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biopet.biopet
Commits
048dc6d5
Commit
048dc6d5
authored
May 13, 2016
by
Wai Yi Leung
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parent
860ab6c3
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12 additions
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13 deletions
+12
-13
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
.../nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
+5
-5
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
...lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
+4
-5
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+1
-1
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
...lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
+1
-1
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
View file @
048dc6d5
...
...
@@ -4,12 +4,12 @@ package nl.lumc.sasc.biopet.extensions.clever
* Created by wyleung on 4-4-16.
*/
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
scala.io.Source
...
...
@@ -125,9 +125,9 @@ object CleverFixVCF extends ToolCommand {
val
inputVCF
=
Source
.
fromFile
(
input
)
val
writer
=
new
PrintWriter
(
output
)
inputVCF
.
getLines
().
foreach
(
x
=>
writer
.
write
(
replaceHeaderLine
(
x
,
vcfColHeader
,
vcfColReplacementHeader
+
commandArgs
.
sampleLabel
,
extraHeader
))
)
inputVCF
.
getLines
().
foreach
(
x
=>
writer
.
write
(
replaceHeaderLine
(
x
,
vcfColHeader
,
vcfColReplacementHeader
+
commandArgs
.
sampleLabel
,
extraHeader
))
)
writer
.
close
()
inputVCF
.
close
()
}
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCFTest.scala
View file @
048dc6d5
...
...
@@ -5,8 +5,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by wyleung on 13-5-16.
*/
* Created by wyleung on 13-5-16.
*/
class
CleverFixVCFTest
extends
TestNGSuite
with
Matchers
{
@Test
...
...
@@ -16,10 +16,9 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
CleverFixVCF
.
vcfColHeader
,
CleverFixVCF
.
vcfColReplacementHeader
+
"testsample"
,
CleverFixVCF
.
extraHeader
)
should
equal
(
CleverFixVCF
.
extraHeader
+
"\n"
+
CleverFixVCF
.
vcfColReplacementHeader
+
"testsample"
+
"\n"
)
)
should
equal
(
CleverFixVCF
.
extraHeader
+
"\n"
+
CleverFixVCF
.
vcfColReplacementHeader
+
"testsample"
+
"\n"
)
}
@Test
def
replacementOther
=
{
val
vcfRecord
=
"chrM\t312\tL743020\t.\t<DEL>\t.\tPASS\tBPWINDOW=313,16189;CILEN=15866,15888;IMPRECISE;SVLEN=-15877;SVTYPE=DEL\tGT:DP\t1/.:103"
...
...
@@ -29,7 +28,7 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
CleverFixVCF
.
vcfColHeader
,
CleverFixVCF
.
vcfColReplacementHeader
+
"testsample"
,
CleverFixVCF
.
extraHeader
)
should
equal
(
vcfRecordExpected
+
"\n"
)
)
should
equal
(
vcfRecordExpected
+
"\n"
)
}
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
View file @
048dc6d5
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.
{
BreakdancerCaller
,
BreakdancerConfig
,
BreakdancerVCF
}
import
nl.lumc.sasc.biopet.extensions.picard.SortVcf
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
View file @
048dc6d5
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.clever.
{
CleverCaller
,
CleverFixVCF
}
import
nl.lumc.sasc.biopet.extensions.clever.
{
CleverCaller
,
CleverFixVCF
}
import
nl.lumc.sasc.biopet.extensions.picard.SortVcf
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
View file @
048dc6d5
...
...
@@ -30,7 +30,7 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
var
inputBams
:
Map
[
String
,
File
]
=
Map
.
empty
val
sampleNameSuffix
:
String
=
config
(
"samplename_suffix"
,
default
=
""
)
val
sampleNameSuffix
:
String
=
config
(
"samplename_suffix"
,
default
=
""
)
def
outputVCF
(
sample
:
String
)
:
Option
[
File
]
=
{
outputVCFs
.
get
(
sample
)
match
{
...
...
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