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vidjil
vidjil
Commits
bb3a5cfc
Commit
bb3a5cfc
authored
Jan 31, 2017
by
Mathieu Giraud
Browse files
tests: update tests
parent
c568f70e
Changes
4
Hide whitespace changes
Inline
Side-by-side
algo/tests/unit-tests/testAffectAnalyser.cpp
View file @
bb3a5cfc
...
...
@@ -342,8 +342,8 @@ void testGetMaximum() {
*/
template
<
template
<
class
>
class
T
>
void
testBugAffectAnalyser
()
{
Fasta
seqV
(
"../../germline/IGHV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/IGHJ.fa"
,
2
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
IGHV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
IGHJ.fa"
,
2
);
Fasta
data
(
"../../data/bug-revcomp.fa"
,
1
,
" "
);
int
k
=
9
;
...
...
algo/tests/unit-tests/testBugs.cpp
View file @
bb3a5cfc
...
...
@@ -9,8 +9,8 @@ using namespace std;
void
testSegmentationBug1
(
IndexTypes
index
,
int
delta_min
)
{
string
buggy_sequences
=
"bugs/kmersegment.fa"
;
Fasta
seqV
(
"../../germline/TRGV.fa"
);
Fasta
seqJ
(
"../../germline/TRGJ.fa"
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
TRGV.fa"
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
TRGJ.fa"
);
Germline
*
germline
;
germline
=
new
Germline
(
"custom"
,
'x'
,
seqV
,
seqV
,
seqJ
,
delta_min
,
"##############"
);
...
...
algo/tests/unit-tests/testSegment.cpp
View file @
bb3a5cfc
...
...
@@ -44,9 +44,9 @@ void testOverlap()
void
testFineSegment
(
IndexTypes
index
)
{
Fasta
seqV
(
"../../germline/IGHV.fa"
,
2
);
Fasta
seqD
(
"../../germline/IGHD.fa"
,
2
);
Fasta
seqJ
(
"../../germline/IGHJ.fa"
,
2
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
IGHV.fa"
,
2
);
Fasta
seqD
(
"../../germline/
homo-sapiens/
IGHD.fa"
,
2
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
IGHJ.fa"
,
2
);
OnlineFasta
data
(
"../../data/Stanford_S22.fasta"
,
1
,
" "
);
data
.
next
();
...
...
@@ -99,8 +99,8 @@ void testFineSegment(IndexTypes index)
*/
void
testSegmentOverlap
(
IndexTypes
index
)
{
Fasta
seqV
(
"../../germline/TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/TRGJ.fa"
,
2
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
TRGJ.fa"
,
2
);
Fasta
data
(
"../../data/bug-segment-overlap.fa"
,
1
,
" "
);
...
...
@@ -135,8 +135,8 @@ void testSegmentOverlap(IndexTypes index)
}
void
testSegmentationCause
(
IndexTypes
index
)
{
Fasta
seqV
(
"../../germline/TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/TRGJ.fa"
,
2
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
TRGJ.fa"
,
2
);
Fasta
data
(
"../../data/segmentation.fasta"
,
1
,
" "
);
...
...
@@ -248,8 +248,8 @@ void testSegmentationCause(IndexTypes index) {
}
void
testExtractor
(
IndexTypes
index
)
{
Fasta
seqV
(
"../../germline/TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/TRGJ.fa"
,
2
);
Fasta
seqV
(
"../../germline/
homo-sapiens/
TRGV.fa"
,
2
);
Fasta
seqJ
(
"../../germline/
homo-sapiens/
TRGJ.fa"
,
2
);
OnlineFasta
data
(
"../../data/segmentation.fasta"
,
1
,
" "
);
...
...
algo/tests/unit-tests/testTools.cpp
View file @
bb3a5cfc
...
...
@@ -49,9 +49,9 @@ void testOnlineFastaMaxNth() {
void
testFastaNbSequences
()
{
TAP_TEST
(
nb_sequences_in_fasta
(
"../../germline/IGHV.fa"
)
==
350
,
TEST_FASTA_NB_SEQUENCES
,
"ccc"
);
TAP_TEST
(
nb_sequences_in_fasta
(
"../../germline/
homo-sapiens/
IGHV.fa"
)
==
350
,
TEST_FASTA_NB_SEQUENCES
,
"ccc"
);
int
a1
=
approx_nb_sequences_in_fasta
(
"../../germline/IGHV.fa"
);
int
a1
=
approx_nb_sequences_in_fasta
(
"../../germline/
homo-sapiens/
IGHV.fa"
);
TAP_TEST
(
a1
>=
345
&&
a1
<=
355
,
TEST_FASTA_NB_SEQUENCES
,
""
);
int
a2
=
nb_sequences_in_fasta
(
"../../data/Stanford_S22.fasta"
,
true
);
...
...
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