estimate.cpp File Reference

#include <algorithm>
#include <deque>
#include <iostream>
#include <math.h>
#include <numeric>
#include <omp.h>
#include <ranges>
#include <stdlib.h>
#include <string>
#include <vector>
#include <seqan3/alphabet/container/concatenated_sequences.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/concept/cereal.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include "estimate.hpp"

Functions
template<class IBFType , bool last_exp, bool normalization, typename exp_t >
void	check_ibf (min_arguments const &args, IBFType const &ibf, std::vector< uint16_t > &estimations_i, seqan3::dna4_vector const &seq, std::vector< float > &prev_counts, exp_t const &expressions, uint16_t const level, std::vector< double > const fprs, std::vector< int > &deleted)
template<typename float_or_int >
void	read_levels (std::vector< std::vector< float_or_int > > &, std::filesystem::path)
template<class IBFType , bool samplewise, bool normalization_method = false>
void	estimate (estimate_ibf_arguments &args, IBFType &ibf, std::filesystem::path file_out, estimate_arguments const &estimate_args)
	Function to estimate expression value.
void	call_estimate (estimate_ibf_arguments &args, estimate_arguments &estimate_args)
	Function, which calls the estimate function.

Function Documentation

call_estimate()

void call_estimate	(	estimate_ibf_arguments &	args,
		estimate_arguments &	estimate_args
	)

Function, which calls the estimate function.

Parameters

args	The arguments estimate and ibf use.
estimate_args	The estimate arguments.

check_ibf()

template<class IBFType , bool last_exp, bool normalization, typename exp_t >

void check_ibf	(	min_arguments const &	args,
		IBFType const &	ibf,
		std::vector< uint16_t > &	estimations_i,
		seqan3::dna4_vector const &	seq,
		std::vector< float > &	prev_counts,
		exp_t const &	expressions,
		uint16_t const	level,
		std::vector< double > const	fprs,
		std::vector< int > &	deleted
	)

estimate()

template<class IBFType , bool samplewise, bool normalization_method = false>

void estimate	(	estimate_ibf_arguments &	args,
		IBFType &	ibf,
		std::filesystem::path	file_out,
		estimate_arguments const &	estimate_args
	)

Function to estimate expression value.

Parameters

args	The arguments.
ibf	The ibf determing what kind ibf is used (compressed or uncompressed).
file_out	The output file.
estimate_args	The estimate arguments.

read_levels()

template<typename float_or_int >

void read_levels	(	std::vector< std::vector< float_or_int > > &	expressions,
		std::filesystem::path	filename
	)