Reads a binary file and write a new one with the sequence as a string

bit_dna.c

// Compile: gcc -o bit2dna bit_dna.c
// Libraries
#include <stdio.h>
#include <string.h>

// Declare constants
#define A 0 // 00
#define C 1 // 01
#define G 2 // 10
#define T 3 // 11
#define BYTES_PER_BATCH 1

// Declare headers and structs
char translate(unsigned int base);
struct NucleotidWord {
  unsigned int base0: 2;
  unsigned int base1: 2;
  unsigned int base2: 2;
  unsigned int base3: 2;
};

// Main function
// It receives as argument the path and read the dna sequence
// ./dna_bit path/to/read.dna path/to/write.seq

int main(int argc, char** params) {
  FILE *read_ptr;
  FILE *write_ptr;

  char* pathToReadFile = params[1];
  char* pathToWriteFile = params[2];

  printf("Welcome to Bit2DNA version 0.0.1\n");
  printf("Input path: %s \n", pathToReadFile);

  read_ptr = fopen(pathToReadFile, "rb");
  write_ptr = fopen(pathToWriteFile, "w");

  // Declare buffer variables:
  struct NucleotidWord buffer;
  char writeBuffer;
  unsigned int bytesRead = 0;

  while (fread(&buffer, 1, 1, read_ptr)) {
    writeBuffer = translate(buffer.base3);
    fwrite(&writeBuffer, sizeof(char), 1, write_ptr);

    writeBuffer = translate(buffer.base2);
    fwrite(&writeBuffer, sizeof(char), 1, write_ptr);

    writeBuffer = translate(buffer.base1);
    fwrite(&writeBuffer, sizeof(char), 1, write_ptr);

    writeBuffer = translate(buffer.base0);
    fwrite(&writeBuffer, sizeof(char), 1, write_ptr);

    bytesRead++;
    printf("\n");
  }
  writeBuffer = '\n';
  fwrite(&writeBuffer, sizeof(char), 1, write_ptr);
  // Closes the file and exit successfuly
  fclose(read_ptr);
  fclose(write_ptr);

  // Print statistics
  printf("Total bytes read: %d\n", bytesRead);
  printf("File read from: %s\n", pathToReadFile);
  printf("File written in: %s\n", pathToWriteFile);

  return 0;
}

char translate(unsigned int base) {
  printf("Translating %d\n", (int)base);
  char nucleotid;

  if (base == A) {
    nucleotid = 'A';
  } else if (base == C) {
    nucleotid = 'C';
  } else if (base == G) {
    nucleotid = 'G';
  } else {
    nucleotid = 'T';
  }

  return nucleotid;
}