Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
vidjil
vidjil
Commits
2ecc174b
Commit
2ecc174b
authored
Dec 03, 2014
by
Mikaël Salson
Browse files
Test: Test unsegmentation cause with long V and J
parent
b43f8672
Changes
2
Hide whitespace changes
Inline
Side-by-side
algo/tests/testSegment.cpp
View file @
2ecc174b
...
...
@@ -157,6 +157,14 @@ void testSegmentationCause() {
TAP_TEST
(
!
ks
.
isSegmented
(),
TEST_KMER_IS_SEGMENTED
,
"fewJ: "
<<
ks
.
getKmerAffectAnalyser
()
->
toString
());
TAP_TEST
(
ks
.
getSegmentationStatus
()
==
UNSEG_TOO_FEW_J
,
TEST_KMER_SEGMENTATION_CAUSE
,
""
);
nb_checked
++
;
}
else
if
(
data
.
read
(
i
).
label
==
"seq-fewV2"
)
{
TAP_TEST
(
!
ks
.
isSegmented
(),
TEST_KMER_IS_SEGMENTED
,
""
);
TAP_TEST
(
ks
.
getSegmentationStatus
()
==
UNSEG_TOO_FEW_V
,
TEST_KMER_SEGMENTATION_CAUSE
,
""
);
nb_checked
++
;
}
else
if
(
data
.
read
(
i
).
label
==
"seq-fewJ2"
)
{
TAP_TEST
(
!
ks
.
isSegmented
(),
TEST_KMER_IS_SEGMENTED
,
"fewJ: "
<<
ks
.
getKmerAffectAnalyser
()
->
toString
());
TAP_TEST
(
ks
.
getSegmentationStatus
()
==
UNSEG_TOO_FEW_J
,
TEST_KMER_SEGMENTATION_CAUSE
,
""
);
nb_checked
++
;
}
else
if
(
data
.
read
(
i
).
label
==
"seq-delta-min-old"
)
{
// This test was a test for delta_min but with the CountKmerAffectAnalyser
// the read is segmented, now. So we keep it, but change the test
...
...
@@ -190,7 +198,7 @@ void testSegmentationCause() {
}
}
TAP_TEST
(
nb_checked
==
1
1
,
TEST_KMER_DATA
,
""
);
TAP_TEST
(
nb_checked
==
1
3
,
TEST_KMER_DATA
,
""
);
delete
multi
;
}
...
...
@@ -218,15 +226,15 @@ void testExtractor() {
WindowsStorage
*
ws
=
we
.
extract
(
&
data
,
multi
,
30
,
labels
);
TAP_TEST
(
we
.
getNbReads
()
==
1
1
,
TEST_EXTRACTOR_NB_READS
,
""
);
TAP_TEST
(
we
.
getNbReads
()
==
1
3
,
TEST_EXTRACTOR_NB_READS
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
SEG_PLUS
)
==
4
,
TEST_EXTRACTOR_NB_SEGMENTED
,
"segPlus: "
<<
we
.
getNbSegmented
(
SEG_PLUS
));
TAP_TEST
(
we
.
getNbSegmented
(
SEG_MINUS
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_SHORT
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_STRAND_NOT_CONSISTENT
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_FEW_ZERO
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_FEW_V
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_FEW_J
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_FEW_V
)
==
2
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_TOO_FEW_J
)
==
2
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_BAD_DELTA_MIN
)
==
0
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
UNSEG_BAD_DELTA_MAX
)
==
1
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
TAP_TEST
(
we
.
getNbSegmented
(
TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW
)
==
2
,
TEST_EXTRACTOR_NB_SEGMENTED
,
""
);
...
...
@@ -237,8 +245,8 @@ void testExtractor() {
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_SHORT
)
==
4
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_STRAND_NOT_CONSISTENT
)
==
36
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_FEW_ZERO
)
==
36
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_FEW_V
)
==
36
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_FEW_J
)
==
36
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_FEW_V
)
==
51
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_TOO_FEW_J
)
==
55
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
UNSEG_BAD_DELTA_MAX
)
==
66
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW
)
==
28.5
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
TAP_TEST
(
we
.
getAverageSegmentationLength
(
TOTAL_SEG_AND_WINDOW
)
==
48
,
TEST_EXTRACTOR_AVG_LENGTH
,
""
);
...
...
data/segmentation.fasta
View file @
2ecc174b
...
...
@@ -10,8 +10,12 @@ tgtgccacctgggacaggAGTTTCTTATAATAATTC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>seq-fewV
AAAAAAAAAAAAAAAAAAGAATTATTATAAGAAACT
>seq-fewV2
AAAAAAAAAAAAAAAAAAGAATTATTATAAGAAACTCTTTGGCAGTGGAACAACACTGGTTGTCAC
>seq-fewJ
tgtgccacctgggacaggAAAAAAAAAAAAAAAAAA
>seq-fewJ2
tgcaaaatctaattaaaaatgattctgggttctattactgtgccacctgggacaggAAAAAAAAAAAAAAAAAA
>seq-delta-min-old
tgtgccacctgggacaggGAATTATTATAAGAAACTtgtgccacctgggacaggGAATTATTATAAGAAACT
>seq-delta-min
...
...
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