MdStringComputationContext()
: T0(256,false), T1(256,false), nm(0)
{
std::fill(T0.begin(),T0.end(),4);
std::fill(T1.begin(),T1.end(),5);
T0['A'] = T0['a'] = T1['A'] = T1['a'] = 0;
T0['C'] = T0['c'] = T1['C'] = T1['c'] = 1;
T0['G'] = T0['g'] = T1['G'] = T1['g'] = 2;
T0['T'] = T0['t'] = T1['T'] = T1['t'] = 3;
auxvec.set("MD");
auxvec.set("NM");
}
void init()
{
rgfilter.set("RG");
pgfilter.set("PG");
std::vector < std::vector<libmaus2::bambam::Chromosome> const * > V;
std::vector < std::vector<libmaus2::bambam::ReadGroup> const * > R;
std::vector< std::string const * > H;
for ( uint64_t i = 0; i < inputbamheaders.size(); ++i )
{
libmaus2::bambam::BamHeader const & header = *inputbamheaders[i];
V.push_back( & (header.getChromosomes()) );
R.push_back( & (header.getReadGroups()) );
H.push_back( & (header.text) );
std::string const SO = libmaus2::bambam::BamHeader::getSortOrderStatic(header.text);
orderedCoordinates = orderedCoordinates && (SO == "coordinate");
orderedNames = orderedNames && (SO == "queryname");
}
libmaus2::bambam::ChromosomeVectorMerge::unique_ptr_type tchromosomeMergeInfo(new libmaus2::bambam::ChromosomeVectorMerge(V));
chromosomeMergeInfo = UNIQUE_PTR_MOVE(tchromosomeMergeInfo);
libmaus2::bambam::ReadGroupVectorMerge::unique_ptr_type treadGroupMergeInfo(new libmaus2::bambam::ReadGroupVectorMerge(R));
readGroupMergeInfo = UNIQUE_PTR_MOVE(treadGroupMergeInfo);
libmaus2::bambam::ProgramHeaderLinesMerge::unique_ptr_type tprogramHeaderLinesMergeInfo(new libmaus2::bambam::ProgramHeaderLinesMerge(H));
programHeaderLinesMergeInfo = UNIQUE_PTR_MOVE(tprogramHeaderLinesMergeInfo);
// get HD line fields
std::vector < std::pair<std::string,std::string> > VHDP;
for ( uint64_t i = 0; i < inputbamheaders.size(); ++i )
{
std::vector<libmaus2::bambam::HeaderLine> VHD = libmaus2::bambam::HeaderLine::extractLinesByType(inputbamheaders[i]->text,"HD");
if ( VHD.size() )
{
libmaus2::bambam::HeaderLine const & H = VHD.front();
for ( std::map<std::string,std::string>::const_iterator ita = H.M.begin(); ita != H.M.end(); ++ita )
VHDP.push_back(*ita);
}
}
// sort by tag
std::sort(VHDP.begin(),VHDP.end());
// extract consistent tags present in all HD lines
std::map<std::string,std::string> MHD;
uint64_t l = 0;
while ( l < VHDP.size() )
{
uint64_t h = l+1;
while ( h < VHDP.size() && VHDP[l].first == VHDP[h].first )
++h;
// we have the right number
if ( h-l == inputbamheaders.size() )
{
// check for consistent value
bool eq = true;
for ( uint64_t i = l+1; i < h; ++i )
eq = eq && (VHDP[i].second == VHDP[l].second);
if ( eq )
MHD[VHDP[l].first] = VHDP[l].second;
}
l = h;
}
std::string const VN = (MHD.find("VN") != MHD.end()) ? MHD.find("VN")->second : "1.5";
std::ostringstream headertextstr;
headertextstr << "@HD\tVN:" << VN;
if ( inputbamheaders.size() == 1 )
headertextstr << "\tSO:" << libmaus2::bambam::BamHeader::getSortOrderStatic(inputbamheaders[0]->text);
else
headertextstr << "\tSO:unknown";
for ( std::map<std::string,std::string>::const_iterator ita = MHD.begin(); ita != MHD.end(); ++ita )
{
std::string const & key = ita->first;
if ( key != "VN" && key != "SO" )
headertextstr << "\t" << key << ":" << ita->second;
}
headertextstr << "\n";
for ( uint64_t i = 0; i < chromosomeMergeInfo->chromosomes.size(); ++i )
headertextstr << chromosomeMergeInfo->chromosomes[i].createLine() << "\n";
for ( uint64_t i = 0; i < readGroupMergeInfo->readgroups.size(); ++i )
headertextstr << readGroupMergeInfo->readgroups[i].createLine() << "\n";
headertextstr << programHeaderLinesMergeInfo->PGtext;
std::vector<std::string> otherlines;
for ( uint64_t i = 0; i < inputbamheaders.size(); ++i )
{
std::vector<libmaus2::bambam::HeaderLine> lines = libmaus2::bambam::HeaderLine::extractLines(inputbamheaders[i]->text);
for ( uint64_t j = 0; j < lines.size(); ++j )
{
libmaus2::bambam::HeaderLine const & line = lines[j];
if (
line.type != "HD" &&
line.type != "SQ" &&
line.type != "RG" &&
line.type != "PG"
)
{
otherlines.push_back(line.line);
}
}
}
std::set<std::string> otherlinesseen;
for ( uint64_t i = 0; i < otherlines.size(); ++i )
if ( otherlinesseen.find(otherlines[i]) == otherlinesseen.end() )
{
headertextstr << otherlines[i] << std::endl;
otherlinesseen.insert(otherlines[i]);
}
// std::cerr << std::string(80,'-') << std::endl;
std::string const headertext = headertextstr.str();
::libmaus2::bambam::BamHeader::unique_ptr_type tbamheader(new ::libmaus2::bambam::BamHeader(headertext));
bamheader = UNIQUE_PTR_MOVE(tbamheader);
// std::cerr << "topologically sorted: " << chromosomeMergeInfo->topological << std::endl;
// std::cerr << bamheader->text;
}