bool ConvertTool::ConvertToolPrivate::RunPileupConversion(BamMultiReader* reader) {
// check for valid BamMultiReader
if ( reader == 0 ) return false;
// set up our pileup format 'visitor'
ConvertPileupFormatVisitor* v = new ConvertPileupFormatVisitor(m_references,
m_settings->FastaFilename,
m_settings->IsPrintingPileupMapQualities,
&m_out);
// set up PileupEngine
PileupEngine pileup;
pileup.AddVisitor(v);
// iterate through data
BamAlignment al;
while ( reader->GetNextAlignment(al) )
pileup.AddAlignment(al);
pileup.Flush();
// clean up
delete v;
v = 0;
// return success
return true;
}
bool CoverageTool::CoverageToolPrivate::Run(void) {
// if output filename given
ofstream outFile;
if ( m_settings->HasOutputFile ) {
// open output file stream
outFile.open(m_settings->OutputFilename.c_str());
if ( !outFile ) {
cerr << "bamtools coverage ERROR: could not open " << m_settings->OutputFilename
<< " for output" << endl;
return false;
}
// set m_out to file's streambuf
m_out.rdbuf(outFile.rdbuf());
}
//open our BAM reader
BamReader reader;
if ( !reader.Open(m_settings->InputBamFilename) ) {
cerr << "bamtools coverage ERROR: could not open input BAM file: " << m_settings->InputBamFilename << endl;
return false;
}
// retrieve references
m_references = reader.GetReferenceData();
// set up our output 'visitor'
CoverageVisitor* cv = new CoverageVisitor(m_references, &m_out);
// set up pileup engine with 'visitor'
PileupEngine pileup;
pileup.AddVisitor(cv);
// process input data
BamAlignment al;
while ( reader.GetNextAlignment(al) )
pileup.AddAlignment(al);
// clean up
reader.Close();
if ( m_settings->HasOutputFile )
outFile.close();
delete cv;
cv = 0;
// return success
return true;
}
void GenericIndividualSnpCall::simpleSnpCall(string &fastaObj, BamReader &bamObj, int chrID, int leftPosition, int rightPosition, vector<Allele> &variantCandidates, map<int,list<tuple<char,int,int,double>>> &bamData)
{
set<int> BlockSnpPositions;
vector<Allele> BlockSnpAlleles;
// rewind
bamObj.Rewind();
// set region
bamObj.SetRegion(chrID, leftPosition, chrID, rightPosition);
BamAlignment al;
// search SNP positions in the region
while (bamObj.GetNextAlignment(al))
{
if (!GenericBamAlignmentTools::goodAlignment(al))
continue;
if (!al.HasTag("MD"))
continue;
vector<long> SnpInAlignment;
GenericBamAlignmentTools::getBamAlignmentMismatches(al, SnpInAlignment);
for (int i=0; i<SnpInAlignment.size(); i++)
{
BlockSnpPositions.insert(SnpInAlignment[i]);
}
}
// pileup visitor
SimpleSnpCallPileupVisitor visitor(&fastaObj, chrID, leftPosition, rightPosition, m_downSample, &BlockSnpPositions, &BlockSnpAlleles, &bamData);
PileupEngine SimpleSnpCallPileupEngine;
SimpleSnpCallPileupEngine.AddVisitor(&visitor);
// rewind
bamObj.Rewind();
// set region
bamObj.SetRegion(chrID, leftPosition, chrID, rightPosition);
// load data
while(bamObj.GetNextAlignment(al))
{
if (!GenericBamAlignmentTools::goodAlignment(al))
continue;
if (!GenericBamAlignmentTools::validMapQuality(al, m_minMapQuality))
continue;
if (!GenericBamAlignmentTools::validReadIdentity(al, m_maxMismatchFrac))
continue;
if (!GenericBamAlignmentTools::validReadLength(al, m_minReadLength))
continue;
if (!al.HasTag("MD"))
continue;
SimpleSnpCallPileupEngine.AddAlignment(al);
}
SimpleSnpCallPileupEngine.Flush();
// Filter SNP candidiate
for (int i=0; i<BlockSnpAlleles.size(); i++)
{
Allele allele = BlockSnpAlleles[i];
if (allele.m_alleleDepth < m_minSnpRead)
continue;
if (allele.m_alleleDepth < m_minSnpFrac*allele.m_globalDepth)
continue;
variantCandidates.push_back(allele);
}
}
