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biopet.biopet
Commits
ec4eb7de
Commit
ec4eb7de
authored
May 15, 2016
by
Peter van 't Hof
Browse files
Style fixes
parent
03360822
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
ec4eb7de
...
...
@@ -3,13 +3,13 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
}
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
}
/**
* Created by pjvanthof on 15/05/16.
...
...
@@ -27,6 +27,7 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
def
mergeStrategies
=
MultisampleMapping
.
MergeStrategy
.
values
def
bamToFastq
=
false
def
correctReadgroups
=
false
def
unmappedToGears
=
false
def
sample1
=
Array
(
true
,
false
)
def
sample2
=
Array
(
true
,
false
)
...
...
@@ -43,7 +44,12 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
var
m
:
Map
[
String
,
Any
]
=
MultisampleMappingTestTrait
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
MultisampleMappingTestTrait
.
sample2
,
m
)
m
++
Map
(
"merge_strategy"
->
merge
.
toString
,
"bam_to_fastq"
->
bamToFastq
,
"correct_readgroups"
->
correctReadgroups
)
m
++
Map
(
"merge_strategy"
->
merge
.
toString
,
"bam_to_fastq"
->
bamToFastq
,
"correct_readgroups"
->
correctReadgroups
,
"unmapped_to_gears"
->
unmappedToGears
)
}
if
(!
sample1
&&
!
sample2
)
{
// When no samples
...
...
@@ -64,7 +70,12 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MergeSam
||
merge
==
MergeStrategy
.
PreProcessMergeSam
))
1
else
0
))
pipeline
.
samples
.
foreach
{
case
(
sampleName
,
sample
)
=>
if
(
merge
==
MergeStrategy
.
None
)
sample
.
bamFile
shouldBe
None
sample
.
summaryStats
shouldBe
Map
()
sample
.
libraries
.
foreach
{
case
(
libraryId
,
library
)
=>
library
.
summaryStats
shouldBe
Map
()
}
}
pipeline
.
summarySettings
.
get
(
"merge_strategy"
)
shouldBe
Some
(
merge
.
toString
)
}
}
}
...
...
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