// 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);
}
bool VcfFileWriter::writeRecord(VcfRecord& record)
{
if(!record.write(myFilePtr, mySiteOnly))
{
myStatus = record.getStatus();
return(false);
}
++myNumRecords;
return(true);
}
void
process_block(const bool is_in_region,
const unsigned end,
VcfRecord& vcfr) const {
if(end>vcfr.GetPos()) {
vcfr.SetInfoVal("END",_intstr.get32(end));
} else {
vcfr.DeleteInfoKeyVal("END");
}
if(is_in_region) make_record_haploid(vcfr);
vcfr.WriteUnaltered(_opt.outfp);
}
void
make_record_haploid(VcfRecord& vcfr) const {
const char* gt(vcfr.GetSampleVal("GT"));
if(NULL == gt) return;
parse_gt(gt,_gti);
if(_gti.size() == 2) { // record is diploid
if(_gti[0] == _gti[1]) {
// change GT:
static const char* unknown(".");
const char* val(unknown);
if(_gti[0]>=0) {
val=_intstr.get32(_gti[0]);
}
vcfr.SetSampleVal("GT",val);
// move PL field to 'backup' OPL field:
const char* pl(vcfr.GetSampleVal("PL"));
if(NULL != pl) {
vcfr.SetSampleVal(_shopt.orig_pl_tag.c_str(),pl);
vcfr.DeleteSampleKeyVal("PL");
}
} else {
vcfr.AppendFilter(_shopt.haploid_conflict_label.c_str());
}
}
}
void ResetVcfRecordFromBam( VcfRecord & vcf_rec, RefStats & rstats, vector<RefSeq*> & REF_SEQ, string & chr, int center, SamFile & samIn, SamFileHeader & samHeader )
{
vector<int> raw_counts; // read-type count vector
raw_counts.resize(18, 0);
setReadCountInSection( raw_counts, chr, center, samIn, samHeader, REF_SEQ ); // set from bam
// set gl & if 1/1 or 1/0, set breakpoint
vector<MergeCell> new_vec;
new_vec.resize(1);
MergeCellPtr merge_ptr = new_vec.begin();
merge_ptr->dups = 1;
merge_ptr->counts = raw_counts;
raw_counts.clear();
merge_ptr->GL.resize(3,0);
rstats.SetRecordGL( merge_ptr );
vcf_rec.SetChrName( chr );
vcf_rec.SetPosition( center );
vcf_rec.UpdateFromMergeCellPtr( merge_ptr );
// if need to refine break point && exist MEI, do refine
if (REFINE_BREAK_POINT && vcf_rec.GetDosage() > 0)
vcf_rec.SetBreakPointAndCIFromBam( samIn, samHeader );
}
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 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);
}
void
process_block(const bool is_in_region,
const unsigned end,
VcfRecord& vcfr) const {
if(! is_in_region) {
if(end>vcfr.GetPos()) {
vcfr.SetInfoVal("END",_intstr.get32(end));
} else {
vcfr.DeleteInfoKeyVal("END");
}
vcfr.WriteUnaltered(_opt.outfp);
} else {
vcfr.DeleteInfoKeyVal("END");
vcfr.WriteUnaltered(_opt.outfp);
while(end>vcfr.GetPos()) {
const int next_pos(vcfr.GetPos()+1);
vcfr.SetPos(next_pos);
vcfr.SetRef(_scp.get_char(vcfr.GetChrom().c_str(),next_pos));
vcfr.WriteUnaltered(_opt.outfp);
}
}
}
bool VcfFileReader::readRecord(VcfRecord& record, VcfSubsetSamples* subset)
{
myStatus = StatGenStatus::SUCCESS;
// Subset the read if there are subsets specified.
VcfSubsetSamples* subsetPtr = subset;
if((subsetPtr == NULL) && myUseSubset)
{
subsetPtr = &mySampleSubset;
}
// Check to see if a new region has been set. If so, setup for that region.
bool searchChrom = false;
if(myNewSection)
{
if(myVcfIndex != NULL)
{
// Have an index file so use
if(!processNewSection())
{
// processNewSection sets the status appropriately on failure.
return(false);
}
}
else if(myTotalRead == 0)
{
// ReadSection without an index only works if no records
// have been read.
searchChrom = true;
myNewSection = false;
}
else
{
myNewSection = false;
myStatus.setStatus(StatGenStatus::FAIL_ORDER,
"Cannot set read section with no index after reading records");
return(false);
}
}
// Keep looping until a desired record is found.
bool recordFound = false;
while(!recordFound)
{
if(!record.read(myFilePtr, mySiteOnly, myRecordDiscardRules, subsetPtr))
{
myStatus = record.getStatus();
myTotalRead += myRecordDiscardRules.getNumDiscarded();
myNumRecords += myRecordDiscardRules.getNumDiscarded();
myRecordDiscardRules.clearNumDiscarded();
return(false);
}
++myTotalRead;
myTotalRead += myRecordDiscardRules.getNumDiscarded();
// Check to see if the record is in the section.
// First check the chromosome.
if(!mySectionChrom.empty() && (mySectionChrom != record.getChromStr()))
{
if(searchChrom)
{
// Still searching for the chromosome, so continue
// to the next record.
continue;
}
// Record is not within the correct chromosome, so return failure.
myStatus = StatGenStatus::NO_MORE_RECS;
return(false);
}
searchChrom = false;
// Check if the record is after the section end if applicable.
if((mySection1BasedEndPos != -1) &&
(record.get1BasedPosition() >= mySection1BasedEndPos))
{
myStatus = StatGenStatus::NO_MORE_RECS;
return(false);
}
// Check if the record is prior to the section start if applicable.
// Determinine the VCF record end position.
// If we are not requiring overlap, then we only need to check
// the start position, but if overlap is required, then it needs
// to incrment the start by the length-1.
int numIncBases = 0;
if(mySectionOverlap)
{
// The VCF record end position is the start position + length of the
// reference string - 1.
numIncBases = record.getNumRefBases() - 1;
}
if((mySection1BasedStartPos != -1) &&
((record.get1BasedPosition() + numIncBases)
< mySection1BasedStartPos))
{
// This record is prior to the section, so keep reading.
continue;
}
++myNumRecords;
myNumRecords += myRecordDiscardRules.getNumDiscarded();
myRecordDiscardRules.clearNumDiscarded();
// Record successfully read, so check to see if it is discarded.
if((myDiscardRules & DISCARD_NON_PHASED) && !record.allPhased())
{
// Not all samples are phased, so discard this record.
continue;
}
if((myDiscardRules & DISCARD_MISSING_GT) &&
!record.hasAllGenotypeAlleles())
{
// discard missing GTs and this record had missing alleles,
// so keep reading.
continue;
}
if((myDiscardRules & DISCARD_FILTERED) &&
!(record.getFilter().passedAllFilters()))
{
// Record was filtered, so discard it.
continue;
}
if((myDiscardRules & DISCARD_MULTIPLE_ALTS) &&
(record.getNumAlts() > 1))
{
// Record had multiple alternates, so discard.
continue;
}
// Check allele counts for discarding.
if(myMinAltAlleleCount != UNSET_MIN_ALT_ALLELE_COUNT)
{
// Count the number of alternates.
int32_t altCount = 0;
for(int sampleNum = 0; sampleNum < record.getNumSamples();
sampleNum++)
{
if((myAltAlleleCountSubset != NULL) &&
!(myAltAlleleCountSubset->keep(sampleNum)))
{
// Skip this sample.
continue;
}
for(int gtNum = 0; gtNum < record.getNumGTs(sampleNum); gtNum++)
{
if(record.getGT(sampleNum, gtNum) > 0)
{
// Alternate, so increment the count.
++altCount;
}
}
}
if(altCount < myMinAltAlleleCount)
{
// Not enough alternates so continue to the next sample.
continue;
}
}
// Check to see if the minimum alternate allele count is met.
if(myMinMinorAlleleCount != UNSET_MIN_MINOR_ALLELE_COUNT)
{
// Get the number of possible alternates.
unsigned int numAlts = record.getNumAlts();
// Verify that each allele has the min count.
bool failMinorAlleleCount = false;
for(unsigned int i = 0; i <= numAlts; i++)
{
if(record.getAlleleCount(i, myMinorAlleleCountSubset)
< myMinMinorAlleleCount)
{
// Not enough of one gt, so not ok.
failMinorAlleleCount = true;
break;
}
}
if(failMinorAlleleCount)
{
// not enough alleles, so continue to the next record.
continue;
}
}
// Record was not discarded.
recordFound = true;
}
// Increment the number of kept records.
++myNumKeptRecords;
return(true);
}
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);
}