Commit b0da36cb authored by Celine Mercier's avatar Celine Mercier

New command: obi align, except it's called obi pouic for now because of

a Cython compilation bug
parent d1f1fd43
This diff is collapsed.
#cython: language_level=3
cpdef align_columns(bytes dms_n,
bytes input_view_1_n,
bytes output_view_n,
bytes input_view_2_n=*,
bytes input_column_1_n=*,
bytes input_column_2_n=*,
bytes input_elt_1_n=*,
bytes input_elt_2_n=*,
bytes id_column_1_n=*,
bytes id_column_2_n=*,
double threshold=*, bint normalize=*,
int reference=*, bint similarity_mode=*,
bint print_seq=*, bint print_count=*,
bytes comments=*,
int thread_count=*)
\ No newline at end of file
This diff is collapsed.
......@@ -4,13 +4,13 @@ from obitools3.dms.capi.obidms cimport OBIDMS_p
from obitools3.dms.capi.obitypes cimport const_char_p
cdef extern from "obi_align.h" nogil:
cdef extern from "obi_lcs.h" nogil:
int obi_lcs_align_one_column(OBIDMS_p dms,
int obi_lcs_align_one_column(const_char_p dms_name,
const_char_p seq_view_name,
const_char_p seq_column_name,
const_char_p seq_elt_name,
const_char_p id_column_name,
const_char_p id_column_name,
const_char_p output_view_name,
const_char_p output_view_comments,
bint print_seq,
......@@ -22,7 +22,7 @@ cdef extern from "obi_align.h" nogil:
int thread_count)
int obi_lcs_align_two_columns(OBIDMS_p dms,
int obi_lcs_align_two_columns(const_char_p dms_name,
const_char_p seq1_view_name,
const_char_p seq2_view_name,
const_char_p seq1_column_name,
......
......@@ -7,7 +7,7 @@
../../../src/hashtable.c
../../../src/linked_list.c
../../../src/murmurhash2.c
../../../src/obi_align.c
../../../src/obi_lcs.c
../../../src/obi_clean.c
../../../src/obi_ecopcr.c
../../../src/libecoPCR/libthermo/nnparams.c
......
......@@ -7,7 +7,7 @@
../../src/hashtable.c
../../src/linked_list.c
../../src/murmurhash2.c
../../src/obi_align.c
../../src/obi_lcs.c
../../src/obi_clean.c
../../src/obi_ecopcr.c
../../src/libecoPCR/libthermo/nnparams.c
......
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