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biopet.biopet
Commits
ede07209
Commit
ede07209
authored
Mar 13, 2016
by
Peter van 't Hof
Browse files
Merge branch 'fix-compile_issues' into 'develop'
Fix compile issues See merge request !352
parents
f3779b52
e6d50ed6
Changes
3
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public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala
View file @
ede07209
...
...
@@ -8,11 +8,10 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by ahbbollen on 3-3-16.
*/
* Created by ahbbollen on 3-3-16.
*/
class
VariantEffectPredictorTest
extends
TestNGSuite
with
Matchers
{
@Test
def
testSummaryStats
=
{
val
file
=
new
File
(
Paths
.
get
(
getClass
.
getResource
(
"/vep.metrics"
).
toURI
).
toString
)
...
...
@@ -31,7 +30,6 @@ class VariantEffectPredictorTest extends TestNGSuite with Matchers {
stats
.
contains
(
"Distribution_of_variants_on_chromosome_1"
)
shouldBe
true
stats
.
contains
(
"Position_in_protein"
)
shouldBe
true
}
}
public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
View file @
ede07209
...
...
@@ -130,7 +130,7 @@ object SeqStat extends ToolCommand {
baseStats
++=
mutable
.
ArrayBuffer
.
fill
(
record
.
length
-
baseStats
.
length
)(
BaseStat
())
}
if
(
readStats
.
lengths
.
length
<=
record
.
length
)
{
if
(
readStats
.
lengths
.
length
<=
record
.
length
)
readStats
.
lengths
++=
mutable
.
ArrayBuffer
.
fill
(
record
.
length
-
readStats
.
lengths
.
length
+
1
)(
0
)
val
readQuality
=
record
.
getBaseQualityString
...
...
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
ede07209
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gentrap
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions._
...
...
@@ -25,7 +25,7 @@ import nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
abstract
class
GentrapTestAbstract
(
val
expressionMeasure
:
String
)
extends
TestNGSuite
with
Matchers
{
...
...
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