genotypekit.hpp File Reference

#include <iostream>
#include <algorithm>
#include <functional>
#include <cmath>
#include <regex>
#include <limits>
#include <unordered_set>
#include <unordered_map>
#include <list>
#include <vg/vg.pb.h>
#include "vg.hpp"
#include "translator.hpp"
#include "hash_map.hpp"
#include "types.hpp"
#include "statistics.hpp"
#include "snarls.hpp"
#include "path_index.hpp"
#include "packer.hpp"

Classes
class	vg::ConsistencyCalculator
class	vg::TraversalSupportCalculator
class	vg::GenotypeLikelihoodCalculator
class	vg::GenotypePriorCalculator
class	vg::VcfRecordConverter
class	vg::VcfRecordFilter
struct	vg::AugmentedGraph
struct	vg::SupportAugmentedGraph
	Augmented Graph that holds some Support annotation data specific to vg call. More...
class	vg::SimpleConsistencyCalculator
class	vg::FixedGenotypePriorCalculator
class	vg::SimpleTraversalSupportCalculator

Namespaces
	vg

Functions
SnarlTraversal	vg::get_traversal_of_snarl (VG &graph, const Snarl *snarl, const SnarlManager &manager, const Path &path)
string	vg::traversal_to_string (VG &graph, const SnarlTraversal &path)
Support	vg::make_support (double forward, double reverse, double quality)
double	vg::total (const Support &support)
Support	vg::support_min (const Support &a, const Support &b)
Support	vg::support_max (const Support &a, const Support &b)
Support	vg::flip (const Support &to_flip)
Support	vg::operator+ (const Support &one, const Support &other)
Support &	vg::operator+= (Support &one, const Support &other)
template<typename Scalar >
Support	vg::operator* (const Support &support, const Scalar &scale)
template<typename Scalar >
Support &	vg::operator*= (Support &support, const Scalar &scale)
template<typename Scalar >
Support	vg::operator* (const Scalar &scale, const Support &support)
template<typename Scalar >
Support	vg::operator/ (const Support &support, const Scalar &scale)
template<typename Scalar >
Support &	vg::operator/= (Support &support, const Scalar &scale)
bool	vg::operator< (const Support &a, const Support &b)
bool	vg::operator> (const Support &a, const Support &b)
ostream &	vg::operator<< (ostream &stream, const Support &support)
string	vg::to_vcf_genotype (const Genotype &gt)