edlib.h

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#ifndef EDLIB_H
#define EDLIB_H

#ifdef __cplusplus
extern "C" {
#endif

// Status codes
#define EDLIB_STATUS_OK 0
#define EDLIB_STATUS_ERROR 1

typedef enum {
    EDLIB_MODE_NW,
    EDLIB_MODE_SHW,
    EDLIB_MODE_HW
} EdlibAlignMode;

typedef enum {
    EDLIB_TASK_DISTANCE,  
    EDLIB_TASK_LOC,       
    EDLIB_TASK_PATH       
} EdlibAlignTask;

typedef enum {
    EDLIB_CIGAR_STANDARD,  
    EDLIB_CIGAR_EXTENDED   
} EdlibCigarFormat;

// Edit operations.
#define EDLIB_EDOP_MATCH 0    
#define EDLIB_EDOP_INSERT 1   
#define EDLIB_EDOP_DELETE 2   
#define EDLIB_EDOP_MISMATCH 3 



    typedef struct {
        int k;

        EdlibAlignMode mode;

        EdlibAlignTask task;
    } EdlibAlignConfig;

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

    EdlibAlignConfig edlibDefaultAlignConfig(void);


    typedef struct {
        int editDistance;
        int* endLocations;
        int* startLocations;
        int numLocations;
        unsigned char* alignment;
        int alignmentLength;
        int alphabetLength;
    } EdlibAlignResult;

    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);



#ifdef __cplusplus
}
#endif

#endif // EDLIB_H