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#cython: language_level=3
from obitools3.dms.capi.kmer_similarity cimport kmer_similarity, Obi_ali_p
from libc.stdint cimport int32_t, uint8_t
from obitools3.dms.capi.obiview cimport Obiview_p
from obitools3.dms.capi.obidmscolumn cimport OBIDMS_column_p
cdef class Ali_shifted:
cdef Obi_ali_p _pointer
cdef inline Obi_ali_p pointer(self)
cpdef free(self)
@staticmethod
cdef Ali_shifted new_ali(Obi_ali_p ali_p)
cdef class Kmer_similarity:
cdef uint8_t kmer_size
cdef int32_t* kmer_pos_array_p
cdef int32_t kmer_pos_array_height_a[1]
cdef int32_t* shift_array_p
cdef int32_t shift_array_height_a[1]
cdef int32_t* shift_count_array_p
cdef int32_t shift_count_array_height_a[1]
cdef Obiview_p view1_p
cdef OBIDMS_column_p column1_p
cdef OBIDMS_column_p qual_col1_p
cdef Obiview_p view2_p
cdef OBIDMS_column_p column2_p
cdef OBIDMS_column_p qual_col2_p
cdef OBIDMS_column_p reversed_col_p
cdef bint build_consensus
cpdef free(self)
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