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DNA sequences are now encoded on 4 bits when they are in IUPAC

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This commit is contained in:
Celine Mercier
2015-11-20 15:32:09 +01:00
parent 87044b41d8
commit 6aa2f92930
5 changed files with 318 additions and 54 deletions
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104
src/encode.h
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@ -18,7 +18,8 @@
#include "obiarray.h"
#define NUC_MASK 0x3 /**< Binary: 11 to use when decoding */
#define NUC_MASK_2B 0x3 /**< Binary: 11 to use when decoding 2 bits sequences */
#define NUC_MASK_4B 0xF /**< Binary: 1111 to use when decoding 4 bits sequences */
/**
@ -26,10 +27,33 @@
*/
enum
{
NUC_A = 0x0, /* binary: 00 */
NUC_C = 0x1, /* binary: 01 */
NUC_G = 0x2, /* binary: 10 */
NUC_T = 0x3, /* binary: 11 */
NUC_A_2b = 0x0, /* binary: 00 */
NUC_C_2b = 0x1, /* binary: 01 */
NUC_G_2b = 0x2, /* binary: 10 */
NUC_T_2b = 0x3, /* binary: 11 */
};
/**
* @brief enum for the 4-bits codes for each of the 15 IUPAC nucleotides.
*/
enum
{
NUC_A_4b = 0x1, /* binary: 0001 */
NUC_C_4b = 0x2, /* binary: 0010 */
NUC_G_4b = 0x3, /* binary: 0011 */
NUC_T_4b = 0x4, /* binary: 0100 */
NUC_R_4b = 0x5, /* binary: 0101 */
NUC_Y_4b = 0x6, /* binary: 0110 */
NUC_S_4b = 0x7, /* binary: 0111 */
NUC_W_4b = 0x8, /* binary: 1000 */
NUC_K_4b = 0x9, /* binary: 1001 */
NUC_M_4b = 0xA, /* binary: 1010 */
NUC_B_4b = 0xB, /* binary: 1011 */
NUC_D_4b = 0xC, /* binary: 1100 */
NUC_H_4b = 0xD, /* binary: 1101 */
NUC_V_4b = 0xE, /* binary: 1110 */
NUC_N_4b = 0xF, /* binary: 1111 */
};
@ -72,10 +96,10 @@ 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
* 00 -> a
* 01 -> c
* 10 -> t
* 11 -> g
*
* @param seq The sequence to decode.
* @param length_seq The initial length of the sequence before it was encoded.
@ -88,6 +112,68 @@ byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
/**
* @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
*
* A or a : 0001
* C or c : 0010
* G or g : 0011
* T or t : 0100
* R or r : 0101
* Y or y : 0110
* S or s : 0111
* W or w : 1000
* K or k : 1001
* M or m : 1010
* B or b : 1011
* D or d : 1100
* H or h : 1101
* V or v : 1110
* N or n : 1111
*
* @warning The DNA sequence must contain only IUPAC 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_4_bits(char* seq, int32_t length);
/**
* @brief Decodes a DNA sequence that is coded with each nucleotide on 4 bits.
*
* A or a : 0001
* C or c : 0010
* G or g : 0011
* T or t : 0100
* R or r : 0101
* Y or y : 0110
* S or s : 0111
* W or w : 1000
* K or k : 1001
* M or m : 1010
* B or b : 1011
* D or d : 1100
* H or h : 1101
* V or v : 1110
* N or n : 1111
*
* @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_4_bits(byte_t* seq_b, int32_t length_seq);
////////// FOR DEBUGGING ///////////
// little endian