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
048dc6d5
Commit
048dc6d5
authored
May 13, 2016
by
Wai Yi Leung
Browse files
Style
parent
860ab6c3
Changes
5
Hide whitespace changes
Inline
Side-by-side
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
{
...
...
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