Primary struct that stores data for a given FASTA file. More...

#include <FastaVector.h>

Data Fields
struct FastaVectorString	sequence
	Storage for sequence data. More...

struct FastaVectorString	header
	Storage for header data. More...

struct FastaVectorMetadataVector	metadata
	Storage for header and sequence metadata. More...

Related Functions
(Note that these are not member functions.)
enum FastaVectorReturnCode	fastaVectorInit (struct FastaVector *fastaVector)
	Initialize an empty `FastaVector` struct. More...

void	fastaVectorDealloc (struct FastaVector *fastaVector)
	Deinitialize `FastaVector` member data. More...

enum FastaVectorReturnCode	fastaVectorReadFasta (const char restrict const fileSrc, struct FastaVector fastaVector)
	Load the given fasta file. More...

enum FastaVectorReturnCode	fastaVectorWriteFasta (const char restrict const filePath, struct FastaVector fastaVector, uint32_t fileLineLength)
	Write a `FastaVector` to a file. More...

enum FastaVectorReturnCode	fastaVectorAddSequenceToList (struct FastaVector fastaVector, char header, size_t headerLength, char *sequence, size_t sequenceLength)
	Add a header and sequence to the given `FastaVector`. More...

void	fastaVectorFastaGetHeader (struct FastaVector fastaVector, size_t headerIndex, char headerPtr, size_t headerLength)
	Gets a header from the given `FastaVector`. More...

void	fastaVectorFastaGetSequence (struct FastaVector fastaVector, size_t sequenceIndex, char sequencePtr, size_t sequenceLength)
	Gets a sequence from the given `FastaVector`. More...

bool	fastaVectorGetLocalSequencePositionFromGlobal (const struct FastaVector const fastaVector, const size_t globalSequencePosition, struct FastaVectorLocalPosition localPosition)
	Gets a local sequence index and position from a `FastaVector`. More...

Detailed Description

Primary struct that stores data for a given FASTA file.

Friends And Related Function Documentation

◆ fastaVectorAddSequenceToList()

enum FastaVectorReturnCode fastaVectorAddSequenceToList	(	struct FastaVector *	fastaVector,
		char *	header,
		size_t	headerLength,
		char *	sequence,
		size_t	sequenceLength
	)

Parameters

fastaVector	the `FastaVector` to modify
header	pointer to the first character in the header
headerLength	length of the header, in bytes
sequence	pointer to the first character in the sequence
sequenceLength	length of the sequence, in bytes

Returns: a status code

The header should not include the leading ">" character, it will be added automatically. The header and sequence will be automatically null-terminated upon insertion into the FastaVector.

The return value is one of:

FASTA_VECTOR_OK
FASTA_VECTOR_ALLOCATION_FAIL

TODO: What if the original FV was not null-terminated?

◆ fastaVectorDealloc()

void fastaVectorDealloc ( struct FastaVector * fastaVector )

Parameters

fastaVector the vector to deinitialize

This function does not deallocate (free) the FastaVector itself, only the member data.

◆ fastaVectorFastaGetHeader()

void fastaVectorFastaGetHeader	(	struct FastaVector *	fastaVector,
		size_t	headerIndex,
		char **	headerPtr,
		size_t *	headerLength
	)

Parameters

fastaVector	the `FastaVector` to read
headerIndex	the index of the header to be retrieved
headerPtr	pointer to store the header
headerLength	pointer to store the header length

If the FastaVector was built with null-terminated headers, the null terminator will be included in the resulting headerPtr and headerLength.

The index is 0-based so, for example, index 4 is the 5th header.

TODO: Should we return a statuc code in case the index was out of bounds?

◆ fastaVectorFastaGetSequence()

void fastaVectorFastaGetSequence	(	struct FastaVector *	fastaVector,
		size_t	sequenceIndex,
		char **	sequencePtr,
		size_t *	sequenceLength
	)

Parameters

fastaVector	the `FastaVector` to read
sequenceIndex	the index of the sequence to be retrieved
sequencePtr	pointer to store the sequence
sequenceLength	pointer to store the sequence length

If the FastaVector was built with null-terminated sequences, the null terminator will be included in the resulting sequencePtr and sequenceLength.

The index is 0-based so, for example, index 4 is the 5th sequence.

◆ fastaVectorGetLocalSequencePositionFromGlobal()

bool fastaVectorGetLocalSequencePositionFromGlobal	(	const struct FastaVector *const	fastaVector,
		const size_t	globalSequencePosition,
		struct FastaVectorLocalPosition *	localPosition
	)

Parameters

fastaVector	the `FastaVector` to inspect
globalSequencePosition	position across the entire sequence collection
localPosition	a pointer to the struct to load the local position data into

Returns: true on success, false on failure

The return value will be false if the given globalSequencePosition is outside the range of positions in the vector of sequences. In other words, if globalSequencePosition is greater than the sum of the lengths of all the sequences in the FastaVector, minus 1.

◆ fastaVectorInit()

enum FastaVectorReturnCode fastaVectorInit ( struct FastaVector * fastaVector )

Parameters

fastaVector the vector to initialize

Returns: a status code

The struct itself must have been allocated before this function is called.

◆ fastaVectorReadFasta()

enum FastaVectorReturnCode fastaVectorReadFasta	(	const char *restrict const	fileSrc,
		struct FastaVector *	fastaVector
	)

Parameters

fileSrc	the path of the FASTA file to load
fastaVector	the vector to load the fasta into
nullTerminateHeaders	whether null characters should be added to headers
nullTerminateSequences	whether null characters should be added to sequences

Returns: a status code

Loads its full contents into the initialized fasta vector. This function takes any properly formed fasta file, and loads all headers and sequences.

If nullTerminateHeaders is set to true, then null characters ('\0') are added after each header to easily denote the end of the header (useful for printing). If nullTerminateSequences is set to true, null characters ('\0') are added after each sequence to easily separate them (useful for printing or separating the sequences in an index).

◆ fastaVectorWriteFasta()

enum FastaVectorReturnCode fastaVectorWriteFasta	(	const char *restrict const	filePath,
		struct FastaVector *	fastaVector,
		uint32_t	fileLineLength
	)

Parameters

filePath	path of the file to be written
fastaVector	the FASTA data to be written
fileLineLength	maximum number of characters per line of sequence

Returns: a status code

This function will overwrite the file at the given path.

Field Documentation

◆ header

struct FastaVectorString FastaVector::header

Storage for header data.

◆ metadata

struct FastaVectorMetadataVector FastaVector::metadata

Storage for header and sequence metadata.

◆ sequence

struct FastaVectorString FastaVector::sequence

Storage for sequence data.

The documentation for this struct was generated from the following file:

src/FastaVector.h

Data Fields

Related Functions

Detailed Description

Friends And Related Function Documentation

◆ fastaVectorAddSequenceToList()

◆ fastaVectorDealloc()

◆ fastaVectorFastaGetHeader()

◆ fastaVectorFastaGetSequence()

◆ fastaVectorGetLocalSequencePositionFromGlobal()

◆ fastaVectorInit()

◆ fastaVectorReadFasta()

◆ fastaVectorWriteFasta()

Field Documentation

◆ header

◆ metadata

◆ sequence