Fasta

Module providing functions for handling FASTA data. More...

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	i_Index   0xFF
	Invalid FASTA index.

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

Module providing functions for handling FASTA data.

Macro Definition Documentation

firstEl

#define firstEl

(

b

)

(b & 0x0F)

Gets the first 4 bits of a byte.

Parameters

b	the byte to get the first 4 bits from

i_Index

#define i_Index   0xFF

Invalid FASTA index.

secondEl

#define secondEl

(

b

)

(b & 0xF0) >> 4

Gets the second 4 bits of a byte.

Parameters

b	the byte to get the second 4 bits from

toByte

#define toByte	(		a,
			b
	)		(uint8_t)a | (b << 4)

Combines two 4 bit numbers into a byte.

Parameters

a	the first 4 bit number
b	the second 4 bit number

Function Documentation

getIUPACchar()

char getIUPACchar	(	uint8_t	index,
		bool	rna
	)

Returns IUPAC FASTA character.

Parameters

index	the code to convert to a character
rna	if true, T will be converted to U

Returns

the IUPAC character

Warning

index must be less than 16, else the function will go out of bounds

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initialize_fasta_binary_mapping()

void initialize_fasta_binary_mapping

(

)

Initializes the FASTA binary mapping.

is_valid_title()

bool is_valid_title	(	const char *	title,
		size_t	len
	)

Checks if a FASTA title is valid.

Parameters

title	the title to check
len	the length of the title

Returns

true if the title is valid, false otherwise

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pack()

static void pack ( uint8_t  values[PACKING_WIDTH], packing_t *  packed  )

inlinestatic

Packs an array of 4-bit values into an integer.

Parameters

values	the array of 4-bit values to pack
packed	the packed value

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Variable Documentation

fasta_binary_mapping

uint8_t fasta_binary_mapping[CHAR_MAX+1]

extern

A lookup table mapping FASTA characters to binary values.

Warning

This table is initialized in the initialize_fasta_binary_mapping