population_8hpp_source.html

#ifndef GENESIS_POPULATION_H_

#define GENESIS_POPULATION_H_


/*

    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 <lucas.czech@sund.ku.dk>

    University of Copenhagen, Globe Institute, Section for GeoGenetics

    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark

*/


#include "genesis/population/filter/filter_stats.hpp"

#include "genesis/population/filter/filter_status.hpp"

#include "genesis/population/filter/sample_counts_filter.hpp"

#include "genesis/population/filter/sample_counts_filter_numerical.hpp"

#include "genesis/population/filter/sample_counts_filter_positional.hpp"

#include "genesis/population/filter/variant_filter.hpp"

#include "genesis/population/filter/variant_filter_numerical.hpp"

#include "genesis/population/filter/variant_filter_positional.hpp"

#include "genesis/population/format/bed_reader.hpp"

#include "genesis/population/format/frequency_table_input_stream.hpp"

#include "genesis/population/format/genome_region_reader.hpp"

#include "genesis/population/format/gff_reader.hpp"

#include "genesis/population/format/hts_file.hpp"

#include "genesis/population/format/map_bim_reader.hpp"

#include "genesis/population/format/sam_flags.hpp"

#include "genesis/population/format/sam_variant_input_stream.hpp"

#include "genesis/population/format/simple_pileup_common.hpp"

#include "genesis/population/format/simple_pileup_input_stream.hpp"

#include "genesis/population/format/simple_pileup_reader.hpp"

#include "genesis/population/format/sync_common.hpp"

#include "genesis/population/format/sync_input_stream.hpp"

#include "genesis/population/format/sync_reader.hpp"

#include "genesis/population/format/vcf_common.hpp"

#include "genesis/population/format/vcf_format_iterator.hpp"

#include "genesis/population/format/vcf_header.hpp"

#include "genesis/population/format/vcf_input_stream.hpp"

#include "genesis/population/format/vcf_record.hpp"

#include "genesis/population/function/diversity_pool_calculator.hpp"

#include "genesis/population/function/diversity_pool_functions.hpp"

#include "genesis/population/function/diversity_pool_processor.hpp"

#include "genesis/population/function/fst_cathedral.hpp"

#include "genesis/population/function/fst_pool_calculator.hpp"

#include "genesis/population/function/fst_pool_functions.hpp"

#include "genesis/population/function/fst_pool_karlsson.hpp"

#include "genesis/population/function/fst_pool_kofler.hpp"

#include "genesis/population/function/fst_pool_processor.hpp"

#include "genesis/population/function/fst_pool_unbiased.hpp"

#include "genesis/population/function/functions.hpp"

#include "genesis/population/function/genome_locus.hpp"

#include "genesis/population/function/genome_locus_set.hpp"

#include "genesis/population/function/genome_region.hpp"

#include "genesis/population/function/subsample.hpp"

#include "genesis/population/function/variant_input_stream.hpp"

#include "genesis/population/function/window_average.hpp"

#include "genesis/population/genome_locus.hpp"

#include "genesis/population/genome_locus_set.hpp"

#include "genesis/population/genome_region.hpp"

#include "genesis/population/genome_region_list.hpp"

#include "genesis/population/plotting/af_spectrum.hpp"

#include "genesis/population/plotting/cathedral_plot.hpp"

#include "genesis/population/plotting/genome_heatmap.hpp"

#include "genesis/population/plotting/heatmap_colorization.hpp"

#include "genesis/population/sample_counts.hpp"

#include "genesis/population/stream/variant_gapless_input_stream.hpp"

#include "genesis/population/stream/variant_input_stream_adapters.hpp"

#include "genesis/population/stream/variant_input_stream.hpp"

#include "genesis/population/stream/variant_input_stream_sources.hpp"

#include "genesis/population/stream/variant_parallel_input_stream.hpp"

#include "genesis/population/variant.hpp"

#include "genesis/population/window/base_window.hpp"

#include "genesis/population/window/base_window_stream.hpp"

#include "genesis/population/window/chromosome_window_stream.hpp"

#include "genesis/population/window/functions.hpp"

#include "genesis/population/window/genome_window_stream.hpp"

#include "genesis/population/window/interval_window_stream.hpp"

#include "genesis/population/window/position_window_stream.hpp"

#include "genesis/population/window/queue_window_stream.hpp"

#include "genesis/population/window/region_window_stream.hpp"

#include "genesis/population/window/sliding_window_generator.hpp"

#include "genesis/population/window/variant_window_stream.hpp"

#include "genesis/population/window/vcf_window.hpp"

#include "genesis/population/window/window.hpp"

#include "genesis/population/window/window_view.hpp"

#include "genesis/population/window/window_view_stream.hpp"


#endif // include guard