Needle
An application for fast and efficient searches of NGS data.
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#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, std::vector< int > &deleted) |
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. | |
void | call_estimate (estimate_ibf_arguments &args, estimate_arguments &estimate_args) |
Function, which calls the estimate function. | |
void call_estimate | ( | estimate_ibf_arguments & | args, |
estimate_arguments & | estimate_args | ||
) |
Function, which calls the estimate function.
args | The arguments estimate and ibf use. |
estimate_args | The estimate arguments. |
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, | ||
std::vector< int > & | deleted | ||
) |
void estimate | ( | estimate_ibf_arguments & | args, |
IBFType & | ibf, | ||
std::filesystem::path | file_out, | ||
estimate_arguments const & | estimate_args | ||
) |
Function to estimate expression value.
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. |
void read_levels | ( | std::vector< std::vector< float_or_int > > & | expressions, |
std::filesystem::path | filename | ||
) |