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cdef extern from "edlib.h" nogil:
ctypedef enum EdlibAlignMode: EDLIB_MODE_NW, EDLIB_MODE_SHW, EDLIB_MODE_HW
ctypedef enum EdlibAlignTask: EDLIB_TASK_DISTANCE, EDLIB_TASK_LOC, EDLIB_TASK_PATH
ctypedef enum EdlibCigarFormat: EDLIB_CIGAR_STANDARD, EDLIB_CIGAR_EXTENDED
ctypedef struct EdlibEqualityPair:
char first
char second
ctypedef struct EdlibAlignConfig:
int k
EdlibAlignMode mode
EdlibAlignTask task
const EdlibEqualityPair* additionalEqualities
int additionalEqualitiesLength
EdlibAlignConfig edlibNewAlignConfig(int k, EdlibAlignMode mode, EdlibAlignTask task,
const EdlibEqualityPair* additionalEqualities,
int additionalEqualitiesLength)
EdlibAlignConfig edlibDefaultAlignConfig()
ctypedef struct EdlibAlignResult:
int status
int editDistance
int* endLocations
int* startLocations
int numLocations
unsigned char* alignment
int alignmentLength
int alphabetLength
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)
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