Bed2Fa::Bed2Fa(bool useName, const string &dbFile, const string &bedFile,
const string &fastaOutFile, bool useFasta, bool useStrand) {
_useName = useName;
_dbFile = dbFile;
_bedFile = bedFile;
_fastaOutFile = fastaOutFile;
_useFasta = useFasta;
_useStrand = useStrand;
_bed = new BedFile(_bedFile);
// Figure out what the output file should be.
if (fastaOutFile == "stdout") {
_faOut = &cout;
}
else {
// Make sure we can open the file.
ofstream fa(fastaOutFile.c_str(), ios::out);
if ( !fa ) {
cerr << "Error: The requested fasta output file (" << fastaOutFile << ") could not be opened. Exiting!" << endl;
exit (1);
}
else {
fa.close();
_faOut = new ofstream(fastaOutFile.c_str(), ios::out);
}
}
// Extract the requested intervals from the FASTA input file.
ExtractDNA();
}
Bed2Fa::Bed2Fa(bool useName, const string &dbFile,
const string &bedFile, const string &fastaOutFile,
bool useFasta, bool useStrand,
bool useBlocks, bool useFullHeader,
bool useBedOut) :
_useName(useName),
_dbFile(dbFile),
_bedFile(bedFile),
_fastaOutFile(fastaOutFile),
_useFasta(useFasta),
_useBedOut(useBedOut),
_useStrand(useStrand),
_useBlocks(useBlocks),
_useFullHeader(useFullHeader)
{
_bed = new BedFile(_bedFile);
// Figure out what the output file should be.
if (fastaOutFile == "stdout" || fastaOutFile == "-") {
_faOut = &cout;
}
else {
// Make sure we can open the file.
ofstream fa(fastaOutFile.c_str(), ios::out);
if ( !fa ) {
cerr << "Error: The requested fasta output file ("
<< fastaOutFile << ") could not be opened. Exiting!"
<< endl;
exit (1);
}
else {
fa.close();
_faOut = new ofstream(fastaOutFile.c_str(), ios::out);
}
}
// Extract the requested intervals from the FASTA input file.
ExtractDNA();
}
