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biopet.biopet
Commits
b4c7ded4
Commit
b4c7ded4
authored
Sep 27, 2016
by
Peter van 't Hof
Browse files
Added more job testing
parent
6f2d19e0
Changes
1
Hide whitespace changes
Inline
Side-by-side
basty/src/test/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTest.scala
View file @
b4c7ded4
...
...
@@ -3,9 +3,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
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.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
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
...
...
@@ -41,10 +42,11 @@ class BastyTest extends TestNGSuite with Matchers {
def
multisampleCalling
:
Boolean
=
true
def
sampleCalling
=
false
def
libraryCalling
=
false
def
dbsnp
=
tru
e
def
dbsnp
=
fals
e
def
svCalling
=
false
def
cnvCalling
=
false
def
annotation
=
false
def
bootRuns
:
Option
[
Int
]
=
None
@Test
(
dataProvider
=
"bastyOptions"
)
def
testBasty
(
f
:
String
,
sample1
:
Boolean
,
sample2
:
Boolean
)
:
Unit
=
{
...
...
@@ -61,7 +63,8 @@ class BastyTest extends TestNGSuite with Matchers {
"use_base_recalibration"
->
baseRecalibration
,
"sv_calling"
->
svCalling
,
"cnv_calling"
->
cnvCalling
,
"annotation"
->
annotation
),
m
)
"annotation"
->
annotation
,
"boot_runs"
->
bootRuns
),
m
)
}
...
...
@@ -105,6 +108,10 @@ class BastyTest extends TestNGSuite with Matchers {
(
if
(
multisampleCalling
)
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
)))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RunGubbins
])
shouldBe
2
}
}
}
...
...
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