simple_pileup_input_stream.hpp

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#ifndef GENESIS_POPULATION_FORMAT_SIMPLE_PILEUP_INPUT_STREAM_H_
#define GENESIS_POPULATION_FORMAT_SIMPLE_PILEUP_INPUT_STREAM_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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/population/format/simple_pileup_reader.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/math/bitvector/helper.hpp"
 
#include <string>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Simple Pileup Input Stream
// =================================================================================================
 
template<class T = SimplePileupReader::Record>
class SimplePileupInputStream
{
public:
 
    // -------------------------------------------------------------------------
    //     Member Types
    // -------------------------------------------------------------------------
 
    using self_type         = SimplePileupInputStream;
    using value_type        = T;
    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
    // -------------------------------------------------------------------------
 
    SimplePileupInputStream() = default;
 
    explicit SimplePileupInputStream(
        std::shared_ptr< utils::BaseInputSource > source,
        SimplePileupReader const&                 reader = {}
    )
        : input_stream_( std::make_shared<utils::InputStream>( source ))
        , reader_( reader )
    {
        // Read the first record of the file.
        increment();
    }
 
    // /* *
    //  * @brief Create an instance that reads from an input source, using only the samples at the
    //  * indices given in the @p sample_indices, and optionally take a SimplePileupReader with
    //  * settings to be used.
    //  */
    // SimplePileupInputStream(
    //     std::shared_ptr< utils::BaseInputSource > source,
    //     std::vector<size_t> const&                sample_indices,
    //     SimplePileupReader const&                 reader = {}
    // )
    //     : input_stream_( std::make_shared<utils::InputStream>( source ))
    //     , reader_( reader )
    //     , use_sample_filter_( true )
    // {
    //     // Prepare the sample filter from the indices.
    //     sample_filter_ = utils::make_bool_vector_from_indices( sample_indices );
    //
    //     // Read the first record of the file.
    //     increment();
    // }
 
    SimplePileupInputStream(
        std::shared_ptr< utils::BaseInputSource > source,
        std::vector<bool> const&                  sample_filter,
        SimplePileupReader 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();
    }
 
    ~SimplePileupInputStream() = default;
 
    SimplePileupInputStream( self_type const& ) = default;
    SimplePileupInputStream( 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
    // -------------------------------------------------------------------------
 
    SimplePileupReader const& reader() const
    {
        return reader_;
    }
 
    T const& record() const
    {
        return record_;
    }
 
    T& record()
    {
        return record_;
    }
 
    T const* operator ->() const
    {
        return &record_;
    }
 
    T* operator ->()
    {
        return &record_;
    }
 
    T const& operator*() const
    {
        return record_;
    }
 
    T& operator*()
    {
        return record_;
    }
 
    // -------------------------------------------------------------------------
    //     Iteration
    // -------------------------------------------------------------------------
 
    self_type& operator ++ ()
    {
        increment();
        return *this;
    }
 
    self_type& operator ++(int)
    {
        increment();
        return *this;
    }
 
    void increment()
    {
        increment_();
    }
 
    bool operator==( self_type const& it ) const
    {
        return good_ == it.good_;
    }
 
    bool operator!=( self_type const& it ) const
    {
        return !(*this == it);
    }
 
    // -------------------------------------------------------------------------
    //     Internal Members
    // -------------------------------------------------------------------------
 
private:
 
    void increment_();
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    // Basic iterator setup and input.
    bool good_ = false;
    std::shared_ptr<utils::InputStream> input_stream_;
 
    // Reading into records
    SimplePileupReader reader_;
    size_t sample_size_ = 0;
    T record_;
 
    // Sample filtering
    std::vector<bool> sample_filter_;
    bool              use_sample_filter_ = false;
};
 
// -------------------------------------------------------------------------
//     Explicit Specialiyations in Namespace Scope
// -------------------------------------------------------------------------
 
template<>
inline void SimplePileupInputStream<SimplePileupReader::Record>::increment_()
{
    // We resize to the size that we had before (or 0 if we are just starting),
    // so that the parser can check the correct sample size.
    // We cannot rely on the samples keeping their size, as the user might have moved the data.
    record_.samples.resize( sample_size_ );
    if( use_sample_filter_ ) {
        good_ = reader_.parse_line_record( *input_stream_, record_, sample_filter_ );
    } else {
        good_ = reader_.parse_line_record( *input_stream_, record_ );
    }
    sample_size_ = record_.samples.size();
}
 
template<>
inline void SimplePileupInputStream<Variant>::increment_()
{
    // Same as above
    record_.samples.resize( sample_size_ );
    if( use_sample_filter_ ) {
        good_ = reader_.parse_line_variant( *input_stream_, record_, sample_filter_ );
    } else {
        good_ = reader_.parse_line_variant( *input_stream_, record_ );
    }
    sample_size_ = record_.samples.size();
}
 
} // namespace population
} // namespace genesis
 
#endif // include guard