Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
0d010c88
Commit
0d010c88
authored
Oct 21, 2015
by
Sander van der Zeeuw
Browse files
changed imports
parent
025740f5
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
0d010c88
...
...
@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.utils.commandline.Input
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
0d010c88
...
...
@@ -49,11 +49,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@DataProvider
(
name
=
"shivaVariantcallingOptions"
)
def
shivaVariantcallingOptions
=
{
val
bool
=
Array
(
true
,
false
)
(
for
(
bams
<-
0
to
3
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
freebayes
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
freebayes
)).
toArray
(
for
(
bams
<-
0
to
3
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
freebayes
<-
bool
)
yield
Array
(
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
freebayes
)).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
...
...
@@ -72,7 +74,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toList
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
freebayes
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftools_singlesample
&&
!
freebayes
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment