int Application::main(int argc,char *argv[])
{
// Process command line
cmd=new CommandLine(argc,argv,"");
if(cmd->numArgs()!=2)
throw String("\ndelete-target-gaps <in.maf> <target-name>\n");
String mafFile=cmd->arg(0);
String targetName=cmd->arg(1);
// Setting up alphabet
alphabet=&DnaDashDotAlphabet::global();
gapSymbols.addMember(alphabet->lookup('-'));
gapSymbols.addMember(alphabet->lookup('.'));
gapSymbols.addMember(alphabet->lookup('N'));
alphabetMap=new DropGapMapping(*alphabet,PureDnaAlphabet::global());
// Load the alignments
//int rootID=phylogeny->getRoot()->getID();
alignment=NULL;
ifstream is(mafFile.c_str());
if(!is.good()) throw String("Can't open file ")+mafFile;
while(!is.eof()) {
MultiAlignment *a=new MultiAlignment;
a->loadMAF(is);
if(a->getNumTracks()>0) {
a->toupper();
MultSeqAlignment *m=new MultSeqAlignment(*a,*alphabet,gapSymbols);
int rootID=m->getTrackByName(targetName).getID();
m->deleteTargetGaps(rootID);
if(!alignment) alignment=m;
else {
alignment->append(*m);
delete m;
}
}
delete a;
}
is.close();
// Emit the processed alignment
alignment->printSlice(cout,0,alignment->getLength(),'+',60);
return 0;
}
