int main(int argc, char* argv[]) {
string cmpFileName, movieFileName;
int argi = 3;
int numMetrics = 8;
map<string,bool> metricOptions;
int maxElements = 0;
//
// Default is all options are true
//
CreateMetricOptions(metricOptions);
string metricList = "";
bool useCcs = false;
bool byRead = false;
bool failOnMissingData = false;
CommandLineParser clp;
bool printVersion = false;
clp.RegisterStringOption("basFileName", &movieFileName, "The input {bas,pls}.h5 or input.fofn.", true);
clp.RegisterStringOption("cmpFileName", &cmpFileName, "The cmp.h5 file to load pulse information into.", true);
clp.RegisterPreviousFlagsAsHidden();
clp.RegisterStringOption("metrics", &metricList, "The a string delimited list of metrics (with no spaces).The "
"valid options are: QualityValue, ClassifierQV, MergeQV, StartFrame,"
"PulseWidth, pkmid, IPD, and Light.");
clp.RegisterFlagOption("useccs", &useCcs, "Load pulse information for CCS sequences and not raw bases.");
clp.RegisterFlagOption("byread", &byRead, "Load pulse information by read rather than buffering an entire pls.h5 file. "
"This option will soon be deprecated and on by default.");
clp.RegisterIntOption("maxElements", &maxElements, "Set a limit on the size of pls/bas file to buffer in.", CommandLineParser::PositiveInteger);
clp.RegisterFlagOption("failOnMissingData", &failOnMissingData, "Exit if any data fields are missing from the bas.h5 or pls.h5 input that are required to load a metric. Defualt is a warning.");
clp.SetProgramSummary("Load pulse information such as inter pulse distance, or quality information into the cmp.h5 file."
"This allows one to analyze kinetic and quality information by alignment column.");
clp.ParseCommandLine(argc, argv);
if (printVersion) {
cout << VERSION << endl;
exit(1);
}
if (metricList == "") {
SetDefaultMetricOptions(metricOptions);
}
else {
ParseMetricsList(metricList, metricOptions);
}
//
// Always read in basecalls since they are used to check the sanity
// of the alignment indices.
//
metricOptions["Basecall"] = true;
//
// Translate from the metrics to be loaded to the ones that are
// required to compute them.
//
vector<string> datasetFields;
RequirementMap fieldRequirements;
BuildRequirementMap(fieldRequirements);
StoreDatasetFieldsFromPulseFields(metricOptions, fieldRequirements, datasetFields);
vector<string> movieFileNames;
vector<string> fofnMovieNames;
FileOfFileNames::StoreFileOrFileList(movieFileName, movieFileNames);
HDFBasReader hdfBasReader;
HDFPlsReader hdfPlsReader;
HDFCCSReader<SMRTSequence> hdfCcsReader;
vector<string> baseFileFields, pulseFileFields;
int fieldIndex;
bool useBaseFile = false, usePulseFile = false;
for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
if (hdfBasReader.ContainsField(datasetFields[fieldIndex])) {
useBaseFile = true;
baseFileFields.push_back(datasetFields[fieldIndex]);
}
}
if (maxElements != 0) {
hdfBasReader.maxAllocNElements = maxElements;
hdfPlsReader.maxAllocNElements = maxElements;
}
//
// For now, all runs will attempt to use information from a .bas
// file, since it's assumed that if one has alignments, one has a
// .bas file.
//
useBaseFile = true;
//
// Add some default fields.
//
hdfBasReader.IncludeField("Basecall");
hdfBasReader.IncludeField("PulseIndex");
hdfBasReader.InitializeFields(baseFileFields);
for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
if (hdfPlsReader.ContainsField(datasetFields[fieldIndex])) {
usePulseFile = true;
pulseFileFields.push_back(datasetFields[fieldIndex]);
}
}
if (usePulseFile) {
hdfPlsReader.InitializeFields(pulseFileFields);
}
hdfPlsReader.IncludeField("NumEvent");
int nMovies = movieFileNames.size();
int movieIndex;
MovieNameToArrayIndex movieNameMap;
//
// Initialize movies. This accomplishes two tasks. First, all movie
// files are opened and initialized, so that if there are data
// fields missing the program will exit now rather than in the
// middle of loading pulses.
// Next, a list of movie names is created in fofnMovieNames. The
// cmp file does not necessarily index movies in the order of the
// fofn, and so when loading pulses from a movie indexed by a cmp
// file, one needs to look up the file name of the movie. This is
// done by scanning the fofnMovieNames list in order until the movie
// is found.
for (movieIndex = 0; movieIndex < nMovies; movieIndex++) {
if (!hdfBasReader.Initialize(movieFileNames[movieIndex])) {
cout << "ERROR, could not initialize HDF file "
<< movieFileNames[movieIndex] << " for reading bases." << endl;
exit(1);
}
else {
fofnMovieNames.push_back(hdfBasReader.GetMovieName());
movieNameMap[hdfBasReader.GetMovieName()] = movieIndex;
hdfBasReader.Close();
}
//
// The pulse file is optional.
//
if (usePulseFile) {
if (hdfPlsReader.Initialize(movieFileNames[movieIndex]) == 0) {
usePulseFile = false;
}
}
}
CmpFile cmpFile;
/*
* These readers pull information from the same pls file.
*/
HDFCmpFile<CmpAlignment> cmpReader;
if (cmpReader.Initialize(cmpFileName, H5F_ACC_RDWR) == 0) {
cout << "ERROR, could not open the cmp file." << endl;
exit(0);
}
cmpReader.Read(cmpFile);
string commandLine;
clp.CommandLineToString(argc, argv, commandLine);
string versionStr(VERSION);
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionStr);
cmpReader.fileLogGroup.AddEntry(commandLine, "Loading pulse metrics", "loadPulses", GetTimestamp(), versionStr);
//
// Group alignment indices by movie so that they may be processed one movie at a time
// later on. The movie indices set keeps track of all indices
// listed in alignment files. This keeps a reference to all
// alignments in memory at once. At the time of writing this, most
// projects will have at most a few million alignments, and so the
// size of this structure is modest.
//
UInt alignmentIndex;
map<int, vector<int> > movieIndexSets;
for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
movieIndexSets[cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId()].push_back(alignmentIndex);
}
vector<float> computedPulseField;
string alignedSequence;
string readSequence;
vector<unsigned char> byteAlignment;
int m;
vector<int> baseToAlignmentMap;
//
// Load pulses from movies in order they appear in the input fofn.
//
int fofnMovieIndex;
for (fofnMovieIndex = 0; fofnMovieIndex < fofnMovieNames.size(); fofnMovieIndex++) {
if (cmpFile.readType == ReadType::CCS or useCcs) {
hdfBasReader.SetReadBasesFromCCS();
hdfCcsReader.Initialize(movieFileNames[fofnMovieIndex]);
}
hdfBasReader.Initialize(movieFileNames[fofnMovieIndex]);
BaseFile baseFile;
PulseFile pulseFile;
if (byRead == false) {
//
// Read the entire bas file at once, and then extract values
// from memory. This can be faster depending on the chunk
// size and size of the movie.
//
hdfBasReader.ReadBaseFile(baseFile);
hdfBasReader.Close();
}
else {
//
// Reads are scanned one by instead of caching all. It is
// still necessary to read in some of the datasets entirely,
// in particular the start positions and hole numbers.
//
// This is repeated below for a pulse file. Since the pulse
// and base files are separate objects, the scan data is
// read into each separately. Somehow later the information
// should be merged into just one.
if (hdfBasReader.scanDataReader.fileHasScanData) {
hdfBasReader.scanDataReader.Read(baseFile.scanData);
}
baseFile.readStartPositions.resize(hdfBasReader.nReads+1);
baseFile.readStartPositions[0] = 0;
hdfBasReader.GetAllReadLengths(baseFile.readLengths);
int i;
assert(baseFile.readLengths.size() + 1 == baseFile.readStartPositions.size());
for (i = 1; i < hdfBasReader.nReads + 1; i++ ) {
baseFile.readStartPositions[i] = baseFile.readLengths[i-1] + baseFile.readStartPositions[i-1];
}
//
// Although the whole bas file isn't being read in, it is
// necessary to read in which hole numbers are contained in this
// bas file since it is possible that the alignment for a
// particular hole number may be in a different input bas.h5
// file even if it is the same movie.
//
hdfBasReader.GetAllHoleNumbers(baseFile.holeNumbers);
}
set<uint32_t> moviePartHoleNumbers;
copy(baseFile.holeNumbers.begin(), baseFile.holeNumbers.end(), inserter(moviePartHoleNumbers, moviePartHoleNumbers.begin()));
if (usePulseFile) {
hdfPlsReader.Initialize(movieFileNames[fofnMovieIndex]);
hdfPlsReader.IncludeField("NumEvent");
hdfPlsReader.IncludeField("StartFrame");
if (byRead == false) {
hdfPlsReader.ReadPulseFile(pulseFile);
hdfPlsReader.Close();
}
else {
if (usePulseFile) {
pulseFile.pulseStartPositions.resize(hdfBasReader.nReads+1);
pulseFile.pulseStartPositions[0] = 0;
hdfPlsReader.GetAllNumEvent(pulseFile.numEvent);
int i;
for (i = 1; i < hdfBasReader.nReads + 1; i++ ) {
pulseFile.pulseStartPositions[i] = pulseFile.numEvent[i-1] + pulseFile.pulseStartPositions[i-1];
}
if (hdfPlsReader.scanDataReader.fileHasScanData) {
hdfPlsReader.scanDataReader.Read(pulseFile.scanData);
}
}
}
}
string cmpFileMovieName;
for (m = 0; m < cmpFile.movieInfo.name.size(); m++) {
//
// First find the file name for the movie 'm'
//
cmpFileMovieName = cmpFile.movieInfo.name[m];
int fofnMovieIndex;
if (baseFile.GetMovieName() == cmpFileMovieName) {
break;
}
}
//
// If the movie specified in the input.fofn is not found in the
// cmp file, that indicates something bad is happeing. Either the
// input.fofn was not used to generate the cmp.h5 file, or no
// alignments were found between the input bas.h5 and the
// reference. That shouldn't happen.
//
if (m == cmpFile.movieInfo.name.size()) {
cout << "WARNING: The movie indexed in the compare file " << cmpFileMovieName << " is not listed in the file " << movieFileName << endl;
continue;
}
//
// Open the movie and load its pulses into memory.
//
movieIndex = cmpFile.movieInfo.id[m];
int movieAlignmentIndex;
float NaN = 0.0/0.0;
UChar missingQualityValue = 255;
HalfWord missingFrameRateValue = USHRT_MAX;
unsigned int missingPulseIndex = UINT_MAX;
//
// Since usePulseFile is set when the input file is a pulseFile,
// and ReadType::CCS becomes the read type when the alignments are
// ccs, when pulse files are specified for de novo ccs alignments,
// they will be opened as pulse files. Since the de novo ccs
// sequences do not have pulse file information, the auto-reading
// of pulse files needs to be disabled. Do that here.
//
if (cmpFile.readType == ReadType::CCS or useCcs) {
usePulseFile = false;
}
//
// Now check the sanity of metric options.
//
map<string,bool>::iterator metricIt;
for (metricIt = metricOptions.begin(); metricIt != metricOptions.end(); ++metricIt) {
if (metricIt->second == false) {
continue;
}
bool metricMayBeComputed = true;
if (cmpFile.readType == ReadType::CCS and
metricIt->first != "QualityValue" and
metricIt->first != "DeletionQV" and
metricIt->first != "SubstitutionQV" and
metricIt->first != "InsertionQV" and
metricIt->first != "DeletionTag" and
metricIt->first != "SubstitutionTag" and
metricIt->first != "Basecall") {
cout << "ERROR! The metric " << metricIt->first << " cannot be loaded into de novo ccs alignemnts." << endl;
// exit(0);
metricMayBeComputed = false;
}
if (metricIt->first == "IPD") {
//
// The field requirements for IPD are special.
//
if ((useBaseFile and !hdfBasReader.FieldIsIncluded("PreBaseFrames")) or
(usePulseFile and (!hdfPlsReader.FieldIsIncluded("StartFrame") and
!hdfPlsReader.FieldIsIncluded("WidthInFrames")))) {
metricMayBeComputed = false;
}
}
else {
if (fieldRequirements.find(metricIt->first) != fieldRequirements.end()) {
//
// There are requirements for this field. Make sure all are
// present before trying to compute this field.
//
int requirementIndex;
for (requirementIndex = 0; requirementIndex < fieldRequirements[metricIt->first].size(); ++requirementIndex) {
string requirement;
requirement = fieldRequirements[metricIt->first][requirementIndex];
if (((useBaseFile == false or ((hdfBasReader.includedFields.find(requirement) == hdfBasReader.includedFields.end() or
hdfBasReader.includedFields[requirement] == false))) and
((usePulseFile == false or (hdfPlsReader.includedFields.find(requirement) == hdfPlsReader.includedFields.end() or
hdfPlsReader.includedFields[requirement] == false))))) {
metricMayBeComputed = false;
}
}
}
else {
//
// There are no requirements for this field, so it must exist as
// a datset in either the bas or pls file.
//
if ((useBaseFile == false or ((hdfBasReader.includedFields.find(metricIt->first) == hdfBasReader.includedFields.end() or
hdfBasReader.includedFields[metricIt->first] == false))) and
(usePulseFile == false or (((hdfPlsReader.includedFields.find(metricIt->first) == hdfPlsReader.includedFields.end() or
hdfPlsReader.includedFields[metricIt->first] == false))))) {
metricMayBeComputed = false;
}
}
}
if (metricMayBeComputed == false) {
if (failOnMissingData) {
cout << "ERROR";
}
else {
cout << "WARNING";
}
cout << ": There is insufficient data to compute metric: " << metricIt->first << " in the file " << movieFileNames[fofnMovieIndex] << " ";
cout << " It will be ignored." << endl;
if (failOnMissingData) {
exit(1);
}
metricOptions[metricIt->first] = false;
}
}
UInt i;
//
// This is currently used as a sentinal for showing that an array
// element does not have a value stored for it, as in deleted
// bases.
//
vector<int> pulseIndexArray;
vector<unsigned int> statTime;
if (metricOptions["WhenStarted"]) {
string whenStarted;
if (hdfPlsReader.scanDataReader.useWhenStarted == false) {
cout << "ERROR! Attempting to read WhenStarted from "
<< movieFileNames[fofnMovieIndex]
<< " but the attriubte does not exist." << endl;
exit(1);
}
hdfPlsReader.scanDataReader.ReadWhenStarted(whenStarted);
if (!cmpReader.movieInfoGroup.whenStartedArray.IsInitialized()) {
cmpReader.movieInfoGroup.whenStartedArray.Initialize(cmpReader.movieInfoGroup.movieInfoGroup, "WhenStarted");
}
cmpReader.movieInfoGroup.whenStartedArray.Write(&whenStarted, 1);
}
if (AnyFieldRequiresFrameRate(datasetFields)) {
if (useBaseFile) {
cmpReader.movieInfoGroup.StoreFrameRate(m, baseFile.GetFrameRate());
}
else if (usePulseFile) {
cmpReader.movieInfoGroup.StoreFrameRate(m, pulseFile.GetFrameRate());
}
}
//
// An index set is a set of indices into the alignment array that
// are of reads generated by this movie. Load pulses for all
// alignments generated for this movie.
//
//
// Movie index sets should be sorted by alignment index. Build a lookup table for this.
//
std::vector<std::pair<int,int> > toFrom;
for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
alignmentIndex = movieIndexSets[movieIndex][movieAlignmentIndex];
toFrom.push_back(std::pair<int,int>(cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId(), movieAlignmentIndex));
}
// orders by first by default.
std::sort(toFrom.begin(), toFrom.end());
//
// Load metrics for alignments from movie 'movieIndex'.
//
cout << "loading " << movieIndexSets[movieIndex].size() << " alignments for movie " << movieIndex << endl;
for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
alignmentIndex = movieIndexSets[movieIndex][toFrom[movieAlignmentIndex].second];
//
// Alignments are groupsd by ref group id then movie id.
//
int refGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetRefGroupId();
int movieId = cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId();
UInt holeNumber = cmpFile.alnInfo.alignments[alignmentIndex].GetHoleNumber();
//
// Since the movie may be split into multiple parts, look to see
// if this hole number is one of the ones covered by this
// set. If it is not, just continue. It will be loaded on
// another pass through a different movie part.
//
if (moviePartHoleNumbers.find(holeNumber) == moviePartHoleNumbers.end()) {
continue;
}
//
// Now locate where this movie is stored.
//
if (cmpReader.refGroupIdToArrayIndex.find(refGroupId) == cmpReader.refGroupIdToArrayIndex.end()) {
cout << "ERROR! An alignment " << alignmentIndex << " is specified with reference group " << endl
<< refGroupId << " that is not found as an alignment group." << endl;
exit(1);
}
int refGroupIndex = cmpReader.refGroupIdToArrayIndex[refGroupId];
//
// Now find the group containing the alignment for this movie.
//
if (cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex.find(movieId) ==
cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex.end()) {
cout << "ERROR! An alignment " << alignmentIndex << " is specified with movie index " << endl
<< movieId << " that is not found in the alignment group " << refGroupIndex << endl;
exit(1);
}
int readGroupIndex = cmpReader.refAlignGroups[refGroupIndex]->movieIdToIndex[movieId];
//
// First do sanity check on the read to make sure the pules and the bases match.
//
//
// Look to see if the output HDF arrays need to be created.
//
UInt offsetBegin, offsetEnd;
offsetBegin = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
offsetEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
int alignedSequenceLength = offsetEnd - offsetBegin;
if (alignedSequenceLength >= 0) {
alignedSequence.resize(alignedSequenceLength);
byteAlignment.resize(alignedSequenceLength);
}
//
// Read the alignment string. All alignments
//
cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin,
offsetEnd,
&byteAlignment[0]);
//
// Convert to something we can compare easily.
//
ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);
//
// Do a sanity check to make sure the pulses and the alignment
// make sense. The main check is to see if the query sequence
// in the alignment is the same as the query sequence in the
// read.
//
//
// First pull out the bases corresponding to this read.
//
int queryStart = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart();
int queryEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd();
// Build a map of where
CreateSequenceToAlignmentMap(byteAlignment,
baseToAlignmentMap);
//
// Condense gaps in the alignment for easy comparison.
//
//
RemoveGaps(alignedSequence, alignedSequence);
//
// Query the cmp file for a way to look up a read based on
// coordinate information. For Astro reads, the coords are
// based on x and y. For Springfield, it is read index. The
// base files should be able to look up reads by x,y or by
// index.
//
int readIndex;
if (cmpFile.platformId == Astro) {
cout << "ASTRO pulse loading is deprecated." << endl;
exit(0);
}
if (baseFile.LookupReadIndexByHoleNumber(holeNumber, readIndex) == false) {
cout << "ERROR! Alignment has hole number " << holeNumber << " that is not in the movie. " << endl;
assert(0);
}
int readStart, readLength, alignBaseStart, alignBaseEnd, alignBaseLength;
readStart = baseFile.readStartPositions[readIndex];
readLength = baseFile.readStartPositions[readIndex+1] - baseFile.readStartPositions[readIndex];
alignBaseStart = readStart + queryStart;
alignBaseEnd = readStart + queryEnd;
alignBaseLength = alignBaseEnd - alignBaseStart;
int pulseStart;
if (usePulseFile) {
pulseStart = pulseFile.pulseStartPositions[readIndex];
}
//
// This maps from pulse to a base, since there are more pulses
// called than bases, and the is one pulse for every base.
//
pulseIndexArray.resize(readLength);
SMRTSequence sourceRead;
unsigned int numPasses;
//
// These are not allocated in the regular allocate function
// since they are only used in loadPulses. (maybe I should
// subclass SMRTSequence here).
//
if (byRead) {
// Read in the data from the bas file if it exsts.
if (useBaseFile) {
hdfBasReader.GetReadAt(readIndex, sourceRead);
if (cmpFile.readType == ReadType::CCS or useCcs) {
numPasses = hdfCcsReader.GetNumPasses(readIndex);
}
}
// Read in the data from the pls file if it exists.
if (usePulseFile) {
hdfPlsReader.GetReadAt(readIndex, sourceRead.pulseIndex, sourceRead);
}
}
else {
//
// The entire base/pulse file was read in, so copy data from that into a read
// For the data used in the read, it is possible to simply
// reference the data, but for the pls file it is necessary
// to copy since there is a packing of data.
//
if (useBaseFile) {
baseFile.CopyReadAt(readIndex, sourceRead);
if (cmpFile.readType == ReadType::CCS or useCcs) {
numPasses = hdfCcsReader.GetNumPasses(readIndex);
}
}
if (usePulseFile) {
//
// Copy the subset of pulses that correspond to the ones called as bases.
//
int i;
for (i = 0; i < readLength; i++) {
pulseIndexArray[i] = pulseStart + baseFile.pulseIndex[readStart + i];
}
pulseFile.CopyReadAt(readIndex, &pulseIndexArray[0], sourceRead);
}
}
readSequence.resize(queryEnd - queryStart);
CapQualityValues(sourceRead);
copy((char*) (sourceRead.seq + queryStart),
(char*) (sourceRead.seq + queryEnd),
readSequence.begin());
bool stringsMatch = true;
if (alignedSequence.size() != readSequence.size() or alignedSequence != readSequence) {
cout << "ERROR, the query sequence does not match the aligned query sequence." << endl;
cout << "HoleNumber: "<< holeNumber << ", MovieName: " << cmpFileMovieName;
cout << " ,ReadIndex: " << (int) readIndex <<
cout << ", qStart: "<< queryStart << ", qEnd: " << queryEnd << endl;
cout << "Aligned sequence: "<< endl;
cout << alignedSequence << endl;
cout << "Original sequence: " << endl;
cout << readSequence << endl;
assert(0);
}
/*
* Compute any necessary data fields. These usually involve
* using differences of pulse indices, pulse widths, etc..
* Missing fields are stored as 0's.
*/
vector<float> readPulseMetric;
vector<float> floatMetric;
vector<UChar> qvMetric;
vector<HalfWord> frameRateMetric;
vector<uint32_t> timeMetric;
int ungappedAlignedSequenceLength = alignedSequence.size();
floatMetric.resize(alignedSequenceLength+1);
readPulseMetric.resize(alignedSequenceLength+1);
qvMetric.resize(alignedSequenceLength+1);
frameRateMetric.resize(alignedSequenceLength+1);
timeMetric.resize(alignedSequenceLength+1);
UInt i;
UInt pi;
HDFCmpExperimentGroup* expGroup = cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
if (cmpFile.readType == ReadType::CCS or useCcs) {
if (!cmpReader.alnInfoGroup.numPasses.IsInitialized()) {
cmpReader.alnInfoGroup.InitializeNumPasses();
}
cmpReader.alnInfoGroup.numPasses.WriteToPos(&numPasses, 1, alignmentIndex);
}
if (metricOptions["StartTimeOffset"] == true) {
if (!expGroup->startTimeOffset.IsInitialized()) {
expGroup->startTimeOffset.Initialize(expGroup->experimentGroup, "StartTimeOffset");
}
unsigned int readStartTimeOffset = sourceRead.startFrame[queryStart];
expGroup->startTimeOffset.WriteToPos(&readStartTimeOffset, 1, alignmentIndex);
}
if (metricOptions["QualityValue"] == true) {
if (!expGroup->qualityValue.IsInitialized()) {
expGroup->qualityValue.Initialize(expGroup->experimentGroup, "QualityValue");
}
// Store start time normalized to frame rate.
fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
qvMetric[baseToAlignmentMap[i]] = sourceRead.qual[queryStart + i];
}
qvMetric[qvMetric.size()-1] = 0;
expGroup->qualityValue.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
}
if (metricOptions["InsertionQV"] == true) {
if (!expGroup->insertionQV.IsInitialized()) {
expGroup->insertionQV.Initialize(expGroup->experimentGroup, "InsertionQV");
}
// Store start time normalized to frame rate.
fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
qvMetric[baseToAlignmentMap[i]] = sourceRead.insertionQV[queryStart+ i];
}
qvMetric[qvMetric.size()-1] = 0;
expGroup->insertionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
}
if (metricOptions["MergeQV"] == true) {
if (!expGroup->mergeQV.IsInitialized()) {
expGroup->mergeQV.Initialize(expGroup->experimentGroup, "MergeQV");
}
// Store start time normalized to frame rate.
fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
qvMetric[baseToAlignmentMap[i]] = sourceRead.mergeQV[queryStart+ i];
}
qvMetric[qvMetric.size()-1] = 0;
expGroup->mergeQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
}
if (metricOptions["DeletionQV"] == true) {
if (!expGroup->deletionQV.IsInitialized()) {
expGroup->deletionQV.Initialize(expGroup->experimentGroup, "DeletionQV");
}
// Store start time normalized to frame rate.
fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
qvMetric[baseToAlignmentMap[i]] = sourceRead.deletionQV[queryStart+i];
}
qvMetric[qvMetric.size()-1] = 0;
expGroup->deletionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
}
if (metricOptions["DeletionTag"] == true) {
if (!expGroup->deletionTag.IsInitialized()) {
expGroup->deletionTag.Initialize(expGroup->experimentGroup, "DeletionTag");
}
vector<char> readDeletionTagMetric;
readDeletionTagMetric.resize(readPulseMetric.size());
// Store start time normalized to frame rate.
for (i = 0; i < readDeletionTagMetric.size()-1; i++ ) {
readDeletionTagMetric[i] = '-';
}
readDeletionTagMetric[i] = '\0';
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
assert(baseToAlignmentMap[i] < readDeletionTagMetric.size());
readDeletionTagMetric[baseToAlignmentMap[i]] = sourceRead.deletionTag[queryStart+i];
}
readDeletionTagMetric[readDeletionTagMetric.size()-1] = 0;
expGroup->deletionTag.WriteToPos(&readDeletionTagMetric[0], readDeletionTagMetric.size(), offsetBegin);
}
if (metricOptions["PulseIndex"] == true) {
if (!expGroup->pulseIndex.IsInitialized()) {
expGroup->pulseIndex.Initialize(expGroup->experimentGroup, "PulseIndex");
}
vector<uint32_t> readPulseIndexMetric;
fill(readPulseIndexMetric.begin(), readPulseIndexMetric.end(), missingPulseIndex);
readPulseIndexMetric.resize(readPulseMetric.size());
// Store start time normalized to frame rate.
assert(readPulseIndexMetric.size() > 0);
for (i = 0; i < readPulseIndexMetric.size(); i++ ) {
readPulseIndexMetric[i] = 0;
}
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
readPulseIndexMetric[baseToAlignmentMap[i]] = sourceRead.pulseIndex[queryStart+i];
}
readPulseIndexMetric[readPulseIndexMetric.size()-1] = 0;
expGroup->pulseIndex.WriteToPos(&readPulseIndexMetric[0], readPulseIndexMetric.size(), offsetBegin);
}
if (metricOptions["SubstitutionTag"] == true) {
if (!expGroup->substitutionTag.IsInitialized()) {
expGroup->substitutionTag.Initialize(expGroup->experimentGroup, "SubstitutionTag");
}
vector<char> readSubstitutionTagMetric;
readSubstitutionTagMetric.resize(readPulseMetric.size());
// Store start time normalized to frame rate.
for (i = 0; i < readSubstitutionTagMetric.size()-1; i++ ) {
readSubstitutionTagMetric[i] = '-';
}
readSubstitutionTagMetric[i] = '\0';
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
readSubstitutionTagMetric[baseToAlignmentMap[i]] = sourceRead.substitutionTag[queryStart+i];
}
readSubstitutionTagMetric[readSubstitutionTagMetric.size()-1] = 0;
expGroup->substitutionTag.WriteToPos(&readSubstitutionTagMetric[0], readSubstitutionTagMetric.size(), offsetBegin);
}
if (metricOptions["SubstitutionQV"] == true) {
if (!expGroup->substitutionQV.IsInitialized()) {
expGroup->substitutionQV.Initialize(expGroup->experimentGroup, "SubstitutionQV");
}
// Store start time normalized to frame rate.
fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
qvMetric[baseToAlignmentMap[i]] = sourceRead.substitutionQV[queryStart+i];
}
qvMetric[qvMetric.size()-1] = 0;
expGroup->substitutionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
}
if (metricOptions["ClassifierQV"] == true) {
if (!expGroup->classifierQV.IsInitialized()) {
expGroup->classifierQV.Initialize(expGroup->experimentGroup, "ClassifierQV");
}
// Store start time normalized to frame rate.
fill(floatMetric.begin(), floatMetric.end(), missingQualityValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
floatMetric[baseToAlignmentMap[i]] = sourceRead.classifierQV[i+queryStart];
}
floatMetric[floatMetric.size()-1] = 0;
expGroup->classifierQV.WriteToPos(&floatMetric[0], floatMetric.size(), offsetBegin);
}
if (metricOptions["StartFrame"] == true) {
if (!expGroup->startTime.IsInitialized()) {
expGroup->startTime.Initialize(expGroup->experimentGroup, "StartFrame");
}
if (useBaseFile) {
sourceRead.startFrame = new unsigned int[sourceRead.length];
copy(sourceRead.preBaseFrames, &sourceRead.preBaseFrames[sourceRead.length], sourceRead.startFrame);
for (i = 0; i < sourceRead.length-1; i++) {
sourceRead.startFrame[i+1] += sourceRead.widthInFrames[i];
}
partial_sum(sourceRead.startFrame, &sourceRead.startFrame[sourceRead.length], sourceRead.startFrame);
}
// Store start time normalized to frame rate.
fill(timeMetric.begin(), timeMetric.end(), missingPulseIndex);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
timeMetric[baseToAlignmentMap[i]] = sourceRead.startFrame[i+queryStart];
}
timeMetric[timeMetric.size()-1] = 0;
expGroup->startTime.WriteToPos(&timeMetric[0], timeMetric.size(), offsetBegin);
}
if (metricOptions["PulseWidth"] == true) {
if (!expGroup->pulseWidth.IsInitialized()) {
expGroup->pulseWidth.Initialize(expGroup->experimentGroup, "PulseWidth");
}
// Store start time normalized to frame rate.
fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
//
// For legacy reasons, it's possible the width in frames is
// stored in the bas file. If this is the case, use the width
// in frames there. Otherwise, use the width in frames stored
// in the pls file.
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[queryStart + i];
}
frameRateMetric[frameRateMetric.size()-1] = 0;
expGroup->pulseWidth.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
}
if (metricOptions["PreBaseFrames"] == true) {
if (!expGroup->preBaseFrames.IsInitialized()) {
expGroup->preBaseFrames.Initialize(expGroup->experimentGroup, "PreBaseFrames");
}
// Compute width in frames normalized to frame rate.
fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i+queryStart];
}
frameRateMetric[frameRateMetric.size()-1] = 0;
expGroup->preBaseFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
}
if (metricOptions["WidthInFrames"] == true) {
if (!expGroup->widthInFrames.IsInitialized()) {
expGroup->widthInFrames.Initialize(expGroup->experimentGroup, "WidthInFrames");
}
// Compute width in frames normalized to frame rate.
fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
if (usePulseFile) {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[i+queryStart];
}
else {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[i+queryStart];
}
}
frameRateMetric[frameRateMetric.size()-1] = 0;
expGroup->widthInFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
}
if (metricOptions["pkmid"] == true) {
if (!expGroup->pkmid.IsInitialized()) {
expGroup->pkmid.Initialize(expGroup->experimentGroup, "pkmid");
}
for (i = 0; i < readPulseMetric.size(); i++ ) {
readPulseMetric[i] = NaN;
}
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
readPulseMetric[baseToAlignmentMap[i]] = sourceRead.midSignal[i+queryStart];
}
readPulseMetric[readPulseMetric.size()-1] = 0;
expGroup->pkmid.WriteToPos(&readPulseMetric[0], readPulseMetric.size(), offsetBegin);
}
if (metricOptions["IPD"] == true) {
if (!expGroup->ipd.IsInitialized()) {
expGroup->ipd.Initialize(expGroup->experimentGroup, "IPD");
}
fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
//
// The IPD is undefined for the first base in a read.
//
if (usePulseFile ) {
if (queryStart == 0 and i == 0) {
frameRateMetric[baseToAlignmentMap[i]] = 0;
}
else {
frameRateMetric[baseToAlignmentMap[i]] = (sourceRead.startFrame[i+queryStart]
- sourceRead.startFrame[i+queryStart-1]
- sourceRead.widthInFrames[i+queryStart-1]);
}
}
else if (useBaseFile) {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i + queryStart];
}
}
frameRateMetric[frameRateMetric.size()-1] = 0;
expGroup->ipd.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
}
if (metricOptions["Light"] == true) {
if (!expGroup->light.IsInitialized()) {
expGroup->light.Initialize(expGroup->experimentGroup, "Light");
}
fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
frameRateMetric[baseToAlignmentMap[i]] = sourceRead.meanSignal[i+queryStart];
frameRateMetric[baseToAlignmentMap[i]] = (frameRateMetric[baseToAlignmentMap[i]] *
sourceRead.widthInFrames[i+queryStart]);
}
frameRateMetric[frameRateMetric.size()-1] = 0;
expGroup->light.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
}
sourceRead.Free();
Free(sourceRead.meanSignal);
Free(sourceRead.maxSignal);
Free(sourceRead.midSignal);
Free(sourceRead.startFrame);
Free(sourceRead.classifierQV);
Free(sourceRead.widthInFrames);
}
if (byRead == true) {
if (useBaseFile) {
hdfBasReader.Close();
}
if (cmpFile.readType == ReadType::CCS or useCcs) {
hdfCcsReader.Close();
}
if (usePulseFile) {
hdfPlsReader.Close();
}
}
} // done loading movies
cmpReader.Close();
}
int main(int argc, char* argv[]) {
string refGenomeFileName = "";
string lengthModelFileName = "";
string outputModelFileName = "";
DNALength numBasesPerFile = 0;
string sourceReadsFileName = "";
string titleTableFileName = "";
int numBasH5Files = 1;
string basH5BaseFileName = "simulated";
string movieName = "m101211_092754_00114_cSIM_s1_p0";
bool doRandGenInit = true;
bool usePosMap = false;
bool printPercentRepeat = false;
string posMapFileName = "";
vector<string> movieNames;
bool useLengthModel = false;
bool useFixedLength = false;
ofstream posMapFile;
int scaledLength = 0;
int fixedLength = 0;
int nBasFiles = 1;
bool useLengthsModel = true;
bool printHelp = false;
// Look to see if the refAsReads flag is specified anywhere before
// parsing the command line.
CommandLineParser clp;
string commandLine;
string helpString;
SetHelp(helpString);
vector<string> fns;
clp.RegisterStringOption("genome", &refGenomeFileName, "");
clp.RegisterIntOption("numBasesPerFile", (int*)&numBasesPerFile, "",
CommandLineParser::PositiveInteger);
clp.RegisterStringOption("sourceReads", &sourceReadsFileName, "");
clp.RegisterStringOption("lengthModel", &lengthModelFileName, "");
clp.RegisterIntOption("fixedLength", &fixedLength, "",
CommandLineParser::PositiveInteger);
clp.RegisterFlagOption("lengthModel", &useLengthModel, "");
clp.RegisterStringOption("movieName", &movieName, "");
clp.RegisterStringOption("titleTable", &titleTableFileName, "");
clp.RegisterStringOption("baseFileName", &basH5BaseFileName, "");
clp.RegisterIntOption("nFiles", &nBasFiles, "",
CommandLineParser::PositiveInteger);
clp.RegisterIntOption("meanLength", &scaledLength, "",
CommandLineParser::PositiveInteger);
clp.RegisterStringOption("posMap", &posMapFileName, "");
clp.RegisterFlagOption("printPercentRepeat", &printPercentRepeat, "");
clp.RegisterFlagOption("h", &printHelp, "");
clp.SetHelp(helpString);
clp.ParseCommandLine(argc, argv, fns);
clp.CommandLineToString(argc, argv, commandLine);
clp.SetProgramName("alchemy");
outputModelFileName = fns[0];
if (argc <= 1 or printHelp or outputModelFileName == "") {
cout << helpString << endl;
exit(0);
}
if (usePosMap) {
CrucialOpen(posMapFileName, posMapFile, std::ios::out);
}
if (sourceReadsFileName == "" and fixedLength == 0) {
useLengthModel = true;
}
if (useLengthModel and fixedLength != 0) {
cout << "ERROR! You must either use a length model or a fixed length." << endl;
exit(1);
}
if (sourceReadsFileName == "" and numBasesPerFile == 0) {
cout << "ERROR! You must specify either a set of read to use as " << endl
<< "original reads for simulation or the total number of bases " << endl
<< "to simulate in each bas.h5 file." << endl;
exit(1);
}
if (sourceReadsFileName == "" and refGenomeFileName == "") {
cout << "ERROR! You must specify a genome to sample reads from or a set of read "<<endl
<< "to use as original reads for simulation." << endl;
exit(1);
}
if (fixedLength != 0 and refGenomeFileName == "") {
cout << "ERROR! You must specify a genome file if using a fixed length." << endl;
exit(1);
}
if ((fixedLength != 0 or scaledLength != 0) and sourceReadsFileName != "") {
cout << "ERROR! You cannot specify a fixed length nor mean length with a source " << endl
<< "reads file. The read lengths are taken from the source reads or the length model." << endl;
exit(1);
}
LengthHistogram lengthHistogram;
OutputSampleListSet outputModel(0);
TitleTable titleTable;
if (doRandGenInit) {
InitializeRandomGeneratorWithTime();
}
//
// Read models.
//
if (titleTableFileName != "") {
titleTable.Read(titleTableFileName);
}
outputModel.Read(outputModelFileName);
if (useLengthModel) {
lengthHistogram.BuildFromAlignmentLengths(outputModel.lengths);
}
vector<int> alignmentLengths;
int meanAlignmentLength;
if (scaledLength != 0 and useLengthModel) {
//
// Scale the histogram so that the average length is 'scaledLength'.
//
// 1. Integrate histogram
long totalLength = 0;
long totalSamples = 0;
int hi;
for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size()-1; hi++) {
int ni;
ni = lengthHistogram.lengthHistogram.cdf[hi+1] - lengthHistogram.lengthHistogram.cdf[hi];
totalLength += ni * lengthHistogram.lengthHistogram.data[hi];
}
totalSamples = lengthHistogram.lengthHistogram.cdf[lengthHistogram.lengthHistogram.cdf.size()-1];
float meanSampleLength = totalLength / (1.0*totalSamples);
float fractionIncrease = scaledLength / meanSampleLength;
for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size(); hi++) {
lengthHistogram.lengthHistogram.data[hi] *= fractionIncrease;
}
}
FASTAReader inReader, seqReader;
vector<FASTASequence> reference;
DNALength refLength = 0;
int i;
if (refGenomeFileName != "") {
inReader.Init(refGenomeFileName);
inReader.ReadAllSequences(reference);
for (i = 0; i < reference.size(); i++) {
refLength += reference[i].length;
}
}
if (sourceReadsFileName != "") {
seqReader.Init(sourceReadsFileName);
}
ofstream readsFile;
//
// Create and simulate bas.h5 files.
//
int baseFileIndex;
bool readsRemain = true;
for (baseFileIndex = 0; ((sourceReadsFileName == "" and baseFileIndex < nBasFiles) // case 1 is reads are generated by file
or (sourceReadsFileName != "" and readsRemain)); // case 2 is reads are generated by an input file.
baseFileIndex++) {
//
// Prep the base file for writing.
//
stringstream fileNameStrm, movieNameStrm;
//string movieName = "m000000_000000_00000_cSIMULATED_s";
movieNameStrm << movieName << baseFileIndex << "_p0";
string fullMovieName = movieNameStrm.str();
fileNameStrm << fullMovieName << ".bas.h5";
HDFBasWriter basWriter;
HDFRegionTableWriter regionWriter;
//
// This is mainly used to create the atributes.
//
RegionTable regionTable;
regionTable.CreateDefaultAttributes();
basWriter.SetPlatform(Springfield);
//
// Use a fixed set of fields for now.
//
// These are all pulled from the outputModel.
basWriter.IncludeField("Basecall");
basWriter.IncludeField("QualityValue");
basWriter.IncludeField("SubstitutionQV");
basWriter.IncludeField("SubstitutionTag");
basWriter.IncludeField("InsertionQV");
basWriter.IncludeField("DeletionQV");
basWriter.IncludeField("DeletionTag");
basWriter.IncludeField("WidthInFrames");
basWriter.IncludeField("PreBaseFrames");
basWriter.IncludeField("PulseIndex");
vector<unsigned char> qualityValue, substitutionQV, substitutionTag, insertionQV, deletionQV, deletionTag;
vector<HalfWord> widthInFrames, preBaseFrames, pulseIndex;
// Just go from 0 .. hole Number
basWriter.IncludeField("HoleNumber");
// Fixed to 0.
basWriter.IncludeField("HoleXY");
if (usePosMap == false) {
basWriter.IncludeField("SimulatedSequenceIndex");
basWriter.IncludeField("SimulatedCoordinate");
}
basWriter.SetChangeListID("1.3.0.50.104380");
DNALength numSimulatedBases = 0;
FASTASequence sampleSeq;
//sampleSeq.length = readLength;
int maxRetry = 10000000;
int retryNumber = 0;
int numReads = 0;
int readLength = 0;
while (numBasesPerFile == 0 or numSimulatedBases < numBasesPerFile) {
DNALength seqIndex, seqPos;
if (useLengthModel or fixedLength) {
if (useLengthModel) {
lengthHistogram.GetRandomLength(readLength);
}
else {
readLength = fixedLength;
}
}
if (refGenomeFileName != "") {
FindRandomPos(reference, seqIndex, seqPos, readLength + (outputModel.keyLength - 1));
sampleSeq.seq = &reference[seqIndex].seq[seqPos];
sampleSeq.length = readLength + (outputModel.keyLength - 1);
assert(reference[seqIndex].length >= sampleSeq.length);
}
else if (sourceReadsFileName != "") {
if (seqReader.GetNext(sampleSeq) == false) {
readsRemain = false;
break;
}
if (sampleSeq.length < outputModel.keyLength) {
continue;
}
//
// Now attempt to parse the position from the fasta title.
//
if (useLengthModel) {
int tryNumber = 0;
readLength = 0;
int maxNTries = 1000;
int tryBuffer[5] = {-1,-1,-1,-1,-1};
while (tryNumber < maxNTries and readLength < outputModel.keyLength) {
lengthHistogram.GetRandomLength(readLength);
readLength = sampleSeq.length = min(sampleSeq.length, (unsigned int) readLength);
tryBuffer[tryNumber%5] = readLength;
tryNumber++;
}
if (tryNumber >= maxNTries) {
cout << "ERROR. Could not generate a read length greater than the " << outputModel.keyLength << " requried " <<endl
<< "minimum number of bases using the length model specified in the alchemy." <<endl
<< "model. Something is either wrong with the model or the context length is too large." <<endl;
cout << "The last few tries were: " << tryBuffer[0] << " " << tryBuffer[1] << " " << tryBuffer[2] << " " << tryBuffer[3] << " " << tryBuffer[4] << endl;
exit(1);
}
}
readLength = sampleSeq.length;
vector<string> tokens;
Tokenize(sampleSeq.title, "|", tokens);
if (tokens.size() == 4) {
seqPos = atoi(tokens[2].c_str());
if (titleTableFileName == "") {
seqIndex = 0;
}
else {
int index;
titleTable.Lookup(tokens[1], index);
seqIndex = index;
}
}
else {
seqPos = 0;
}
}
//
// If this is the first read printed to the base file, initialize it.
//
if (numSimulatedBases == 0) {
basWriter.Initialize(fileNameStrm.str(), movieNameStrm.str(), Springfield);
regionWriter.Initialize(basWriter.pulseDataGroup);
}
numSimulatedBases += readLength;
int p;
// create the sample sequence
int contextLength = outputModel.keyLength;
int contextMiddle = contextLength / 2;
string outputString;
int nDel = 0;
int nIns = 0;
//
// Simulate to beyond the sample length.
//
qualityValue.clear();
substitutionQV.clear();
substitutionTag.clear();
insertionQV.clear();
deletionQV.clear();
deletionTag.clear();
pulseIndex.clear();
widthInFrames.clear();
preBaseFrames.clear();
assert(sampleSeq.length > contextMiddle + 1);
for (p = contextMiddle;
p < sampleSeq.length - contextMiddle - 1; p++) {
string refContext;
refContext.assign((const char*) &sampleSeq.seq[p-contextMiddle], contextLength);
string outputContext;
int contextWasFound;
OutputSample sample;
int i;
for (i = 0; i < refContext.size(); i++) {
refContext[i] = toupper(refContext[i]);
}
outputModel.SampleRandomSample(refContext, sample);
if (sample.type == OutputSample::Deletion ) {
//
// There was a deletion. Advance in reference, then output
// the base after the deletion.
//
p++;
++nDel;
}
int cp;
//
// Add the sampled context, possibly multiple characters because of an insertion.
//
for (i = 0; i < sample.nucleotides.size(); i++) {
outputString.push_back(sample.nucleotides[i]);
qualityValue.push_back(sample.qualities[i].qv[0]);
deletionQV.push_back(sample.qualities[i].qv[1]);
insertionQV.push_back(sample.qualities[i].qv[2]);
substitutionQV.push_back(sample.qualities[i].qv[3]);
deletionTag.push_back(sample.qualities[i].tags[0]);
substitutionTag.push_back(sample.qualities[i].tags[1]);
pulseIndex.push_back(sample.qualities[i].frameValues[0]);
preBaseFrames.push_back(sample.qualities[i].frameValues[1]);
widthInFrames.push_back(sample.qualities[i].frameValues[2]);
}
nIns += sample.qualities.size() - 1;
}
if (outputString.find('N') != outputString.npos or
outputString.find('n') != outputString.npos) {
cout << "WARNING! The sampled string " << endl << outputString << endl
<< "should not contain N's, but it seems to. This is being ignored "<<endl
<< "for now so that simulation may continue, but this shouldn't happen"<<endl
<< "and is really a bug." << endl;
numSimulatedBases -= readLength;
continue;
}
//
// Ok, done creating the read, now time to create some quality values!!!!!
//
SMRTSequence read;
read.length = outputString.size();
read.Allocate(read.length);
memcpy(read.seq, outputString.c_str(), read.length * sizeof(unsigned char));
assert(qualityValue.size() == read.length * sizeof(unsigned char));
memcpy(read.qual.data, &qualityValue[0], read.length * sizeof(unsigned char));
memcpy(read.deletionQV.data, &deletionQV[0], read.length * sizeof(unsigned char));
memcpy(read.insertionQV.data, &insertionQV[0], read.length * sizeof(unsigned char));
memcpy(read.substitutionQV.data, &substitutionQV[0], read.length * sizeof(unsigned char));
memcpy(read.deletionTag, &deletionTag[0], read.length * sizeof(unsigned char));
memcpy(read.substitutionTag, &substitutionTag[0], read.length * sizeof(unsigned char));
memcpy(read.pulseIndex, &pulseIndex[0], read.length * sizeof(int));
memcpy(read.preBaseFrames, &preBaseFrames[0], read.length * sizeof(HalfWord));
memcpy(read.widthInFrames, &widthInFrames[0], read.length * sizeof(HalfWord));
//
// The pulse index for now is just fake data.
//
int i;
for (i = 0; i < read.length; i++) {
read.pulseIndex[i] = 1;
}
read.xy[0] = seqIndex;
read.xy[1] = seqPos;
read.zmwData.holeNumber = numReads;
basWriter.Write(read);
// Record where this was simulated from.
if (usePosMap == false) {
basWriter.WriteSimulatedCoordinate(seqPos);
basWriter.WriteSimulatedSequenceIndex(seqIndex);
}
else {
posMapFile << fullMovieName << "/" << numReads << "/0_" << read.length << " " << seqIndex << " "<< seqPos;
if (printPercentRepeat) {
DNALength nRepeat = sampleSeq.GetRepeatContent();
posMapFile << " " << nRepeat*1.0/sampleSeq.length;
}
posMapFile << endl;
}
RegionAnnotation region;
region.row[0] = read.zmwData.holeNumber;
region.row[1] = 1;
region.row[2] = 0;
region.row[3] = read.length;
region.row[4] = 1000; // Should be enough.
regionWriter.Write(region);
region.row[1] = 2; // Rewrite for hq region encompassing everything.
regionWriter.Write(region);
if (sourceReadsFileName != "") {
sampleSeq.Free();
}
read.Free();
++numReads;
}
regionWriter.Finalize(regionTable.columnNames,
regionTable.regionTypes,
regionTable.regionDescriptions,
regionTable.regionSources);
basWriter.Close();
numReads = 0;
//
// The bas writer should automatically flush on closing.
//
}
if (usePosMap) {
posMapFile.close();
}
for (i = 0; i < reference.size(); i++) {
reference[i].Free();
}
}
int main(int argc, char* argv[]) {
#ifdef USE_GOOGLE_PROFILER
char *profileFileName = getenv("CPUPROFILE");
if (profileFileName != NULL) {
ProfilerStart(profileFileName);
}
else {
ProfilerStart("google_profile.txt");
}
#endif
// Register inputs and outputs.
string samFileName, refFileName, outFileName;
CommandLineParser clp;
clp.RegisterStringOption("file.sam", &samFileName,
"Input SAM file.");
clp.RegisterStringOption("reference.fasta", &refFileName,
"Reference used to generate reads.");
clp.RegisterStringOption("out.sam", &outFileName,
"Output SAM file.");
clp.RegisterPreviousFlagsAsHidden();
// Register filter criteria options.
int minAlnLength = 50;
float minPctSimilarity = 70, minPctAccuracy = 70;
string hitPolicyStr = "randombest";
bool useScoreCutoff = false;
int scoreCutoff = INF_INT;
int scoreSignInt = -1;
RegisterFilterOptions(clp, minAlnLength, minPctSimilarity,
minPctAccuracy, hitPolicyStr, useScoreCutoff,
scoreSignInt, scoreCutoff);
int seed = 1;
clp.RegisterIntOption("seed", &seed,
"(1) Seed for random number generator.\n"
"If seed is 0, then use current time as seed.",
CommandLineParser::Integer);
string holeNumberStr;
Ranges holeNumberRanges;
clp.RegisterStringOption("holeNumbers", &holeNumberStr,
"A string of comma-delimited hole number ranges to output hits, "
"such as '1,2,10-12'. "
"This requires hit titles to be in SMRT read title format.");
bool parseSmrtTitle = false;
clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
"Use this option when filtering alignments generated by "
"programs other than blasr, e.g. bwa-sw or gmap. "
" Parse read coordinates from the SMRT read title. "
"The title is in the format /name/hole/coordinates, where"
" coordinates are in the format \\d+_\\d+, and represent "
"the interval of the read that was aligned.");
/* This experimental option can be useful for metagenomics, in which case
* there are hundreds of sequences in the target, of which many titles are
* long and may contain white spaces (e.g., ' ', '\t').
* In order to save disc space and avoid the (possibly) none unique mapping
* between full and short reference names, one may call blasr with
* -titleTable option to represent all target sequences in the output
* by their indices in the title table.*/
string titleTableName = "";
clp.RegisterStringOption("titleTable", &titleTableName,
"Use this experimental option when filtering alignments generated by "
"blasr with -titleTable titleTableName, in which case "
"reference titles in SAM are represented by their "
"indices (e.g., 0, 1, 2, ...) in the title table.");
string adapterGffFileName = "";
clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName,
"Use this option to remove reads which can only map to adapters "
"specified in the GFF file.");
bool verbose = false;
clp.RegisterFlagOption("v", &verbose, "Be verbose.");
clp.SetExamples(
"Because SAM has optional tags that have different meanings"
" in different programs, careful usage is required in order "
"to have proper output. The \"xs\" tag in bwa-sw is used to "
"show the suboptimal score, but in PacBio SAM (blasr) it is "
"defined as the start in the query sequence of the alignment.\n"
"When \"-smrtTitle\" is specified, the xs tag is ignored, but "
"when it is not specified, the coordinates given by the xs and "
"xe tags are used to define the interval of a read that is "
"aligned. The CIGAR string is relative to this interval.");
clp.ParseCommandLine(argc, argv);
// Set random number seed.
if (seed == 0) {
srand(time(NULL));
} else {
srand(seed);
}
scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE;
Score s(static_cast<float>(scoreCutoff), scoreSign);
FilterCriteria filterCriteria(minAlnLength, minPctSimilarity,
minPctAccuracy, true, s);
filterCriteria.Verbose(verbose);
HitPolicy hitPolicy(hitPolicyStr, scoreSign);
string errMsg;
if (not filterCriteria.MakeSane(errMsg)) {
cout << errMsg << endl;
exit(1);
}
// Parse hole number ranges.
if (holeNumberStr.size() != 0) {
if (not holeNumberRanges.setRanges(holeNumberStr)) {
cout << "Could not parse hole number ranges: "
<< holeNumberStr << "." << endl;
exit(1);
}
}
// Open output file.
ostream * outFilePtr = &cout;
ofstream outFileStrm;
if (outFileName != "") {
CrucialOpen(outFileName, outFileStrm, std::ios::out);
outFilePtr = &outFileStrm;
}
GFFFile adapterGffFile;
if (adapterGffFileName != "")
adapterGffFile.ReadAll(adapterGffFileName);
SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
FASTAReader fastaReader;
//
// Initialize samReader and fastaReader.
//
samReader.Initialize(samFileName);
fastaReader.Initialize(refFileName);
//
// Configure the file log.
//
string command;
CommandLineParser::CommandLineToString(argc, argv, command);
string log = "Filter sam hits.";
string program = "samFilter";
string versionString = VERSION;
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
//
// Read necessary input.
//
vector<FASTASequence> references;
fastaReader.ReadAllSequences(references);
// If the SAM file is generated by blasr with -titleTable,
// then references in the SAM are represented by
// their corresponding indices in the title table.
// In that case, we need to convert reference titles in fasta file
// to their corresponding indices in the title table, such that
// references in both SAM and fasta files are represented
// by title table indices and therefore can match.
if (titleTableName != "") {
ConvertTitlesToTitleTableIndices(references, titleTableName);
}
AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
vector<string> allHeaders = samReader.ReadHeader(alignmentSet);
// Process SAM Header.
string commandLineString;
clp.CommandLineToString(argc, argv, commandLineString);
allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \
"\tCL:" + program + " " + commandLineString);
for (int i = 0; i < allHeaders.size(); i++) {
outFileStrm << allHeaders[i] << endl;
}
//
// The order of references in vector<FASTASequence> references and
// AlignmentSet<, , >alignmentSet.references can be different.
// Rearrange alignmentSet.references such that they are ordered in
// exactly the same way as vector<FASTASequence> references.
//
alignmentSet.RearrangeReferences(references);
// Map reference name obtained from SAM file to indices
map<string, int> refNameToIndex;
for (int i = 0; i < references.size(); i++) {
string refName = alignmentSet.references[i].GetSequenceName();
refNameToIndex[refName] = i;
}
//
// Store the alignments.
//
SAMAlignment samAlignment;
int alignIndex = 0;
//
// For 150K, each chip produces about 300M sequences
// (not including quality values and etc.).
// Let's assume that the sam file and reference data can
// fit in the memory.
// Need to scale for larger sequal data in the future.
//
vector<SAMAlignment> allSAMAlignments;
while (samReader.GetNextAlignment(samAlignment)) {
if (samAlignment.rName == "*") {
continue;
}
if (parseSmrtTitle and holeNumberStr.size() != 0) {
string movieName;
int thisHoleNumber;
if (not ParsePBIReadName(samAlignment.qName,
movieName,
thisHoleNumber)) {
cout << "ERROR, could not parse SMRT title: "
<< samAlignment.qName << "." << endl;
exit(1);
}
if (not holeNumberRanges.contains(UInt(thisHoleNumber))) {
if (verbose)
cout << thisHoleNumber << " is not in range." << endl;
continue;
}
}
if (samAlignment.cigar.find('P') != string::npos) {
cout << "WARNING. Could not process SAM record with 'P' in "
<< "its cigar string." << endl;
continue;
}
vector<AlignmentCandidate<> > convertedAlignments;
SAMAlignmentsToCandidates(samAlignment,
references, refNameToIndex,
convertedAlignments, parseSmrtTitle, false);
if (convertedAlignments.size() > 1) {
cout << "WARNING. Ignore multiple segments." << endl;
continue;
}
for (int i = 0; i < 1; i++) {
AlignmentCandidate<> & alignment = convertedAlignments[i];
//score func does not matter
DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc;
ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
alignment.tAlignedSeq.seq, distFunc);
// Check whether this alignment can only map to adapters in
// the adapter GFF file.
if (adapterGffFileName != "" and
CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) {
if (verbose)
cout << alignment.qName << " filter adapter only."
<< endl;
continue;
}
// Assign score to samAlignment.
samAlignment.score = samAlignment.as;
if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) {
continue;
}
allSAMAlignments.push_back( samAlignment );
alignment.FreeSubsequences();
}
++alignIndex;
}
// Sort all SAM alignments by qName, score and target position.
sort(allSAMAlignments.begin(), allSAMAlignments.end(),
byQNameScoreTStart);
unsigned int groupBegin = 0;
unsigned int groupEnd = -1;
vector<SAMAlignment> filteredSAMAlignments;
while(groupBegin < allSAMAlignments.size()) {
// Get the next group of SAM alignments which have the same qName
// from allSAMAlignments[groupBegin ... groupEnd)
GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd);
vector<unsigned int> hitIndices = ApplyHitPolicy(
hitPolicy, allSAMAlignments, groupBegin, groupEnd);
for(unsigned int i = 0; i < hitIndices.size(); i++) {
filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]);
}
groupBegin = groupEnd;
}
// Sort all SAM alignments by reference name and query name
sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(),
byRNameQName);
for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) {
filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm);
}
if (outFileName != "") {
outFileStrm.close();
}
#ifdef USE_GOOGLE_PROFILER
ProfilerStop();
#endif
return 0;
}
