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vidjil
vidjil
Commits
05050b0d
Commit
05050b0d
authored
Apr 24, 2015
by
Mathieu Giraud
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core/segment.{h,cpp}: e-value test for each germline
parent
11351f69
Changes
2
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2 changed files
with
25 additions
and
25 deletions
+25
-25
algo/core/segment.cpp
algo/core/segment.cpp
+23
-23
algo/core/segment.h
algo/core/segment.h
+2
-2
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algo/core/segment.cpp
View file @
05050b0d
...
...
@@ -191,7 +191,7 @@ ostream &operator<<(ostream &out, const Segmenter &s)
KmerSegmenter
::
KmerSegmenter
()
{
kaa
=
0
;
}
KmerSegmenter
::
KmerSegmenter
(
Sequence
seq
,
Germline
*
germline
,
int
multiplier
)
KmerSegmenter
::
KmerSegmenter
(
Sequence
seq
,
Germline
*
germline
,
double
threshold
,
int
multiplier
)
{
label
=
seq
.
label
;
sequence
=
seq
.
sequence
;
...
...
@@ -252,7 +252,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, int multiplier)
}
strand
=
nb_strand
[
0
]
>
nb_strand
[
1
]
?
-
1
:
1
;
computeSegmentation
(
strand
,
max12
.
first
,
max12
.
second
,
multiplier
);
computeSegmentation
(
strand
,
max12
.
first
,
max12
.
second
,
threshold
,
multiplier
);
if
(
!
detected
)
because
=
UNSEG_TOO_FEW_ZERO
;
...
...
@@ -283,7 +283,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, int multiplier)
return
;
}
computeSegmentation
(
strand
,
before
,
after
,
multiplier
);
computeSegmentation
(
strand
,
before
,
after
,
threshold
,
multiplier
);
}
// endif Pseudo-germline
...
...
@@ -343,7 +343,7 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
{
Germline
*
germline
=
*
it
;
KmerSegmenter
*
kseg
=
new
KmerSegmenter
(
seq
,
germline
,
multiplier
);
KmerSegmenter
*
kseg
=
new
KmerSegmenter
(
seq
,
germline
,
threshold
,
multiplier
);
bool
keep_seg
=
false
;
if
(
out_unsegmented
)
...
...
@@ -396,24 +396,6 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
delete
kseg
;
}
}
// end for (Germlines)
// E-value threshold
if
(
threshold_nb_expected
>
NO_LIMIT_VALUE
)
if
(
the_kseg
->
isSegmented
())
{
if
(
the_kseg
->
evalue
>
threshold_nb_expected
)
{
// Detail the unsegmentation cause
if
(
the_kseg
->
evalue_left
>
threshold_nb_expected
&&
the_kseg
->
evalue_right
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_TOO_FEW_ZERO
);
}
else
if
(
the_kseg
->
evalue_left
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_TOO_FEW_V
);
}
else
if
(
the_kseg
->
evalue_right
>
threshold_nb_expected
)
{
the_kseg
->
setSegmentationStatus
(
UNSEG_TOO_FEW_J
);
}
else
// left and right are <= threshold, but their sum is > threshold
the_kseg
->
setSegmentationStatus
(
UNSEG_TOO_FEW_ZERO
);
}
}
}
KmerMultiSegmenter
::~
KmerMultiSegmenter
()
{
...
...
@@ -421,7 +403,7 @@ KmerMultiSegmenter::~KmerMultiSegmenter() {
delete
the_kseg
;
}
void
KmerSegmenter
::
computeSegmentation
(
int
strand
,
KmerAffect
before
,
KmerAffect
after
,
int
multiplier
)
{
void
KmerSegmenter
::
computeSegmentation
(
int
strand
,
KmerAffect
before
,
KmerAffect
after
,
double
threshold
,
int
multiplier
)
{
// Try to segment, computing 'Vend' and 'Jstart'
// If not segmented, put the cause of unsegmentation in 'because'
...
...
@@ -433,6 +415,24 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
evalue_right
=
pvalues
.
second
*
multiplier
;
evalue
=
evalue_left
+
evalue_right
;
// E-value threshold
if
(
threshold
>
NO_LIMIT_VALUE
&&
evalue
>
threshold
)
{
// Detail the unsegmentation cause
if
(
evalue_left
>
threshold
&&
evalue_right
>
threshold
)
because
=
UNSEG_TOO_FEW_ZERO
;
else
if
(
evalue_left
>
threshold
)
because
=
UNSEG_TOO_FEW_V
;
else
if
(
evalue_right
>
threshold
)
because
=
UNSEG_TOO_FEW_J
;
else
// left and right are <= threshold, but their sum is > threshold
because
=
UNSEG_TOO_FEW_ZERO
;
return
;
}
//
// We labeled it detected if there were both enough affect_5 and enough affect_3
detected
=
(
max
.
nb_before_left
+
max
.
nb_before_right
>=
DETECT_THRESHOLD
)
&&
(
max
.
nb_after_left
+
max
.
nb_after_right
>=
DETECT_THRESHOLD
);
...
...
algo/core/segment.h
View file @
05050b0d
...
...
@@ -185,7 +185,7 @@ class KmerSegmenter : public Segmenter
* @param seq: An object read from a FASTA/FASTQ file
* @param germline: the germline
*/
KmerSegmenter
(
Sequence
seq
,
Germline
*
germline
,
int
multiplier
=
1
);
KmerSegmenter
(
Sequence
seq
,
Germline
*
germline
,
double
threshold
=
THRESHOLD_NB_EXPECTED
,
int
multiplier
=
1
);
KmerSegmenter
(
const
KmerSegmenter
&
seg
);
...
...
@@ -199,7 +199,7 @@ class KmerSegmenter : public Segmenter
void
toJsonList
(
JsonList
*
seg
);
private:
void
computeSegmentation
(
int
strand
,
KmerAffect
left
,
KmerAffect
right
,
int
multiplier
);
void
computeSegmentation
(
int
strand
,
KmerAffect
left
,
KmerAffect
right
,
double
threshold
,
int
multiplier
);
};
...
...
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