void CAgpCompSpanSplitter::SaveRow(const string& s, CRef<CAgpRow> row, TRangeColl* runs_of_Ns)
{
if( row ) {
comp_or_gap_printed=true;
if(object_name != row->GetObject() ) {
object_name = row->GetObject();
part_number = 1; // row->GetPartNumber();
}
CRef<CAgpRow> tmp_row( row->Clone() );
if(runs_of_Ns && runs_of_Ns->size()) {
if( row->GetVersion() == eAgpVersion_auto ) {
cerr << "FATAL: need AGP version (for adding gap lines). Please use -v 1.1 or -v 2.0\n";
exit(1);
}
/*
CAgpRow tmp_gap_row = *row; // to retain the object name
tmp_gap_row.GetComponentType() = "N";
tmp_gap_row.is_gap = true;
tmp_gap_row.linkage = true;
tmp_gap_row.gap_type = row->GetVersion() == eAgpVersion_1_1 ? CAgpRow::eGapFragment : CAgpRow::eGapScaffold;
tmp_gap_row.linkage_evidence_flags = CAgpRow::fLinkageEvidence_unspecified;'
*/
CRef<CAgpRow> tmp_gap_row( CAgpRow::New(NULL, row->GetVersion(), NULL) );
tmp_gap_row->FromString(
row->GetObject()+
"\t1\t100\t1\tN\t100\t"+
string(row->GetVersion() == eAgpVersion_1_1 ? "fragment\tyes\t" : "scaffold\tyes\tunspecified")
);
int comp2obj_ofs = row->object_beg - row->component_beg;
for(TRangeColl::const_iterator it = runs_of_Ns->begin(); it != runs_of_Ns->end(); ++it) {
if( (TSeqPos) tmp_row->component_beg < it->GetFrom() ) {
// component line
tmp_row->component_end = it->GetFrom()-1;
tmp_row->object_end = comp2obj_ofs + tmp_row->component_end;
tmp_row->part_number = part_number;
(*m_out) << tmp_row->ToString() << endl;
part_number++;
}
// gap line
tmp_gap_row->object_beg = comp2obj_ofs + it->GetFrom();
tmp_gap_row->object_end = comp2obj_ofs + it->GetTo();
tmp_gap_row->gap_length = it->GetTo() - it->GetFrom() + 1;
tmp_gap_row->part_number = part_number;
(*m_out) << tmp_gap_row->ToString(true) << endl; // true: use linkage_evidence_flags
part_number++;
tmp_row->component_beg = it->GetTo() + 1;
tmp_row->object_beg = comp2obj_ofs + tmp_row->component_beg;
}
if(tmp_row->component_beg <= row->component_end) {
// this component does not end with Ns => need to print the final component span
tmp_row->component_end = row->component_end;
tmp_row->object_end = row->object_end;
}
else return; // ends with Ns => skip printing the component row below
}
tmp_row->part_number = part_number;
(*m_out) << tmp_row->ToString() << endl;
part_number++;
}
else if(!comp_or_gap_printed){
// comment line (only at the head of file, to comply with AGP 2.0)
(*m_out) << s << endl;
}
}
