int VcfConvert::execute(int argc, char **argv)
{
String refFile = "";
String inputVcf = "";
String outputVcf = "";
String refName = "";
bool uncompress = false;
bool params = false;
bool noeof = false;
// Read in the parameters.
ParameterList inputParameters;
BEGIN_LONG_PARAMETERS(longParameterList)
LONG_PARAMETER_GROUP("Required Parameters")
LONG_STRINGPARAMETER("in", &inputVcf)
LONG_STRINGPARAMETER("out", &outputVcf)
LONG_PARAMETER_GROUP("Optional Parameters")
LONG_PARAMETER("uncompress", &uncompress)
LONG_STRINGPARAMETER("refName", &refName)
LONG_PARAMETER("noeof", &noeof)
LONG_PARAMETER("params", ¶ms)
LONG_PHONEHOME(VERSION)
END_LONG_PARAMETERS();
inputParameters.Add(new LongParameters ("Input Parameters",
longParameterList));
inputParameters.Read(argc-1, &(argv[1]));
// Check that all files were specified.
if(inputVcf == "")
{
usage();
inputParameters.Status();
std::cerr << "Missing \"--in\", a required parameter.\n\n";
return(-1);
}
if(outputVcf == "")
{
usage();
inputParameters.Status();
std::cerr << "Missing \"--out\", a required parameter.\n\n";
return(-1);
}
if(params)
{
inputParameters.Status();
}
// If no eof block is required for a bgzf file, set the bgzf file type to
// not look for it.
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
VcfFileReader inFile;
VcfFileWriter outFile;
VcfHeader header;
// Open the file.
inFile.open(inputVcf, header);
if(refName != "")
{
inFile.setReadSection(refName.c_str());
}
if(uncompress)
{
outFile.open(outputVcf, header, InputFile::DEFAULT);
}
else
{
outFile.open(outputVcf, header);
}
VcfRecord record;
int numRecords = 0;
while(inFile.readRecord(record))
{
++numRecords;
outFile.writeRecord(record);
}
inFile.close();
std::cerr << "NumRecords: " << numRecords << "\n";
return(0);
}
int VcfSplit::execute(int argc, char **argv)
{
String refFile = "";
String inputVcf = "";
String outputVcfBase = "";
String refName = "";
bool uncompress = false;
bool params = false;
bool noeof = false;
// Read in the parameters.
ParameterList inputParameters;
BEGIN_LONG_PARAMETERS(longParameterList)
LONG_PARAMETER_GROUP("Required Parameters")
LONG_STRINGPARAMETER("in", &inputVcf)
LONG_STRINGPARAMETER("obase", &outputVcfBase)
LONG_PARAMETER_GROUP("Optional Parameters")
LONG_PARAMETER("uncompress", &uncompress)
LONG_STRINGPARAMETER("refName", &refName)
LONG_PARAMETER("noeof", &noeof)
LONG_PARAMETER("params", ¶ms)
LONG_PHONEHOME(VERSION)
END_LONG_PARAMETERS();
inputParameters.Add(new LongParameters ("Input Parameters",
longParameterList));
inputParameters.Read(argc-1, &(argv[1]));
// Check that all files were specified.
if(inputVcf == "")
{
usage();
inputParameters.Status();
std::cerr << "Missing \"--in\", a required parameter.\n\n";
return(-1);
}
if(outputVcfBase == "")
{
usage();
inputParameters.Status();
std::cerr << "Missing \"--obase\", a required parameter.\n\n";
return(-1);
}
outputVcfBase += ".";
if(params)
{
inputParameters.Status();
}
// If no eof block is required for a bgzf file, set the bgzf file type to
// not look for it.
if(noeof)
{
// Set that the eof block is not required.
BgzfFileType::setRequireEofBlock(false);
}
VcfFileReader inFile;
std::map<std::string, VcfFileWriter*> outFiles;
VcfHeader header;
// Open the file.
inFile.open(inputVcf, header);
if(refName != "")
{
inFile.setReadSection(refName.c_str());
}
VcfRecord record;
int numRecords = 0;
std::string prevChr = "";
std::string chr = "";
VcfFileWriter* outFilePtr = 0;
std::string outName = "";
while(inFile.readRecord(record))
{
++numRecords;
chr = record.getChromStr();
if((outFilePtr == 0) || (chr != prevChr))
{
outFilePtr = outFiles[chr];
if(outFilePtr == 0)
{
outFilePtr = new VcfFileWriter();
outFiles[chr] = outFilePtr;
outName = outputVcfBase.c_str();
if(chr.substr(0,3) != "chr")
{
outName += "chr";
}
outName += chr + ".vcf";
// chr not in outFile list.
if(uncompress)
{
outFilePtr->open(outName.c_str(), header, InputFile::DEFAULT);
}
else
{
outName += ".gz";
outFilePtr->open(outName.c_str(), header);
}
}
}
outFilePtr->writeRecord(record);
}
inFile.close();
for (std::map<std::string,VcfFileWriter*>::iterator it = outFiles.begin();
it != outFiles.end(); ++it)
{
if(it->second != 0)
{
it->second->close();
it->second = 0;
}
}
std::cerr << "NumRecords: " << numRecords << "\n";
return(0);
}
