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 ()
	Initializes the FASTA binary mapping.

Variables
uint8_t	fasta_binary_mapping [CHAR_MAX+1]
	A lookup table mapping FASTA characters to binary values.

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