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

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a Cython compilation bug
This commit is contained in:
Celine Mercier
2018-11-07 16:05:48 +01:00
parent d1f1fd432e
commit b0da36cb48
6 changed files with 296 additions and 242 deletions
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8
python/obitools3/dms/capi/obialign.pxd
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@@ -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,

2
python/obitools3/dms/dms.cfiles
View File

@@ -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