int main(int argc, char* argv[]) {
// set srand
srand(1);
CConsole::Initialize();
ConfigurationSettings settings;
string commandLine;
for ( int i = 0; i < argc; ++i )
commandLine = commandLine + argv[i] + " ";
printf("------------------------------------------------------------------------------\n");
printf("Mosaik"); CConsole::Red(); printf("Aligner"); CConsole::Reset();
printf(" %u.%u.%u %s\n",
MOSAIK_MAJOR_VERSION, MOSAIK_MINOR_VERSION, MOSAIK_BUILD_VERSION, MOSAIK_VERSION_DATE);
printf("Michael Stromberg & Wan-Ping Lee Marth Lab, Boston College Biology Department\n");
printf("------------------------------------------------------------------------------\n\n");
// =================================
// configure the command line parser
// =================================
// set general info about the program
COptions::SetProgramInfo("MosaikAligner", "pairwise aligns a MOSAIK read file", "-in <filename> -out <filename> -ia <filename>");
// add the input/output options
OptionGroup* pIoOpts = COptions::CreateOptionGroup("Input/output: (required)");
COptions::AddValueOption("-ia", "MOSAIK reference filename", "the input reference file", "An input MOSAIK reference file", settings.HasReferencesFilename, settings.ReferencesFilename, pIoOpts);
COptions::AddValueOption("-in", "MOSAIK read filename", "the input read file", "An input MOSAIK read file", settings.HasReadsFilename, settings.ReadsFilename, pIoOpts);
COptions::AddValueOption("-out", "MOSAIK alignment filename", "the output alignment file", "An output MOSAIK alignment file", settings.HasAlignmentsFilename, settings.AlignmentsFilename, pIoOpts);
COptions::AddValueOption("-ibs", "MOSAIK reference filename", "enables colorspace to basespace conversion using the supplied BASESPACE reference archive", "", settings.HasBasespaceReferencesFilename, settings.BasespaceReferencesFilename, pIoOpts);
COptions::AddValueOption("-annpe", "Neural network filename", "", "", settings.HasPeNeuralNetworkFilename, settings.PeNeuralNetworkFilename, pIoOpts);
COptions::AddValueOption("-annse", "Neural network filename", "", "", settings.HasSeNeuralNetworkFilename, settings.SeNeuralNetworkFilename, pIoOpts);
// add the essential options
OptionGroup* pEssentialOpts = COptions::CreateOptionGroup("Essential parameters");
COptions::AddValueOption("-a", "algorithm", "alignment algorithm: [fast, single, multi, all]", "", settings.HasAlgorithm, settings.Algorithm, pEssentialOpts, DEFAULT_ALGORITHM);
COptions::AddValueOption("-m", "mode", "alignment mode: [unique, all]", "", settings.HasMode, settings.Mode, pEssentialOpts, DEFAULT_MODE);
COptions::AddValueOption("-hs", "hash size", "hash size [4 - 32]", "", settings.HasHashSize, settings.HashSize, pEssentialOpts, DEFAULT_HASH_SIZE);
// add the filtering options
OptionGroup* pFilterOpts = COptions::CreateOptionGroup("Filtering");
COptions::AddValueOption("-act", "threshold", "the alignment candidate threshold (length)", "", settings.EnableAlignmentCandidateThreshold, settings.AlignmentCandidateThreshold, pFilterOpts);
//COptions::AddOption("-dh", "require at least two hash hits", settings.EnableDoubleHashHits, pFilterOpts);
COptions::AddValueOption("-ls", "radius", "enable local alignment search for PE reads", "", settings.HasLocalAlignmentSearchRadius, settings.LocalAlignmentSearchRadius, pFilterOpts);
//COptions::AddValueOption("-lsh", "mapping quality", "MQ threshold", "", settings.HasLocalAlignmentSearchHighMqThreshold, settings.LocalAlignmentSearchHighMqThreshold, pFilterOpts );
//COptions::AddValueOption("-lsl", "mapping quality", "MQ threshold; when the best MQ is higher than -lsh and the second best is lower than -lsl, local alignment search is enabled.", "", settings.HasLocalAlignmentSearchLowMqThreshold, settings.LocalAlignmentSearchLowMqThreshold, pFilterOpts );
COptions::AddValueOption("-mhp", "hash positions", "the maximum # of positions stored per seed", "", settings.LimitHashPositions, settings.HashPositionThreshold, pFilterOpts);
COptions::AddValueOption("-mhr", "hash regionss", "the maximum # of regions for aligning", "", settings.LimitHashRegions, settings.HashRegionThreshold, pFilterOpts);
COptions::AddValueOption("-min", "nucleotides", "the minimum # of aligned nucleotides", "", settings.CheckMinAlignment, settings.MinimumAlignment, pFilterOpts);
COptions::AddValueOption("-minp", "percent", "the minimum alignment percentage [0.0 - 1.0]", "", settings.CheckMinAlignmentPercent, settings.MinimumAlignmentPercentage, pFilterOpts);
COptions::AddValueOption("-mm", "mismatches", "the # of mismatches allowed", "", settings.CheckNumMismatches, settings.NumMismatches, pFilterOpts);
COptions::AddValueOption("-mmp", "threshold", "the percentage of mismatches allowed [0.0 - 1.0]", "", settings.CheckMismatchPercent, settings.MismatchPercent, pFilterOpts);
COptions::AddOption( "-ncg", "not count gaps as mismatches", settings.NotCountGapAsMismatch, pFilterOpts);
//COptions::AddOption("-mmal", "when enabled, unaligned portions of the read will not count as a mismatch", settings.UseAlignedLengthForMismatches, pFilterOpts);
// TODO: we need to move the alignment quality calculation up to ApplyReadFilters in order to make this option useable
//COptions::AddValueOption("-aq", "threshold", "enable an alignment quality threshold", "", settings.CheckAlignmentQuality, settings.AlignmentQualityThreshold, pFilterOpts);
// add the performance options
OptionGroup* pPerformanceOpts = COptions::CreateOptionGroup("Performance");
COptions::AddValueOption("-p", "processors", "uses the specified number of processors", "", settings.HasNumThreads, settings.NumThreads, pPerformanceOpts);
COptions::AddValueOption("-bw", "bandwidth", "specifies the Smith-Waterman bandwidth", "", settings.HasBandwidth, settings.Bandwidth, pPerformanceOpts, DEFAULT_BANDWIDTH);
COptions::AddOption("-lm", "enable low-memory functions", settings.UseLowMemory, pPerformanceOpts);
// add the jump database options
OptionGroup* pJumpOpts = COptions::CreateOptionGroup("Jump database");
COptions::AddValueOption("-j", "filename stub", "uses the specified jump database", "", settings.UseJumpDB, settings.JumpFilenameStub, pJumpOpts);
//COptions::AddValueOption("-jc", "# of hashes", "caches the most recently used hashes", "", settings.HasJumpCacheMemory, settings.JumpCacheMemory, pJumpOpts);
COptions::AddOption("-kd", "keeps the keys file on disk", settings.KeepJumpKeysOnDisk, pJumpOpts);
COptions::AddOption("-pd", "keeps the positions file on disk", settings.KeepJumpPositionsOnDisk, pJumpOpts);
COptions::AddValueOption("-sref", "reference prefixes", "specifies the prefixes of special references", "", settings.HasSpecialReferencePrefix, settings.SpecialReferencePrefix, pJumpOpts);
COptions::AddValueOption("-srefn", "hashes", "the maximum special hashes", "", settings.HasSpecialHashCount, settings.SpecialHashCount, pJumpOpts);
// add the reporting options
OptionGroup* pReportingOpts = COptions::CreateOptionGroup("Reporting");
COptions::AddValueOption("-statmq", "threshold", "enable mapping quality threshold for statistical map [0 - 255]", "", settings.HasStatMappingQuality, settings.StatMappingQuality, pReportingOpts);
COptions::AddOption("-omi", "output chrmosome ids and positions of multiply mapped alignments in the multiple.bam", settings.OutputMultiplyIncomplete, pReportingOpts);
COptions::AddOption("-om", "output complete multiply mapped alignments in the multiple.bam", settings.OutputMultiplyComplete, pReportingOpts);
COptions::AddOption("-zn", "output zn tags",settings.EnableZnTag, pReportingOpts);
//COptions::AddValueOption("-rur", "FASTQ filename", "stores unaligned reads in a FASTQ file", "", settings.RecordUnalignedReads, settings.UnalignedReadsFilename, pReportingOpts);
// add the pairwise alignment scoring options
OptionGroup* pPairwiseOpts = COptions::CreateOptionGroup("Pairwise Alignment Scores");
COptions::AddValueOption("-ms", "match score", "the match score", "", settings.HasMatchScore, settings.MatchScore, pPairwiseOpts, CPairwiseUtilities::MatchScore);
COptions::AddValueOption("-mms", "mismatch score", "the mismatch score", "", settings.HasMismatchScore, settings.MismatchScore, pPairwiseOpts, CPairwiseUtilities::MismatchScore);
COptions::AddValueOption("-gop", "gap open penalty", "the gap open penalty", "", settings.HasGapOpenPenalty, settings.GapOpenPenalty, pPairwiseOpts, CPairwiseUtilities::GapOpenPenalty);
COptions::AddValueOption("-gep", "gap extend penalty", "the gap extend penalty", "", settings.HasGapExtendPenalty, settings.GapExtendPenalty, pPairwiseOpts, CPairwiseUtilities::GapExtendPenalty);
COptions::AddValueOption("-hgop", "gap open penalty", "enables the homopolymer gop", "", settings.HasHomoPolymerGapOpenPenalty, settings.HomoPolymerGapOpenPenalty, pPairwiseOpts, CPairwiseUtilities::HomoPolymerGapOpenPenalty);
// add interface options
OptionGroup* pInterface = COptions::CreateOptionGroup("Interface Options");
COptions::AddOption("-quiet", "disable progress bars and counters", settings.IsQuietMode, pInterface);
// parse the current command line
COptions::Parse(argc, argv);
// =============================
// check for missing information
// =============================
bool foundError = false;
ostringstream errorBuilder;
const string ERROR_SPACER(7, ' ');
//if(settings.EnableAlignmentCandidateThreshold && settings.EnableDoubleHashHits) {
// errorBuilder << ERROR_SPACER << "Please specify either an alignment candidate threshold (-act) or double-hash hits (-dh). Double-hash hits are equivalent to '-act <hash size + 1>." << endl;
// foundError = true;
//}
if((settings.HasJumpCacheMemory || settings.KeepJumpKeysOnDisk || settings.KeepJumpPositionsOnDisk) && !settings.UseJumpDB) {
errorBuilder << ERROR_SPACER << "Jump database settings were specified, but the jump database was not explicitly chosen. Please use the -j parameter." << endl;
foundError = true;
}
if(settings.UseJumpDB) {
string keysFilename = settings.JumpFilenameStub + "_keys.jmp";
string metaFilename = settings.JumpFilenameStub + "_meta.jmp";
string positionsFilename = settings.JumpFilenameStub + "_positions.jmp";
CFileUtilities::CheckFile(keysFilename.c_str(), true);
CFileUtilities::CheckFile(metaFilename.c_str(), true);
CFileUtilities::CheckFile(positionsFilename.c_str(), true);
if(!settings.KeepJumpKeysOnDisk && !settings.KeepJumpPositionsOnDisk && settings.HasJumpCacheMemory)
settings.HasJumpCacheMemory = false;
}
if(!settings.CheckNumMismatches && !settings.CheckMismatchPercent ) {
//settings.CheckNumMismatches = true;
settings.CheckMismatchPercent = true;
}
// figure out which algorithm to use
CSequenceUtilities::LowercaseSequence(settings.Algorithm);
CAlignmentThread::AlignerAlgorithmType algorithmType = CAlignmentThread::AlignerAlgorithm_ALL;
if(settings.Algorithm == "fast") algorithmType = CAlignmentThread::AlignerAlgorithm_FAST;
else if(settings.Algorithm == "single") algorithmType = CAlignmentThread::AlignerAlgorithm_SINGLE;
else if(settings.Algorithm == "multi") algorithmType = CAlignmentThread::AlignerAlgorithm_MULTI;
else if(settings.Algorithm == "all") algorithmType = CAlignmentThread::AlignerAlgorithm_ALL;
else {
errorBuilder << ERROR_SPACER << "Unknown algorithm type. Please choose between 'fast', 'single', 'multi', or 'all'. The default value is '" << DEFAULT_ALGORITHM << "'." << endl;
foundError = true;
}
// set the hash positions threshold
if ( ( settings.LimitHashPositions ) && ( settings.HashPositionThreshold == 0 ) )
settings.LimitHashPositions = false;
if ( settings.LimitHashPositions ) {
// make sure we're using the all algorithm
if ( algorithmType != CAlignmentThread::AlignerAlgorithm_ALL ) {
errorBuilder << ERROR_SPACER << "Setting the hash positions threshold is only applicable when using the 'all' algorithm. This can be set by using the '-a all' parameter. Or turn off the hash positions threshold by using '-mhp 0'" << endl;
foundError = true;
}
// won't be the case
//if ( settings.HashPositionThreshold == 0 ) {
// errorBuilder << ERROR_SPACER << "The hash position threshold should be larger than 0. Use the -mhp parameter to change the hash position threshold." << endl;
// foundError = true;
//}
}
if ( settings.LimitHashRegions ) {
if ( settings.HashRegionThreshold == 0 ) {
errorBuilder << ERROR_SPACER << "The hash region threshold should be larger than 0. Use the -mhr parameter to change the hash position threshold." << endl;
foundError = true;
}
}
// figure out which alignment mode to use
CSequenceUtilities::LowercaseSequence(settings.Algorithm);
CAlignmentThread::AlignerModeType modeType = CAlignmentThread::AlignerMode_ALL;
if(settings.Mode == "unique") modeType = CAlignmentThread::AlignerMode_UNIQUE;
else if(settings.Mode == "all") modeType = CAlignmentThread::AlignerMode_ALL;
else {
errorBuilder << ERROR_SPACER << "Unknown mode type. Please choose between 'unique' or 'all'. The default value is '" << DEFAULT_MODE << "'." << endl;
foundError = true;
}
// set the maximum mismatch percentage
if(settings.CheckMismatchPercent) {
// make sure our value is within bounds
if((settings.MismatchPercent < 0.0) || (settings.MismatchPercent > 1.0)) {
errorBuilder << ERROR_SPACER << "The maximum mismatch percentage should be between 0.0 and 1.0." << endl;
foundError = true;
}
CPairwiseUtilities::MaxMismatchPercent = settings.MismatchPercent;
CPairwiseUtilities::UseMismatchPercentFilter = true;
}
// set the minimum aligned percentage
if(settings.CheckMinAlignmentPercent) {
// make sure our value is within bounds
if((settings.MinimumAlignmentPercentage < 0.0) || (settings.MinimumAlignmentPercentage > 1.0)) {
errorBuilder << ERROR_SPACER << "The minimum alignment percentage should be between 0.0 and 1.0." << endl;
foundError = true;
}
// assign the minimum percentage alignment
CPairwiseUtilities::MinPercentAlignment = settings.MinimumAlignmentPercentage;
CPairwiseUtilities::UseMinAlignmentPercentFilter = true;
}
// check the minimum alignment quality
//if(settings.CheckAlignmentQuality && (settings.AlignmentQualityThreshold > 99)) {
// errorBuilder << ERROR_SPACER << "The alignment quality threshold should be between 0 and 99." << endl;
// foundError = true;
//}
// set the hash size
if(settings.HasHashSize && ((settings.HashSize < MIN_HASH_SIZE) || (settings.HashSize > MAX_HASH_SIZE))) {
errorBuilder << ERROR_SPACER << "The hash size should be between " << MIN_HASH_SIZE << " and " << MAX_HASH_SIZE << ". The default value is " << DEFAULT_HASH_SIZE << "." << endl;
foundError = true;
}
// set the number of threads
if(settings.HasNumThreads && (settings.NumThreads < 1)) {
errorBuilder << ERROR_SPACER << "At least one processor should be specified. Use the -p parameter to change the number of desired processors." << endl;
foundError = true;
}
// test if the specified input files exist and are in the right format
SequencingTechnologies seqTech;
ReadStatus readStatus;
MosaikReadFormat::CReadReader::CheckFile(settings.ReadsFilename, seqTech, readStatus, true);
MosaikReadFormat::CReferenceSequenceReader::CheckFile(settings.ReferencesFilename, true);
// set defaults of act, ls and bw
{
MosaikReadFormat::CReadReader reader;
reader.Open( settings.ReadsFilename );
uint64_t nReads, nBases;
nReads = reader.GetNumReads();
nBases = reader.GetNumBases();
// sanity checker
if ( nBases < nReads )
errorBuilder << ERROR_SPACER << "The number of reads is smaller than the number of total bases in " << settings.ReadsFilename;
double readLength = nBases/nReads;
if ( ( readStatus & RS_PAIRED_END_READ ) != 0 )
readLength /= 2;
// act
if ( settings.EnableAlignmentCandidateThreshold ) {
if ( settings.AlignmentCandidateThreshold == 0 ) {
settings.EnableAlignmentCandidateThreshold = false;
settings.AlignmentCandidateThreshold = 0;
}
} else {
if ( seqTech == ST_454 ) {
settings.EnableAlignmentCandidateThreshold = true;
settings.AlignmentCandidateThreshold = ( readLength > 350.0 ) ? 55 : 26;
} else {
settings.EnableAlignmentCandidateThreshold = true;
settings.AlignmentCandidateThreshold = (unsigned char)floor( 13 + ( readLength / 5 ) );
}
}
// bw
if ( settings.HasBandwidth ) {
if ( settings.Bandwidth == 0 ) {
settings.HasBandwidth = false;
settings.Bandwidth = 0;
}
} else {
if ( settings.CheckNumMismatches ) {
settings.HasBandwidth = true;
settings.Bandwidth = static_cast<unsigned int>(ceil( 2.5 * settings.NumMismatches ));
if ( ( settings.Bandwidth % 2 ) != 1 ) ++settings.Bandwidth;
} else if ( settings.CheckMismatchPercent ) {
settings.HasBandwidth = true;
settings.Bandwidth = static_cast<unsigned int>(ceil( 2.5 * settings.MismatchPercent * ceil(readLength) ));
if ( ( settings.Bandwidth % 2 ) != 1 ) ++settings.Bandwidth;
} else {
settings.HasBandwidth = false;
settings.Bandwidth = 0;
}
}
// ls
// only for paired-end data and the -mfl setting in the given archive != 0
MosaikReadFormat::ReadGroup readGroup = reader.GetReadGroup();
if ( settings.HasLocalAlignmentSearchRadius ) {
if ( settings.LocalAlignmentSearchRadius == 0 ) {
settings.HasLocalAlignmentSearchRadius = false;
settings.LocalAlignmentSearchRadius = 0;
} else {
if ( ( readStatus & RS_PAIRED_END_READ ) == 0 ) {
cout << "WARNING: Local alignment search only works for paired-end data." << endl;
settings.HasLocalAlignmentSearchRadius = false;
settings.LocalAlignmentSearchRadius = 0;
}
}
} else {
if ( ( readStatus & RS_PAIRED_END_READ ) != 0 ) {
if ( readGroup.MedianFragmentLength == 0 ) {
cout << "WARNING: Paired-end data is detected, but the median fragment length is not specified." << endl;
cout << " Accordingly, local alignment search is not enabled." << endl;
cout << " The median fragment length (-mfl parameter) can be specified in MosaikBuild.\n" << endl;
} else {
settings.HasLocalAlignmentSearchRadius = true;
settings.LocalAlignmentSearchRadius = readGroup.MedianFragmentLength;
}
}
}
if ( !settings.HasLocalAlignmentSearchRadius && settings.HasLocalAlignmentSearchHighMqThreshold )
cout << "WARNING: -lsh is enabled but -ls is not." << endl;
if ( !settings.HasLocalAlignmentSearchRadius && settings.HasLocalAlignmentSearchLowMqThreshold )
cout << "WARNING: -lsl is enabled but -ls is not." << endl;
if ( settings.HasLocalAlignmentSearchHighMqThreshold || settings.HasLocalAlignmentSearchLowMqThreshold ) {
if ( settings.LocalAlignmentSearchLowMqThreshold > settings.LocalAlignmentSearchHighMqThreshold ) {
errorBuilder << ERROR_SPACER << "The high MQ threshold (-lsh) must be larger than low MQ threshold (-lsl)." << endl;
foundError = true;
}
}
// Note: These two statements are always tru
//if (settings.LocalAlignmentSearchHighMqThreshold > 255) {
// errorBuilder << ERROR_SPACER << "The range of high MQ threshold (-lsh) is 0-255." << endl;
// foundError = true;
//}
//if ( settings.LocalAlignmentSearchLowMqThreshold > 255 ) {
// errorBuilder << ERROR_SPACER << "The range of low MQ threshold (-lsl) is 0-255." << endl;
// foundError = true;
//}
reader.Close();
}
// set the Smith-Waterman bandwidth
if ( settings.HasBandwidth && ( ( settings.Bandwidth % 2 ) != 1 ) ) {
errorBuilder << ERROR_SPACER << "The bandwidth must be an odd number. Use the -bw parameter to change the bandwidth." << endl;
foundError = true;
}
switch(seqTech) {
case ST_454:
if(!settings.HasHomoPolymerGapOpenPenalty) {
CPairwiseUtilities::UseHomoPolymerGapOpenPenalty = true;
settings.HasHomoPolymerGapOpenPenalty = true;
settings.HomoPolymerGapOpenPenalty = CPairwiseUtilities::HomoPolymerGapOpenPenalty;
}
break;
case ST_SOLID:
settings.EnableColorspace = true;
break;
}
// check if we have a supplied basespace reference archive when aligning a SOLiD read archive
if(seqTech == ST_SOLID) {
// force -ibs to be basespace and -ia to be colorspace if aligning SOLiD reads
if(settings.HasBasespaceReferencesFilename && settings.HasReferencesFilename) {
MosaikReadFormat::CReferenceSequenceReader csRef, bsRef;
// retrieve the colorspace status
csRef.Open(settings.ReferencesFilename);
ReferenceSequenceStatus csStatus = csRef.GetStatus();
csRef.Close();
// retrieve the basespace status
bsRef.Open(settings.BasespaceReferencesFilename);
ReferenceSequenceStatus bsStatus = bsRef.GetStatus();
bsRef.Close();
if(csStatus != REF_COLORSPACE) {
errorBuilder << ERROR_SPACER << "Expected to find a colorspace reference sequence archive (" << settings.ReferencesFilename << ") with the -ia parameter, but found a basespace reference sequence archive." << endl;
foundError = true;
}
if(bsStatus != REF_UNKNOWN) {
errorBuilder << ERROR_SPACER << "Expected to find a basespace reference sequence archive (" << settings.BasespaceReferencesFilename << ") with the -ibs parameter, but found a colorspace reference sequence archive." << endl;
foundError = true;
}
}
if(!settings.HasBasespaceReferencesFilename) {
errorBuilder << ERROR_SPACER << "When aligning SOLiD read archives, both a colorspace reference archive AND a basespace reference archive are required. Use the -ibs parameter to supply the basespace reference archive filename." << endl;
foundError = true;
}
//if( settings.UseLowMemory ) {
// errorBuilder << ERROR_SPACER << "The low-memory algorithm does not support for SOLiD reads yet." << endl;
// foundError = true;
//}
}
// files for neural network for mapping quality calculation
if (!settings.HasPeNeuralNetworkFilename) {
errorBuilder << ERROR_SPACER << "An input paired-end neural-network file was not specified. Please use the -annpe parameter." << endl
<< ERROR_SPACER << " The file is on src/networkFile/2.1.26.pe.100.0065.ann." << endl;
foundError = true;
} else { // test the exietence of the file
// doesn't show error message
CFileUtilities::CheckFile(settings.PeNeuralNetworkFilename.c_str(), true);
}
if (!settings.HasSeNeuralNetworkFilename) {
errorBuilder << ERROR_SPACER << "An input single-end neural-network file was not specified. Please use the -annse parameter." << endl
<< ERROR_SPACER << " The file is on src/networkFile/2.1.26.se.100.005.ann." << endl;
foundError = true;
} else { // test the exietence of the file
CFileUtilities::CheckFile(settings.SeNeuralNetworkFilename.c_str(), true);
}
if (settings.OutputMultiplyIncomplete && settings.OutputMultiplyComplete) {
foundError = true;
errorBuilder << ERROR_SPACER << "-omi and -om are incompatible." << endl;
}
// print the errors if any were found
if(foundError) {
CConsole::Red();
printf("ERROR: Some problems were encountered when parsing the command line options:\n");
CConsole::Reset();
printf("%s\n", errorBuilder.str().c_str());
printf("For a complete list of command line options, type \"%s -h\"\n", argv[0]);
exit(1);
}
// ===================================================
// Parse configuration strings and set class variables
// ===================================================
// set the minimum alignment quality
//if(settings.CheckAlignmentQuality) {
// CPairwiseUtilities::MinAlignmentQuality = settings.AlignmentQualityThreshold;
// CPairwiseUtilities::UseMinAlignmentQualityFilter = true;
//}
// set the maximum number of mismatches
if(settings.CheckNumMismatches) {
CPairwiseUtilities::MaxNumMismatches = settings.NumMismatches;
CPairwiseUtilities::UseMismatchFilter = true;
}
// set the minimum number of aligned nucleotides
if(settings.CheckMinAlignment) {
CPairwiseUtilities::MinAlignment = settings.MinimumAlignment;
CPairwiseUtilities::UseMinAlignmentFilter = true;
}
// set the Smith-Waterman scores
if(settings.HasMatchScore || settings.HasMismatchScore || settings.HasGapOpenPenalty || settings.HasGapExtendPenalty) {
if(settings.HasMatchScore) CPairwiseUtilities::MatchScore = settings.MatchScore;
if(settings.HasMismatchScore) CPairwiseUtilities::MismatchScore = settings.MismatchScore;
if(settings.HasGapOpenPenalty) CPairwiseUtilities::GapOpenPenalty = settings.GapOpenPenalty;
if(settings.HasGapExtendPenalty) CPairwiseUtilities::GapExtendPenalty = settings.GapExtendPenalty;
}
// set the Smith-Waterman h**o-polymer gap open penalty
if(settings.HasHomoPolymerGapOpenPenalty) {
CPairwiseUtilities::HomoPolymerGapOpenPenalty = settings.HomoPolymerGapOpenPenalty;
CPairwiseUtilities::UseHomoPolymerGapOpenPenalty = true;
}
// show warning message about unique alignments
if(((readStatus & RS_PAIRED_END_READ) != 0) && (modeType != CAlignmentThread::AlignerMode_ALL)) {
cout << "WARNING: A paired-end read archive was detected and the aligner mode (-m parameter) was not set to 'all'. Paired-end resolution in MosaikSort will be limited to unique vs unique reads.\n" << endl << endl;
}
// show warning messages dealing with the local alignment search radius
if(settings.HasLocalAlignmentSearchRadius) {
// show the warning message if we have a SE read archive
if( ( readStatus & RS_SINGLE_END_READ ) != 0 ) {
cout << "WARNING: A single-end read archive was detected and the local alignment search was enabled. Local alignment search only works with paired-end reads.\n" << endl << endl;
settings.HasLocalAlignmentSearchRadius = false;
} else {
// show the warning message if we have a PE read archive with no mean fragment length
MosaikReadFormat::CReadReader in;
in.Open(settings.ReadsFilename);
MosaikReadFormat::ReadGroup readGroup = in.GetReadGroup();
in.Close();
if( readGroup.MedianFragmentLength == 0 ) {
cout << "WARNING: Local alignment search only works when the median fragment length (-mfl parameter) has been specified in MosaikBuild.\n" << endl << endl;
settings.HasLocalAlignmentSearchRadius = false;
}
}
}
// show warning message about using the local alignment search with SE read archives
if(((readStatus & RS_SINGLE_END_READ) != 0) && settings.HasLocalAlignmentSearchRadius) {
cout << "WARNING: A single-end read archive was detected and the local alignment search was enabled. Local alignment search only works with paired-end reads.\n" << endl << endl;
settings.HasLocalAlignmentSearchRadius = false;
}
// start benchmarking
CBenchmark bench;
bench.Start();
// create our aligner
CMosaikAligner ma(settings.HashSize, algorithmType, modeType, settings.NumThreads, commandLine );
// ===============
// enable features
// ===============
// set zn tag reporting
if (settings.EnableZnTag) ma.EnableZnTag();
// set neural network filename
if (settings.HasPeNeuralNetworkFilename) ma.SetPeNeuralNetworkFilename(settings.PeNeuralNetworkFilename);
if (settings.HasSeNeuralNetworkFilename) ma.SetSeNeuralNetworkFilename(settings.SeNeuralNetworkFilename);
// output multiply mapped alignments
ma.OutputMultiply(settings.OutputMultiplyIncomplete, settings.OutputMultiplyComplete);
// enable quiet mode
if (settings.IsQuietMode) ma.SetQuietMode();
// enable the hash positions threshold
if(settings.LimitHashPositions) ma.EnableHashPositionThreshold(settings.HashPositionThreshold);
// enable the hash region threshold
if(settings.LimitHashRegions) ma.EnableHashRegionThreshold(settings.HashRegionThreshold);
// enable the alignment candidate threshold
if(settings.EnableAlignmentCandidateThreshold) ma.EnableAlignmentCandidateThreshold(settings.AlignmentCandidateThreshold);
// enable unaligned read reporting if specified
//if(settings.RecordUnalignedReads) ma.EnableUnalignedReadReporting(settings.UnalignedReadsFilename);
// enable colorspace (SOLiD)
if(settings.EnableColorspace) ma.EnableColorspace(settings.BasespaceReferencesFilename);
// enable double-hash hits
//if(settings.EnableDoubleHashHits) ma.EnableAlignmentCandidateThreshold(settings.HashSize + 1);
// enable entire read length mismatch checking
if(settings.UseAlignedLengthForMismatches) ma.UseAlignedReadLengthForMismatchCalculation();
// enable the jump database
if(settings.UseJumpDB) ma.EnableJumpDB(settings.JumpFilenameStub, settings.JumpCacheMemory, !settings.KeepJumpKeysOnDisk, !settings.KeepJumpPositionsOnDisk);
// enable the local alignment search
if(settings.HasLocalAlignmentSearchRadius) ma.EnableLocalAlignmentSearch(settings.LocalAlignmentSearchRadius);
// set the Smith-Waterman bandwidth
if(settings.HasBandwidth) ma.EnableBandedSmithWaterman(settings.Bandwidth);
// enable low-memory algorithm
if(settings.UseLowMemory) ma.EnableLowMemory();
// not count gasp as mismatches
if(settings.NotCountGapAsMismatch) ma.NotCountGapAsMismatch();
// enables special references checker
if(settings.HasSpecialReferencePrefix) {
ma.EnableSpecialReference(settings.SpecialReferencePrefix);
if ( settings.HasSpecialHashCount )
ma.SetSpecialHashCount(settings.SpecialHashCount);
else
ma.SetSpecialHashCount(DEFAULT_SPECIAL_HASHES);
}
// set the trigger condition of local search
if ( settings.HasLocalAlignmentSearchHighMqThreshold || settings.HasLocalAlignmentSearchLowMqThreshold )
ma.SetLocalAlignmentSearchMqThreshold ( settings.LocalAlignmentSearchHighMqThreshold, settings.LocalAlignmentSearchLowMqThreshold );
// set the mapping quality threshold for stat map
if ( settings.HasStatMappingQuality ) ma.SetStatMappingQuality( settings.StatMappingQuality );
// =============
// set filenames
// =============
ma.SetFilenames(settings.ReadsFilename, settings.AlignmentsFilename, settings.ReferencesFilename);
// ====================
// echo enabled options
// ====================
cout << "- Using the following alignment algorithm: ";
switch(algorithmType) {
case CAlignmentThread::AlignerAlgorithm_FAST:
cout << "single position (fast)" << endl;
break;
case CAlignmentThread::AlignerAlgorithm_SINGLE:
cout << "single position" << endl;
break;
case CAlignmentThread::AlignerAlgorithm_MULTI:
cout << "multiple position" << endl;
break;
case CAlignmentThread::AlignerAlgorithm_ALL:
cout << "all positions" << endl;
break;
default:
cout << "ERROR: Unknown alignment algorithm specified." << endl;
exit(1);
break;
}
cout << "- Using the following alignment mode: ";
switch(modeType) {
case CAlignmentThread::AlignerMode_ALL:
cout << "aligning reads to all possible locations" << endl;
break;
case CAlignmentThread::AlignerMode_UNIQUE:
cout << "only aligning unique reads" << endl;
break;
default:
cout << "ERROR: Unknown alignment mode specified." << endl;
exit(1);
break;
}
//if(settings.CheckAlignmentQuality) cout << "- Using an alignment quality threshold of " << CPairwiseUtilities::MinAlignmentQuality << endl;
if(settings.CheckNumMismatches) cout << "- Using a maximum mismatch threshold of " << CPairwiseUtilities::MaxNumMismatches << endl;
if(settings.CheckMismatchPercent) cout << "- Using a maximum mismatch percent threshold of " << CPairwiseUtilities::MaxMismatchPercent << endl;
if(settings.CheckMinAlignment) cout << "- Using a minimum alignment threshold of " << CPairwiseUtilities::MinAlignment << endl;
if(settings.CheckMinAlignmentPercent) cout << "- Using a minimum percent alignment threshold of " << CPairwiseUtilities::MinPercentAlignment << endl;
if(settings.HasHashSize) cout << "- Using a hash size of " << (unsigned int)settings.HashSize << endl;
//if(settings.EnableDoubleHashHits) cout << "- Using double-hash hits" << endl;
if(settings.EnableColorspace) cout << "- Aligning in colorspace (SOLiD)" << endl;
if(settings.HasNumThreads) cout << "- Using " << (short)settings.NumThreads << (settings.NumThreads > 1 ? " processors" : " processor") << endl;
if(settings.HasBandwidth) cout << "- Using a Smith-Waterman bandwidth of " << settings.Bandwidth << endl;
if(settings.EnableAlignmentCandidateThreshold)
cout << "- Using an alignment candidate threshold of " << (unsigned short)settings.AlignmentCandidateThreshold << "bp." << endl;
if(settings.HasLocalAlignmentSearchRadius)
cout << "- Using a local alignment search radius of " << settings.LocalAlignmentSearchRadius << "bp." << endl;
if(settings.LimitHashPositions) cout << "- Setting hash position threshold to " << settings.HashPositionThreshold << endl;
if(settings.UseJumpDB) {
cout << "- Using a jump database for hashing";
if(settings.HasJumpCacheMemory) cout << " with a " << settings.JumpCacheMemory << " element cache";
cout << ".";
if(!settings.KeepJumpKeysOnDisk && !settings.KeepJumpPositionsOnDisk) cout << " Storing keys & positions in memory.";
else if(!settings.KeepJumpKeysOnDisk && settings.KeepJumpPositionsOnDisk) cout << " Storing keys in memory.";
else if(settings.KeepJumpKeysOnDisk && !settings.KeepJumpPositionsOnDisk) cout << " Storing positions in memory.";
cout << endl;
}
//if(settings.RecordUnalignedReads)
// cout << "- Reporting all unaligned reads to " << settings.UnalignedReadsFilename << "." << endl;
if(settings.HasHomoPolymerGapOpenPenalty)
cout << "- Using a h**o-polymer gap open penalty of " << CPairwiseUtilities::HomoPolymerGapOpenPenalty << endl;
if(settings.HasMatchScore || settings.HasMismatchScore || settings.HasGapOpenPenalty || settings.HasGapExtendPenalty)
cout << "- Updating Smith-Waterman scoring scheme (match, mismatch, gap open, gap extend): (" <<
CPairwiseUtilities::MatchScore << ", " << CPairwiseUtilities::MismatchScore << ", " <<
CPairwiseUtilities::GapOpenPenalty << ", " << CPairwiseUtilities::GapExtendPenalty << ")" << endl;
// ==============
// Start aligning
// ==============
ma.AlignReadArchiveLowMemory();
//ma.AlignReadArchive();
// ==================
// Show total runtime
// ==================
// stop benchmarking
bench.Stop();
// show the benchmarking results
cout << endl;
bench.DisplayTime("MosaikAligner");
return 0;
}
void CMosaikAligner::AlignReadArchiveLowMemory(void) {
// ==============
// initialization
// ==============
// retrieve the concatenated reference sequence length
// vector<ReferenceSequence> referenceSequences;
MosaikReadFormat::CReferenceSequenceReader refseq;
refseq.Open(mSettings.ReferenceFilename);
refseq.GetReferenceSequences(referenceSequences);
mReferenceLength = refseq.GetReferenceSequenceLength();
const unsigned int numRefSeqs = refseq.GetNumReferenceSequences();
refseq.Close();
// retrieve the basespace reference filenames
//char** pBsRefSeqs = NULL;
if(mFlags.EnableColorspace) {
MosaikReadFormat::CReferenceSequenceReader bsRefSeq;
bsRefSeq.Open(mSettings.BasespaceReferenceFilename);
if(!bsRefSeq.HasSameReferenceSequences(referenceSequences)) {
printf("ERROR: The basespace and colorspace reference sequence archives do not seem to represent the same FASTA file.\n");
exit(1);
}
bsRefSeq.Close();
}
// initialize our hash tables
//InitializeHashTables(CalculateHashTableSize(mReferenceLength, mSettings.HashSize));
// hash the concatenated reference sequence
//if(!mFlags.IsUsingJumpDB) {
// InitializeHashTables(CalculateHashTableSize(mReferenceLength, mSettings.HashSize), 0, 0, 0);
// HashReferenceSequence(refseq);
//}
//cout << "- loading reference sequence... ";
//cout.flush();
//refseq.LoadConcatenatedSequence(mReference);
//cout << "finished." << endl;
// create our reference sequence LUTs
//unsigned int* pRefBegin = new unsigned int[numRefSeqs];
//unsigned int* pRefEnd = new unsigned int[numRefSeqs];
//
//for(unsigned int j = 0; j < numRefSeqs; j++) {
// pRefBegin[j] = referenceSequences[j].Begin;
// pRefEnd[j] = referenceSequences[j].End;
//}
string inputReadArchiveFilename = mSettings.InputReadArchiveFilename;
if ( !mFlags.UseLowMemory ) {
// prepare BS reference sequence for SOLiD data
char** pBsRefSeqs = NULL;
if(mFlags.EnableColorspace) {
cout << "- loading basespace reference sequences... ";
cout.flush();
MosaikReadFormat::CReferenceSequenceReader bsRefSeq;
bsRefSeq.Open(mSettings.BasespaceReferenceFilename);
bsRefSeq.CopyReferenceSequences(pBsRefSeqs);
bsRefSeq.Close();
cout << "finished." << endl;
}
// prepare reference sequence
refseq.Open(mSettings.ReferenceFilename);
cout << "- loading reference sequence... ";
cout.flush();
refseq.LoadConcatenatedSequence(mReference);
cout << "finished." << endl;
refseq.Close();
unsigned int* pRefBegin = new unsigned int[numRefSeqs];
unsigned int* pRefEnd = new unsigned int[numRefSeqs];
for(unsigned int j = 0; j < numRefSeqs; j++) {
pRefBegin[j] = referenceSequences[j].Begin;
pRefEnd[j] = referenceSequences[j].End;
}
// initialize our hash tables
if(!mFlags.IsUsingJumpDB) {
InitializeHashTables(CalculateHashTableSize(mReferenceLength, mSettings.HashSize), 0, 0, 0, mFlags.UseLowMemory, 0);
HashReferenceSequence(refseq);
}
else {
InitializeHashTables(CalculateHashTableSize(mReferenceLength, mSettings.HashSize), pRefBegin[0], pRefEnd[numRefSeqs - 1], 0, mFlags.UseLowMemory, 0);
mpDNAHash->LoadKeysNPositions();
}
// set the hash positions threshold
if(mFlags.IsUsingHashPositionThreshold && (mAlgorithm == CAlignmentThread::AlignerAlgorithm_ALL))
mpDNAHash->RandomizeAndTrimHashPositions(mSettings.HashPositionThreshold);
// localize the read archive filenames
string outputReadArchiveFilename = mSettings.OutputReadArchiveFilename;
// define our read format reader and writer
MosaikReadFormat::CReadReader in;
in.Open(inputReadArchiveFilename);
MosaikReadFormat::ReadGroup readGroup = in.GetReadGroup();
ReadStatus readStatus = in.GetStatus();
mSettings.SequencingTechnology = readGroup.SequencingTechnology;
mSettings.MedianFragmentLength = readGroup.MedianFragmentLength;
vector<MosaikReadFormat::ReadGroup> readGroups;
readGroups.push_back(readGroup);
// set the alignment status flags
AlignmentStatus alignmentStatus = AS_UNSORTED_READ | readStatus;
if(mMode == CAlignmentThread::AlignerMode_ALL) alignmentStatus |= AS_ALL_MODE;
else alignmentStatus |= AS_UNIQUE_MODE;
MosaikReadFormat::CAlignmentWriter out;
out.Open(mSettings.OutputReadArchiveFilename.c_str(), referenceSequences, readGroups, alignmentStatus, ALIGNER_SIGNATURE);
AlignReadArchive(in, out, pRefBegin, pRefEnd, pBsRefSeqs);
// close open file streams
in.Close();
// solid references should be one-base longer after converting back to basespace
if(mFlags.EnableColorspace) out.AdjustSolidReferenceBases();
out.Close();
// free memory
if(mFlags.IsUsingJumpDB) mpDNAHash->FreeMemory();
if(pRefBegin) delete [] pRefBegin;
if(pRefEnd) delete [] pRefEnd;
if(mReference) delete [] mReference;
if(pBsRefSeqs) {
for(unsigned int i = 0; i < numRefSeqs; ++i) delete [] pBsRefSeqs[i];
delete [] pBsRefSeqs;
}
pRefBegin = NULL;
pRefEnd = NULL;
mReference = NULL;
pBsRefSeqs = NULL;
}
else {
// grouping reference and store information in referenceGroups vector
// vector< pair <unsigned int, unsigned int> > referenceGroups;
GroupReferences();
// get hash statistics for adjusting mhp for each reference group and reserve memory
vector< unsigned int > nHashs; // the numbers of hash positions in each reference group
vector< unsigned int > expectedMemories; // the numbers of hashs in each reference group
uint64_t nTotalHash;
GetHashStatistics( nHashs, expectedMemories, nTotalHash );
// align reads again per chromosome group
for ( unsigned int i = 0; i < referenceGroups.size(); i++) {
unsigned int startRef = referenceGroups[i].first;
unsigned int endRef = referenceGroups[i].first + referenceGroups[i].second - 1;
CConsole::Heading();
if ( referenceGroups[i].second > 1 )
cout << endl << "Aligning chromosome " << startRef + 1 << "-" << endRef + 1 << " (of " << numRefSeqs << "):" << endl;
else
cout << endl << "Aligning chromosome " << startRef + 1 << " (of " << numRefSeqs << "):" << endl;
CConsole::Reset();
// initialize our hash tables
// calculate expected memories for jump data
unsigned int expectedMemory = nHashs[i] + expectedMemories[i];
// reserve 3% more memory for unexpected usage
expectedMemory = expectedMemory * 1.03;
InitializeHashTables(0, referenceSequences[startRef].Begin, referenceSequences[endRef].End, referenceSequences[startRef].Begin, mFlags.UseLowMemory, expectedMemory);
// set the hash positions threshold
if(mFlags.IsUsingHashPositionThreshold && (mAlgorithm == CAlignmentThread::AlignerAlgorithm_ALL)) {
double ratio = nHashs[i] / (double)nTotalHash;
unsigned int positionThreshold = ceil(ratio * (double)mSettings.HashPositionThreshold);
//cout << positionThreshold << endl;
mpDNAHash->RandomizeAndTrimHashPositions(positionThreshold);
}
// load jump data
mpDNAHash->LoadKeysNPositions();
// set reference information
unsigned int* pRefBegin = new unsigned int[referenceGroups[i].second];
unsigned int* pRefEnd = new unsigned int[referenceGroups[i].second];
for ( unsigned int j = 0; j < referenceGroups[i].second; j++ ){
pRefBegin[j] = referenceSequences[startRef+j].Begin - referenceSequences[startRef].Begin;
pRefEnd[j] = referenceSequences[startRef+j].End - referenceSequences[startRef].Begin;
}
// prepare BS reference sequence for SOLiD data
char** pBsRefSeqs = NULL;
if(mFlags.EnableColorspace) {
cout << "- loading basespace reference sequences... ";
cout.flush();
MosaikReadFormat::CReferenceSequenceReader bsRefSeq;
bsRefSeq.Open(mSettings.BasespaceReferenceFilename);
bsRefSeq.CopyReferenceSequences(pBsRefSeqs, startRef, referenceGroups[i].second);
bsRefSeq.Close();
cout << "finished." << endl;
}
// prepare reference sequence
refseq.Open(mSettings.ReferenceFilename);
cout << "- loading reference sequence... ";
cout.flush();
//refseq.LoadConcatenatedSequence(mReference);
refseq.LoadConcatenatedSequence(mReference, startRef, referenceGroups[i].second);
refseq.Close();
// trim reference sequence
//unsigned int chrLength = referenceSequences[endRef].End - referenceSequences[startRef].Begin + 1;
//char* chrReference = new char[ chrLength + 1 ];
//char* mReferencePtr = mReference + referenceSequences[startRef].Begin;
//memcpy( chrReference, mReferencePtr, chrLength);
//chrReference[chrLength] = 0;
//delete [] mReference;
//mReference = chrReference;
cout << "finished." << endl;
// localize the read archive filenames
// get a temporary file name
string tempFilename;
CFileUtilities::GetTempFilename(tempFilename);
outputFilenames.push_back(tempFilename);
// define our read format reader and writer
MosaikReadFormat::CReadReader in;
in.Open(inputReadArchiveFilename);
MosaikReadFormat::ReadGroup readGroup = in.GetReadGroup();
ReadStatus readStatus = in.GetStatus();
mSettings.SequencingTechnology = readGroup.SequencingTechnology;
mSettings.MedianFragmentLength = readGroup.MedianFragmentLength;
vector<MosaikReadFormat::ReadGroup> readGroups;
readGroups.push_back(readGroup);
// set the alignment status flags
AlignmentStatus alignmentStatus = AS_UNSORTED_READ | readStatus;
if(mMode == CAlignmentThread::AlignerMode_ALL) alignmentStatus |= AS_ALL_MODE;
else alignmentStatus |= AS_UNIQUE_MODE;
// prepare a new vector for the current chromosome for opening out archive
vector<ReferenceSequence> smallReferenceSequences;
for ( unsigned int j = 0; j < referenceGroups[i].second; j++ ){
smallReferenceSequences.push_back(referenceSequences[startRef+j]);
}
MosaikReadFormat::CAlignmentWriter out;
out.Open(tempFilename.c_str(), smallReferenceSequences, readGroups, alignmentStatus, ALIGNER_SIGNATURE);
out.AdjustPartitionSize(20000/referenceGroups.size());
AlignReadArchive(in, out, pRefBegin, pRefEnd, pBsRefSeqs);
// close open file streams
in.Close();
// solid references should be one-base longer after converting back to basespace
if(mFlags.EnableColorspace) out.AdjustSolidReferenceBases();
out.Close();
// free memory
if(mFlags.IsUsingJumpDB) mpDNAHash->FreeMemory();
if(pRefBegin) delete [] pRefBegin;
if(pRefEnd) delete [] pRefEnd;
if(mReference) delete [] mReference;
if(pBsRefSeqs) {
for(unsigned int j = 0; j < referenceGroups[i].second; j++)
delete [] pBsRefSeqs[j];
delete [] pBsRefSeqs;
}
pRefBegin = NULL;
pRefEnd = NULL;
mReference = NULL;
pBsRefSeqs = NULL;
}
}
if ( mFlags.UseLowMemory )
MergeArchives();
PrintStatistics();
}