Main header file, containing all public functions and structures. More...

Classes
struct	EdlibAlignConfig
	Configuration object for edlibAlign() function. More...

struct	EdlibAlignResult

Macros
#define	EDLIB_STATUS_OK 0

#define	EDLIB_STATUS_ERROR 1

#define	EDLIB_EDOP_MATCH 0
	Match.

#define	EDLIB_EDOP_INSERT 1
	Insertion to target = deletion from query.

#define	EDLIB_EDOP_DELETE 2
	Deletion from target = insertion to query.

#define	EDLIB_EDOP_MISMATCH 3
	Mismatch.

Enumerations
enum	EdlibAlignMode { EDLIB_MODE_NW, EDLIB_MODE_SHW, EDLIB_MODE_HW }

enum	EdlibAlignTask { EDLIB_TASK_DISTANCE, EDLIB_TASK_LOC, EDLIB_TASK_PATH }

enum	EdlibCigarFormat { EDLIB_CIGAR_STANDARD, EDLIB_CIGAR_EXTENDED }

Functions
EdlibAlignConfig	edlibNewAlignConfig (int k, EdlibAlignMode mode, EdlibAlignTask task)

EdlibAlignConfig	edlibDefaultAlignConfig (void)

void	edlibFreeAlignResult (EdlibAlignResult result)

EdlibAlignResult	edlibAlign (const char query, int queryLength, const char target, int targetLength, const EdlibAlignConfig config)

char *	edlibAlignmentToCigar (const unsigned char *alignment, int alignmentLength, EdlibCigarFormat cigarFormat)

Detailed Description

Main header file, containing all public functions and structures.

Author: Martin Sosic

Enumeration Type Documentation

§ EdlibAlignMode

enum EdlibAlignMode

Alignment methods - how should Edlib treat gaps before and after query?

Enumerator
EDLIB_MODE_NW	Global method. This is the standard method. Useful when you want to find out how similar is first sequence to second sequence.
EDLIB_MODE_SHW	Prefix method. Similar to global method, but with a small twist - gap at query end is not penalized. What that means is that deleting elements from the end of second sequence is "free"! For example, if we had "AACT" and "AACTGGC", edit distance would be 0, because removing "GGC" from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at the beginning of second sequence.
EDLIB_MODE_HW	Infix method. Similar as prefix method, but with one more twist - gaps at query end and start are not penalized. What that means is that deleting elements from the start and end of second sequence is "free"! For example, if we had ACT and CGACTGAC, edit distance would be 0, because removing CG from the start and GAC from the end of second sequence is "free" and does not count into total edit distance. This method is appropriate when you want to find out how well first sequence fits at any part of second sequence. For example, if your second sequence was a long text and your first sequence was a sentence from that text, but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in that text. In bioinformatics, this method is appropriate for aligning read to a sequence.

§ EdlibAlignTask

enum EdlibAlignTask

Alignment tasks - what do you want Edlib to do?

Enumerator
EDLIB_TASK_DISTANCE	Find edit distance and end locations.
EDLIB_TASK_LOC	Find edit distance, end locations and start locations.
EDLIB_TASK_PATH	Find edit distance, end locations and start locations and alignment path.

§ EdlibCigarFormat

enum EdlibCigarFormat

Describes cigar format.

See also: http://samtools.github.io/hts-specs/SAMv1.pdf; http://drive5.com/usearch/manual/cigar.html

Enumerator
EDLIB_CIGAR_STANDARD	Match: 'M', Insertion: 'I', Deletion: 'D', Mismatch: 'M'.
EDLIB_CIGAR_EXTENDED	Match: '=', Insertion: 'I', Deletion: 'D', Mismatch: 'X'.

Function Documentation

§ edlibAlign()

EdlibAlignResult edlibAlign	(	const char *	query,
		int	queryLength,
		const char *	target,
		int	targetLength,
		const EdlibAlignConfig	config
	)

Aligns two sequences (query and target) using edit distance (levenshtein distance). Through config parameter, this function supports different alignment methods (global, prefix, infix), as well as different modes of search (tasks). It always returns edit distance and end locations of optimal alignment in target. It optionally returns start locations of optimal alignment in target and alignment path, if you choose appropriate tasks.

Parameters

[in]	query	First sequence. Character codes should be in range [0, 127].
[in]	queryLength	Number of characters in first sequence.
[in]	target	Second sequence. Character codes should be in range [0, 127].
[in]	targetLength	Number of characters in second sequence.
[in]	config	Additional alignment parameters, like alignment method and wanted results.

Returns: Result of alignment, which can contain edit distance, start and end locations and alignment path. Make sure to clean up the object using edlibFreeAlignResult() or by manually freeing needed members.

§ edlibAlignmentToCigar()

char* edlibAlignmentToCigar	(	const unsigned char *	alignment,
		int	alignmentLength,
		EdlibCigarFormat	cigarFormat
	)

Builds cigar string from given alignment sequence.

Parameters

[in]	alignment	Alignment sequence. 0 stands for match. 1 stands for insertion to target. 2 stands for insertion to query. 3 stands for mismatch.
[in]	alignmentLength
[in]	cigarFormat	Cigar will be returned in specified format.

Returns: Cigar string. I stands for insertion. D stands for deletion. X stands for mismatch. (used only in extended format) = stands for match. (used only in extended format) M stands for (mis)match. (used only in standard format) String is null terminated. Needed memory is allocated and given pointer is set to it. Do not forget to free it later using free()!

§ edlibDefaultAlignConfig()

EdlibAlignConfig edlibDefaultAlignConfig ( void )

Returns: Default configuration object, with following defaults: k = -1, mode = EDLIB_MODE_NW, task = EDLIB_TASK_DISTANCE.

§ edlibFreeAlignResult()

void edlibFreeAlignResult ( EdlibAlignResult result )

Frees memory in EdlibAlignResult that was allocated by edlib. If you do not use it, make sure to free needed members manually using free().

§ edlibNewAlignConfig()

EdlibAlignConfig edlibNewAlignConfig	(	int	k,
		EdlibAlignMode	mode,
		EdlibAlignTask	task
	)

Helper method for easy construction of configuration object.

Returns: Configuration object filled with given parameters.

Classes

Macros

Enumerations

Functions