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;
}
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;
}