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biopet.biopet
Commits
81e75fbd
Commit
81e75fbd
authored
Sep 28, 2016
by
Peter van 't Hof
Browse files
Format fix
parent
1aea2582
Changes
1
Hide whitespace changes
Inline
Side-by-side
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
81e75fbd
package
nl.lumc.sasc.biopet.pipelines.basty
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.
{
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.
{
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.extensions.gatk.
{
BaseRecalibrator
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.tools.
{
BastyGenerateFasta
,
VcfStats
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
BastyGenerateFasta
,
VcfStats
}
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
}
/**
* Created by pjvanthof on 27/09/16.
*/
* Created by pjvanthof on 27/09/16.
*/
class
BastyTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Basty
=
{
new
Basty
()
{
...
...
@@ -27,7 +27,6 @@ class BastyTest extends TestNGSuite with Matchers {
}
}
@DataProvider
(
name
=
"bastyOptions"
)
def
bastyOptions
=
{
for
(
...
...
@@ -110,8 +109,8 @@ class BastyTest extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
(
if
(
multisampleCalling
)
2
else
0
)
+
(
if
(
sampleCalling
)
numberSamples
*
2
else
0
)
+
(
if
(
libraryCalling
)
numberLibs
*
2
else
0
))
(
if
(
sampleCalling
)
numberSamples
*
2
else
0
)
+
(
if
(
libraryCalling
)
numberLibs
*
2
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BastyGenerateFasta
])
shouldBe
2
+
(
2
*
numberSamples
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
Raxml
])
shouldBe
(
2
*
(
2
+
bootRuns
.
getOrElse
(
100
)))
...
...
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