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;
}
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;
}