSize);
_fileReader->setFileName(_filename.c_str());
_fileReader->setInputStream(_bufStreamMgr);
if (!_fileReader->open()) {
cerr << "Error: Types determined but can't open file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
_context->setInputFileType(_contextFileIdx, _fileType);
_context->setInputRecordType(_contextFileIdx, _recordType);
//if this is a database file, and the numFields is greater than the numFields in other DB files, update.
// TBD: This is one of many things that will need to be changed to support multiple database files in future versions.
int numFields = _bufStreamMgr->getTypeChecker().getNumFields();
if (_context->hasIntersectMethods()) {
if (_contextFileIdx == (static_cast<ContextIntersect *>(_context))->getDatabaseFileIdx() && numFields >
(static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields()) {
(static_cast<ContextIntersect *>(_context))->setMaxNumDatabaseFields(numFields);
}
}
if (_fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
_context->setHeader(_contextFileIdx, _fileReader->getHeader());
_context->setReferences(_contextFileIdx, static_cast<BamFileReader *>(_fileReader)->getReferences());
_headerSet = true;
}
return true;
}
