Public Member Functions
	gkArrays (char *tags_file, uint threshold, bool use_bitvector=false, uint tag_length=0, bool stranded=false, uint nb_threads=1)
	gkArrays (char tags_file1, char tags_file2, uint threshold, bool use_bitvector=false, uint tag_length=0, bool stranded=false, uint nb_threads=1)
uintSA	convertPposToQpos (uintSA i)
uintSA	getEndPosOfTagNum (uint tag_num)
uintSA	getGkCFA (uintSA i)
uintSA	getGkCFALength ()
uintSA	getGkISA (uintSA i)
uintSA	getGkSA (uintSA i)
uintSA	getGkSALength ()
uintSA	getNbPposition (uintSA nb_reads)
uint	getNbTags ()
uint	getNbTagsWithFactor (uint tag_num, uint pos_factor, bool multiplicity=0)
uint	getNbThreads ()
uint	getPair (uint i)
uintSA	getPosInCommon (uint tag_num, uint pos_factor)
readsReader *	getReads ()
uintSA	getStartPosOfTagNum (uint tag_num)
uintSA	getStartQPosOfTagNum (uint tag_num)
uint *	getSupport (uint i)
uint	getSupportLength (uint i=0)
char *	getTag (uint i)
uint	getTagLength (uint i=0)
char *	getTagFactor (uint i, uint p, uint l)
uint	getTagNum (uintSA pos)
std::pair< uint, uint >	getTagNumAndPosFromAbsolutePos (uintSA pos)
uint *	getTagNumWithFactor (uint tag_num, uint pos_factor)
std::pair< uint, uint > *	getTagsWithFactor (uint tag_num, uint pos_factor)
std::pair< uint, uint > *	getTagsWithFactor (char *factor, uint factor_length, uint &nb_fact)
char *	getTextFactor (uintSA pos, uint length)
uint	getThreshold ()
array_type	getType ()
bool	isLarge ()
bool	isPposition (uintSA pos)
bool	isStranded ()
bool	isTheFirstMemberOfPair (uint i)
Static Public Member Functions
static bool	isDiscarded (uint actual_length, uint theoretical_length=0, uint k=0)

Constructor & Destructor Documentation

gkarrays::gkArrays::gkArrays	(	char *	tags_file,
		uint	threshold,
		bool	use_bitvector = `false`,
		uint	tag_length = `0`,
		bool	stranded = `false`,
		uint	nb_threads = `1`
	)

Construct the read index

Parameters:

tags_file	Name of the file containg the reads
threshold	length of k-mers we have to use
use_bitvector,:	true iff we must store the array using a bit vector (slower but more space efficient)
tag_length	length of the reads. If a shorter read is found, it raises an error. If a longer read is found, only the prefix of tag_length characters is kept. If tag_length == 0 (default), just gess what the read length is.
stranded,:	true iff we know which strand has been sequenced and, therefore, (for instance) AACG must not be considered as equal to its revcomp (CGTT).
nb_threads	allows to build GkSA on a multi-thread architecture

gkarrays::gkArrays::gkArrays	(	char *	tags_file1,
		char *	tags_file2,
		uint	threshold,
		bool	use_bitvector = `false`,
		uint	tag_length = `0`,
		bool	stranded = `false`,
		uint	nb_threads = `1`
	)

Alternative to construct the read index with paired-end reads

Parameters:

tags_file1	Name of the file containing the reads of the first pair
tags_file2	Name of the file containing the reads of the second pair
threshold	length of k-mers we have to use
use_bitvector,:	true iff we must store the array using a bit vector (slower but more space efficient)
tag_length	length of the reads. If a shorter read is found, it raises an error. If a longer read is found, only the prefix of tag_length characters is kept. If tag_length == 0 (default), just gess what the read length is.
stranded,:	true iff we know which strand has been sequenced and, therefore, (for instance) AACG must not be considered as equal to its revcomp (CGTT).
nb_threads	allows to build GkSA on a multi-thread architecture

Member Function Documentation

uintSA gkarrays::gkArrays::convertPposToQpos ( uintSA i )

Convert a position from P-position to Q-position (if you do not understand this, please read our article!). That converts a position as in the concatenation of reads to the position in GkIFA (for example). In the article, values of GkSA are also renumbered to Q-position but we do not renumber them in practice (it is quite useless).

Parameters:

i,:	a P-position

Returns:: a Q-position

uintSA gkarrays::gkArrays::getEndPosOfTagNum ( uint tag_num )

Gives the end position of a given read in the concatenation of reads.

Parameters:

tag_num,: tag number

Returns:: the end position of the read #tag_num in C_R (the concatenation of reads)

uintSA gkarrays::gkArrays::getGkCFA ( uintSA i )

Parameters:

i	the index position in the array (starting at 0).

Returns:: the value of GkCFA at the given index ie. the number of k-factors of rank i, where i is the requested index.

uintSA gkarrays::gkArrays::getGkCFALength ( )

Returns:: the number of elements in the GkCFA array. In other terms it corresponds to the number of distinct k-mers in the input.

uintSA gkarrays::gkArrays::getGkISA ( uintSA i )

Parameters:

i	the index position in the array (starting at 0).

Returns:: the value of GkISA at the given index ie. the rank of the k-factor at position P-position i.

uintSA gkarrays::gkArrays::getGkSA ( uintSA i )

Parameters:

i	the index position in the array (starting at 0).

Returns:: the value of GkSA at the given index ie. the P-position of the k-factor whose rank is i

uintSA gkarrays::gkArrays::getGkSALength ( )

Returns:: the number of entries in gkSA (ie. the number of P-positions)

uintSA gkarrays::gkArrays::getNbPposition ( uintSA nb_reads )

Returns:: the number of P-positions in Cr from a number of reads (fixed length or not) This function is available before the construction of gkSA.

uint gkarrays::gkArrays::getNbTags ( )

Returns:: the number of tags (or reads) indexed in the Gk Arrays

uint gkarrays::gkArrays::getNbTagsWithFactor	(	uint	tag_num,
		uint	pos_factor,
		bool	multiplicity = `0`
	)

Parameters:

tag_num	The number of the tag in the index
pos_factor	Position of the factor in the tag
multiplicity	Counts (if false) only once a tag that contains the factor many times

Returns:: Return the number of tags sharing the factor starting at position pos_factor in the tag tag_num. This is the number of elements returned by the function getTagsWithFactor(.)

uint gkarrays::gkArrays::getNbThreads ( )

Returns:: the number of threads the GkArrays have been told to use. The threads can be used for the construction.

uint gkarrays::gkArrays::getPair ( uint i )

Parameters:

i	The number of the tag in the index

Returns:: the tag number of the paired-end read associated with i or -1 if reads are not paired-end.

uintSA gkarrays::gkArrays::getPosInCommon	(	uint	tag_num,
		uint	pos_factor
	)

Returns:: the rank of the P-k factor starting at position pos_factor in the read number tag_num.

readsReader * gkarrays::gkArrays::getReads ( )

Returns:: the object that allows to get a readIterator

uintSA gkarrays::gkArrays::getStartPosOfTagNum ( uint tag_num )

Gives the start position of a given read in the concatenation of reads.

Parameters:

tag_num,: tag number

Returns:: the start position of the read #tag_num in C_R (the concatenation of reads)

uintSA gkarrays::gkArrays::getStartQPosOfTagNum ( uint tag_num )

Gives the start Q-position of a given read in the ISA array

Parameters:

tag_num,: tag number

Returns:: the start Q-position of the read #tag_num in GkISA.

uint * gkarrays::gkArrays::getSupport ( uint i )

Parameters:

i	Tag number

Returns:: an array whose length is getSupportLength(i) and where the value at position k is the number of occurrences of the k-factor starting at position k in the reads among all the Pk-factors.

uint gkarrays::gkArrays::getSupportLength ( uint i = 0 )

Return the length of the support.

Returns:: getTagLength(i) - getThreshold()+1

char * gkarrays::gkArrays::getTag ( uint i )

Parameters:

i	the read number to be retrieved

Returns:: the read number i.

char * gkarrays::gkArrays::getTagFactor	(	uint	i,
		uint	p,
		uint	l
	)

Parameters:

i	The number of the tag in the index
p	Position of the factor in the tag
l	The length of the factor

Returns:: the factor at the position p in the tag number i

uint gkarrays::gkArrays::getTagLength ( uint i = 0 )

Parameters:

i	Tag number (if the length is not constant)

Returns:: the length of the read.

uint gkarrays::gkArrays::getTagNum ( uintSA pos )

Gives the number of a read

Parameters:

pos	a position in SA or in the concatenated sequence of reads

Returns:: the read number where this position lies

std::pair< uint, uint > gkarrays::gkArrays::getTagNumAndPosFromAbsolutePos ( uintSA pos )

Return the number of tag and the relative position in that tag corresponding to a given position in the concatenation of reads

Parameters:

pos	position in the concatenation of reads

Returns:: a pair whose fist element is the tag number and the second element is the position in the tag.

uint * gkarrays::gkArrays::getTagNumWithFactor	(	uint	tag_num,
		uint	pos_factor
	)

Parameters:

tag_num	The number of the tag in the index
pos_factor	Position of the factor in the tag

Returns:: Return an array that contains each tag number where the factors matches.

Postcondition:: The array is sorted

pair< uint, uint > * gkarrays::gkArrays::getTagsWithFactor	(	uint	tag_num,
		uint	pos_factor
	)

Parameters:

tag_num	The number of the tag in the index
pos_factor	Position of the factor in the tag

Returns:: Return an array composed of pairs (tag, pos) corresponding to all the Pk-factors equal to the Pk-factor starting at position pos_factor in the tag tag_num.

Postcondition:: The array is sorted according to read number and read position

pair< uint, uint > * gkarrays::gkArrays::getTagsWithFactor	(	char *	factor,
		uint	factor_length,
		uint &	nb_fact
	)

Parameters:

factor	the pattern to be searched.
factor_length	the length of the factor, should be <= getThreshold()
nb_fact	nb_fact is used to give the number of occurrences in the array.

Returns:: Return an array composed of pairs (tag, pos) corresponding to all the Pk-factors equal to the k-factor factor

char * gkarrays::gkArrays::getTextFactor	(	uintSA	pos,
		uint	length
	)

Parameters:

pos	The position from where we want to retrieve a text subtring. The position must be given in the original text (not the filtered one).
length	the length of the substring to be retrieved.

Returns:: text factor at position pos of length length. The returned string is NULL-terminated.

uint gkarrays::gkArrays::getThreshold ( )

Returns:: return the length of the k-factors (ie. return k).

array_type gkarrays::gkArrays::getType ( )

Returns:: the array type used for building GkSA and GkISA (either SMALL_ARRAY, LARGE_ARRAY or OPTIMAL_ARRAY).

bool gkarrays::gkArrays::isDiscarded	(	uint	actual_length,
		uint	theoretical_length = `0`,
		uint	k = `0`
	)		`[static]`

Returns:: true iff the read is not suitable ie. if it is shorter than the specified length (if any) or shorter than the specified k-mer length.

bool gkarrays::gkArrays::isLarge ( )

Returns:: true if the nbPposition > 2^32

bool gkarrays::gkArrays::isPposition ( uintSA pos )

Returns:: true iff the position does not lie in the threshold - 1 last characters of a read, ie. if it is a P-position.

bool gkarrays::gkArrays::isStranded ( )

Returns:: true iff the GkArrays have been built as a strand-dependant index. Therefore a k-mer and its revcomp won't be considered as equal.

bool gkarrays::gkArrays::isTheFirstMemberOfPair ( uint i )

Parameters:

i	the number of the tag in the index

Returns:: true if the tag is the first member of is pair in case of paired-end files. False either

The documentation for this class was generated from the following files:

gkArrays.h
gkArrays.cpp

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation