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biopet.biopet
Commits
ca5dcca3
Commit
ca5dcca3
authored
Apr 29, 2016
by
Peter van 't Hof
Browse files
Reduced number of test in shiva
parent
c7cca543
Changes
1
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Inline
Side-by-side
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
ca5dcca3
...
...
@@ -33,7 +33,7 @@ import org.testng.annotations.{ DataProvider, Test }
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaTest
extends
TestNGSuite
with
Matchers
{
trait
ShivaTest
Trait
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Shiva
=
{
new
Shiva
()
{
override
def
configNamespace
=
"shiva"
...
...
@@ -45,24 +45,33 @@ class ShivaTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"shivaOptions"
)
def
shivaOptions
=
{
val
bool
=
Array
(
true
,
false
)
for
(
s1
<-
bool
;
s2
<-
bool
;
multi
<-
bool
;
dbsnp
<-
bool
;
realign
<-
bool
;
baseRecalibration
<-
bool
)
yield
Array
(
""
,
s1
,
s2
,
multi
,
dbsnp
,
realign
,
baseRecalibration
)
s1
<-
sample1
;
s2
<-
sample2
;
realign
<-
realignProvider
;
baseRecalibration
<-
baseRecalibrationProvider
)
yield
Array
(
""
,
s1
,
s2
,
realign
,
baseRecalibration
)
}
def
sample1
=
Array
(
false
,
true
)
def
sample2
=
Array
(
false
,
true
)
def
realignProvider
=
Array
(
false
,
true
)
def
baseRecalibrationProvider
=
Array
(
false
,
true
)
def
multisampleCalling
:
Boolean
=
true
def
sampleCalling
=
false
def
libraryCalling
=
false
def
dbsnp
:
Boolean
=
true
@Test
(
dataProvider
=
"shivaOptions"
)
def
testShiva
(
f
:
String
,
sample1
:
Boolean
,
sample2
:
Boolean
,
multi
:
Boolean
,
dbsnp
:
Boolean
,
realign
:
Boolean
,
baseRecalibration
:
Boolean
)
:
Unit
=
{
val
map
=
{
var
m
:
Map
[
String
,
Any
]
=
ShivaTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample2
,
m
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test.vcf.gz"
),
m
)
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_variantcalling"
->
multi
,
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_variantcalling"
->
multisampleCalling
,
"single_sample_variantcalling"
->
sampleCalling
,
"library_variantcalling"
->
libraryCalling
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
)
...
...
@@ -87,11 +96,37 @@ class ShivaTest extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
numberLibs
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
if
(
multi
)
2
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
(
if
(
multisampleCalling
)
2
else
0
)
+
(
if
(
sampleCalling
)
numberSamples
*
2
else
0
)
+
(
if
(
libraryCalling
)
numberLibs
*
2
else
0
))
}
}
}
class
ShivaDefaultTest
extends
ShivaTestTrait
class
ShivaNoDbsnpTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
realignProvider
=
Array
(
true
)
override
def
dbsnp
=
false
}
class
ShivaLibraryCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
,
false
)
override
def
sample2
=
Array
(
false
,
true
)
override
def
realignProvider
=
Array
(
false
)
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
libraryCalling
=
true
}
class
ShivaSampleCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
,
false
)
override
def
sample2
=
Array
(
false
,
true
)
override
def
realignProvider
=
Array
(
false
)
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
sampleCalling
=
true
}
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
...
...
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