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vidjil
vidjil
Commits
f5098f53
Commit
f5098f53
authored
Mar 27, 2014
by
Mathieu Giraud
Browse files
segment.cpp: info_extra field to store anything that is not constrained by .vdj.fa
'removeChevauchement' and possibly other infos
parent
bea5d4bd
Changes
2
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Inline
Side-by-side
algo/core/segment.cpp
View file @
f5098f53
...
...
@@ -84,7 +84,7 @@ string Segmenter::removeChevauchement()
if
(
Vend
>=
Jstart
)
{
int
middle
=
(
Vend
+
Jstart
)
/
2
;
chevauchement
=
"!"
+
string_of_int
(
Vend
-
Jstart
)
+
"!"
;
chevauchement
=
"
!"
+
string_of_int
(
Vend
-
Jstart
)
+
"!"
;
Vend
=
middle
;
Jstart
=
middle
+
1
;
}
...
...
@@ -141,6 +141,7 @@ ostream &operator<<(ostream &out, const Segmenter &s)
{
out
<<
">"
<<
s
.
label
<<
" "
;
out
<<
(
s
.
segmented
?
""
:
"! "
)
<<
s
.
info
;
out
<<
" "
<<
s
.
info_extra
;
out
<<
endl
;
if
(
s
.
segmented
)
...
...
@@ -166,6 +167,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, IKmerStore<KmerAffect> *index,
label
=
seq
.
label
;
sequence
=
seq
.
sequence
;
info
=
""
;
info_extra
=
"seed"
;
segmented
=
false
;
Dend
=
0
;
...
...
@@ -217,7 +219,8 @@ KmerSegmenter::KmerSegmenter(Sequence seq, IKmerStore<KmerAffect> *index,
because
=
reversed
?
SEG_MINUS
:
SEG_PLUS
;
info
=
string_of_int
(
Vend
+
FIRST_POS
)
+
" "
+
string_of_int
(
Jstart
+
FIRST_POS
)
;
info
+=
" "
+
removeChevauchement
();
// removeChevauchement is called once info was already computed: it is only to output info_extra
info_extra
+=
removeChevauchement
();
finishSegmentation
();
}
}
...
...
@@ -441,7 +444,7 @@ FineSegmenter::FineSegmenter(Sequence seq, Fasta &rep_V, Fasta &rep_J,
int
delta_min
,
int
delta_max
,
Cost
segment_c
)
{
info_extra
=
""
;
label
=
seq
.
label
;
sequence
=
seq
.
sequence
;
Dend
=
0
;
...
...
algo/core/segment.h
View file @
f5098f53
...
...
@@ -49,7 +49,8 @@ protected:
string
code
;
string
code_short
;
string
code_light
;
string
info
;
string
info
;
// .vdj.fa header, fixed fields
string
info_extra
;
// .vdj.fa header, other information, at the end of the header
int
best_V
,
best_J
;
int
del_V
,
del_D_left
,
del_D_right
,
del_J
;
string
seg_V
,
seg_N
,
seg_J
;
...
...
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