Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
vidjil
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Issues
1,712
Issues
1,712
List
Boards
Labels
Service Desk
Milestones
Merge Requests
87
Merge Requests
87
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Incidents
Environments
Packages & Registries
Packages & Registries
Container Registry
Analytics
Analytics
CI / CD
Repository
Value Stream
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
vidjil
vidjil
Commits
32ee38d5
Commit
32ee38d5
authored
Apr 01, 2015
by
Mikaël Salson
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
segment.cpp: Add a UNSEG_NOISY cause when the e-value is not high enough
parent
ef8e47fc
Changes
4
Hide whitespace changes
Inline
Side-by-side
Showing
4 changed files
with
24 additions
and
1 deletion
+24
-1
algo/core/segment.cpp
algo/core/segment.cpp
+5
-0
algo/core/segment.h
algo/core/segment.h
+7
-1
algo/tests/testSegment.cpp
algo/tests/testSegment.cpp
+10
-0
algo/tests/tests.h
algo/tests/tests.h
+2
-0
No files found.
algo/core/segment.cpp
View file @
32ee38d5
...
...
@@ -396,6 +396,11 @@ int Segmenter::getSegmentationStatus() const {
return
because
;
}
void
Segmenter
::
setSegmentationStatus
(
int
status
)
{
because
=
status
;
segmented
=
(
status
==
SEG_PLUS
||
status
==
SEG_MINUS
);
}
// FineSegmenter
void
best_align
(
int
overlap
,
string
seq_left
,
string
seq_right
,
...
...
algo/core/segment.h
View file @
32ee38d5
...
...
@@ -32,13 +32,14 @@ using namespace std;
enum
SEGMENTED
{
DONT_KNOW
,
SEG_PLUS
,
SEG_MINUS
,
UNSEG_TOO_SHORT
,
UNSEG_STRAND_NOT_CONSISTENT
,
UNSEG_TOO_FEW_ZERO
,
UNSEG_TOO_FEW_V
,
UNSEG_TOO_FEW_J
,
UNSEG_BAD_DELTA_MIN
,
UNSEG_BAD_DELTA_MAX
,
UNSEG_AMBIGUOUS
,
UNSEG_BAD_DELTA_MIN
,
UNSEG_BAD_DELTA_MAX
,
UNSEG_AMBIGUOUS
,
UNSEG_NOISY
,
TOTAL_SEG_AND_WINDOW
,
TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW
,
STATS_SIZE
}
;
const
char
*
const
segmented_mesg
[]
=
{
"?"
,
"SEG_+"
,
"SEG_-"
,
"UNSEG too short"
,
"UNSEG strand"
,
"UNSEG too few (0)"
,
"UNSEG too few V"
,
"UNSEG too few J"
,
"UNSEG < delta_min"
,
"UNSEG > delta_max"
,
"UNSEG ambiguous"
,
"UNSEG noisy"
,
"= SEG, with window"
,
"= SEG, no window"
,
}
;
...
...
@@ -136,6 +137,11 @@ protected:
string
getInfoLine
()
const
;
/**
* @post status == SEG_PLUS || status == SEG_MINUS <==> isSegmented()
*/
void
setSegmentationStatus
(
int
status
);
friend
ostream
&
operator
<<
(
ostream
&
out
,
const
Segmenter
&
s
);
};
...
...
algo/tests/testSegment.cpp
View file @
32ee38d5
...
...
@@ -120,6 +120,16 @@ void testSegmentationCause() {
TEST_KMER_JUNCTION
,
""
);
TAP_TEST
(
ks
.
getLeft
()
==
17
,
TEST_KMER_LEFT
,
"left = "
<<
ks
.
getLeft
());
TAP_TEST
(
ks
.
getRight
()
==
18
,
TEST_KMER_RIGHT
,
"right = "
<<
ks
.
getRight
());
ks
.
setSegmentationStatus
(
DONT_KNOW
);
TAP_TEST
(
!
ks
.
isSegmented
(),
TEST_SET_SEGMENTATION_CAUSE
,
""
);
TAP_TEST
(
ks
.
getSegmentationStatus
()
==
DONT_KNOW
,
TEST_SET_SEGMENTATION_CAUSE
,
""
);
ks
.
setSegmentationStatus
(
UNSEG_NOISY
);
TAP_TEST
(
!
ks
.
isSegmented
(),
TEST_SET_SEGMENTATION_CAUSE
,
""
);
TAP_TEST
(
ks
.
getSegmentationStatus
()
==
UNSEG_NOISY
,
TEST_SET_SEGMENTATION_CAUSE
,
""
);
ks
.
setSegmentationStatus
(
SEG_PLUS
);
TAP_TEST
(
ks
.
isSegmented
(),
TEST_SET_SEGMENTATION_CAUSE
,
""
);
TAP_TEST
(
ks
.
getSegmentationStatus
(),
TEST_SET_SEGMENTATION_CAUSE
,
""
);
nb_checked
++
;
}
else
if
(
data
.
read
(
i
).
label
==
"seq-seg-"
)
{
TAP_TEST
(
ks
.
isSegmented
(),
TEST_KMER_IS_SEGMENTED
,
""
);
...
...
algo/tests/tests.h
View file @
32ee38d5
...
...
@@ -101,6 +101,7 @@ enum {
/* Kmer segmentation */
TEST_KMER_IS_SEGMENTED
,
TEST_KMER_SEGMENTATION_CAUSE
,
TEST_SET_SEGMENTATION_CAUSE
,
TEST_KMER_JUNCTION
,
TEST_KMER_DATA
,
TEST_KMER_LEFT
,
...
...
@@ -237,6 +238,7 @@ inline void declare_tests() {
RECORD_TAP_TEST
(
TEST_KMER_IS_SEGMENTED
,
"Test isSegmented() in KmerSegmenter"
);
RECORD_TAP_TEST
(
TEST_KMER_SEGMENTATION_CAUSE
,
"Test getSegmentationStatus() in KmerSegmenter"
);
RECORD_TAP_TEST
(
TEST_SET_SEGMENTATION_CAUSE
,
"Test setSegmentationStatus() in KmerSegmenter"
);
RECORD_TAP_TEST
(
TEST_KMER_JUNCTION
,
"Test getJunction() in KmerSegmenter"
);
RECORD_TAP_TEST
(
TEST_KMER_DATA
,
"Test that data is consistent with what we expect for KmerSegmenter"
);
RECORD_TAP_TEST
(
TEST_KMER_LEFT
,
"Test V end (resp. J start) with KmerSegmenter on fwd (resp bwd) strand"
);
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment