fasta.h File Reference

Header file for the FASTA module. More...

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

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Macros
#define	firstEl(b)   (b & 0x0F)
	Gets the first 4 bits of a byte.
#define	secondEl(b)   (b & 0xF0) >> 4
	Gets the second 4 bits of a byte.
#define	toByte(a, b)   (uint8_t)a | (b << 4)
	Combines two 4 bit numbers into a byte.
#define	PACKING_WIDTH   sizeof(packing_t) * 2
#define	ROUND_NUM   7
#define	PACKING_ROUND(packed_size)   (((packed_size) + ROUND_NUM) & ~ROUND_NUM)
#define	i_Index   0xFF
	Invalid FASTA index.

Typedefs
typedef uint64_t	packing_t

Functions
static void	pack (uint8_t values[PACKING_WIDTH], packing_t *packed)
	Packs an array of 4-bit values into an integer.
bool	is_valid_title (const char *title, size_t len)
	Checks if a FASTA title is valid.
char	getIUPACchar (uint8_t index, bool rna)
	Returns IUPAC FASTA character.
void	initialize_fasta_binary_mapping (uint8_t fasta_binary_mapping[CHAR_MAX+1])
	Initializes the FASTA binary mapping.

Detailed Description

Header file for the FASTA module.

This module provides common functions that we use for handling FASTA data

Macro Definition Documentation

PACKING_ROUND

#define PACKING_ROUND

(

packed_size

)

(((packed_size) + ROUND_NUM) & ~ROUND_NUM)

PACKING_WIDTH

#define PACKING_WIDTH   sizeof(packing_t) * 2

ROUND_NUM

#define ROUND_NUM   7

Typedef Documentation

packing_t

typedef uint64_t packing_t