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vidjil
vidjil
Commits
5b0a0833
Commit
5b0a0833
authored
Feb 02, 2016
by
Mathieu Giraud
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core/segment.{h,cpp}: AlignBox, ostream &operator<<
parent
b311fa68
Changes
2
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2 changed files
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25 additions
and
11 deletions
+25
-11
algo/core/segment.cpp
algo/core/segment.cpp
+14
-7
algo/core/segment.h
algo/core/segment.h
+11
-4
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algo/core/segment.cpp
View file @
5b0a0833
...
...
@@ -46,6 +46,18 @@ string AlignBox::getSequence(string sequence) {
}
ostream
&
operator
<<
(
ostream
&
out
,
const
AlignBox
&
box
)
{
out
<<
"[/"
<<
box
.
del_left
<<
" "
;
out
<<
"@"
<<
box
.
start
<<
" "
;
out
<<
box
.
ref_label
<<
"("
<<
box
.
ref_nb
<<
") "
;
out
<<
"@"
<<
box
.
end
<<
" "
;
out
<<
box
.
del_right
<<
"/]"
;
return
out
;
}
Segmenter
::~
Segmenter
()
{}
...
...
@@ -621,14 +633,9 @@ bool comp_pair (pair<int,int> i,pair<int,int> j)
* @param reverse_ref: if true, reverse the reference sequences (VkVk)
* @param reverse_both: if true, reverse both the read and the reference sequences (J segment)
* @param local: if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
* @param box: the AligBox to fill
* @param segment_cost: the cost used by the dynamic programing
* @return score: the maximized score, together with the following values:
* @return tag: - the name of the sequence
* @return del: - the number of deletions at the end of the reference sequence (or at the start if 'reverse_both')
* @return del2: - the number of deletions at the start of the reference sequence (used with 'local')
* @return begin: - the start position of the aligned segment in the read
* @return length: - the length of the alignmed segment in the read
* @return best_best_i: ?
* @post box is filled
*/
int
align_against_collection
(
string
&
read
,
Fasta
&
rep
,
bool
reverse_ref
,
bool
reverse_both
,
bool
local
,
...
...
algo/core/segment.h
View file @
5b0a0833
...
...
@@ -68,6 +68,10 @@ const char* const segmented_mesg[] = { "?",
/**
* An alignment box (AlignBox) gather all parameters for a recombined gene segment (V, D, J, other D...)
**/
class
AlignBox
{
public:
...
...
@@ -76,16 +80,19 @@ class AlignBox
int
end
;
int
del_right
;
AlignBox
();
string
getSequence
(
string
sequence
);
/* Identifier, label and sequence of the reference sequence (the best one) */
int
ref_nb
;
string
ref_label
;
string
ref
;
vector
<
pair
<
int
,
int
>
>
score
;
string
getSequence
(
string
sequence
);
AlignBox
();
/* Identifiers and scores of other possible reference sequence */
vector
<
pair
<
int
,
int
>
>
score
;
};
ostream
&
operator
<<
(
ostream
&
out
,
const
AlignBox
&
box
);
/**
* Check whether there is an overlap between two boxes,
...
...
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