bool checkCigarValid(
::libmaus::bambam::BamAlignment const & alignment,
::libmaus::bambam::BamHeader const & bamheader,
::libmaus::autoarray::AutoArray < ::libmaus::autoarray::AutoArray<uint8_t>::unique_ptr_type > const & text
)
{
if ( alignment.isUnmap() )
return true;
if ( ! alignment.isCigarLengthConsistent() )
{
std::cerr << "[E] inconsistent cigar " << alignment.getCigarString() << " for " << alignment.getName() << std::endl;
return false;
}
if ( alignment.getRefID() < 0 || alignment.getRefID() >= static_cast<int64_t>(bamheader.chromosomes.size()) )
{
std::cerr << "[E] reference id " << alignment.getRefID() << " out of range for " << alignment.getName() << std::endl;
return false;
}
::libmaus::autoarray::AutoArray<uint8_t> const & ctext = *(text[alignment.getRefID()]);
int64_t refpos = alignment.getPos();
int64_t seqpos = 0;
bool alok = true;
std::string const read = alignment.getRead();
for ( uint64_t i = 0; alok && i < alignment.getNCigar(); ++i )
{
char const cop = alignment.getCigarFieldOpAsChar(i);
int64_t const clen = alignment.getCigarFieldLength(i);
switch ( cop )
{
// match/mismatch, increment both
case '=':
case 'X':
case 'M':
{
for ( int64_t j = 0; alok && j < clen; ++j, ++refpos, ++ seqpos )
{
if ( refpos < 0 || refpos >= static_cast<int64_t>(ctext.size()) )
{
std::cerr << "[E] " << cop << " operation outside of chromosome coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
else if ( seqpos >= alignment.getLseq() )
{
std::cerr << "[E] " << cop << " operation outside of sequence coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
else if ( cop == '=' && toupper(ctext[refpos]) != toupper(read[seqpos]) )
{
std::cerr << "[E] " << cop << " operation but mismatch between reference and query." << std::endl;
alok = false;
}
else if ( cop == 'X' && toupper(ctext[refpos]) == toupper(read[seqpos]) )
{
std::cerr << "[E] " << cop << " operation but mismatch between reference and query." << std::endl;
alok = false;
}
}
break;
}
// insert into reference, increment seq
case 'P':
case 'I':
{
for ( int64_t j = 0; alok && j < clen; ++j, ++seqpos )
{
if ( seqpos >= alignment.getLseq() )
{
std::cerr << "[E] " << cop << " operation outside of sequence coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
}
break;
}
// delete from reference, increment ref
case 'D':
{
for ( int64_t j = 0; alok && j < clen; ++j, ++refpos )
{
if ( refpos < 0 || refpos >= static_cast<int64_t>(ctext.size()) )
{
std::cerr << "[E] " << cop << " operation outside of reference coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
}
break;
}
// soft clipping, increment seq
case 'S':
{
for ( int64_t j = 0; alok && j < clen; ++j, ++seqpos )
{
if ( seqpos >= alignment.getLseq() )
{
std::cerr << "[E] " << cop << " operation outside of sequence coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
}
break;
}
// hard clipping, do nothing
case 'H':
{
break;
}
// skip region in reference, increment ref
case 'N':
{
for ( int64_t j = 0; alok && j < clen; ++j, ++refpos )
{
if ( refpos < 0 || refpos >= static_cast<int64_t>(ctext.size()) )
{
std::cerr << "[E] " << cop << " operation outside of reference coordinate range " << " for " << alignment.getName() << std::endl;
alok = false;
}
}
break;
}
}
}
return alok;
}
