Esempio n. 1
0
Record *FileRecordMgr::allocateAndGetNextRecord()
{
	if (!_fileReader->isOpen()) {
		return NULL;
	}
	if (!_fileReader->readEntry()) {
		return NULL;
	}
	if (!_headerSet && _fileReader->hasHeader()) {
		_context->setHeader(_contextFileIdx, _fileReader->getHeader());
		_headerSet = true;
	}
	Record *record = NULL;
	record = _recordMgr->allocateRecord();
	if (!record->initFromFile(_fileReader)) {
		_recordMgr->deleteRecord(record);
		return NULL;
	}
	// In the rare case of Bam records where both the read and it's mate failed to map,
	// Ignore the record. Delete and return null
	if (!(record->isUnmapped() && record->isMateUnmapped())) {
		if (!record->coordsValid()) {
			cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
			exit(1);
		}

		//test for sorted order, if necessary.
		if (_context->getSortedInput()) {
			testInputSortOrder(record);
		}
	}
	assignChromId(record);
	_totalRecordLength += (unsigned long)(record->getEndPos() - record->getStartPos());
	return record;
}
Esempio n. 2
0
Record *FileRecordMgr::getNextRecord(RecordKeyList *keyList)
{
	if (!_fileReader->isOpen()) {
		return NULL;
	}
	if (!_fileReader->readEntry()) {
		return NULL;
	}
	Record *record = NULL;
	record = _recordMgr->allocateRecord();
	if (!record->initFromFile(_fileReader)) {
		_recordMgr->deleteRecord(record);
		return NULL;
	}

	// If the record is unmapped, don't test for valid coords or sort order,
	// but still return it so the -v (noHit) option and the like will still
	// see it.

	if (!record->isUnmapped()) {
		if (!record->coordsValid()) {
			cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
			exit(1);
		}

		//test for sorted order, if necessary.
		if (_isSortedInput) {
			testInputSortOrder(record);
		}
	}
	assignChromId(record);
	_totalRecordLength += (unsigned long)(record->getEndPos() - record->getStartPos());
	if (keyList != NULL) {
		keyList->setKey(record);
	}
	return record;
}