#include <chopper/layout/hibf_statistics.hpp>
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| static void | print_header_to (std::ostream &stream, bool const verbose=true) |
| | Prints a column names of the summary to the command line. More...
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| static std::string | byte_size_to_formatted_str (size_t const bytes) |
| | Round bytes to the appropriate unit and convert to string with unit. More...
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◆ bin_kind
The kind of bin that is stored.
| Enumerator |
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| split | A single user bin, split into 1 or more bins (even though 1 is not technically split).
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| merged | Multiple user bins are merged into a single technical bin.
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◆ hibf_statistics() [1/4]
| chopper::layout::hibf_statistics::hibf_statistics |
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delete |
Deleted. Holds reference members.
◆ hibf_statistics() [2/4]
| chopper::layout::hibf_statistics::hibf_statistics |
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hibf_statistics const & |
b | ) |
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delete |
Deleted. Holds const member.
◆ hibf_statistics() [3/4]
Deleted. Holds const member.
◆ ~hibf_statistics()
| chopper::layout::hibf_statistics::~hibf_statistics |
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default |
◆ hibf_statistics() [4/4]
| chopper::layout::hibf_statistics::hibf_statistics |
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configuration const & |
config_, |
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std::vector< seqan::hibf::sketch::hyperloglog > const & |
sketches_, |
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std::vector< size_t > const & |
kmer_counts |
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Construct an empty HIBF with an empty top level IBF.
- Parameters
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| [in] | config_ | User configuration for the HIBF. |
| [in] | sketches_ | The sketches of the input. |
| [in] | kmer_counts | The original user bin weights (kmer counts). |
◆ byte_size_to_formatted_str()
| std::string chopper::layout::hibf_statistics::byte_size_to_formatted_str |
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size_t const |
bytes | ) |
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Round bytes to the appropriate unit and convert to string with unit.
◆ collect_bins()
| void chopper::layout::hibf_statistics::collect_bins |
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◆ compute_cardinalities()
| void chopper::layout::hibf_statistics::compute_cardinalities |
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level & |
curr_level | ) |
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◆ compute_total_query_cost()
| void chopper::layout::hibf_statistics::compute_total_query_cost |
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level & |
curr_level | ) |
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Computes the estimated query cost.
◆ finalize()
| void chopper::layout::hibf_statistics::finalize |
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Gather all statistics to have all members ready.
◆ gather_statistics()
| void chopper::layout::hibf_statistics::gather_statistics |
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level const & |
curr_level, |
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size_t const |
level_summary_index |
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private |
Recursively gather all the statistics from the bins.
- Parameters
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| [in] | curr_level | The current IBF from which the statistics will be extracted. |
| [in] | level_summary_index | The index of curr_level in summeries. |
◆ operator=() [1/2]
Deleted. Holds const member.
◆ operator=() [2/2]
Deleted. Holds const member.
◆ print_header_to()
| void chopper::layout::hibf_statistics::print_header_to |
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std::ostream & |
stream, |
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bool const |
verbose = true |
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Prints a column names of the summary to the command line.
◆ print_summary_to()
| void chopper::layout::hibf_statistics::print_summary_to |
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size_t & |
t_max_64_memory, |
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std::ostream & |
stream, |
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bool const |
verbose = true |
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Prints a tab-separated summary of the statistics of this HIBF to the command line.
◆ to_formatted_BF_size()
| std::string chopper::layout::hibf_statistics::to_formatted_BF_size |
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size_t const |
number_of_kmers_to_be_stored | ) |
const |
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private |
Compute the Bloom Filter size from number_of_kmers_to_be_stored and return it as a formatted string with the appropriate unit.
- Parameters
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| [in] | number_of_kmers_to_be_stored | |
◆ total_hibf_size_in_byte()
| size_t chopper::layout::hibf_statistics::total_hibf_size_in_byte |
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Return the total corrected size of the HIBF in bytes.
◆ config
Copy of the user configuration for this HIBF.
◆ counts
| std::vector<size_t> const& chopper::layout::hibf_statistics::counts |
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private |
A reference to the input counts.
◆ expected_HIBF_query_cost
| double chopper::layout::hibf_statistics::expected_HIBF_query_cost {0.0} |
The estimated query cost relative to the total k-mer count in the data set.
◆ fp_correction
| std::vector<double> const chopper::layout::hibf_statistics::fp_correction {} |
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private |
The split bin false positive correction factors to use for the statistics.
◆ hibf_layout
| seqan::hibf::layout::layout chopper::layout::hibf_statistics::hibf_layout |
A reference to the input counts.
◆ merged_fpr_correction_factor
| double const chopper::layout::hibf_statistics::merged_fpr_correction_factor {} |
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private |
The merged bin false positive correction factors to use for the statistics.
◆ sketches
| std::vector<seqan::hibf::sketch::hyperloglog> const& chopper::layout::hibf_statistics::sketches |
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private |
A reference to the input sketches.
◆ summaries
| std::map<size_t, level_summary> chopper::layout::hibf_statistics::summaries |
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The gathered summary of statistics for each level of this HIBF.
◆ top_level_ibf
| level chopper::layout::hibf_statistics::top_level_ibf |
The top level IBF of this HIBF, often starting point for recursions.
◆ total_kmer_count
| size_t const chopper::layout::hibf_statistics::total_kmer_count {} |
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private |
The original kmer count of all user bins.
◆ total_query_cost
| double chopper::layout::hibf_statistics::total_query_cost {0.0} |
The estimated query cost of every single kmer in this HIBF.
The documentation for this class was generated from the following files:
