void Styler_Syntax::DoStyle(StyleRun& sr, unsigned int offset, const auto_vector<stxmatch>& matches) { const unsigned int rstart = sr.GetRunStart(); const unsigned int rend = sr.GetRunEnd(); const unsigned int styleStart = offset < rstart ? rstart - offset : 0; const stxmatch m(wxEmptyString, NULL, styleStart, 0, 0, 0, NULL); if (matches.empty()) return; auto_vector<stxmatch>::const_iterator p = lower_bound(matches.begin(), matches.end(), &m, stxmatch_start_less()); if (p != matches.begin()) --p; for (; p != matches.end(); ++p) { const unsigned int mStart = (*p)->start+offset; const unsigned int mEnd = (*p)->end+offset; if (mStart > rend) break; // Check for overlap if (mEnd > rstart && mStart < rend) { const unsigned int start = wxMax(rstart, mStart); const unsigned int end = wxMin(rend, mEnd); const style* st = (*p)->st; if (st) { if (st->foregroundcolor != wxNullColour) sr.SetForegroundColor(start, end, st->foregroundcolor); if (st->backgroundcolor != wxNullColour) { sr.SetBackgroundColor(start, end, st->backgroundcolor); if (mEnd > rend) sr.SetExtendBgColor(st->backgroundcolor); } if (st->fontflags != wxFONTFLAG_DEFAULT) sr.SetFontStyle(start, end, st->fontflags); } // Check if there are submatches if ((*p)->subMatch.get()) { DoStyle(sr, (*p)->start+offset, (*p)->subMatch->matches); } } } }
int main(int argc,char** argv) { const char* exonFile=0; int optind=1; char* faidxfile=NULL; while(optind < argc) { if(strcmp(argv[optind],"-h")==0) { this->usage(cerr,argc,argv); return(EXIT_FAILURE); } else if(strcmp(argv[optind],"-f")==0 && optind+1< argc) { faidxfile = argv[++optind]; } else if(strcmp(argv[optind],"-g")==0 && optind+1< argc) { exonFile=argv[++optind]; } else if(strcmp(argv[optind],"--")==0) { ++optind; break; } else if(argv[optind][0]=='-') { cerr << "unknown option '" << argv[optind]<< "'" << endl; this->usage(cerr,argc,argv); return EXIT_FAILURE; } else { break; } ++optind; } if(faidxfile==0) { cerr << "no fasta genome defined." << endl; this->usage(cerr,argc,argv); return EXIT_FAILURE; } this->faidx.reset(new IndexedFasta(faidxfile)); if(exonFile==0) { cerr << "no bed for exons defined." << endl; this->usage(cerr,argc,argv); return EXIT_FAILURE; } if(optind==argc) { cerr << "BAM files missing"<< endl; return EXIT_FAILURE; } else { while(optind< argc) { char* bamfile=argv[optind++]; WHERE("Open "<< bamfile); BamFile2* bam=new BamFile2(bamfile); this->bamFiles.push_back(bam); bam->open(true); } } //open exon file igzstreambuf buf(exonFile); istream in(&buf); this->readExons(in); buf.close(); if(exons.empty()) { cerr << "No exon.\n"; return EXIT_FAILURE; } run(); for(size_t i=0;i< bamFiles.size();++i) { bamFiles[i]->close(); } return EXIT_SUCCESS; }
void run(std::istream& in) { vector<string> tokens; string line; int chromCol=0; int posCol=1; int idCol=2; int refCol=3; int altCol=4; int sampleCol=-1; while(getline(in,line,'\n')) { if(AbstractApplication::stopping()) break; if(line.empty() || line[0]=='#') continue; tokenizer.split(line,tokens); string chrom=tokens[chromCol]; chat *p2; int pos=(int)strtol(tokens[posCol].c_str(),&p2,10); string id=tokens[idCol]; string ref=tokens[refCol]; string alt=tokens[altCol]; string sampleName=tokens[sampleCol]; Row* therow=NULL; if(!rows.empty() && rows.back()->pos->chrom.compare(chrom)==0 && rows.back()->pos->pos==pos && rows.back()->ref.compare(ref)==0 && rows.back()->alt.compare(alt)==0 ) { therow=rows.back(); } else { therow=new Row; therow->pos=new ChromPosition(chrom,pos); therow->id.assign(id); therow->ref.assign(ref); therow->alt.assign(alt); rows.push_back(therow); } int index_sample=0; if(sampleCol==-1) { if(sample2col.empty()) { Sample* sample=new Sample; sample->name.assign("Sample"); sample->column_index=0; samples.push_back(sample); } index_sample=0; } else { map<string,Sample*>::iterator r= sample2col.find(sampleName); if(r==sample2col.end()) { Sample* sample=new Sample; sample->name.assign(sampleName); sample->column_index=sample2col.size(); index_sample=sample->column_index; samples.push_back(sample); sample2col.put(sample->name,sample); } else { index_sample=r->second->column_index; } } if(index_sample>=therow->data.size()) { therow->data.resize(index_sample+1); } Data* data=new Data; therow->data.assign(index_sample,data); } }