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Fix Diversity Pool Processor and add test case
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,134 @@ | ||
| /* | ||
| Genesis - A toolkit for working with phylogenetic data. | ||
| Copyright (C) 2014-2024 Lucas Czech | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| Contact: | ||
| Lucas Czech <[email protected]> | ||
| University of Copenhagen, Globe Institute, Section for GeoGenetics | ||
| Oster Voldgade 5-7, 1350 Copenhagen K, Denmark | ||
| */ | ||
|
|
||
| /** | ||
| * @brief | ||
| * | ||
| * @file | ||
| * @ingroup test | ||
| */ | ||
|
|
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| #include "src/common.hpp" | ||
|
|
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| #include "genesis/population/sample_counts.hpp" | ||
| #include "genesis/population/variant.hpp" | ||
| #include "genesis/population/stream/variant_input_stream.hpp" | ||
| #include "genesis/population/stream/variant_input_stream_sources.hpp" | ||
| #include "genesis/population/stream/variant_input_stream_adapters.hpp" | ||
| #include "genesis/population/filter/sample_counts_filter.hpp" | ||
| #include "genesis/population/filter/variant_filter.hpp" | ||
| #include "genesis/population/function/functions.hpp" | ||
| #include "genesis/utils/math/random.hpp" | ||
|
|
||
| #include <cmath> | ||
| #include <limits> | ||
|
|
||
| using namespace genesis::population; | ||
| using namespace genesis::utils; | ||
|
|
||
| // ================================================================================================= | ||
| // Random Fuzzy | ||
| // ================================================================================================= | ||
|
|
||
| /** | ||
| * @brief This is a helper function to create random Variants, to be used for testing. | ||
| * | ||
| * Just to avoid code duplication in the test cases. | ||
| */ | ||
| std::vector<Variant> test_create_random_variants_( size_t min_count ) | ||
| { | ||
| // Number of samples per variant | ||
| auto const n_positions = 100; | ||
| auto const n_samples = permuted_congruential_generator( 2, 10 ); | ||
|
|
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| // Create a list of Variants and samples, with random content | ||
| std::vector<Variant> data; | ||
| data.resize( n_positions ); | ||
| for( size_t n_var = 0; n_var < n_positions; ++n_var ) { | ||
| auto& variant = data[n_var]; | ||
| variant.chromosome = "1"; | ||
| variant.position = n_var + 1; | ||
| variant.status.set( | ||
| permuted_congruential_generator( | ||
| static_cast<int>( VariantFilterTag::kEnd ) - 1 | ||
| ) | ||
| ); | ||
|
|
||
| // Fill the variant with samples | ||
| variant.samples.resize( n_samples ); | ||
| for( size_t n_smp = 0; n_smp < n_samples; ++n_smp ) { | ||
| auto& sample = variant.samples[n_smp]; | ||
|
|
||
| // Make a selection of how many of the counts we want to fill. | ||
| // This makes sure that we are not underrepresenting low counts. | ||
| auto const num_non_empty = permuted_congruential_generator( 4 ); | ||
| switch( num_non_empty ) { | ||
| case 0: { | ||
| break; | ||
| } | ||
| case 1: { | ||
| sample.a_count = permuted_congruential_generator( 1, 10 ); | ||
| break; | ||
| } | ||
| case 2: { | ||
| sample.a_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.c_count = permuted_congruential_generator( 1, 10 ); | ||
| break; | ||
| } | ||
| case 3: { | ||
| sample.a_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.c_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.g_count = permuted_congruential_generator( 1, 10 ); | ||
| break; | ||
| } | ||
| case 4: { | ||
| sample.a_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.c_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.g_count = permuted_congruential_generator( 1, 10 ); | ||
| sample.t_count = permuted_congruential_generator( 1, 10 ); | ||
| break; | ||
| } | ||
| } | ||
|
|
||
| // Also set a random status | ||
| sample.status.set( | ||
| permuted_congruential_generator( | ||
| static_cast<int>( SampleCountsFilterTag::kEnd ) - 1 | ||
| ) | ||
| ); | ||
|
|
||
| // Lastly, to avoid missing data issues in the computation, | ||
| // we always set the status to missing if there are no counts. | ||
| // Our filters would usually catch that, so it's fair to do this here as well. | ||
| if( nucleotide_sum( sample ) < min_count ) { | ||
| sample.status.reset( SampleCountsFilterTag::kMissing ); | ||
| } | ||
| } | ||
| } | ||
| return data; | ||
| } | ||
|
|
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| std::vector<Variant> test_create_random_variants_() | ||
| { | ||
| return test_create_random_variants_( 0 ); | ||
| } |