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biopet.biopet
Commits
fbc7a317
Commit
fbc7a317
authored
Apr 29, 2016
by
Peter van 't Hof
Browse files
Fixed tests
parent
b53183a5
Changes
3
Hide whitespace changes
Inline
Side-by-side
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
fbc7a317
...
...
@@ -15,20 +15,20 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
java.nio.file.Paths
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import
nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelConfig
,
PindelVCF
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.extensions.pindel.
{
PindelCaller
,
PindelConfig
,
PindelVCF
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
...
...
@@ -152,9 +152,9 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
Map
(
"bam"
->
ShivaSvCallingTest
.
inputTouch
(
"bam"
+
".bam"
))
intercept
[
IllegalArgumentException
]
{
pipeline
.
init
()
pipeline
.
script
()
}
Logging
.
errors
.
clear
()
}
private
def
resourcePath
(
p
:
String
)
:
String
=
{
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
fbc7a317
...
...
@@ -84,7 +84,7 @@ class ShivaTest extends TestNGSuite with Matchers {
// Gatk preprocess
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
numberLibs
else
0
)
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
)
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
fbc7a317
...
...
@@ -15,7 +15,6 @@ import nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
...
...
@@ -53,9 +52,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
(
for
(
bams
<-
0
to
2
;
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
(
for
(
bams
<-
0
to
2
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
,
freebayes
,
varscanCnsSinglesample
)
).
toArray
...
...
@@ -89,7 +86,7 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(
callers
.
isEmpty
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
callers
.
isEmpty
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
@@ -113,10 +110,6 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
)
}
}
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
ShivaVariantcallingTest
.
outputDir
)
}
}
class
ShivaVariantcallingNoVariantcallersTest
extends
ShivaVariantcallingTestTrait
...
...
@@ -165,6 +158,7 @@ class ShivaVariantcallingVarscanCnsSinglesampleTest extends ShivaVariantcallingT
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
outputDir
.
deleteOnExit
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
...
...
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