241 lines
6.3 KiB
C
Executable File
241 lines
6.3 KiB
C
Executable File
/****************************************************************************
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* Encoding header file *
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****************************************************************************/
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/**
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* @file encode.h
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* @author Celine Mercier
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* @date November 18th 2015
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* @brief Header file for encoding DNA sequences.
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*/
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#ifndef ENCODE_H_
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#define ENCODE_H_
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#include <stdlib.h>
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#include <stdio.h>
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#include <stdint.h>
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#include <stdbool.h>
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#include "obitypes.h"
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#define NUC_MASK_2B 0x3 /**< Binary: 11 to use when decoding 2 bits sequences
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*/
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#define NUC_MASK_4B 0xF /**< Binary: 1111 to use when decoding 4 bits sequences
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*/
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/**
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* @brief enum for the 2-bits codes for each of the 4 nucleotides.
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*/
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enum
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{
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NUC_A_2b = 0x0, /* binary: 00 */
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NUC_C_2b = 0x1, /* binary: 01 */
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NUC_G_2b = 0x2, /* binary: 10 */
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NUC_T_2b = 0x3, /* binary: 11 */
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};
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/**
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* @brief enum for the 4-bits codes for each of the 15 IUPAC nucleotides.
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*/
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enum
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{
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NUC_A_4b = 0x1, /* binary: 0001 */
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NUC_C_4b = 0x2, /* binary: 0010 */
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NUC_G_4b = 0x3, /* binary: 0011 */
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NUC_T_4b = 0x4, /* binary: 0100 */
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NUC_R_4b = 0x5, /* binary: 0101 */
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NUC_Y_4b = 0x6, /* binary: 0110 */
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NUC_S_4b = 0x7, /* binary: 0111 */
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NUC_W_4b = 0x8, /* binary: 1000 */
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NUC_K_4b = 0x9, /* binary: 1001 */
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NUC_M_4b = 0xA, /* binary: 1010 */
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NUC_B_4b = 0xB, /* binary: 1011 */
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NUC_D_4b = 0xC, /* binary: 1100 */
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NUC_H_4b = 0xD, /* binary: 1101 */
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NUC_V_4b = 0xE, /* binary: 1110 */
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NUC_N_4b = 0xF, /* binary: 1111 */
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};
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/**
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* @brief Checks if there are only 'atgcuATGCU' characters in a
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* character string.
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*
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* @param seq The sequence to check.
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*
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* @returns A boolean value indicating if there are only
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* 'atgcATGC' characters in a character string.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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bool only_ATGC(const char* seq);
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/**
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* @brief Checks if there are only IUPAC DNA characters in a
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* character string.
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*
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* @param seq The sequence to check.
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*
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* @returns A boolean value indicating if there are only
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* IUPAC DNA characters in a character string.
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*
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* @since May 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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bool only_IUPAC_DNA(const char* seq);
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/**
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* @brief Checks if a character string can be read as a DNA sequence encoded
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* with ACGT or IUPAC characters (in capital letters or not).
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*
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* @param seq The sequence to check.
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*
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* @returns A boolean value indicating if the character string
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* can be read as a DNA sequence.
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*
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* @since May 2017
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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bool is_a_DNA_seq(const char* seq);
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/**
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* @brief Returns a nucleotide from a DNA sequence encoded
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* with each nucleotide on 2 or 4 bits.
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*
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* @param seq The encoded sequence.
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* @param idx The index (in the decoded sequence) of the nucleotide to get.
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* @param encoding An integer indicating whether the sequence is encoded with each nucleotide on 2 or 4 bits.
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*
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* @returns The (still encoded) nucleotide at the given index.
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* @retval 255 if an error occurred.
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*
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* @see decode_seq_on_2_bits() and decode_seq_on_4_bits()
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* @since January 2019
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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byte_t get_nucleotide_from_encoded_seq(byte_t* seq, int32_t idx, uint8_t encoding);
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/**
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* @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
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*
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* A or a : 00
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* C or c : 01
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* T or t or U or u : 10
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* G or g : 11
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*
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* @warning The DNA sequence must contain only 'atgcuATGCU' characters.
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* @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
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*
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* @param seq The sequence to encode.
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* @param length The length of the sequence to encode.
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*
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* @returns The encoded sequence.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
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/**
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* @brief Decodes a DNA sequence that is coded with each nucleotide on 2 bits.
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*
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* 00 -> a
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* 01 -> c
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* 10 -> t
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* 11 -> g
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*
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* @param seq_b The sequence to decode.
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* @param length_seq The initial length of the sequence before it was encoded.
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*
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* @returns The decoded sequence ended with '\0'.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
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/**
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* @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
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*
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* A or a : 0001
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* C or c : 0010
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* G or g : 0011
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* T or t or U or u : 0100
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* R or r : 0101
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* Y or y : 0110
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* S or s : 0111
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* W or w : 1000
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* K or k : 1001
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* M or m : 1010
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* B or b : 1011
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* D or d : 1100
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* H or h : 1101
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* V or v : 1110
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* N or n : 1111
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*
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* @warning The DNA sequence must contain only IUPAC characters.
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* @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
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*
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* @param seq The sequence to encode.
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* @param length The length of the sequence to encode.
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*
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* @returns The encoded sequence.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
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/**
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* @brief Decodes a DNA sequence that is coded with each nucleotide on 4 bits.
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*
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* A or a : 0001
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* C or c : 0010
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* G or g : 0011
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* T or t : 0100
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* R or r : 0101
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* Y or y : 0110
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* S or s : 0111
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* W or w : 1000
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* K or k : 1001
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* M or m : 1010
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* B or b : 1011
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* D or d : 1100
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* H or h : 1101
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* V or v : 1110
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* N or n : 1111
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*
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* @param seq_b The sequence to decode.
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* @param length_seq The initial length of the sequence before it was encoded.
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*
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* @returns The decoded sequence ended with '\0'.
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*
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* @since November 2015
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
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////////// FOR DEBUGGING ///////////
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// little endian
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void print_bits(void* ptr, int32_t length);
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#endif /* ENCODE_H_ */
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