sync_input_iterator.hpp

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#ifndef GENESIS_POPULATION_FORMATS_SYNC_INPUT_ITERATOR_H_
#define GENESIS_POPULATION_FORMATS_SYNC_INPUT_ITERATOR_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2022 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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/population/formats/sync_reader.hpp"
#include "genesis/utils/io/input_source.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Simple Pileup Input Iterator
// =================================================================================================
 
class SyncInputIterator
{
public:
 
    // -------------------------------------------------------------------------
    //     Member Types
    // -------------------------------------------------------------------------
 
    using self_type         = SyncInputIterator;
    using value_type        = Variant;
    using pointer           = value_type*;
    using reference         = value_type&;
    using const_reference   = value_type const&;
    using difference_type   = std::ptrdiff_t;
    using iterator_category = std::input_iterator_tag;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    SyncInputIterator() = default;
 
    explicit SyncInputIterator(
        std::shared_ptr< utils::BaseInputSource > source,
        SyncReader const&                         reader = {}
    )
        : input_stream_( std::make_shared<utils::InputStream>( source ))
        , reader_( reader )
    {
        // Read the first record of the file.
        increment();
    }
 
    SyncInputIterator(
        std::shared_ptr< utils::BaseInputSource > source,
        std::vector<bool> const&                  sample_filter,
        SyncReader const&                         reader = {}
    )
        : input_stream_( std::make_shared<utils::InputStream>( source ))
        , reader_( reader )
        , sample_filter_( sample_filter )
        , use_sample_filter_( true )
    {
        // Read the first record of the file.
        increment();
    }
 
    ~SyncInputIterator() = default;
 
    SyncInputIterator( self_type const& ) = default;
    SyncInputIterator( self_type&& )      = default;
 
    self_type& operator= ( self_type const& ) = default;
    self_type& operator= ( self_type&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Comparators
    // -------------------------------------------------------------------------
 
    explicit operator bool() const
    {
        return good_;
    }
 
    bool good() const
    {
        return good_;
    }
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    Variant const& variant() const
    {
        return variant_;
    }
 
    Variant& variant()
    {
        return variant_;
    }
 
    Variant const* operator ->() const
    {
        return &variant_;
    }
 
    Variant* operator ->()
    {
        return &variant_;
    }
 
    Variant const& operator*() const
    {
        return variant_;
    }
 
    Variant& operator*()
    {
        return variant_;
    }
 
    // -------------------------------------------------------------------------
    //     Iteration
    // -------------------------------------------------------------------------
 
    self_type& operator ++ ()
    {
        increment();
        return *this;
    }
 
    self_type& operator ++(int)
    {
        increment();
        return *this;
    }
 
    void increment()
    {
        // Read into temp object, so that we have the previous one still available.
        // Same logic as SimplePileupInputIterator<Variant>::increment_(), see there for details.
        Variant tmp;
        tmp.samples.resize( variant_.samples.size() );
        if( use_sample_filter_ ) {
            good_ = reader_.parse_line( *input_stream_, tmp, sample_filter_ );
        } else {
            good_ = reader_.parse_line( *input_stream_, tmp );
        }
 
        // Make sure that the input is sorted.
        if( good_ &&
            (
                ( tmp.chromosome  < variant_.chromosome ) ||
                ( tmp.chromosome == variant_.chromosome && tmp.position <= variant_.position )
            )
        ) {
            throw std::runtime_error(
                "Malformed pileup " + input_stream_->source_name() + " at " + input_stream_->at() +
                ": unordered chromosomes and positions"
            );
        }
        variant_ = std::move( tmp );
    }
 
    bool operator==( self_type const& it ) const
    {
        return good_ == it.good_;
    }
 
    bool operator!=( self_type const& it ) const
    {
        return !(*this == it);
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    // Basic iterator setup and input.
    bool good_ = false;
    std::shared_ptr<utils::InputStream> input_stream_;
 
    // Reading into variants
    Variant variant_;
    SyncReader reader_;
 
    // Sample filtering
    std::vector<bool> sample_filter_;
    bool              use_sample_filter_ = false;
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard