C++ BamReader::GetReferenceCount方法代码示例

// 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());
//.........这里部分代码省略.........