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biopet.biopet
Commits
62308c50
Commit
62308c50
authored
10 years ago
by
Peter van 't Hof
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Added star-2pass and stampy to data provider, not having 192 unit tests
parent
d70e8930
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public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+2
-3
2 additions, 3 deletions
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
with
2 additions
and
3 deletions
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+
2
−
3
View file @
62308c50
...
@@ -32,7 +32,7 @@ class MappingTest extends TestNGSuite with Matchers {
...
@@ -32,7 +32,7 @@ class MappingTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"mappingOptions"
,
parallel
=
true
)
@DataProvider
(
name
=
"mappingOptions"
,
parallel
=
true
)
def
mappingOptions
=
{
def
mappingOptions
=
{
val
aligners
=
Array
(
"bwa"
,
"bwa-aln"
,
"star"
,
"
bowtie
"
)
val
aligners
=
Array
(
"bwa"
,
"bwa-aln"
,
"star"
,
"
star-2pass"
,
"bowtie"
,
"stampy
"
)
val
paired
=
Array
(
true
,
false
)
val
paired
=
Array
(
true
,
false
)
val
chunks
=
Array
(
1
,
5
,
10
,
100
)
val
chunks
=
Array
(
1
,
5
,
10
,
100
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
...
@@ -77,7 +77,6 @@ class MappingTest extends TestNGSuite with Matchers {
...
@@ -77,7 +77,6 @@ class MappingTest extends TestNGSuite with Matchers {
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaAln
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
2
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaAln
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
2
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSampe
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
1
else
0
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSampe
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
1
else
0
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSamse
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
0
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSamse
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
(
if
(
paired
)
0
else
1
)
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Star
])
shouldBe
((
if
(
aligner
==
"star"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Star
])
shouldBe
((
if
(
aligner
==
"star"
)
1
else
if
(
aligner
==
"star-2pass"
)
3
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Star
])
shouldBe
((
if
(
aligner
==
"star"
)
1
else
if
(
aligner
==
"star-2pass"
)
3
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Bowtie
])
shouldBe
((
if
(
aligner
==
"bowtie"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Bowtie
])
shouldBe
((
if
(
aligner
==
"bowtie"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Stampy
])
shouldBe
((
if
(
aligner
==
"stampy"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Stampy
])
shouldBe
((
if
(
aligner
==
"stampy"
)
1
else
0
)
*
chunks
)
...
@@ -109,7 +108,7 @@ object MappingTest {
...
@@ -109,7 +108,7 @@ object MappingTest {
"bwa"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"star"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"bowtie"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
),
"stampy"
->
Map
(
"exe"
->
"test"
,
"genome"
->
"test"
,
"hash"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
)
"samtools"
->
Map
(
"exe"
->
"test"
)
)
)
}
}
\ No newline at end of file
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