seqan::hibf::layout::data_store Struct Reference

Contains information used for the layout. More...

#include <hibf/layout/data_store.hpp>

Classes
struct	previous_level
	Stores information of the previous level of a given IBF. More...

Public Member Functions
void	validate () const

Public Attributes
References to global instances of the HIBF.
layout *	hibf_layout
	The layout that is built by layout::hierarchical_binning.
std::vector< size_t > const *	kmer_counts {}
	The kmer counts associated with the above files used to layout user bin into technical bins.
std::vector< sketch::hyperloglog > const *	sketches {}
	The hyperloglog sketches of all input files to estimate their size and similarities.
Local Storage one IBF in the HIBF.
These member variables change on each IBF of the HIBF s.t. the current IBF can be constructed from the current subset of data. The same data is also used for the top level IBF that holds all the data.
std::vector< size_t >	positions
	The input is sorted and rearranged. To keep track without changing the input we store the positions.
std::vector< double >	fpr_correction {}
	The false positive correction based on fp_rate, num_hash_functions and requested_max_tb.
double	relaxed_fpr_correction {}
	The correction factor for merged bins which are allowed to have a relaxed FPR.
previous_level	previous {}
	Information about previous levels of the IBF if the algorithm is called recursively.
std::vector< uint64_t >	union_estimates {}
	Matrix of estimates of merged bin cardinalites.
bool	user_bins_arranged {false}
	The input is sorted and rearranged. To keep track without changing the input we store the positions.
concurrent_timer	union_estimation_timer {}
	Tracks the time the algorithm spends on estimating the union of user bins (merged bins).
concurrent_timer	rearrangement_timer {}
	Tracks the time the algorithm spends on rearranging user bins (merged bins).

Detailed Description

Contains information used for the layout.

Member Data Documentation

positions

std::vector<size_t> seqan::hibf::layout::data_store::positions

Initial value:

= [this]()
    {
        std::vector<size_t> ps;
        if (this->kmer_counts == nullptr)
            return ps; 
        ps.resize(this->kmer_counts->size());
        std::iota(ps.begin(), ps.end(), 0);
        return ps;
    }()

The input is sorted and rearranged. To keep track without changing the input we store the positions.

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The documentation for this struct was generated from the following file:

• data_store.hpp