/****************************************************************************
 * Encoding header file	                                                    *
 ****************************************************************************/

/**
 * @file encode.h
 * @author Celine Mercier
 * @date November 18th 2015
 * @brief Header file for encoding DNA sequences.
 */


#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>
#include <stdbool.h>

#include "obiarray.h"


#define NUC_MASK 0x3   /**< Binary: 11 to use when decoding */


/**
 * @brief enum for the 2-bits codes for each of the 4 nucleotides.
 */
enum
{
    NUC_A = 0x0,   /* binary: 00 */
    NUC_C = 0x1,   /* binary: 01 */
    NUC_G = 0x2,   /* binary: 10 */
    NUC_T = 0x3,   /* binary: 11 */
};


/**
 * @brief Checks if there are only 'atgcATGC' characters in a
 *        character string.
 *
 * @param seq The sequence to check.
 *
 * @returns A boolean value indicating if there are only
 *          'atgcATGC' characters in a character string.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
bool only_ATGC(char* seq);


/**
 * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
 *
 *    A or a : 00
 *    C or c : 01
 *    T or t : 10
 *    G or g : 11
 *
 * @warning The DNA sequence must contain only 'atgcATGC' characters.
 *
 * @param seq The sequence to encode.
 * @param length The length of the sequence to encode.
 *
 * @returns The encoded sequence.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
byte_t* encode_seq_on_2_bits(char* seq, int32_t length);


/**
 * @brief Decodes a DNA sequence that is coded with each nucleotide on 2 bits.
 *
 *    A or a : 00
 *    C or c : 01
 *    T or t : 10
 *    G or g : 11
 *
 * @param seq The sequence to decode.
 * @param length_seq The initial length of the sequence before it was encoded.
 *
 * @returns The decoded sequence ended with '\0'.
 *
 * @since November 2015
 * @author Celine Mercier (celine.mercier@metabarcoding.org)
 */
char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);


////////// FOR DEBUGGING ///////////

// little endian
void print_bits(void* ptr, int32_t length);