fasta_query.h

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// ReferenceGenome: A class for querying a reference genome FASTA file.
 
#ifndef FASTA_QUERY_H
#define FASTA_QUERY_H
 
#include <string>
#include <map>
#include <unordered_map>
#include <vector>
// #include <mutex>
#include <shared_mutex>
#include <string_view>
 
class ReferenceGenome {
    private:
        std::string fasta_filepath;
        std::vector<std::string> chromosomes;
        std::unordered_map<std::string, std::string> chr_to_seq;
        std::map<std::string, uint32_t> chr_to_length;
        std::shared_mutex& shared_mutex;
 
    public:
        ReferenceGenome(std::shared_mutex& shared_mutex) : shared_mutex(shared_mutex) {}
    
        int setFilepath(std::string fasta_filepath);
        std::string getFilepath() const;
        std::string_view query(const std::string& chr, uint32_t pos_start, uint32_t pos_end) const;
        bool compare(const std::string& chr, uint32_t pos_start, uint32_t pos_end, const std::string& compare_seq, float match_threshold) const;
 
        // Get the chromosome contig lengths in VCF header format
        std::string getContigHeader() const;
 
        // Get the list of chromosomes, used for whole genome analysis
        std::vector<std::string> getChromosomes() const;
 
        // Get the length of a chromosome
        uint32_t getChromosomeLength(std::string chr) const;
};
 
#endif // FASTA_QUERY_H