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biopet.biopet
Commits
717a50df
Commit
717a50df
authored
Mar 01, 2017
by
Peter van 't Hof
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Fixing small issues
parent
81108a2a
Changes
1
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21 additions
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14 deletions
+21
-14
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
...asc/biopet/pipelines/mapping/MultisampleMappingTest.scala
+21
-14
No files found.
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
717a50df
...
...
@@ -14,27 +14,32 @@
*/
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.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.extensions.centrifuge.Centrifuge
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
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.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Created by pjvanthof on 15/05/16.
*/
trait
MultisampleMappingTestTrait
extends
TestNGSuite
with
Matchers
{
val
outputDir
=
MultisampleMappingTestTrait
.
outputDir
val
configMap
=
MultisampleMappingTestTrait
.
config
(
outputDir
)
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
MultisampleMapping
=
{
new
MultisampleMapping
()
{
override
def
configNamespace
=
"multisamplemapping"
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
MultisampleMappingTestTrait
.
config
))
override
def
globalConfig
=
new
Config
(
ConfigUtils
.
mergeMaps
(
map
,
configMap
))
qSettings
=
new
QSettings
qSettings
.
runName
=
"test"
}
...
...
@@ -59,7 +64,7 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
@Test
(
dataProvider
=
"mappingOptions"
)
def
testMultisampleMapping
(
merge
:
MultisampleMapping.MergeStrategy.Value
,
sample1
:
Boolean
,
sample2
:
Boolean
)
:
Unit
=
{
val
map
:
Map
[
String
,
Any
]
=
{
var
m
:
Map
[
String
,
Any
]
=
MultisampleMappingTestTrait
.
config
var
m
:
Map
[
String
,
Any
]
=
configMap
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample2
,
m
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample3
,
m
)
...
...
@@ -111,6 +116,11 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
pipeline
.
summarySettings
.
get
(
"merge_strategy"
)
shouldBe
Some
(
merge
.
toString
)
}
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
FileUtils
.
deleteDirectory
(
outputDir
)
}
}
class
MultisampleMappingTest
extends
MultisampleMappingTestTrait
{
...
...
@@ -162,12 +172,7 @@ class MultisampleMappingBamToFastqTest extends MultisampleMappingTestTrait {
}
object
MultisampleMappingTestTrait
{
private
var
dirs
:
List
[
File
]
=
Nil
def
outputDir
=
{
val
dir
=
Files
.
createTempDir
()
dirs
:+=
dir
dir
}
def
outputDir
=
Files
.
createTempDir
()
val
inputDir
=
Files
.
createTempDir
()
...
...
@@ -179,7 +184,9 @@ object MultisampleMappingTestTrait {
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
val
os
=
new
FileOutputStream
(
new
File
(
inputDir
,
name
))
val
out
=
new
File
(
inputDir
,
name
)
out
.
deleteOnExit
()
val
os
=
new
FileOutputStream
(
out
)
org
.
apache
.
commons
.
io
.
IOUtils
.
copy
(
is
,
os
)
os
.
close
()
}
...
...
@@ -189,7 +196,7 @@ object MultisampleMappingTestTrait {
copyFile
(
"ref.fa.fai"
)
copyFile
(
"empty.sam"
)
def
config
=
Map
(
def
config
(
outputDir
:
File
)
=
Map
(
"skip_write_dependencies"
->
true
,
"name_prefix"
->
"test"
,
"cache"
->
true
,
...
...
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