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biopet.biopet
Commits
000e1325
Commit
000e1325
authored
May 14, 2016
by
Peter van 't Hof
Browse files
Adding tests on normalize step
parent
43253296
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
000e1325
...
...
@@ -5,20 +5,21 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetPipe
import
nl.lumc.sasc.biopet.extensions.Freebayes
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
CombineVariants
,
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
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
...
...
@@ -48,6 +49,9 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
def
freebayes
:
Boolean
=
false
def
varscanCnsSinglesample
:
Boolean
=
false
def
normalize
=
false
def
decompose
=
false
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
(
for
(
bams
<-
0
to
2
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
...
...
@@ -79,7 +83,11 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
if
(
haplotypeCaller
)
callers
.
append
(
"haplotypecaller"
)
if
(
freebayes
)
callers
.
append
(
"freebayes"
)
if
(
varscanCnsSinglesample
)
callers
.
append
(
"varscan_cns_singlesample"
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
,
"execute_vt_normalize"
->
normalize
,
"execute_vt_decompose"
->
decompose
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
n
.
toString
->
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toMap
...
...
@@ -106,6 +114,8 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
UnifiedGenotyper
])
shouldBe
(
if
(
unifiedGenotyper
)
1
else
0
)
+
(
if
(
unifiedGenotyperAllele
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
1
+
callers
.
size
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtNormalize
])
shouldBe
(
if
(
normalize
)
callers
.
size
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VtDecompose
])
shouldBe
(
if
(
decompose
)
callers
.
size
else
0
)
}
}
}
...
...
@@ -153,6 +163,20 @@ class ShivaVariantcallingFreebayesTest extends ShivaVariantcallingTestTrait {
class
ShivaVariantcallingVarscanCnsSinglesampleTest
extends
ShivaVariantcallingTestTrait
{
override
def
varscanCnsSinglesample
:
Boolean
=
true
}
class
ShivaVariantcallingNormalizeTest
extends
ShivaVariantcallingTestTrait
{
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
normalize
=
true
}
class
ShivaVariantcallingDecomposeTest
extends
ShivaVariantcallingTestTrait
{
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
decompose
=
true
}
class
ShivaVariantcallingNormalizeDecomposeTest
extends
ShivaVariantcallingTestTrait
{
override
def
unifiedGenotyper
:
Boolean
=
true
override
def
normalize
=
true
override
def
decompose
=
true
}
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
...
...
@@ -189,6 +213,7 @@ object ShivaVariantcallingTest {
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
),
"input_alleles"
->
"test.vcf.gz"
,
"varscan_jar"
->
"test"
"varscan_jar"
->
"test"
,
"vt"
->
Map
(
"exe"
->
"test"
)
)
}
\ No newline at end of file
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