//---------------------------------------------------------
// Copyright 2017 Ontario Institute for Cancer Research
// Written by Jared Simpson (jared.simpson@oicr.on.ca)
//---------------------------------------------------------
//
// nanopolish_read_db -- database of reads and their
// associated signal data
//
#ifndef NANOPOLISH_READ_DB
#define NANOPOLISH_READ_DB

#include <map>
#include "htslib/faidx.h"

struct ReadDBData
{
    // path to the signal-level data for this read
    std::string signal_data_path;
};

class ReadDB
{
    public:
        ReadDB();
        ~ReadDB();

        //
        // I/O
        //

        //  construct the database from an input reads file
        void build(const std::string& reads_filename);

        // save the database to disk
        void save() const;

        // restore the database from disk
        void load(const std::string& reads_filename);

        //
        // Data Access
        // 

        // set the signal path for the given read
        void add_signal_path(const std::string& read_id, const std::string& path);
        
        // returns the path to the signal data for the given read
        std::string get_signal_path(const std::string& read_id) const;
        
        // returns true if a read with this ID is in the DB
        bool has_read(const std::string& read_id) const;

        // returns the basecalled sequence for the given read
        std::string get_read_sequence(const std::string& read_id) const;

        // returns the number of reads in the database
        size_t get_num_reads() const { return m_data.size(); }
 
        //
        // Summaries and sanity checks
        //

        // return the number of reads with a fast5 file
        size_t get_num_reads_with_path() const;

        // returns true if all reads in the database have paths to their signal-level data
        bool check_signal_paths() const;

        // print some summary stats about the database
        void print_stats() const;

    private:
        
        //
        void import_reads(const std::string& input_filename, const std::string& output_fasta_filename);

        // the filename of the indexed data, after converting to fasta
        std::string m_indexed_reads_filename;

        //
        std::map<std::string, ReadDBData> m_data;

        //
        faidx_t* m_fai;
};

#endif