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yangao07yangao07
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add edlib
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‎.gitmodules‎

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[submodule "WFA2-lib"]
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path = WFA2-lib
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url = https://github.com/smarco/WFA2-lib.git
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ignore = dirty
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[submodule "edlib"]
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path = edlib
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url = https://github.com/Martinsos/edlib.git
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ignore = dirty

‎edlib‎

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‎edlib/include/edlib.h‎

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#ifndef EDLIB_H
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#define EDLIB_H
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/**
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* @file
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* @author Martin Sosic
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* @brief Main header file, containing all public functions and structures.
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*/
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// Define EDLIB_API macro to properly export symbols
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#ifdef EDLIB_SHARED
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# ifdef _WIN32
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# ifdef EDLIB_BUILD
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# define EDLIB_API __declspec(dllexport)
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# else
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# define EDLIB_API __declspec(dllimport)
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# endif
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# else
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# define EDLIB_API __attribute__ ((visibility ("default")))
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# endif
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#else
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# define EDLIB_API
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#endif
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#ifdef __cplusplus
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extern "C" {
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#endif
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// Status codes
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#define EDLIB_STATUS_OK 0
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#define EDLIB_STATUS_ERROR 1
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/**
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* Alignment methods - how should Edlib treat gaps before and after query?
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*/
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typedef enum {
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/**
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* Global method. This is the standard method.
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* Useful when you want to find out how similar is first sequence to second sequence.
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*/
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EDLIB_MODE_NW,
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/**
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* Prefix method. Similar to global method, but with a small twist - gap at query end is not penalized.
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* What that means is that deleting elements from the end of second sequence is "free"!
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* For example, if we had "AACT" and "AACTGGC", edit distance would be 0, because removing "GGC" from the end
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* of second sequence is "free" and does not count into total edit distance. This method is appropriate
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* when you want to find out how well first sequence fits at the beginning of second sequence.
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*/
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EDLIB_MODE_SHW,
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/**
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* Infix method. Similar as prefix method, but with one more twist - gaps at query end and start are
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* not penalized. What that means is that deleting elements from the start and end of second sequence is "free"!
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* For example, if we had ACT and CGACTGAC, edit distance would be 0, because removing CG from the start
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* and GAC from the end of second sequence is "free" and does not count into total edit distance.
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* This method is appropriate when you want to find out how well first sequence fits at any part of
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* second sequence.
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* For example, if your second sequence was a long text and your first sequence was a sentence from that text,
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* but slightly scrambled, you could use this method to discover how scrambled it is and where it fits in
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* that text. In bioinformatics, this method is appropriate for aligning read to a sequence.
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*/
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EDLIB_MODE_HW
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} EdlibAlignMode;
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/**
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* Alignment tasks - what do you want Edlib to do?
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*/
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typedef enum {
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EDLIB_TASK_DISTANCE, //!< Find edit distance and end locations.
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EDLIB_TASK_LOC, //!< Find edit distance, end locations and start locations.
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EDLIB_TASK_PATH //!< Find edit distance, end locations and start locations and alignment path.
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} EdlibAlignTask;
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/**
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* Describes cigar format.
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* @see http://samtools.github.io/hts-specs/SAMv1.pdf
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* @see http://drive5.com/usearch/manual/cigar.html
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*/
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typedef enum {
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EDLIB_CIGAR_STANDARD, //!< Match: 'M', Insertion: 'I', Deletion: 'D', Mismatch: 'M'.
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EDLIB_CIGAR_EXTENDED //!< Match: '=', Insertion: 'I', Deletion: 'D', Mismatch: 'X'.
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} EdlibCigarFormat;
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// Edit operations.
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#define EDLIB_EDOP_MATCH 0 //!< Match.
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#define EDLIB_EDOP_INSERT 1 //!< Insertion to target = deletion from query.
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#define EDLIB_EDOP_DELETE 2 //!< Deletion from target = insertion to query.
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#define EDLIB_EDOP_MISMATCH 3 //!< Mismatch.
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/**
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* @brief Defines two given characters as equal.
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*/
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typedef struct {
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char first;
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char second;
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} EdlibEqualityPair;
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/**
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* @brief Configuration object for edlibAlign() function.
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*/
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typedef struct {
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/**
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* Set k to non-negative value to tell edlib that edit distance is not larger than k.
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* Smaller k can significantly improve speed of computation.
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* If edit distance is larger than k, edlib will set edit distance to -1.
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* Set k to negative value and edlib will internally auto-adjust k until score is found.
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*/
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int k;
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/**
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* Alignment method.
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* EDLIB_MODE_NW: global (Needleman-Wunsch)
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* EDLIB_MODE_SHW: prefix. Gap after query is not penalized.
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* EDLIB_MODE_HW: infix. Gaps before and after query are not penalized.
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*/
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EdlibAlignMode mode;
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/**
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* Alignment task - tells Edlib what to calculate. Less to calculate, faster it is.
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* EDLIB_TASK_DISTANCE - find edit distance and end locations of optimal alignment paths in target.
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* EDLIB_TASK_LOC - find edit distance and start and end locations of optimal alignment paths in target.
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* EDLIB_TASK_PATH - find edit distance, alignment path (and start and end locations of it in target).
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*/
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EdlibAlignTask task;
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/**
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* List of pairs of characters, where each pair defines two characters as equal.
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* This way you can extend edlib's definition of equality (which is that each character is equal only
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* to itself).
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* This can be useful if you have some wildcard characters that should match multiple other characters,
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* or e.g. if you want edlib to be case insensitive.
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* Can be set to NULL if there are none.
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*/
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const EdlibEqualityPair* additionalEqualities;
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/**
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* Number of additional equalities, which is non-negative number.
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* 0 if there are none.
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*/
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int additionalEqualitiesLength;
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} EdlibAlignConfig;
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/**
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* Helper method for easy construction of configuration object.
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* @return Configuration object filled with given parameters.
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*/
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EDLIB_API EdlibAlignConfig edlibNewAlignConfig(
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int k, EdlibAlignMode mode, EdlibAlignTask task,
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const EdlibEqualityPair* additionalEqualities,
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int additionalEqualitiesLength
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);
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/**
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* @return Default configuration object, with following defaults:
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* k = -1, mode = EDLIB_MODE_NW, task = EDLIB_TASK_DISTANCE, no additional equalities.
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*/
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EDLIB_API EdlibAlignConfig edlibDefaultAlignConfig(void);
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/**
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* Container for results of alignment done by edlibAlign() function.
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*/
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typedef struct {
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/**
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* EDLIB_STATUS_OK or EDLIB_STATUS_ERROR. If error, all other fields will have undefined values.
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*/
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int status;
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/**
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* -1 if k is non-negative and edit distance is larger than k.
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*/
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int editDistance;
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/**
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* Array of zero-based positions in target where optimal alignment paths end.
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* If gap after query is penalized, gap counts as part of query (NW), otherwise not.
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* Set to NULL if edit distance is larger than k.
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* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
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*/
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int* endLocations;
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/**
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* Array of zero-based positions in target where optimal alignment paths start,
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* they correspond to endLocations.
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* If gap before query is penalized, gap counts as part of query (NW), otherwise not.
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* Set to NULL if not calculated or if edit distance is larger than k.
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* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
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*/
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int* startLocations;
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/**
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* Number of end (and start) locations.
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*/
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int numLocations;
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/**
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* Alignment is found for first pair of start and end locations.
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* Set to NULL if not calculated.
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* Alignment is sequence of numbers: 0, 1, 2, 3.
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* 0 stands for match.
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* 1 stands for insertion to target.
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* 2 stands for insertion to query.
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* 3 stands for mismatch.
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* Alignment aligns query to target from beginning of query till end of query.
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* If gaps are not penalized, they are not in alignment.
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* If you do not free whole result object using edlibFreeAlignResult(), do not forget to use free().
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*/
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unsigned char* alignment;
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/**
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* Length of alignment.
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*/
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int alignmentLength;
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/**
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* Number of different characters in query and target together.
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*/
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int alphabetLength;
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} EdlibAlignResult;
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/**
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* Frees memory in EdlibAlignResult that was allocated by edlib.
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* If you do not use it, make sure to free needed members manually using free().
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*/
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EDLIB_API void edlibFreeAlignResult(EdlibAlignResult result);
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/**
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* Aligns two sequences (query and target) using edit distance (levenshtein distance).
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* Through config parameter, this function supports different alignment methods (global, prefix, infix),
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* as well as different modes of search (tasks).
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* It always returns edit distance and end locations of optimal alignment in target.
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* It optionally returns start locations of optimal alignment in target and alignment path,
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* if you choose appropriate tasks.
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* @param [in] query First sequence.
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* @param [in] queryLength Number of characters in first sequence.
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* @param [in] target Second sequence.
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* @param [in] targetLength Number of characters in second sequence.
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* @param [in] config Additional alignment parameters, like alignment method and wanted results.
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* @return Result of alignment, which can contain edit distance, start and end locations and alignment path.
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* Make sure to clean up the object using edlibFreeAlignResult() or by manually freeing needed members.
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*/
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EDLIB_API EdlibAlignResult edlibAlign(
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const char* query, int queryLength,
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const char* target, int targetLength,
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const EdlibAlignConfig config
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);
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/**
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* Builds cigar string from given alignment sequence.
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* @param [in] alignment Alignment sequence.
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* 0 stands for match.
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* 1 stands for insertion to target.
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* 2 stands for insertion to query.
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* 3 stands for mismatch.
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* @param [in] alignmentLength
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* @param [in] cigarFormat Cigar will be returned in specified format.
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* @return Cigar string.
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* I stands for insertion.
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* D stands for deletion.
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* X stands for mismatch. (used only in extended format)
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* = stands for match. (used only in extended format)
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* M stands for (mis)match. (used only in standard format)
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* String is null terminated.
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* Needed memory is allocated and given pointer is set to it.
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* Do not forget to free it later using free()!
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*/
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EDLIB_API char* edlibAlignmentToCigar(
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const unsigned char* alignment, int alignmentLength,
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EdlibCigarFormat cigarFormat
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);
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#ifdef __cplusplus
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}
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#endif
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#endif // EDLIB_H

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