// ValidateReaders checks that all the readers point to BAM files representing
// alignments against the same set of reference sequences, and that the
// sequences are identically ordered. If these checks fail the operation of
// the multireader is undefined, so we force program exit.
void BamMultiReader::ValidateReaders(void) const {
int firstRefCount = readers.front().first->GetReferenceCount();
BamTools::RefVector firstRefData = readers.front().first->GetReferenceData();
for (vector<pair<BamReader*, BamAlignment*> >::const_iterator it = readers.begin(); it != readers.end(); ++it) {
BamReader* reader = it->first;
BamTools::RefVector currentRefData = reader->GetReferenceData();
BamTools::RefVector::const_iterator f = firstRefData.begin();
BamTools::RefVector::const_iterator c = currentRefData.begin();
if (reader->GetReferenceCount() != firstRefCount || firstRefData.size() != currentRefData.size()) {
cerr << "ERROR: mismatched number of references in " << reader->GetFilename()
<< " expected " << firstRefCount
<< " reference sequences but only found " << reader->GetReferenceCount() << endl;
exit(1);
}
// this will be ok; we just checked above that we have identically-sized sets of references
// here we simply check if they are all, in fact, equal in content
while (f != firstRefData.end()) {
if (f->RefName != c->RefName || f->RefLength != c->RefLength) {
cerr << "ERROR: mismatched references found in " << reader->GetFilename()
<< " expected: " << endl;
for (BamTools::RefVector::const_iterator a = firstRefData.begin(); a != firstRefData.end(); ++a)
cerr << a->RefName << " " << a->RefLength << endl;
cerr << "but found: " << endl;
for (BamTools::RefVector::const_iterator a = currentRefData.begin(); a != currentRefData.end(); ++a)
cerr << a->RefName << " " << a->RefLength << endl;
exit(1);
}
++f; ++c;
}
}
}
// ValidateReaders checks that all the readers point to BAM files representing
// alignments against the same set of reference sequences, and that the
// sequences are identically ordered. If these checks fail the operation of
// the multireader is undefined, so we force program exit.
bool BamMultiReaderPrivate::ValidateReaders() const
{
m_errorString.clear();
// skip if 0 or 1 readers opened
if (m_readers.empty() || (m_readers.size() == 1)) return true;
// retrieve first reader
const MergeItem& firstItem = m_readers.front();
const BamReader* firstReader = firstItem.Reader;
if (firstReader == 0) return false;
// retrieve first reader's header data
const SamHeader& firstReaderHeader = firstReader->GetHeader();
const std::string& firstReaderSortOrder = firstReaderHeader.SortOrder;
// retrieve first reader's reference data
const RefVector& firstReaderRefData = firstReader->GetReferenceData();
const int firstReaderRefCount = firstReader->GetReferenceCount();
const int firstReaderRefSize = firstReaderRefData.size();
// iterate over all readers
std::vector<MergeItem>::const_iterator readerIter = m_readers.begin();
std::vector<MergeItem>::const_iterator readerEnd = m_readers.end();
for (; readerIter != readerEnd; ++readerIter) {
const MergeItem& item = (*readerIter);
BamReader* reader = item.Reader;
if (reader == 0) continue;
// get current reader's header data
const SamHeader& currentReaderHeader = reader->GetHeader();
const std::string& currentReaderSortOrder = currentReaderHeader.SortOrder;
// check compatible sort order
if (currentReaderSortOrder != firstReaderSortOrder) {
const std::string message =
std::string("mismatched sort order in ") + reader->GetFilename() + ", expected " +
firstReaderSortOrder + ", but found " + currentReaderSortOrder;
SetErrorString("BamMultiReader::ValidateReaders", message);
return false;
}
// get current reader's reference data
const RefVector currentReaderRefData = reader->GetReferenceData();
const int currentReaderRefCount = reader->GetReferenceCount();
const int currentReaderRefSize = currentReaderRefData.size();
// init reference data iterators
RefVector::const_iterator firstRefIter = firstReaderRefData.begin();
RefVector::const_iterator firstRefEnd = firstReaderRefData.end();
RefVector::const_iterator currentRefIter = currentReaderRefData.begin();
// compare reference counts from BamReader ( & container size, in case of BR error)
if ((currentReaderRefCount != firstReaderRefCount) ||
(firstReaderRefSize != currentReaderRefSize)) {
std::stringstream s;
s << "mismatched reference count in " << reader->GetFilename() << ", expected "
<< firstReaderRefCount << ", but found " << currentReaderRefCount;
SetErrorString("BamMultiReader::ValidateReaders", s.str());
return false;
}
// this will be ok; we just checked above that we have identically-sized sets of references
// here we simply check if they are all, in fact, equal in content
while (firstRefIter != firstRefEnd) {
const RefData& firstRef = (*firstRefIter);
const RefData& currentRef = (*currentRefIter);
// compare reference name & length
if ((firstRef.RefName != currentRef.RefName) ||
(firstRef.RefLength != currentRef.RefLength)) {
std::stringstream s;
s << "mismatched references found in" << reader->GetFilename()
<< "expected: " << std::endl;
// print first reader's reference data
RefVector::const_iterator refIter = firstReaderRefData.begin();
RefVector::const_iterator refEnd = firstReaderRefData.end();
for (; refIter != refEnd; ++refIter) {
const RefData& entry = (*refIter);
std::stringstream s;
s << entry.RefName << ' ' << std::endl;
}
s << "but found: " << std::endl;
// print current reader's reference data
refIter = currentReaderRefData.begin();
refEnd = currentReaderRefData.end();
for (; refIter != refEnd; ++refIter) {
const RefData& entry = (*refIter);
s << entry.RefName << ' ' << entry.RefLength << std::endl;
}
SetErrorString("BamMultiReader::ValidateReaders", s.str());
return false;
}
// update iterators
++firstRefIter;
++currentRefIter;
}
}
// if we get here, everything checks out
return true;
}
