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vidjil
vidjil
Commits
24b6dc53
Commit
24b6dc53
authored
Apr 25, 2015
by
Mathieu Giraud
Browse files
core/segment.{h,cpp}: extract method getInfoLineWithAffects()
parent
90e0102c
Changes
2
Hide whitespace changes
Inline
Side-by-side
algo/core/segment.cpp
View file @
24b6dc53
...
...
@@ -163,6 +163,22 @@ string Segmenter::getInfoLine() const
return
s
;
}
string
KmerSegmenter
::
getInfoLineWithAffects
()
const
{
stringstream
ss
;
ss
<<
"# "
<<
right
<<
setw
(
3
)
<<
score
<<
" "
<<
left
<<
setw
(
30
)
<<
getInfoLine
()
;
if
(
getSegmentationStatus
()
!=
UNSEG_TOO_SHORT
)
ss
<<
getKmerAffectAnalyser
()
->
toString
();
return
ss
.
str
();
}
ostream
&
operator
<<
(
ostream
&
out
,
const
Segmenter
&
s
)
{
out
<<
">"
<<
s
.
label
<<
" "
;
...
...
@@ -313,17 +329,7 @@ KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermlin
if
(
out_unsegmented
)
{
// Debug, display k-mer affectation and segmentation result for this germline
*
out_unsegmented
<<
"# "
<<
right
<<
setw
(
3
)
<<
kseg
->
score
<<
" "
<<
left
<<
setw
(
30
)
<<
kseg
->
getInfoLine
()
<<
endl
;
if
(
kseg
->
getSegmentationStatus
()
!=
UNSEG_TOO_SHORT
)
{
*
out_unsegmented
<<
kseg
->
getKmerAffectAnalyser
()
->
toString
();
*
out_unsegmented
<<
endl
;
}
*
out_unsegmented
<<
kseg
->
getInfoLineWithAffects
()
<<
endl
;
}
// Always remember the first kseg
...
...
algo/core/segment.h
View file @
24b6dc53
...
...
@@ -192,6 +192,7 @@ class KmerSegmenter : public Segmenter
*/
KmerAffectAnalyser
*
getKmerAffectAnalyser
()
const
;
string
getInfoLineWithAffects
()
const
;
void
toJsonList
(
JsonList
*
seg
);
private:
...
...
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