I'm quite new to C++, but I'm used to some coding with R language. I started, a few weeks ago, to put together a small application that should copy and rename file pairs (.seq/.ab1). Result from a DNA sequencer analysis (renaming hundreds of them manually would be a real time waste, specially because we have lists with their new names).
Everything seemed to be fine, but the new files (those copied) appear with a "special character" in their names (right before the file type), it seeems like a space, but its not (I've replaced it with a space, and the file opened correctly). After deleting it the file can be oppened by its associated application, but with it, the aplication acusses the file to be corrupted.
The issue seems to come from the code related to ostringstream::str member function, but I honestly don't know how to fix it. I wonder if its not inserting a null character there, before I append the file type...
Here is the part of the code responsible. It gets the old and new names from a 2 column csv file, data separated by ";". Original data, and new (renamed files) data are kept in diferent directories, thats the reason I need to create a string with each file path inside a for loop. I intend to check old and new files content later, probably with memcmp. But first I need them to be correctly renamed.
I'm on a Ubuntu 14.04 (64 bit) machine with gcc 4.8.4 as compiler. I already excuse myself for the probably poor coding and bad english, I'm not a native speaker (writer, actually).
fNew.open(filename);
std::ostringstream oldSeqName (std::ostringstream::ate);
std::ostringstream newSeqName (std::ostringstream::ate);
std::ostringstream oldAb1Name (std::ostringstream::ate);
std::ostringstream newAb1Name (std::ostringstream::ate);
std::fstream log;
time_t now = time(0);
for (std::string nOld, nNew; getline(fNew, nOld, ';') && getline(fNew, nNew); )
{
std::cout << "Old Name: " << nOld << " -> New Name: " << nNew << std::endl;
// Keep a log of the name changes
log.open("NameChangesLog.txt", std::fstream::out | std::fstream::app);
log << ctime(&now) << " - " << "Old Name: " << nOld << " -> New Name: " << nNew << std::endl;
log.close();
// Create old seq files paths string
oldSeqName.str(nOld);
oldSeqName << ".seq";
std::string osn = "./Seq/" + oldSeqName.str();
// Create new seq files paths string
newSeqName.str(nNew);
newSeqName << ".seq";
std::string nsn = "./renamed/" + newSeqName.str();
std::ifstream ifseq(osn, std::ios::binary);
std::ofstream ofseq(nsn, std::ios::binary);
ofseq << ifseq.rdbuf();
ifseq.close();
ofseq.close();
// Create old ab1 files paths string
oldAb1Name.str(nOld);
oldAb1Name << ".ab1";
std::string oan = "./Seq/" + oldAb1Name.str();
// Create new abq files paths string
newAb1Name.str(nNew);
newAb1Name << ".ab1";
std::string nan = "./renamed/" + newAb1Name.str();
std::ifstream ifab1(oan, std::ios::binary);
std::ofstream ofab1(nan, std::ios::binary);
ofab1 << ifab1.rdbuf();
ifab1.close();
ofab1.close();
}
fNew.close();
