Includes all API relevant to computing a hierarchical layout for building an HIBF. More...

Topics
	Prefixes
	Prefixes for writing the layout file.

Classes
struct	seqan::hibf::layout::data_store
	Contains information used for the layout. More...

struct	seqan::hibf::layout::fpr_correction_parameters
	Contains parameters for compute_fpr_correction. More...

struct	seqan::hibf::layout::graph
	Contains the layout graph structure. More...

class	seqan::hibf::layout::hierarchical_binning
	Hierarchical binning algorithm. More...

struct	seqan::hibf::layout::layout
	The layout. More...

class	seqan::hibf::layout::simple_binning
	Distributes x Technical Bins across y User Bins while minimizing the maximal Technical Bin size. More...

Functions
std::vector< double >	seqan::hibf::layout::compute_fpr_correction (fpr_correction_parameters const &params)
	Precompute f_h factors that adjust the split bin size to prevent FPR inflation due to multiple testing.

layout	seqan::hibf::layout::compute_layout (config const &config, std::vector< size_t > const &kmer_counts, std::vector< sketch::hyperloglog > const &sketches, std::vector< size_t > &&positions, concurrent_timer &union_estimation_timer, concurrent_timer &rearrangement_timer)
	Computes the layout.

void	seqan::hibf::sketch::compute_sketches (config const &config, std::vector< sketch::hyperloglog > &hll_sketches)
	Computes the kmer_counts and sketches and stores them in the respective vectors for further use.

template<typename matrix_type , typename matrix_value_type >
void	seqan::hibf::layout::print_matrix (matrix_type const &matrix, size_t const row_bound, size_t const column_bound, matrix_value_type const inf)
	Helper function to print a matrix when debugging.

Detailed Description

Includes all API relevant to computing a hierarchical layout for building an HIBF.

Function Documentation

std::vector< double > seqan::hibf::layout::compute_fpr_correction ( fpr_correction_parameters const & params )

Precompute f_h factors that adjust the split bin size to prevent FPR inflation due to multiple testing.

layout seqan::hibf::layout::compute_layout	(	config const &	config,
		std::vector< size_t > const &	kmer_counts,
		std::vector< sketch::hyperloglog > const &	sketches,
		std::vector< size_t > &&	positions,
		concurrent_timer &	union_estimation_timer,
		concurrent_timer &	rearrangement_timer )

Computes the layout.

Parameters

[in]	config	The configuration to compute the layout with.
[in]	kmer_counts	The vector that will store the kmer counts (estimations).
[in]	sketches	The vector that will store the sketches.
[in]	positions	Specifies which user bins the layout should be calculated on (positions in the other vectors).
[in,out]	union_estimation_timer	The timer that measures the union estimation time.
[in,out]	rearrangement_timer	The timer that measures the rearrangement time.

void seqan::hibf::sketch::compute_sketches	(	config const &	config,
		std::vector< sketch::hyperloglog > &	hll_sketches )

Computes the kmer_counts and sketches and stores them in the respective vectors for further use.

Parameters

[in]	config	The configuration to compute the layout with.
[in,out]	hll_sketches	The vector that will store the sketches.