//TEMPLATE FUNCTION DepthFromMaxValue
template<class Type> inline
int RealAllowableLeastDepth(ImageDisplay::Matrix<Type>& matrix)
{
ImageDisplay::Matrix<Type>::iterator it = std::max_element(matrix.begin(), matrix.end());
double MaxValue = (double)(*it);
Enforce(MaxValue>0, "Matrix data is empty or all negative");
int bit = ceil(log(MaxValue+1)/log(2.0));//plus 1 means: for value 1024 depth should be 11
return bit;
}
std::vector<Doublet> Higgs::Doublets(boca::Event const& event, std::function<boost::optional<Doublet>(Doublet&)> const& function) const
{
INFO0;
auto jets = event.Jets();
auto jet_range = MomentumRange{Id::higgs, Id::higgs};
auto doublets = UnorderedPairs(jet_range.SofterThanMax(jets), [&](boca::Jet const & jet_1, boca::Jet const & jet_2) {
auto doublet = Doublet{jet_1, jet_2};
if (!jet_range.BelowUpperBound(doublet)) throw boca::Problematic();
if (auto optional = function(doublet)) return *optional;
throw boca::Problematic();
});
for (auto const & jet : jet_range.HarderThanMin(jets)) {
auto doublet = Doublet{};
doublet.Enforce(jet);
if (auto optional = function(doublet)) doublets.emplace_back(*optional);
}
return doublets;
}
void MerlinParameters::Read(int argc, char ** argv, int start)
{
ParameterList::Read(argc, argv, start);
globalRandom.Reset(random_seed);
// The number of analysis steps between markers must be positive
if (FamilyAnalysis::steps_per_interval < 0)
FamilyAnalysis::steps_per_interval = 0;
// Memory usage limit should be positive
if (maxMegabytes < 0)
maxMegabytes = 0;
// The bit limit for analysis should be positive
if (FamilyAnalysis::maxBits < 0)
FamilyAnalysis::maxBits = 0;
// The number of sampled haplotypes should be positive
if (FamilyAnalysis::sampledHaplotypes < 0)
FamilyAnalysis::sampledHaplotypes = 0;
// Clustering distance must be positive
if (clusterDistance < 0.0)
clusterDistance = _NAN_;
// Clustering r-squared must be between 0 and 1
if (clusterRsquared < 0.0)
clusterRsquared = 0.0;
if (clusterRsquared > 1.0)
clusterRsquared = 1.0;
// Limited range of options available with error modelling
if (FuzzyInheritanceTree::perAlleleError != 0.0 ||
FuzzyInheritanceTree::perGenotypeError != 0.0 ||
fitErrorRate)
{
char * reason = "The --%s option is disabled when error modeling is enabled";
Enforce(clusterDistance, _NAN_, reason, "distance");
Enforce(clusterRsquared, _NAN_, reason, "rsq");
Enforce(clusterFile, "", reason, "clusters");
}
// Limited range of options in two-point mode
if (FamilyAnalysis::twopoint)
{
char * reason = "The %s option is disabled during "
"singlepoint analysis.\n";
// No between marker analyses
Enforce(FamilyAnalysis::steps_per_interval, 0, reason, "--steps");
Enforce(FamilyAnalysis::minDistance, _NAN_, reason, "--minStep");
Enforce(FamilyAnalysis::maxDistance, _NAN_, reason, "--maxStep");
Enforce(FamilyAnalysis::grid, _NAN_, reason, "--grid");
// No error checking
Enforce(FamilyAnalysis::findErrors, false, reason, "--flag");
// No haplotyping
Enforce(FamilyAnalysis::bestHaplotype, false, reason, "--best");
Enforce(FamilyAnalysis::sampledHaplotypes, 0, reason, "--sample");
Enforce(FamilyAnalysis::allHaplotypes, false, reason, "--all");
// Positions along chromosome not meaningful
Enforce(FamilyAnalysis::useMarkerNames, true,
"The --markerNames option is automatically enabled during singlepoint analysis\n");
}
// Limited range of options when using imaginary components for recombination fraction
if (MerlinCore::imaginaryTheta < 0.0)
MerlinCore::imaginaryTheta = 0.0;
if (MerlinCore::imaginaryTheta > 0.0)
{
const char * reason = "The %s option is disabled when complex "
"recombination fractions are in use\n";
// No error checking
Enforce(FamilyAnalysis::findErrors, false, reason, "--flag");
// No haplotyping
Enforce(FamilyAnalysis::bestHaplotype, false, reason, "--best");
Enforce(FamilyAnalysis::sampledHaplotypes, 0, reason, "--sample");
Enforce(FamilyAnalysis::allHaplotypes, false, reason, "--all");
}
if (FamilyAnalysis::allHaplotypes)
{
char * reason = "The --%s option is disabled when listing all haplotypes\n";
Enforce(clusterDistance, _NAN_, reason, "distance");
Enforce(clusterRsquared, _NAN_, reason, "rsq");
Enforce(clusterFile, "", reason, "clusters");
}
// Limited range of options when using simwalk2
if (FamilyAnalysis::simwalk2)
{
const char * reason = "The %s option is disabled when creating "
"intermediate results for SimWalk2\n";
// No between marker analyses
Enforce(FamilyAnalysis::steps_per_interval, 0, reason, "--steps");
Enforce(FamilyAnalysis::minDistance, _NAN_, reason, "--minStep");
Enforce(FamilyAnalysis::maxDistance, _NAN_, reason, "--maxStep");
Enforce(FamilyAnalysis::grid, _NAN_, reason, "--grid");
Enforce(FamilyAnalysis::start, _NAN_, reason, "--start");
Enforce(FamilyAnalysis::stop, _NAN_, reason, "--stop");
const char * reason2 = " %s option enabled when creating "
"intermediate results for SimWalk2\n";
// Simwalk2 might want the marker names
Enforce(FamilyAnalysis::useMarkerNames, true, reason2, "--markerNames");
if (KongAndCox::nplPairs)
messages += "The --pairs option will ignore inbreeding "
"to allow joint analysis with Simwalk2\n";
// Non-parametric statistics are required
Enforce(KongAndCox::nplAll, true, reason2, "--npl");
Enforce(KongAndCox::nplPairs, true, reason2, "--pairs");
}
// Checked that proportion of unlinked families is within range
if (VarianceComponents::unlinkedFraction < 0.0 ||
VarianceComponents::unlinkedFraction >= 1.0)
VarianceComponents::unlinkedFraction = 0.0;
// Limited range of options zero recombination is assumed
if (MerlinCore::zeroRecombination)
{
const char * reason = "The --%s option is incompatible with the --zero flag\n"
"and will be disabled\n";
Enforce(associationAnalysis, false, reason, "--assoc options");
Enforce(FamilyAnalysis::findErrors, false, reason, "--flag / --error option");
}
if (reruns > 1)
Enforce(simulateNull, true, "The --reruns option automatically enables the --simulate option\n");
FamilyAnalysis::storeKinshipForVc = varianceComponents;
FamilyAnalysis::storeKinshipForAssoc = associationAnalysis;
// With the --infer parameter, we actively output all information
if (FamilyAnalysis::inferGenotypes)
GenotypeInference::inferBest = GenotypeInference::inferExpected =
GenotypeInference::inferProbabilities = true;
// With the specific options, we enable genotype inference but don't
// touch the individual flags
if (GenotypeInference::inferBest || GenotypeInference::inferExpected ||
GenotypeInference::inferProbabilities)
FamilyAnalysis::inferGenotypes = true;
// The infer genotypes flag controls inference, whereas the output
// flag determines whether results get saved to disk
if (FamilyAnalysis::inferGenotypes)
FamilyAnalysis::outputInferredGenotypes = true;
if (associationAnalysis || FamilyAnalysis::fastAssociationAnalysis)
FamilyAnalysis::inferGenotypes = true;
// Some basic calculations to convert megabyte memory usage
// limit into maximum TreeNode count
BasicTree::maxNodes = (1024 * 1024) / sizeof(TreeNode) * maxMegabytes;
// If we are saving replicated data, then we should also
// be simulating it!
simulateNull |= saveReplicate;
// The max bit parameters for processing haplotype clusters
// should be the same as for other analyses
FamilyHaplos::maxBits = MerlinCore::maxBits;
}
