Needle
An application for fast and efficient searches of NGS data.
Functions
estimate.cpp File Reference
#include <deque>
#include <iostream>
#include <math.h>
#include <numeric>
#include <omp.h>
#include <stdlib.h>
#include <string>
#include <vector>
#include <algorithm>
#include <ranges>
#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.h"

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< uint32_t > &prev_counts, exp_t const &expressions, uint16_t const k, std::vector< double > const fprs)
 
template<typename float_or_int >
void read_levels (std::vector< std::vector< float_or_int >> &expressions, std::filesystem::path filename)
 
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. More...
 
void call_estimate (estimate_ibf_arguments &args, estimate_arguments &estimate_args)
 Function, which calls the estimate function. More...
 

Function Documentation

◆ call_estimate()

void call_estimate ( estimate_ibf_arguments args,
estimate_arguments estimate_args 
)

Function, which calls the estimate function.

Parameters
argsThe arguments estimate and ibf use.
estimate_argsThe 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< uint32_t > &  prev_counts,
exp_t const &  expressions,
uint16_t const  k,
std::vector< double > const  fprs 
)

◆ 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
argsThe arguments.
ibfThe ibf determing what kind ibf is used (compressed or uncompressed).
file_outThe output file.
estimate_argsThe estimate arguments.

◆ read_levels()

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