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biopet.biopet
Commits
08bcca4d
Commit
08bcca4d
authored
Oct 15, 2015
by
Peter van 't Hof
Browse files
Each aligner has his own class now
parent
ba0cf48a
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping
Test
.scala
→
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/
AbstractTest
Mapping.scala
View file @
08bcca4d
...
...
@@ -36,7 +36,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
*
* Created by pjvan_thof on 2/12/15.
*/
class
Mapping
Test
extends
TestNGSuite
with
Matchers
{
abstract
class
AbstractTest
Mapping
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Mapping
=
{
new
Mapping
{
override
def
configName
=
"mapping"
...
...
@@ -46,6 +46,8 @@ class MappingTest extends TestNGSuite with Matchers {
}
}
val
aligner
:
String
@DataProvider
(
name
=
"mappingOptions"
)
def
mappingOptions
=
{
val
aligners
=
Array
(
"bwa-mem"
,
"bwa-aln"
,
"star"
,
"star-2pass"
,
"bowtie"
,
"stampy"
,
"gsnap"
,
"tophat"
)
...
...
@@ -56,7 +58,6 @@ class MappingTest extends TestNGSuite with Matchers {
val
zipped
=
Array
(
true
,
false
)
for
(
aligner
<-
aligners
;
pair
<-
paired
;
chunk
<-
chunks
;
skipMarkDuplicate
<-
skipMarkDuplicates
;
...
...
@@ -99,7 +100,42 @@ class MappingTest extends TestNGSuite with Matchers {
}
}
class
MappingBwaMemTest
extends
AbstractTestMapping
{
val
aligner
=
"bwa-mem"
}
class
MappingBwaAlnTest
extends
AbstractTestMapping
{
val
aligner
=
"bwa-aln"
}
class
MappingStarTest
extends
AbstractTestMapping
{
val
aligner
=
"star"
}
class
MappingStar2PassTest
extends
AbstractTestMapping
{
val
aligner
=
"star-2pass"
}
class
MappingBowtieTest
extends
AbstractTestMapping
{
val
aligner
=
"bowtie"
}
class
MappingStampyTest
extends
AbstractTestMapping
{
val
aligner
=
"stampy"
}
class
MappingGsnapTest
extends
AbstractTestMapping
{
val
aligner
=
"gsnap"
}
class
MappingTophatTest
extends
AbstractTestMapping
{
val
aligner
=
"tophat"
}
object
MappingTest
{
val
aligners
=
Array
(
"bwa-mem"
,
"bwa-aln"
,
"star"
,
"star-2pass"
,
"bowtie"
,
"stampy"
,
"gsnap"
,
"tophat"
)
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
...
...
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