int main(int argc, char* argv[]) {
string plsFileName, fastaOutName;
if (argc < 2) {
cout << "usage: pls2fasta file.pls.h5 file.fasta " << endl;
cout << "Print reads stored in hdf as fasta." << endl;
exit(1);
}
vector<string> plsFileNames;
plsFileName = argv[1];
fastaOutName = argv[2];
if (FileOfFileNames::IsFOFN(plsFileName)) {
FileOfFileNames::FOFNToList(plsFileName, plsFileNames);
}
else {
plsFileNames.push_back(plsFileName);
}
int plsFileIndex;
for (plsFileIndex = 0; plsFileIndex < plsFileNames.size(); plsFileIndex++) {
ReaderAgglomerate reader;
reader.IgnoreCCS();
reader.Initialize(plsFileNames[plsFileIndex]);
ofstream fastaOut;
CrucialOpen(fastaOutName, fastaOut);
SMRTSequence seq;
int seqIndex = 0;
while (reader.GetNext(seq)) {
seq.PrintQualSeq(fastaOut);
}
}
}
