Kseq Paired End Fastx reader in chunks

kseq_chunks.cpp

// to compile: gcc this_prog.c -lz
#include <zlib.h>
#include <cstdio>
#include "kseq.h"
#include <iostream>
#include <vector>

KSEQ_INIT(gzFile, gzread)

using namespace std;

class kseqReader {

private:
    bool END = false;
    string R1_fastx, R2_fastx;
    int chunk_size;
    gzFile fp_r1, fp_r2;
    kseq_t *seq_1, *seq_2;


public:
    struct peRead {
        string R1_seq;
        string R2_seq;
        string R1_name;
        string R2_name;
    };

    std::vector<peRead> chunk_reads;


    kseqReader(string R1File, string R2File, int chunk_size) {
        this->chunk_size = chunk_size;
        this->R1_fastx = R1File;
        this->R2_fastx = R2File;
        fp_r1 = gzopen(R1File.c_str(), "r");
        fp_r2 = gzopen(R2File.c_str(), "r");
        seq_1 = kseq_init(fp_r1);
        seq_2 = kseq_init(fp_r2);
    };

    std::vector<peRead> *next_chunk() {
        this->chunk_reads.clear();
        for (int i = 0; i < this->chunk_size && ((kseq_read(seq_1)) >= 0 && (kseq_read(seq_2)) >= 0); i++) {
            this->chunk_reads.emplace_back(peRead{seq_1->seq.s, seq_2->seq.s, seq_1->name.s, seq_2->name.s});
        }

        if ((int) this->chunk_reads.size() != this->chunk_size) {
            this->END = true;
        }

        return &this->chunk_reads;
    }

    [[nodiscard]] bool end() const {
        return this->END;
    }

    ~kseqReader() {
        kseq_destroy(this->seq_1);
        kseq_destroy(this->seq_2);

        gzclose(this->fp_r1);
        gzclose(this->fp_r2);
    }

};

int main(int argc, char *argv[]) {

    if (argc < 4) {
        fprintf(stderr, "Usage: %s <in_1.fasta> <in_2.fasta> <chunk_size>\n", argv[0]);
        return 1;
    }

    string R1_file = argv[1];
    string R2_file = argv[2];
    int chunkSize = stoi(argv[3]);

    auto *PEReader = new kseqReader(R1_file, R2_file, chunkSize);

    while (!PEReader->end()) {
        for (auto &PE : *PEReader->next_chunk()) {
            cout << PE.R1_name << endl;
            cout << PE.R1_seq << endl;
            cout << endl;
        }
    }


    delete PEReader;

    return 0;
}