33 lines
1.1 KiB
Cython
Executable File
33 lines
1.1 KiB
Cython
Executable File
#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) |