// The VcfRecord passed in should already be set with a record.
bool findPos(bool newChrom, const char* chrom1, int pos1, VcfRecord& record2, VcfFileReader& vcf2)
{
const char* chrom2 = record2.getChromStr();
int pos2 = record2.get1BasedPosition();
// Loop until the chrom/pos is found in vcf2.
bool sameChrom = (strcmp(chrom2, chrom1) == 0);
while(((pos2 < pos1) && sameChrom) ||
(newChrom && !sameChrom))
{
if(vcf2.readRecord(record2))
{
chrom2 = record2.getChromStr();
pos2 = record2.get1BasedPosition();
sameChrom = (strcmp(chrom2, chrom1) == 0);
}
else
{
// no more records.
chrom2 = NULL;
pos2 = UNSET_POS;
return(false);
}
}
// If we wind up here, chrom2 is either at the correct
// position, or it is past the correct position.
if((!sameChrom) || (pos2 != pos1))
{
// Position not found.
return(false);
}
return(true);
}
int VcfCleaner::execute(int argc, char **argv)
{
String refFile = "";
String inputVcf = "";
String outputVcf = "";
bool uncompress = false;
bool params = 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_PARAMETER("params", ¶ms)
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();
}
VcfFileReader inFile;
VcfFileWriter outFile;
VcfHeader header;
VcfRecord record;
// Open the file.
inFile.open(inputVcf, header);
if(uncompress)
{
outFile.open(outputVcf, header, InputFile::DEFAULT);
}
else
{
outFile.open(outputVcf, header);
}
int numReadRecords = 0;
int numWrittenRecords = 0;
int returnVal = 0;
// Set to only store/write the GT field.
VcfRecordGenotype::addStoreField("GT");
while(inFile.readRecord(record))
{
++numReadRecords;
// Check if any samples are missing GT or if any are not phased.
if(!record.hasAllGenotypeAlleles() || !record.allPhased())
{
// Missing a GT or not phased, so continue without writing.
continue;
}
// Clear the INFO field.
record.getInfo().clear();
// Write the record.
if(!outFile.writeRecord(record))
{
// Write error.
std::cerr << "Failed writing a vcf record.\n";
returnVal = -1;
}
++numWrittenRecords;
}
inFile.close();
outFile.close();
std::cerr << "NumReadRecords: " << numReadRecords
<< "; NumWrittenRecords: " << numWrittenRecords << "\n";
return(returnVal);
}
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);
}
int VcfMac::execute(int argc, char **argv)
{
String inputVcf = "";
int minAC = -1;
String sampleSubset = "";
String filterList = "";
bool params = false;
IntervalTree<int> regions;
std::vector<int> intersection;
// Read in the parameters.
ParameterList inputParameters;
BEGIN_LONG_PARAMETERS(longParameterList)
LONG_PARAMETER_GROUP("Required Parameters")
LONG_STRINGPARAMETER("in", &inputVcf)
LONG_PARAMETER_GROUP("Optional Parameters")
LONG_STRINGPARAMETER("sampleSubset", &sampleSubset)
LONG_INTPARAMETER("minAC", &minAC)
LONG_STRINGPARAMETER("filterList", &filterList)
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(params)
{
inputParameters.Status();
}
// Open the two input files.
VcfFileReader inFile;
VcfHeader header;
VcfRecord record;
// Open the file
if(sampleSubset.IsEmpty())
{
inFile.open(inputVcf, header);
}
else
{
inFile.open(inputVcf, header, sampleSubset, NULL, NULL);
}
// Add the discard rule for minor allele count.
if(minAC >= 0)
{
inFile.addDiscardMinMinorAlleleCount(minAC, NULL);
}
if(!filterList.IsEmpty())
{
// Open the filter list.
IFILE regionFile = ifopen(filterList, "r");
String regionLine;
StringArray regionColumn;
int start;
int end;
int intervalVal = 1;
if(regionFile == NULL)
{
std::cerr << "Failed to open " << filterList
<< ", so keeping all positions\n";
filterList.Clear();
}
else
{
while( regionFile->isOpen() && !regionFile->ifeof())
{
// Read the next interval
regionLine.Clear();
regionLine.ReadLine(regionFile);
if(regionLine.IsEmpty())
{
// Nothing on this line, continue to the next.
continue;
}
regionColumn.ReplaceColumns(regionLine, ' ');
if(regionColumn.Length() != 2)
{
std::cerr << "Improperly formatted region line: "
<< regionLine << "; skipping to the next line.\n";
continue;
}
// Convert the columns to integers.
if(!regionColumn[0].AsInteger(start))
{
// The start position (1st column) is not an integer.
std::cerr << "Improperly formatted region line, start position "
<< "(1st column) is not an integer: "
<< regionColumn[0]
<< "; Skipping to the next line.\n";
continue;
}
if(!regionColumn[1].AsInteger(end))
{
// The start position (1st column) is not an integer.
std::cerr << "Improperly formatted region line, end position "
<< "(2nd column) is not an integer: "
<< regionColumn[1]
<< "; Skipping to the next line.\n";
continue;
}
// Add 1-based inclusive intervals.
regions.add(start,end, intervalVal);
}
}
}
int numReadRecords = 0;
while( inFile.readRecord(record))
{
if(!filterList.IsEmpty())
{
// Check if the region should be kept.
intersection.clear();
regions.get_intersecting_intervals(record.get1BasedPosition(), intersection);
if(intersection.empty())
{
// not in the interval, so continue to the next record.
continue;
}
}
++numReadRecords;
// Loop through the number of possible alternates.
unsigned int numAlts = record.getNumAlts();
int minAlleleCount = -1;
int curAlleleCount = 0;
int totalAlleleCount = 0;
for(unsigned int i = 0; i <= numAlts; i++)
{
curAlleleCount = record.getAlleleCount(i);
if((minAlleleCount == -1) ||
(curAlleleCount < minAlleleCount))
{
minAlleleCount = curAlleleCount;
}
totalAlleleCount += curAlleleCount;
}
if(totalAlleleCount != 0)
{
double maf = (double)minAlleleCount/totalAlleleCount;
std::cout << record.getIDStr()
<< "\t" << minAlleleCount
<< "\t" << maf << "\n";
}
}
inFile.close();
// std::cerr << "\n\t# Records: " << numReadRecords << "\n";
// return success.
return(0);
}
