Includes all API relevant to computing a hierarchical layout for building an HIBF.
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| Prefixes |
| Prefixes for writing the layout file.
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std::vector< double > | seqan::hibf::layout::compute_fpr_correction (fpr_correction_parameters const ¶ms) |
| Precompute f_h factors that adjust the split bin size to prevent FPR inflation due to multiple testing.
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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.
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double | seqan::hibf::layout::compute_relaxed_fpr_correction (relaxed_fpr_correction_parameters const ¶ms) |
| Precompute size correction factor for merged bins which are allowed to have a relaxed FPR.
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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.
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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.
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Includes all API relevant to computing a hierarchical layout for building an HIBF.
◆ compute_fpr_correction()
◆ compute_layout()
Computes the layout.
- Parameters
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[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. |
- Returns
- layout
◆ compute_sketches()
Computes the kmer_counts and sketches and stores them in the respective vectors for further use.
- Parameters
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[in] | config | The configuration to compute the layout with. |
[in,out] | hll_sketches | The vector that will store the sketches. |