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vidjil
vidjil
Commits
6aef087f
Commit
6aef087f
authored
Apr 24, 2015
by
Mathieu Giraud
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Plain Diff
core/segment.cpp: use getInfoLine() for .affects debug output (-K)
We thus get evalues.
parent
5b80a9cd
Changes
3
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3 changed files
with
14 additions
and
13 deletions
+14
-13
algo/core/segment.cpp
algo/core/segment.cpp
+12
-11
algo/core/segment.h
algo/core/segment.h
+1
-1
algo/core/windowExtractor.cpp
algo/core/windowExtractor.cpp
+1
-1
No files found.
algo/core/segment.cpp
View file @
6aef087f
...
...
@@ -149,9 +149,8 @@ bool Segmenter::finishSegmentationD()
string
Segmenter
::
getInfoLine
()
const
{
string
s
=
"
>
"
;
string
s
=
""
;
s
+=
label
+
" "
;
s
+=
(
segmented
?
""
:
"! "
)
+
info
;
s
+=
" "
+
info_extra
;
s
+=
" "
+
segmented_germline
->
code
;
...
...
@@ -170,6 +169,7 @@ string Segmenter::getInfoLine() const
ostream
&
operator
<<
(
ostream
&
out
,
const
Segmenter
&
s
)
{
out
<<
">"
<<
s
.
label
<<
" "
;
out
<<
s
.
getInfoLine
()
<<
endl
;
if
(
s
.
segmented
)
...
...
@@ -349,16 +349,17 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
if
(
out_unsegmented
)
{
// Debug, display k-mer affectation and segmentation result for this germline
*
out_unsegmented
<<
"#"
<<
left
<<
setw
(
4
)
<<
kseg
->
segmented_germline
->
cod
e
<<
" "
<<
left
<<
setw
(
20
)
<<
segmented_mesg
[
kseg
->
getSegmentationStatus
()]
<<
" "
;
*
out_unsegmented
<<
right
<<
setw
(
3
)
<<
kseg
->
score
<<
" "
;
*
out_unsegmented
<<
"#
"
<<
right
<<
setw
(
3
)
<<
kseg
->
scor
e
<<
" "
<<
left
<<
setw
(
30
)
<<
kseg
->
getInfoLine
()
<<
endl
;
if
(
kseg
->
getSegmentationStatus
()
!=
UNSEG_TOO_SHORT
)
*
out_unsegmented
<<
kseg
->
getKmerAffectAnalyser
()
->
toString
();
*
out_unsegmented
<<
endl
;
if
(
kseg
->
getSegmentationStatus
()
!=
UNSEG_TOO_SHORT
)
{
*
out_unsegmented
<<
kseg
->
getKmerAffectAnalyser
()
->
toString
();
*
out_unsegmented
<<
endl
;
}
}
// Always remember the first kseg
...
...
algo/core/segment.h
View file @
6aef087f
...
...
@@ -57,7 +57,6 @@ const char* const segmented_mesg[] = { "?",
class
Segmenter
{
protected:
string
label
;
string
sequence
;
int
Vend
,
Jstart
;
int
Dstart
,
Dend
;
...
...
@@ -71,6 +70,7 @@ protected:
public:
Germline
*
segmented_germline
;
string
label
;
string
code
;
string
code_short
;
string
code_light
;
...
...
algo/core/windowExtractor.cpp
View file @
6aef087f
...
...
@@ -83,7 +83,7 @@ WindowsStorage *WindowExtractor::extract(OnlineFasta *reads, MultiGermline *mult
// Last line of detailed affects output
if
(
out_affects
)
{
*
out_affects
<<
"#
"
<<
seg
->
getInfoLine
()
<<
endl
;
*
out_affects
<<
"#
>"
<<
seg
->
label
<<
" "
<<
seg
->
getInfoLine
()
<<
endl
<<
endl
;
}
// Progress bar
...
...
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