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biopet.biopet
Commits
9cae1c11
Commit
9cae1c11
authored
Oct 15, 2015
by
Peter van 't Hof
Browse files
Gentrap test are now divided over 7 threads
parent
f8785ed4
Changes
1
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Inline
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public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
9cae1c11
...
...
@@ -28,7 +28,7 @@ import org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
class
GentrapTest
extends
TestNGSuite
with
Matchers
{
abstract
class
GentrapTest
Abstract
(
val
expressionMeasure
:
String
)
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Gentrap
=
{
new
Gentrap
()
{
...
...
@@ -70,7 +70,7 @@ class GentrapTest extends TestNGSuite with Matchers {
.
toMap
)
private
lazy
val
validExpressionMeasures
=
Set
(
val
validExpressionMeasures
=
Set
(
"fragments_per_gene"
,
"fragments_per_exon"
,
"bases_per_gene"
,
"bases_per_exon"
,
"cufflinks_strict"
,
"cufflinks_guided"
,
"cufflinks_blind"
)
...
...
@@ -96,7 +96,7 @@ class GentrapTest extends TestNGSuite with Matchers {
for
{
sampleConfig
<-
sampleConfigs
.
toArray
expressionMeasure
<-
expressionMeasures
//
expressionMeasure <- expressionMeasures
strandProtocol
<-
strandProtocols
}
yield
Array
(
sampleConfig
,
List
(
expressionMeasure
),
strandProtocol
)
}
...
...
@@ -175,6 +175,14 @@ class GentrapTest extends TestNGSuite with Matchers {
}
}
class
GentrapFragmentsPerGeneTest
extends
GentrapTestAbstract
(
"fragments_per_gene"
)
class
GentrapFragmentsPerExonTest
extends
GentrapTestAbstract
(
"fragments_per_exon"
)
class
GentrapBasesPerGeneTest
extends
GentrapTestAbstract
(
"bases_per_gene"
)
class
GentrapBasesPerExonTest
extends
GentrapTestAbstract
(
"bases_per_exon"
)
class
GentrapCufflinksStrictTest
extends
GentrapTestAbstract
(
"cufflinks_strict"
)
class
GentrapCufflinksGuidedTest
extends
GentrapTestAbstract
(
"cufflinks_guided"
)
class
GentrapCufflinksBlindTest
extends
GentrapTestAbstract
(
"cufflinks_blind"
)
object
GentrapTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
...
...
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