// locate (& load) index files for BAM readers that don't already have one loaded
bool BamMultiReaderPrivate::LocateIndexes(const BamIndex::IndexType& preferredType)
{
bool errorsEncountered = false;
m_errorString.clear();
// iterate over readers
std::vector<MergeItem>::iterator readerIter = m_readers.begin();
std::vector<MergeItem>::iterator readerEnd = m_readers.end();
for (; readerIter != readerEnd; ++readerIter) {
MergeItem& item = (*readerIter);
BamReader* reader = item.Reader;
if (reader == 0) continue;
// if reader has no index, try to locate one
if (!reader->HasIndex()) {
if (!reader->LocateIndex(preferredType)) {
m_errorString.append(1, '\t');
m_errorString.append(reader->GetErrorString());
m_errorString.append(1, '\n');
errorsEncountered = true;
}
}
}
// check for errors encountered before returning success/fail
if (errorsEncountered) {
const std::string currentError = m_errorString;
const std::string message =
std::string("error while locating index files: \n") + currentError;
SetErrorString("BamMultiReader::LocatingIndexes", message);
return false;
} else
return true;
}
// creates index files for BAM files that don't have them
bool BamMultiReaderPrivate::CreateIndexes(const BamIndex::IndexType& type) {
bool errorsEncountered = false;
m_errorString.clear();
// iterate over readers
vector<MergeItem>::iterator itemIter = m_readers.begin();
vector<MergeItem>::iterator itemEnd = m_readers.end();
for ( ; itemIter != itemEnd; ++itemIter ) {
MergeItem& item = (*itemIter);
BamReader* reader = item.Reader;
if ( reader == 0 ) continue;
// if reader doesn't have an index, create one
if ( !reader->HasIndex() ) {
if ( !reader->CreateIndex(type) ) {
m_errorString.append(1, '\t');
m_errorString.append(reader->GetErrorString());
m_errorString.append(1, '\n');
errorsEncountered = true;
}
}
}
// check for errors encountered before returning success/fail
if ( errorsEncountered ) {
const string currentError = m_errorString;
const string message = string("error while creating index files: ") + "\n" + currentError;
SetErrorString("BamMultiReader::CreateIndexes", message);
return false;
} else
return true;
}
void getRefAltCounts(BamReader& reader, const BamRegion &r, int& nReadsRef, int& nReadsAlt, vcfRecord record)
{
// Return the number of reads aligning reference and alternate allele
if (!reader.IsOpen())
{
cout << "Can't access BAM file" << endl;
return;
}
if (!reader.HasIndex())
{
cout << "Can't access BAM file index" << endl;
return;
}
BamAlignment al;
assert(reader.SetRegion(r));
while ( reader.GetNextAlignment(al) )
{
// int baseAlignment = al.Position;
bool found = false;
int index = 0;
int indexPosition = al.Position;
for ( size_t i = 0; i < al.CigarData.size(); i++ )
{
switch ( al.CigarData.at(i).Type )
{
case 'H' : break; // Hard clip
case 'S' : break; // Soft clip
case 'M' : // Match or mismatch
case 'D' :
case 'N' :
case 'P' :
if ( indexPosition + al.CigarData.at(i).Length > (record.pos-1) )
{
index += (record.pos-1) - indexPosition;
found = true;
}
else
{
index += al.CigarData.at(i).Length;
indexPosition += al.CigarData.at(i).Length;
}
break;
case 'I' :
index += al.CigarData.at(i).Length;
break;
}
if ( found )
break;
}
if ( !found || index >= al.AlignedBases.size())
{
cerr << "Problem with finding variant in read:\n";
for ( unsigned int i = 0; i < al.AlignedBases.size(); i++ )
cout << al.AlignedBases.at(i) << " ";
cout << endl;
for ( unsigned int i = 0; i < al.CigarData.size(); i++ )
cout << al.CigarData.at(i).Type << al.CigarData.at(i).Length << " ";
cout << endl;
cout << "Read position: " << al.RefID+1 << " " << al.Position+1 << endl;
cout << "Variant position: " << record.chr << " " << record.pos << endl;
exit(1);
}
if ( al.AlignedBases.at(index) == record.ref.at(0) )
nReadsRef++;
else if ( al.AlignedBases.at(index) == record.alt.at(0) )
nReadsAlt++;
}
}
