HIBF 1.0.0-rc.1
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Layout

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...
 
struct  seqan::hibf::layout::relaxed_fpr_correction_parameters
 Contains parameters for compute_relaxed_fpr_correction. 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.
 
double seqan::hibf::layout::compute_relaxed_fpr_correction (relaxed_fpr_correction_parameters const &params)
 Precompute size correction factor for merged bins which are allowed to have a relaxed FPR.
 
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

◆ compute_fpr_correction()

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.

See also
https://godbolt.org/z/zTj1v9W94

◆ compute_layout()

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]configThe configuration to compute the layout with.
[in]kmer_countsThe vector that will store the kmer counts (estimations).
[in]sketchesThe vector that will store the sketches.
[in]positionsSpecifies which user bins the layout should be calculated on (positions in the other vectors).
[in,out]union_estimation_timerThe timer that measures the union estimation time.
[in,out]rearrangement_timerThe timer that measures the rearrangement time.
Returns
layout

◆ compute_sketches()

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]configThe configuration to compute the layout with.
[in,out]hll_sketchesThe vector that will store the sketches.