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biopet.biopet
Commits
c0d8c129
Commit
c0d8c129
authored
Oct 15, 2015
by
Peter van 't Hof
Browse files
Remove some test and optimize code
parent
08bcca4d
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/AbstractTestMapping.scala
View file @
c0d8c129
...
...
@@ -15,28 +15,24 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.extensions.bwa.
{
BwaAln
,
BwaMem
,
BwaSampe
,
BwaSamse
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
AddOrReplaceReadGroups
,
MarkDuplicates
,
MergeSamFiles
,
SortSam
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import
nl.lumc.sasc.biopet.extensions.tools.
{
FastqSync
,
SeqStat
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Test class for [[Mapping]]
*
* Created by pjvan_thof on 2/12/15.
*/
abstract
class
AbstractTestMapping
extends
TestNGSuite
with
Matchers
{
abstract
class
AbstractTestMapping
(
val
aligner
:
String
)
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Mapping
=
{
new
Mapping
{
override
def
configName
=
"mapping"
...
...
@@ -46,13 +42,10 @@ abstract class AbstractTestMapping 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"
)
val
paired
=
Array
(
true
,
false
)
val
chunks
=
Array
(
1
,
5
,
10
,
100
)
val
chunks
=
Array
(
1
,
5
)
val
skipMarkDuplicates
=
Array
(
true
,
false
)
val
skipFlexipreps
=
Array
(
true
,
false
)
val
zipped
=
Array
(
true
,
false
)
...
...
@@ -100,42 +93,17 @@ abstract class AbstractTestMapping 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"
}
class
MappingBwaMemTest
extends
AbstractTestMapping
(
"bwa-mem"
)
class
MappingBwaAlnTest
extends
AbstractTestMapping
(
"bwa-aln"
)
class
MappingStarTest
extends
AbstractTestMapping
(
"star"
)
class
MappingStar2PassTest
extends
AbstractTestMapping
(
"star-2pass"
)
class
MappingBowtieTest
extends
AbstractTestMapping
(
"bowtie"
)
class
MappingStampyTest
extends
AbstractTestMapping
(
"stampy"
)
class
MappingGsnapTest
extends
AbstractTestMapping
(
"gsnap"
)
class
MappingTophatTest
extends
AbstractTestMapping
(
"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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