position BamAlignmentReader::GetLastPositionInBam(const std::string& bamPath, Region::SharedPtr regionPtr)
	{
		BamTools::BamReader bamReader;
		if (!bamReader.Open(bamPath))
		{
			throw "Unable to open bam file";
		}

		bamReader.LocateIndex();
		int refID = bamReader.GetReferenceID(regionPtr->getReferenceID());
		auto referenceData = bamReader.GetReferenceData();
		bamReader.Close();
		return referenceData[refID].RefLength;
	}
Beispiel #2
0
void Config::InitializationClustering() {
    struct stat st;
    if(stat(Workspace.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Workspace directory already present");
    else if (mkdir(Workspace.c_str(), 0755) != 0) {
        Log("[Error] Could not create workspace directory: " + Workspace);
        exit(1);
    }
    RunningTasksFile = Workspace + "/" + FilePrefix + "running.tasks";
    StatsFile = Workspace + "/" + FilePrefix + "stats";
    BinClusterFile = Workspace + "/" + FilePrefix + "bpc";
    clusterFile = new ClusterFile(BinClusterFile);
    clusterDir = Workspace + "/clusters/";
    if(stat(clusterDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Cluster directory already present");
    else if (mkdir(clusterDir.c_str(), 0755) != 0) {
        Log("[Error] Could not create cluster directory: " + clusterDir);
        exit(1);
    }
    insertsizeDir = Workspace + "/insertsize/";
    if(stat(insertsizeDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Insertsize directory already present");
    else if (mkdir(insertsizeDir.c_str(), 0755) != 0) {
        Log("[Error] Could not create insertsize directory: " + insertsizeDir);
        exit(1);
    }
    coverageDir = Workspace + "/coverage/";
    if(stat(coverageDir.c_str(),&st) == 0 and st.st_mode and S_IFDIR != 0) Log("[Warning] Coverage directory already present");
    else if (mkdir(coverageDir.c_str(), 0755) != 0) {
        Log("[Error] Could not create coverage directory: " + coverageDir);
        exit(1);
    }
    
    if (!ForwardBam.empty() && !ReverseBam.empty() && PairedBam.empty()) {
        UsePairedBam = false;
    } else if (ForwardBam.empty() && ReverseBam.empty() && !PairedBam.empty()) {
        UsePairedBam = true;
    } else {
        Log("[Error] No correct bam file(s)");
        exit(1);
    }
    
    BamTools::BamAlignment alignment;
    BamTools::BamReader BamReader;
    
    if (UsePairedBam) {
        BamReader.Open(PairedBam);
        if (not BamReader.IsOpen()) {
            Log("[Error] Could not open paired bam");
            exit(1);
        }
        if (PairedIndex.empty()) {
            if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
                PairedIndex = PairedBam.substr(0,PairedBam.find_last_of(".bam")-3) + ".bai";
                BamReader.OpenIndex(PairedIndex);
            }
            if (not BamReader.HasIndex()) {
                Log("[Error] No index for bamfile");
                exit(1);
            }
        }
        BamTools::SamHeader header = BamReader.GetHeader();
        for (BamTools::SamReadGroupIterator it = header.ReadGroups.Begin(); it != header.ReadGroups.End(); it++) {
            BamTools::SamReadGroup* readgroup = &*it;
            readNameConverter.TrimName(readgroup->ID);
            readNameConverter.AddReadGroup(readgroup->ID);
        }
        long int count = 0;
        while (BamReader.GetNextAlignment(alignment)) {
            string RG;
            if (alignment.GetTag("RG", RG)) {
                if (not NameTrim.empty()) readNameConverter.TrimName(RG);
                if (readNameConverter.AddReadGroup(RG)) {
                    Log("[Warning] Readgroup '" + RG + "' found in reads but not in header");
                    count = 0;
                }
            }
            count++;
            if (count > 10000) break;
        }
        BamReader.Close();
    } else {
        BamReader.Open(ForwardBam);
        if (not BamReader.IsOpen()) {
            Log("[Error] Could not open first/forward bam");
            exit(1);
        }
        if (ForwardIndex.empty()) {
            if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
                ForwardIndex = ForwardBam.substr(0,ForwardBam.find_last_of(".bam")-3) + ".bai";
                BamReader.OpenIndex(ForwardIndex);
            }
            if (not BamReader.HasIndex()) {
                Log("[Error] No index for forward bamfile");
                exit(1);
            }
        }
        BamTools::SamHeader forwardheader = BamReader.GetHeader();
        for (BamTools::SamReadGroupIterator it = forwardheader.ReadGroups.Begin(); it != forwardheader.ReadGroups.End(); it++) {
            BamTools::SamReadGroup* readgroup = &*it;
            readNameConverter.TrimName(readgroup->ID);
            readNameConverter.AddReadGroup(readgroup->ID);
        }
        long int count = 0;
        while (BamReader.GetNextAlignment(alignment)) {
            string RG;
            if (alignment.GetTag("RG", RG)) {
                if (!NameTrim.empty()) readNameConverter.TrimName(RG);
                if (readNameConverter.AddReadGroup(RG)) {
                    Log("[Warning] Readgroup '" + RG + "' found in forward reads but not in header");
                    count = 0;
                }
            }
            count++;
            if (count > 10000) break;
        }
        BamReader.Close();
        BamReader.Open(ReverseBam);
        if (not BamReader.IsOpen()) {
            Log("[Error] Could not open second/reverse bam");
            exit(1);
        }
        if (ReverseIndex.empty()) {
            if (not BamReader.LocateIndex(BamTools::BamIndex::STANDARD)) {
                ReverseIndex = ReverseBam.substr(0,ReverseBam.find_last_of(".bam")-3) + ".bai";
                BamReader.OpenIndex(ReverseIndex);
            }
            if (not BamReader.HasIndex()) {
                Log("[Error] No index for reverse bamfile");
                exit(1);
            }
        }
        BamTools::SamHeader reverseheader = BamReader.GetHeader();
        for (BamTools::SamReadGroupIterator it = reverseheader.ReadGroups.Begin(); it != reverseheader.ReadGroups.End(); it++) {
            BamTools::SamReadGroup* readgroup = &*it;
            readNameConverter.TrimName(readgroup->ID);
            if (readNameConverter.AddReadGroup(readgroup->ID)) {
                Log("[Warning] Readgroup '" + readgroup->ID + "' found in reverse but not in forward");
            }
        }
        count = 0;
        while (BamReader.GetNextAlignment(alignment)) {
            string RG;
            if (alignment.GetTag("RG", RG)) {
                if (!NameTrim.empty()) readNameConverter.TrimName(RG);
                if (readNameConverter.AddReadGroup(RG)) {
                    Log("[Warning] Readgroup '" + RG + "' found in reverse reads but not in header");
                    count = 0;
                } 
            }
            count++;
            if (count > 10000) break;
        }
        BamReader.Close();
    }
    
    for(map<string, int>::iterator it = readNameConverter.ReadGroups.begin(); it!=readNameConverter.ReadGroups.end(); ++it) {
        ostringstream logBuffer;
        logBuffer << "Readgroup found: " << it->second << " - " << it->first;
        Log(logBuffer.str());
    }
    
    writeConfigFile(Workspace + FilePrefix + "config");
}
//
// Main
//
int somaticVariantFiltersMain(int argc, char** argv)
{
    parseSomaticVariantFiltersOptions(argc, argv);

    Timer* pTimer = new Timer(PROGRAM_IDENT);
    
    // Load Reference
    ReadTable refTable(opt::referenceFile, SRF_NO_VALIDATION);
    refTable.indexReadsByID();

    // Load BAMs
    BamTools::BamReader* pTumorBamReader = new BamTools::BamReader;
    pTumorBamReader->Open(opt::tumorBamFile);
    pTumorBamReader->LocateIndex();

    assert(pTumorBamReader->HasIndex());

    BamTools::BamReader* pNormalBamReader = new BamTools::BamReader;
    pNormalBamReader->Open(opt::normalBamFile);
    pNormalBamReader->LocateIndex();
    assert(pNormalBamReader->HasIndex());

    // Track duplicated variants
    HashSet<std::string> duplicateHash;

    std::ifstream input(opt::vcfFile.c_str());
    std::string line;

    while(getline(input, line))
    {
        if(line.empty())
            continue;

        if(line[0] == '#')
        {
            std::cout << line << "\n";
            continue;
        }
        
        // parse record
        VCFRecord record(line);
        if(record.isMultiAllelic())
        {
            std::cerr << "Error: multi-allelic VCF found, please run vcfbreakmulti\n";
            exit(EXIT_FAILURE);
        }

        // Check if we've seen this variant already
        std::string key = makeVariantKey(record);
        if(duplicateHash.find(key) != duplicateHash.end())
            continue;
        else
            duplicateHash.insert(key);

        if(opt::verbose > 0)
        {
            std::stringstream ss;
            ss << "Variant: " << record << "\n";
            fprintf(stderr, "===============================================\n%s", ss.str().c_str());
        }

        StringStringHash tagHash;
        makeTagHash(record, tagHash);

        StringVector fail_reasons;

        int hplen = 0;
        if(!getTagValue(tagHash, "HPLen", hplen))
            hplen = calculateHomopolymerLength(record, &refTable);
        if(hplen > opt::maxHPLen)
            fail_reasons.push_back("Homopolymer");

        double dust = 0.0f;
        if(!getTagValue(tagHash, "Dust", dust))
            dust = HapgenUtil::calculateDustScoreAtPosition(record.refName, 
                                                            record.refPosition, 
                                                            &refTable);

        if(dust > opt::maxDust)
            fail_reasons.push_back("LowComplexity");
        
        double af;
        if(getTagValue(tagHash, "AF", af) && af < opt::minAF)
            fail_reasons.push_back("LowAlleleFrequency");

        int varDP;
        if(getTagValue(tagHash, "VarDP", varDP) && varDP < opt::minVarDP)
            fail_reasons.push_back("LowVarDP");

        double strandBias;
        if(getTagValue(tagHash, "SB", strandBias) && strandBias >= opt::maxStrandBias)
            fail_reasons.push_back("StrandBias");

        CoverageStats tumor_stats = getVariantCoverage(pTumorBamReader, record, &refTable);
        CoverageStats normal_stats = getVariantCoverage(pNormalBamReader, record, &refTable);

        if(opt::verbose > 0)
        {
            fprintf(stderr, "Tumor: [%zu %zu]\n",  tumor_stats.n_total_reads, tumor_stats.n_evidence_reads);
            fprintf(stderr, "Normal: [%zu %zu]\n", normal_stats.n_total_reads, normal_stats.n_evidence_reads);
        }

        if(normal_stats.n_evidence_reads > opt::maxNormalReads)
            fail_reasons.push_back("NormalEvidence");
        
        if(normal_stats.n_total_reads < opt::minNormalDepth)
            fail_reasons.push_back("LowNormalDepth");

        if(!tumor_stats.snv_evidence_quals.empty())
        {
            double median_quality = median(tumor_stats.snv_evidence_quals);
            if(median_quality < opt::minMedianQuality)
                fail_reasons.push_back("LowQuality");
        }

        if(tumor_stats.median_mapping_quality < opt::minMedianQuality)
            fail_reasons.push_back("LowMappingQuality");

        if(!fail_reasons.empty())
        {
            if(record.passStr != "PASS" && record.passStr != ".")
                fail_reasons.insert(fail_reasons.begin(), record.passStr);

            std::stringstream strss;
            std::copy(fail_reasons.begin(), fail_reasons.end(), std::ostream_iterator<std::string>(strss, ";"));
            record.passStr = strss.str();
            record.passStr.erase(record.passStr.size() - 1); // erase trailing ;
        }

        std::cout << record << "\n";
    }
    
    // Cleanup
    delete pTumorBamReader;
    delete pNormalBamReader;
    delete pTimer;

    return 0;
}
Beispiel #4
0
inline int
run(Config const& c, TSingleHit)
{
  // Create library objects
  typedef std::map<std::string, LibraryInfo> TLibraryMap;
  typedef std::map<std::string, TLibraryMap> TSampleLibrary;
  TSampleLibrary sampleLib;

  // Scan libraries
  for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
    // Get a sample name
    std::string sampleName(c.files[file_c].stem().string());

    // Check that all input bam files exist
    BamTools::BamReader reader;
    if ( ! reader.Open(c.files[file_c].string()) ) {
      std::cerr << "Could not open input bam file: " << c.files[file_c].string() << std::endl;
      reader.Close();
      return -1;
    }
    
    // Check that all input bam files are indexed
    reader.LocateIndex();
    if ( !reader.HasIndex() ) {
      std::cerr << "Missing bam index file: " << c.files[file_c].string() << std::endl;
      reader.Close();
      return -1;
    }

    // Get library parameters and overall maximum insert size
    TLibraryMap libInfo;
    getLibraryParams(c.files[file_c], libInfo, 0, 5);
    sampleLib.insert(std::make_pair(sampleName, libInfo));
  }

  // Read all SV intervals
  typedef std::vector<StructuralVariantRecord> TSVs;
  TSVs svs;
  std::map<unsigned int, std::string> idToName;
  unsigned int intervalCount=1;
  if (boost::filesystem::exists(c.int_file) && boost::filesystem::is_regular_file(c.int_file) && boost::filesystem::file_size(c.int_file)) {
    Memory_mapped_file interval_file(c.int_file.string().c_str());
    char interval_buffer[Memory_mapped_file::MAX_LINE_LENGTH];
    while (interval_file.left_bytes() > 0) {
      interval_file.read_line(interval_buffer);
      // Read single interval line
      StructuralVariantRecord sv;
      Tokenizer token(interval_buffer, Memory_mapped_file::MAX_LINE_LENGTH);
      std::string interval_rname;
      token.getString(sv.chr);
      sv.svStart = token.getUInt();
      sv.svEnd = token.getUInt() + 1;
      std::string svName;
      token.getString(svName);
      idToName.insert(std::make_pair(intervalCount, svName));
      sv.id = intervalCount++;
      svs.push_back(sv);
    }
    interval_file.close();
  } else {
    // Create artificial intervals
    BamTools::BamReader readerRef;
    if ( ! readerRef.Open(c.files[0].string()) ) return -1;
    BamTools::RefVector references = readerRef.GetReferenceData();
    typename BamTools::RefVector::const_iterator itRef = references.begin();
    for(int refIndex=0;itRef!=references.end();++itRef, ++refIndex) {
      int32_t pos = 0;
      while (pos < references[refIndex].RefLength) {
	int32_t window_len = pos+c.window_size;
	if (window_len > references[refIndex].RefLength) window_len = references[refIndex].RefLength;
	StructuralVariantRecord sv;
	sv.chr = references[refIndex].RefName;
	sv.svStart = pos;
	sv.svEnd = window_len;
	std::stringstream s; 
	s << sv.chr << ":" << sv.svStart << "-" << sv.svEnd;
	idToName.insert(std::make_pair(intervalCount, s.str()));
	sv.id = intervalCount++;
	svs.push_back(sv);
	pos += c.window_offset;
      }
    }
  }

  // Output data types
  typedef std::pair<std::string, int> TSampleSVPair;
  typedef std::pair<int, int> TBpRead;
  typedef std::map<TSampleSVPair, TBpRead> TCountMap;
  TCountMap countMap;

  // Annotate coverage
  annotateCoverage(c.files, c.minMapQual, c.inclCigar, sampleLib, svs, countMap, TSingleHit());

  // Output library statistics
  std::cout << "Library statistics" << std::endl;
  TSampleLibrary::const_iterator sampleIt=sampleLib.begin();
  for(;sampleIt!=sampleLib.end();++sampleIt) {
    std::cout << "Sample: " << sampleIt->first << std::endl;
    TLibraryMap::const_iterator libIt=sampleIt->second.begin();
    for(;libIt!=sampleIt->second.end();++libIt) {
      std::cout << "RG: ID=" << libIt->first << ",Median=" << libIt->second.median << ",MAD=" << libIt->second.mad << ",Orientation=" << (int) libIt->second.defaultOrient << ",MappedReads=" << libIt->second.mappedReads << ",DuplicatePairs=" << libIt->second.non_unique_pairs << ",UniquePairs=" << libIt->second.unique_pairs << std::endl;
    }
  }

  // Output file
  boost::iostreams::filtering_ostream dataOut;
  dataOut.push(boost::iostreams::gzip_compressor());
  dataOut.push(boost::iostreams::file_sink(c.outfile.string().c_str(), std::ios_base::out | std::ios_base::binary));

  // Iterate all SVs
  typename TSVs::const_iterator itSV = svs.begin();
  typename TSVs::const_iterator itSVEnd = svs.end();
  for(;itSV!=itSVEnd;++itSV) {
    dataOut << itSV->chr << "\t" << itSV->svStart << "\t" << itSV->svEnd << "\t" << idToName.find(itSV->id)->second;
    // Iterate all samples
    for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
      // Get the sample name
      std::string sampleName(c.files[file_c].stem().string());
      TSampleSVPair sampleSVPair = std::make_pair(sampleName, itSV->id);
      typename TCountMap::iterator countMapIt=countMap.find(sampleSVPair);
      dataOut << "\t";
      if (c.avg_flag) dataOut << ( (countMapIt->second.first) / (double) (itSV->svEnd - itSV->svStart)) << "\t";
      if (c.bp_flag) dataOut << countMapIt->second.first << "\t";
      dataOut << countMapIt->second.second;
    }
    dataOut << std::endl;
  }

  // End
  boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
  std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Done." << std::endl;;
  return 0;
}
Beispiel #5
0
inline int
run(Config const& c, TCoverageType covType)
{
  // Create library objects
  typedef boost::unordered_map<std::string, LibraryInfo> TLibraryMap;
  typedef boost::unordered_map<std::string, TLibraryMap> TSampleLibrary;
  TSampleLibrary sampleLib;

  // Scan libraries
  for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
    // Get a sample name
    std::string sampleName(c.files[file_c].stem().string());

    // Check that all input bam files exist
    BamTools::BamReader reader;
    if ( ! reader.Open(c.files[file_c].string()) ) {
      std::cerr << "Could not open input bam file: " << c.files[file_c].string() << std::endl;
      reader.Close();
      return -1;
    }
    
    // Check that all input bam files are indexed
    reader.LocateIndex();
    if ( !reader.HasIndex() ) {
      std::cerr << "Missing bam index file: " << c.files[file_c].string() << std::endl;
      reader.Close();
      return -1;
    }

    // Get library parameters and overall maximum insert size
    TLibraryMap libInfo;
    getLibraryParams(c.files[file_c], libInfo, 0, 5);
    sampleLib.insert(std::make_pair(sampleName, libInfo));
  }

  // Get references
  BamTools::BamReader readerRef;
  if ( ! readerRef.Open(c.files[0].string()) ) return -1;
  BamTools::RefVector references = readerRef.GetReferenceData();

  // Read all SV intervals
  typedef std::vector<CovRecord> TSVs;
  TSVs svs;
  std::map<unsigned int, std::string> idToName;
  unsigned int intervalCount=1;
  if (boost::filesystem::exists(c.int_file) && boost::filesystem::is_regular_file(c.int_file) && boost::filesystem::file_size(c.int_file)) {
    typedef boost::unordered_map<std::string, unsigned int> TMapChr;
    TMapChr mapChr;
    typename BamTools::RefVector::const_iterator itRef = references.begin();
    for(unsigned int i = 0;itRef!=references.end();++itRef, ++i) mapChr[ itRef->RefName ] = i;
    std::ifstream interval_file(c.int_file.string().c_str(), std::ifstream::in);
    if (interval_file.is_open()) {
      while (interval_file.good()) {
	std::string intervalLine;
	getline(interval_file, intervalLine);
	typedef boost::tokenizer< boost::char_separator<char> > Tokenizer;
	boost::char_separator<char> sep(" \t,;");
	Tokenizer tokens(intervalLine, sep);
	Tokenizer::iterator tokIter = tokens.begin();
	if (tokIter!=tokens.end()) {
	  std::string chrName=*tokIter++;
	  TMapChr::const_iterator mapChrIt = mapChr.find(chrName);
	  if (mapChrIt != mapChr.end()) {
	    if (tokIter!=tokens.end()) {
	      CovRecord sv;	  
	      sv.chr = mapChrIt->second;
	      sv.svStart = boost::lexical_cast<int32_t>(*tokIter++);
	      sv.svEnd = boost::lexical_cast<int32_t>(*tokIter++) + 1;
	      std::string svName = *tokIter;
	      idToName.insert(std::make_pair(intervalCount, svName));
	      sv.id = intervalCount++;
	      svs.push_back(sv);
	    }
	  }
	}
      }
      interval_file.close();
    }
  } else {
    // Create artificial intervals
    typename BamTools::RefVector::const_iterator itRef = references.begin();
    for(int refIndex=0;itRef!=references.end();++itRef, ++refIndex) {
      int32_t pos = 0;
      unsigned int wSize = c.window_size;
      unsigned int wOffset = c.window_offset;
      if (c.window_num>0) {
	wSize=(itRef->RefLength / c.window_num) + 1;
	wOffset=wSize;
      }
      while (pos < references[refIndex].RefLength) {
	int32_t window_len = pos+wSize;
	if (window_len > references[refIndex].RefLength) window_len = references[refIndex].RefLength;
	CovRecord sv;
	sv.chr = refIndex;
	sv.svStart = pos;
	sv.svEnd = window_len;
	std::stringstream s; 
	s << references[sv.chr].RefName << ":" << sv.svStart << "-" << sv.svEnd;
	idToName.insert(std::make_pair(intervalCount, s.str()));
	sv.id = intervalCount++;
	svs.push_back(sv);
	pos += wOffset;
      }
    }
  }

  // Output data types
  typedef std::pair<std::string, int> TSampleSVPair;
  typedef std::pair<int, int> TBpRead;
  typedef std::map<TSampleSVPair, TBpRead> TCountMap;
  TCountMap countMap;

  // Annotate coverage
  if (c.inclCigar) annotateCoverage(c.files, c.minGenoQual, sampleLib, svs, countMap, BpLevelType<BpLevelCount>(), covType);
  else annotateCoverage(c.files, c.minGenoQual, sampleLib, svs, countMap, BpLevelType<NoBpLevelCount>(), covType);

  // Output library statistics
  std::cout << "Library statistics" << std::endl;
  TSampleLibrary::const_iterator sampleIt=sampleLib.begin();
  for(;sampleIt!=sampleLib.end();++sampleIt) {
    std::cout << "Sample: " << sampleIt->first << std::endl;
    TLibraryMap::const_iterator libIt=sampleIt->second.begin();
    for(;libIt!=sampleIt->second.end();++libIt) {
      std::cout << "RG: ID=" << libIt->first << ",Median=" << libIt->second.median << ",MAD=" << libIt->second.mad << ",Orientation=" << (int) libIt->second.defaultOrient << std::endl;
    }
  }

  // Output file
  boost::iostreams::filtering_ostream dataOut;
  dataOut.push(boost::iostreams::gzip_compressor());
  dataOut.push(boost::iostreams::file_sink(c.outfile.string().c_str(), std::ios_base::out | std::ios_base::binary));

  // Print header
  dataOut << "#chr\tstart\tend\tid";
  for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
    std::string sampleName(c.files[file_c].stem().string());
    dataOut << "\t";
    if (c.avg_flag) dataOut << sampleName << "_avgcov" << "\t";
    if (c.bp_flag) dataOut << sampleName << "_bpcount" << "\t";
    if ((c.bp_flag) || (c.avg_flag)) dataOut << sampleName << "_readcount";
    else dataOut << sampleName;
  }
  dataOut << std::endl;

  // Iterate all SVs
  typename TSVs::const_iterator itSV = svs.begin();
  typename TSVs::const_iterator itSVEnd = svs.end();
  for(;itSV!=itSVEnd;++itSV) {
    dataOut << references[itSV->chr].RefName << "\t" << itSV->svStart << "\t" << itSV->svEnd << "\t" << idToName.find(itSV->id)->second;
    // Iterate all samples
    for(unsigned int file_c = 0; file_c < c.files.size(); ++file_c) {
      // Get the sample name
      std::string sampleName(c.files[file_c].stem().string());
      TSampleSVPair sampleSVPair = std::make_pair(sampleName, itSV->id);
      typename TCountMap::iterator countMapIt=countMap.find(sampleSVPair);
      dataOut << "\t";
      if (c.avg_flag) dataOut << ( (countMapIt->second.first) / (double) (itSV->svEnd - itSV->svStart)) << "\t";
      if (c.bp_flag) dataOut << countMapIt->second.first << "\t";
      dataOut << countMapIt->second.second;
    }
    dataOut << std::endl;
  }

  // End
  boost::posix_time::ptime now = boost::posix_time::second_clock::local_time();
  std::cout << '[' << boost::posix_time::to_simple_string(now) << "] Done." << std::endl;;
  return 0;
}