//
// Main
//
int filterBAMMain(int argc, char** argv)
{
parseFilterBAMOptions(argc, argv);
// Read the graph if distance-filtering mode is enabled
StringGraph* pGraph = NULL;
if(!opt::asqgFile.empty())
pGraph = SGUtil::loadASQG(opt::asqgFile, 0, false);
// Read the BWTs if depth-filtering mode is enabled
BWT* pBWT = NULL;
BWT* pRBWT = NULL;
if(!opt::fmIndexPrefix.empty())
{
pBWT = new BWT(opt::fmIndexPrefix + BWT_EXT, opt::sampleRate);
pRBWT = new BWT(opt::fmIndexPrefix + RBWT_EXT, opt::sampleRate);
}
Timer* pTimer = new Timer(PROGRAM_IDENT);
//
int numPairsTotal = 0;
int numPairsFilteredByDistance = 0;
int numPairsFilteredByER = 0;
int numPairsFilteredByQuality = 0;
int numPairsFilteredByDepth = 0;
int numPairsUnmapped = 0;
int numPairsWrote = 0;
// Open the bam files for reading/writing
BamTools::BamReader* pBamReader = new BamTools::BamReader;
pBamReader->Open(opt::bamFile);
BamTools::BamWriter* pBamWriter = new BamTools::BamWriter;
pBamWriter->Open(opt::outFile, pBamReader->GetHeaderText(), pBamReader->GetReferenceData());
const BamTools::RefVector& referenceVector = pBamReader->GetReferenceData();
BamTools::BamAlignment record1;
BamTools::BamAlignment record2;
bool done = false;
while(!done)
{
if(numPairsTotal++ % 200000 == 0)
printf("[sga filterBAM] Processed %d pairs\n", numPairsTotal);
done = !readAlignmentPair(pBamReader, record1, record2);
if(done)
break;
if(!record1.IsMapped() || !record2.IsMapped())
{
numPairsUnmapped += 1;
continue;
}
// Ensure the pairing is correct
if(record1.Name != record2.Name)
{
std::cout << "NAME FAIL: " << record1.Name << " " << record2.Name << "\n";
}
assert(record1.Name == record2.Name);
bool bPassedFilters = true;
// Check if the error rate is below the max
double er1 = getErrorRate(record1);
double er2 = getErrorRate(record2);
if(er1 > opt::maxError || er2 > opt::maxError)
{
bPassedFilters = false;
numPairsFilteredByER += 1;
}
if(record1.MapQuality < opt::minQuality || record2.MapQuality < opt::minQuality)
{
bPassedFilters = false;
numPairsFilteredByQuality += 1;
}
// Perform depth check for pairs aligning to different contigs
if(bPassedFilters && (pBWT != NULL && pRBWT != NULL && opt::maxKmerDepth > 0) && (record1.RefID != record2.RefID))
{
int maxDepth1 = getMaxKmerDepth(record1.QueryBases, pBWT, pRBWT);
int maxDepth2 = getMaxKmerDepth(record1.QueryBases, pBWT, pRBWT);
if(maxDepth1 > opt::maxKmerDepth || maxDepth2 > opt::maxKmerDepth)
{
bPassedFilters = false;
numPairsFilteredByDepth += 1;
}
}
// Perform short-insert pair check
if(pGraph != NULL)
{
bPassedFilters = bPassedFilters && filterByGraph(pGraph, referenceVector, record1, record2);
numPairsFilteredByDistance += 1;
}
if(bPassedFilters)
{
pBamWriter->SaveAlignment(record1);
pBamWriter->SaveAlignment(record2);
numPairsWrote += 1;
}
}
std::cout << "Total pairs: " << numPairsTotal << "\n";
std::cout << "Total pairs output: " << numPairsWrote << "\n";
std::cout << "Total filtered because one pair is unmapped: " << numPairsUnmapped << "\n";
std::cout << "Total filtered by distance: " << numPairsFilteredByDistance << "\n";
std::cout << "Total filtered by error rate: " << numPairsFilteredByER << "\n";
std::cout << "Total filtered by quality: " << numPairsFilteredByQuality << "\n";
std::cout << "Total filtered by depth: " << numPairsFilteredByDepth << "\n";
if(pGraph != NULL)
delete pGraph;
if(pBWT != NULL)
delete pBWT;
if(pRBWT != NULL)
delete pRBWT;
pBamWriter->Close();
pBamReader->Close();
delete pTimer;
delete pBamReader;
delete pBamWriter;
return 0;
}
