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biopet.biopet
Commits
fcb1e2f5
Commit
fcb1e2f5
authored
Jan 20, 2016
by
Sander van der Zeeuw
Browse files
Merge remote-tracking branch 'origin/feature-VarscanIntoShiva' into feature-VarscanIntoShiva
parents
6073f6aa
30696cab
Changes
4
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
View file @
fcb1e2f5
...
...
@@ -15,20 +15,15 @@
*/
package
nl.lumc.sasc.biopet.extensions.varscan
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetJavaCommandLineFunction
}
abstract
class
Varscan
extends
BiopetJavaCommandLineFunction
{
abstract
class
Varscan
extends
BiopetJavaCommandLineFunction
with
Version
{
override
def
subPath
=
"varscan"
::
super
.
subPath
jarFile
=
config
(
"varscan_jar"
)
/**
* TODO: test version
* override def versionCommand = super.commandLine
* override val versionRegex = """VarScan v(.*)""".r
*/
override
def
defaultCoreMemory
=
5.0
def
versionCommand
=
super
.
commandLine
def
versionRegex
=
"""VarScan v(.*)"""
.
r
}
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/VarscanMpileup2cns.scala
View file @
fcb1e2f5
...
...
@@ -39,6 +39,8 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
var
vcfSampleList
:
Option
[
File
]
=
config
(
"vcf_sample_list"
)
var
variants
:
Option
[
Int
]
=
config
(
"variants"
)
override
def
defaultCoreMemory
=
6.0
override
def
beforeGraph
()
:
Unit
=
{
val
validValues
:
Set
[
Int
]
=
Set
(
0
,
1
)
// check for boolean vars that are passed as ints
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @
fcb1e2f5
...
...
@@ -5,7 +5,7 @@ import java.io.PrintWriter
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.extensions.varscan.
{
FixMpileup
,
VarscanMpileup2cns
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
fcb1e2f5
...
...
@@ -77,7 +77,7 @@ class ShivaVariantcallingTest 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
||
(!
raw
&&
!
bcftools
&&
!
bcftoolsSinglesample
&&
!
freebayes
)
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
bcftoolsSinglesample
&&
!
freebayes
&&
!
varscanCnsSinglesample
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
@@ -86,7 +86,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
if
(!
illegalArgumentException
)
{
pipeline
.
script
()
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
1
+
(
if
(
raw
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
(
1
+
(
if
(
raw
)
1
else
0
)
+
(
if
(
varscanCnsSinglesample
)
1
else
0
))
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
Freebayes
])
shouldBe
(
if
(
freebayes
)
1
else
0
)
...
...
@@ -133,6 +133,7 @@ object ShivaVariantcallingTest {
"freebayes"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
)
"tabix"
->
Map
(
"exe"
->
"test"
),
"varscan_jar"
->
"test"
)
}
\ No newline at end of file
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