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vidjil
vidjil
Commits
bec109c6
Commit
bec109c6
authored
Jul 03, 2015
by
Mathieu Giraud
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core/segment.{cpp,h}: FineSegmenter computes and checks left and right e-values
parent
43c73d8a
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2
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+11
-2
algo/core/segment.cpp
algo/core/segment.cpp
+10
-2
algo/core/segment.h
algo/core/segment.h
+1
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algo/core/segment.cpp
View file @
bec109c6
...
...
@@ -738,6 +738,11 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
score_J
=
score_minus_J
;
}
/* E-values */
int
multiplier
=
1
;
evalue_left
=
multiplier
*
segment_cost
.
toPValue
(
score_V
[
0
].
first
);
evalue_right
=
multiplier
*
segment_cost
.
toPValue
(
score_J
[
0
].
first
);
evalue
=
evalue_left
+
evalue_right
;
/* Unsegmentation causes */
if
(
Jstart
-
Vend
<
germline
->
delta_min
)
...
...
@@ -747,14 +752,17 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
if
(
Vend
==
(
int
)
string
::
npos
)
{
because
=
UNSEG_TOO_FEW_V
;
evalue_left
=
BAD_EVALUE
;
}
if
(
Jstart
==
(
int
)
string
::
npos
)
{
because
=
UNSEG_TOO_FEW_J
;
evalue_right
=
BAD_EVALUE
;
}
double
threshold
=
THRESHOLD_NB_EXPECTED
;
checkLeftRightEvaluesThreshold
(
threshold
,
reversed
?
-
1
:
1
);
if
(
because
!=
NOT_PROCESSED
)
{
segmented
=
false
;
...
...
algo/core/segment.h
View file @
bec109c6
...
...
@@ -32,6 +32,7 @@
#define JSON_REMEMBER_BEST 4
/* The number of V/D/J predictions to keep */
#define NO_LIMIT_VALUE -1
#define BAD_EVALUE 1e10
#define THRESHOLD_NB_EXPECTED 1.0
/* Threshold of the accepted expected value for number of found k-mers */
...
...
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