void CSamMdFormatter::FormatDeletion( const char * t, int count )
{
FormatTerminal();
m_data += "^";
while( count-- ) {
char ref = CIupacnaBase( CNcbi8naBase( t++ ) );
switch( ref ) {
case 'A': case 'C': case 'G': case 'T': m_data += ref; break;
default: m_data += 'N';
}
}
}
void CSamMdFormatter::FormatAligned( const char * s, const char * t, int count )
{
while( count-- ) {
char query = *s++;
char subj = CIupacnaBase( CNcbi8naBase( t++ ) );
if( query == subj ) { ++m_keepCount; }
else {
FormatTerminal();
switch( subj ) {
case 'A': case 'C': case 'G': case 'T': m_data += subj; break;
default: m_data += 'N';
}
}
}
}
static CIupacnaBase Any() { return CIupacnaBase('N'); }
int CAlignTest::Execute()
{
CScoreTbl scoreTbl( m_identityScore, m_mismatchScore, m_gapOpeningScore, m_gapExtentionScore );
auto_ptr<IAligner> aligner( CreateAligner( m_algo, &scoreTbl ) );
CAlignerBase::SetPrintDebug( true );
if( m_flags & fAlign_colorspace )
THROW( logic_error, "Colorspace option is not immplemented" );
if( GetArgIndex() + 2 > GetArgCount() )
THROW( runtime_error, "Two sequences are required!" );
if( m_offsetQuery < 0 || m_offsetSubject < 0 )
THROW( runtime_error, "Offset should never be negative" );
const char * qs = GetArg( GetArgIndex() );
const char * ss = GetArg( GetArgIndex() + 1 );
int ql = strlen( qs );
int sl = strlen( ss );
cerr << DISPLAY( qs ) << DISPLAY( ql ) << endl;
cerr << DISPLAY( ss ) << DISPLAY( sl ) << endl;
if( ql == 0 || sl == 0 )
THROW( runtime_error, "Sequences should have at least one base!" );
vector<char> query;
vector<char> subject;
query.reserve( ql );
subject.reserve( sl );
while( *qs ) query.push_back( CNcbi8naBase( CIupacnaBase( *qs++ ) ) );
while( *ss ) subject.push_back( CNcbi8naBase( CIupacnaBase( *ss++ ) ) );
qs = &query[0];
ss = &subject[0];
qs += m_offsetQuery; ql -= m_offsetQuery;
ss += m_offsetSubject; sl -= m_offsetSubject;
if( ql <= 0 || sl <= 0 )
THROW( runtime_error, "Offset is too big" );
if( GetFlags( fQuery_reverse ) ) { qs = qs + ql; ql = -ql; }
if( GetFlags( fSubject_reverse ) ) { ss = ss + sl; sl = -sl; }
int aflags = CAlignerBase::fComputePicture | CAlignerBase::fComputeScore | CAlignerBase::fPictureSubjectStrand;
aligner->SetBestPossibleQueryScore( min( ql, sl ) * m_identityScore );
aligner->Align( CSeqCoding::eCoding_ncbi8na, qs, ql, CSeqCoding::eCoding_ncbi8na, ss, sl, aflags );
const CAlignerBase& abase = aligner->GetAlignerBase();
cout << ( GetFlags( fQuery_reverse ) ? 3 : 5 ) << "'=" << abase.GetQueryString() << "=" << ( GetFlags( fQuery_reverse ) ? 5 : 3 ) << "'\n";
cout << " " << abase.GetAlignmentString() << " "
<< " i=" << abase.GetIdentityCount()
<< ", m=" << abase.GetMismatchCount()
<< ", g=" << abase.GetIndelCount()
<< ", s=" << abase.GetRawScore() << "/" << abase.GetBestQueryScore() << "=" << abase.GetScore() << "%\n";
cout << "5'=" << abase.GetSubjectString() << "=3'\n";
return 0;
}
