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biopet.biopet
Commits
b55361cd
Commit
b55361cd
authored
Jun 24, 2016
by
Wai Yi Leung
Browse files
add test for WipeReads, check on instance in Gentrap
parent
c7be8c6d
Changes
1
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Inline
Side-by-side
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
b55361cd
...
...
@@ -14,20 +14,20 @@
*/
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.core.
{
BiopetFifoPipe
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.gmap.Gsnap
import
nl.lumc.sasc.biopet.extensions.hisat.Hisat2
import
nl.lumc.sasc.biopet.extensions.tools.BaseCounter
import
nl.lumc.sasc.biopet.extensions.tools.
{
BaseCounter
,
WipeReads
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
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
,
val
aligner
:
Option
[
String
])
extends
TestNGSuite
with
Matchers
{
...
...
@@ -146,6 +146,10 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
assert
(
gentrap
.
functions
.
exists
(
_
.
isInstanceOf
[
Ln
]))
}
if
(
gentrap
.
removeRibosomalReads
)
{
assert
(
gentrap
.
functions
.
exists
(
_
.
isInstanceOf
[
WipeReads
]))
}
val
classMap
=
Map
(
"gsnap"
->
classOf
[
Gsnap
],
"tophat"
->
classOf
[
Tophat
],
...
...
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