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OBITools
OBITools3
Commits
f03928c6
Commit
f03928c6
authored
Jul 06, 2017
by
Celine Mercier
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Committing minor comments before merging branch with master
parent
717ee46f
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5 changed files
with
14 additions
and
3 deletions
+14
-3
conf.py
doc/conf.py
+1
-1
linked_list.h
src/linked_list.h
+1
-1
obi_align.c
src/obi_align.c
+9
-0
obiview.c
src/obiview.c
+2
-0
upperband.c
src/upperband.c
+1
-1
No files found.
doc/conf.py
View file @
f03928c6
...
...
@@ -33,7 +33,7 @@ extensions = [
'sphinx.ext.autodoc'
,
'sphinx.ext.todo'
,
'sphinx.ext.coverage'
,
'sphinx.ext.
pn
gmath'
,
'sphinx.ext.
im
gmath'
,
'sphinx.ext.ifconfig'
,
'sphinx.ext.viewcode'
,
'breathe'
,
...
...
src/linked_list.h
View file @
f03928c6
...
...
@@ -90,7 +90,7 @@ Linked_list_node_p ll_get(Linked_list_node_p head, int idx);
* @param idx The index of the node to delete.
*
* @returns A pointer on the new head node of the linked list.
* @retval NULL if an error occurred.
* @retval NULL if an error occurred.
// TODO or if list is now empty...
*
* @since February 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
...
...
src/obi_align.c
View file @
f03928c6
...
...
@@ -883,6 +883,10 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
return
-
1
;
}
// TODO check this
if
(
!
similarity_mode
&&
normalize
&&
(
threshold
>
0
))
threshold
=
1
.
0
-
threshold
;
seq1_count
=
(
seq1_view
->
infos
)
->
line_count
;
seq2_count
=
(
seq2_view
->
infos
)
->
line_count
;
...
...
@@ -932,6 +936,11 @@ int obi_lcs_align_two_columns(OBIDMS_p dms,
// Compute alignment score
if
((
threshold
==
0
)
||
(
score
==
-
1
.
0
))
// no threshold, or filter passed: align
score
=
obiblob_sse_banded_lcs_align
(
blob1
,
blob2
,
threshold
,
normalize
,
reference
,
similarity_mode
,
&
lcs_length
,
&
ali_length
);
// TODO check this
// if (print && !lcsmode && normalize)
// score = 1.0 - score;
}
if
((
score
>=
0
)
&&
(((
normalize
||
similarity_mode
)
&&
(
score
>=
threshold
))
||
((
!
similarity_mode
&&
!
normalize
)
&&
(
score
<=
threshold
))))
...
...
src/obiview.c
View file @
f03928c6
...
...
@@ -1188,6 +1188,8 @@ static int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* colum
}
}
// TODO add line_max
if
(((
*
line_nb_p
)
+
1
)
>
(
view
->
infos
)
->
line_count
)
{
if
(
update_lines
(
view
,
((
*
line_nb_p
)
+
1
))
<
0
)
...
...
src/upperband.c
View file @
f03928c6
...
...
@@ -230,7 +230,7 @@ int thresholdLCS4(int32_t reflen, int32_t lcs)
}
Kmer_table_p
hash_seq_column
(
Obiview_p
view
,
OBIDMS_column_p
seq_col
,
index_t
seq_idx
)
Kmer_table_p
hash_seq_column
(
Obiview_p
view
,
OBIDMS_column_p
seq_col
,
index_t
seq_idx
)
// TODO move in another file (obi_align.c)
{
size_t
i
;
size_t
seq_count
;
...
...
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