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vidjil
vidjil
Commits
34068e0b
Commit
34068e0b
authored
Apr 06, 2015
by
Mathieu Giraud
Browse files
core/segment.{h,cpp}: e-value threshold is now on both left and right sides
Store and check getLeftRightProbabilityAtLeastOrAbove()
parent
0045c06c
Changes
2
Hide whitespace changes
Inline
Side-by-side
algo/core/segment.cpp
View file @
34068e0b
...
...
@@ -159,6 +159,11 @@ string Segmenter::getInfoLine() const
if
(
evalue
>
NO_LIMIT_VALUE
)
s
+=
" "
+
scientific_string_of_double
(
evalue
);
if
(
evalue_left
>
NO_LIMIT_VALUE
)
s
+=
" "
+
scientific_string_of_double
(
evalue_left
);
if
(
evalue_right
>
NO_LIMIT_VALUE
)
s
+=
"/"
+
scientific_string_of_double
(
evalue_right
);
return
s
;
}
...
...
@@ -360,6 +365,17 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
if
(
the_kseg
->
evalue
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_NOISY
);
}
pair
<
double
,
double
>
p
=
the_kseg
->
getKmerAffectAnalyser
()
->
getLeftRightProbabilityAtLeastOrAbove
();
the_kseg
->
evalue_left
=
p
.
first
;
the_kseg
->
evalue_right
=
p
.
second
;
if
(
the_kseg
->
evalue_left
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_NOISY
);
// TOO_FEW_V ?
}
if
(
the_kseg
->
evalue_right
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_NOISY
);
// TOO_FEW_J ?
}
}
}
...
...
@@ -567,6 +583,8 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
Dend
=
0
;
segment_cost
=
segment_c
;
evalue
=
NO_LIMIT_VALUE
;
evalue_left
=
NO_LIMIT_VALUE
;
evalue_right
=
NO_LIMIT_VALUE
;
CDR3start
=
-
1
;
CDR3end
=
-
1
;
...
...
@@ -931,6 +949,10 @@ void KmerSegmenter::toJsonList(JsonList *seg)
if
(
evalue
>
NO_LIMIT_VALUE
)
seg
->
add
(
"_evalue"
,
scientific_string_of_double
(
evalue
));
if
(
evalue_left
>
NO_LIMIT_VALUE
)
seg
->
add
(
"_evalue_left"
,
scientific_string_of_double
(
evalue_left
));
if
(
evalue_right
>
NO_LIMIT_VALUE
)
seg
->
add
(
"_evalue_right"
,
scientific_string_of_double
(
evalue_right
));
JsonList
*
json_affectValues
;
json_affectValues
=
new
JsonList
();
...
...
algo/core/segment.h
View file @
34068e0b
...
...
@@ -77,6 +77,8 @@ protected:
int
best_D
;
double
evalue
;
double
evalue_left
;
double
evalue_right
;
string
seg_N1
,
seg_D
,
seg_N2
;
Cost
segment_cost
;
...
...
Vidjil Team
@vidjilteam
Mentioned in issue
#1493 (closed)
·
Nov 29, 2016
Mentioned in issue
#1493 (closed)
Mentioned in issue #1493
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