int main(int argc, char* argv[]) {
string alignmentFileName, geneDBFileName;
if (argc < 3) {
cout << "usage: printDuplicates alignemntFile genedb " << endl;
exit(1);
}
alignmentFileName = argv[1];
geneDBFileName = argv[2];
GeneDB genedb;
genedb.Read(geneDBFileName);
genedb.IndexChromosomes();
ifstream alignmentIn;
CrucialOpen(alignmentFileName, alignmentIn, std::ios::in);
while(alignmentIn) {
string line;
getline(alignmentIn, line);
if (line == "###") {
// found the end of an entry
}
else {
string chrName, genome, source;
int start, end, identity;
char a, strand, b;
string annotationString;
stringstream strm(line);
strm >> chrName >> genome >> source >> start >> end >> a >> strand >> b >> annotationString;
vector<string> annotations;
if (source != "exon") {
continue;
}
ParseSeparatedList(annotationString, annotations, ';');
GeneDBChromosome *chromosomePtr;
chromosomePtr = genedb.Find(chrName);
if (chromosomePtr == NULL) {
cout << "chromosome " << chromosomePtr << " not found in database." << endl;
continue;
}
int exonIndex;
if ( chromosomePtr->LookupIndexByStart(start, exonIndex) ) {
if (chromosomePtr->exons[exonIndex].start <= start and
chromosomePtr->exons[exonIndex].end >= end) {
chromosomePtr->exons[exonIndex].Print(cout);
}
}
else {
}
}
}
}
bool ParsePBIReadName(std::string &readName, std::string &movieName, int &holeNumber) {
std::vector<std::string> tokens;
ParseSeparatedList(readName, tokens, '/');
if (tokens.size() < 2) {
movieName = "";
holeNumber = 0;
return false;
}
else {
movieName = tokens[0];
holeNumber = atoi(tokens[1].c_str());
return true;
}
}
