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biopet.biopet
Commits
f6bfca5d
Commit
f6bfca5d
authored
Jun 03, 2016
by
Peter van 't Hof
Browse files
Switch to Queue 3.6
parent
e5d79321
Changes
5
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biopet-core/pom.xml
View file @
f6bfca5d
...
...
@@ -56,7 +56,7 @@
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue
</artifactId>
<version>
3.
5
</version>
<version>
3.
6
</version>
<exclusions>
<exclusion>
<groupId>
org.broadinstitute.gatk
</groupId>
...
...
@@ -67,7 +67,7 @@
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue-extensions-public
</artifactId>
<version>
3.
5
</version>
<version>
3.
6
</version>
</dependency>
<dependency>
<groupId>
org.scalatra.scalate
</groupId>
...
...
biopet-tools/pom.xml
View file @
f6bfca5d
...
...
@@ -65,7 +65,7 @@
<dependency>
<groupId>
com.github.broadinstitute
</groupId>
<artifactId>
picard
</artifactId>
<version>
1.14
1
</version>
<version>
2.4.
1
</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
View file @
f6bfca5d
...
...
@@ -177,10 +177,10 @@ object VcfWithVcf extends ToolCommand {
def
getSecondaryRecords
(
secondaryReader
:
VCFFileReader
,
record
:
VariantContext
,
matchAllele
:
Boolean
)
:
List
[
VariantContext
]
=
{
if
(
matchAllele
)
{
secondaryReader
.
query
(
record
.
getContig
,
record
.
getStart
,
record
.
getEnd
).
toList
.
filter
(
x
=>
record
.
getAlternateAlleles
.
exists
(
x
.
hasAlternateAllele
))
secondaryReader
.
query
(
record
.
getContig
,
record
.
getStart
,
record
.
getEnd
).
filter
(
x
=>
record
.
getAlternateAlleles
.
exists
(
x
.
hasAlternateAllele
))
.
toList
}
else
{
secondaryReader
.
query
(
record
.
getContig
,
record
.
getStart
,
record
.
getEnd
).
toList
secondaryReader
.
query
(
record
.
getContig
,
record
.
getStart
,
record
.
getEnd
).
toIterable
.
toList
}
}
...
...
biopet-utils/pom.xml
View file @
f6bfca5d
...
...
@@ -66,7 +66,7 @@
<dependency>
<groupId>
com.github.samtools
</groupId>
<artifactId>
htsjdk
</artifactId>
<version>
1.14
1
</version>
<version>
2.4.
1
</version>
</dependency>
<dependency>
<groupId>
org.scala-lang
</groupId>
...
...
gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/impute/Impute2VcfTest.scala
View file @
f6bfca5d
...
...
@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by pjvan_thof on 31-5-16.
*/
* Created by pjvan_thof on 31-5-16.
*/
class
Impute2VcfTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Impute2Vcf
=
{
new
Impute2Vcf
{
...
...
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