Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
2b479c4c
Commit
2b479c4c
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Fixed unit tests
parent
e5d7f321
Changes
2
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
2b479c4c
...
...
@@ -125,7 +125,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
}
else
None
def
bamFile
:
Option
[
File
]
=
mapping
match
{
case
Some
(
m
)
=>
Some
(
m
.
final
BamFile
)
case
Some
(
m
)
=>
Some
(
m
.
merged
BamFile
)
case
_
if
inputBam
.
isDefined
=>
Some
(
new
File
(
libDir
,
s
"$sampleId-$libId.bam"
))
case
_
=>
None
}
...
...
@@ -249,7 +249,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
case
MergeStrategy
.
None
=>
case
(
MergeStrategy
.
MergeSam
)
if
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
size
==
1
=>
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
head
,
bamFile
.
get
)
:
_
*
)
case
(
MergeStrategy
.
PreProcessMergeSam
|
MergeStrategy
.
PreProcessMarkDuplicates
)
if
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
size
==
1
=>
case
(
MergeStrategy
.
PreProcessMergeSam
)
if
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
size
==
1
=>
add
(
Ln
.
linkBamFile
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
head
,
bamFile
.
get
)
:
_
*
)
case
MergeStrategy
.
MergeSam
=>
add
(
MergeSamFiles
(
qscript
,
libraries
.
flatMap
(
_
.
_2
.
bamFile
).
toList
,
bamFile
.
get
,
isIntermediate
=
!
keepMergedFiles
))
...
...
@@ -312,7 +312,8 @@ class MultisampleMapping(val parent: Configurable) extends QScript with Multisam
object
MultisampleMapping
extends
PipelineCommand
{
object
MergeStrategy
extends
Enumeration
{
val
None
,
MergeSam
,
MarkDuplicates
,
PreProcessMergeSam
,
PreProcessMarkDuplicates
,
PreProcessSambambaMarkdup
=
Value
val
None
,
MergeSam
,
MarkDuplicates
,
PreProcessMergeSam
,
PreProcessMarkDuplicates
,
PreProcessSambambaMarkdup
=
Value
}
/** When file is not absolute an error is raise att the end of the script of a pipeline */
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala
View file @
2b479c4c
...
...
@@ -14,19 +14,20 @@
*/
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.extensions.sambamba.SambambaMarkdup
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.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
/**
* Created by pjvanthof on 15/05/16.
...
...
@@ -96,11 +97,17 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
val
pipesJobs
=
pipeline
.
functions
.
filter
(
_
.
isInstanceOf
[
BiopetCommandLineFunction
])
.
flatMap
(
_
.
asInstanceOf
[
BiopetCommandLineFunction
].
pipesJobs
)
if
(
merge
==
MultisampleMapping
.
MergeStrategy
.
PreProcessMarkDuplicates
)
{
""
}
import
MultisampleMapping.MergeStrategy
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberFastqLibs
+
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MarkDuplicates
||
merge
==
MergeStrategy
.
PreProcessMarkDuplicates
)
)
1
else
0
))
(
if
(
merge
==
MergeStrategy
.
MarkDuplicates
||
merge
==
MergeStrategy
.
PreProcessMarkDuplicates
)
numberSamples
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
(
if
(
sample2
&&
(
merge
==
MergeStrategy
.
MergeSam
||
merge
==
MergeStrategy
.
PreProcessMergeSam
))
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
SambambaMarkdup
])
shouldBe
(
if
(
merge
==
MergeStrategy
.
PreProcessSambambaMarkdup
)
numberSamples
else
0
)
pipeline
.
samples
.
foreach
{
case
(
sampleName
,
sample
)
=>
if
(
merge
==
MergeStrategy
.
None
)
sample
.
bamFile
shouldBe
None
...
...
@@ -211,6 +218,7 @@ object MultisampleMappingTestTrait {
"sickle"
->
Map
(
"exe"
->
"test"
),
"cutadapt"
->
Map
(
"exe"
->
"test"
),
"bwa"
->
Map
(
"exe"
->
"test"
),
"sambamba"
->
Map
(
"exe"
->
"test"
),
"samtools"
->
Map
(
"exe"
->
"test"
),
"igvtools"
->
Map
(
"exe"
->
"test"
,
"igvtools_jar"
->
"test"
),
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
...
...
@@ -232,7 +240,7 @@ object MultisampleMappingTestTrait {
)))
val
sample2
=
Map
(
"samples"
->
Map
(
"sample
3
"
->
Map
(
"libraries"
->
Map
(
"samples"
->
Map
(
"sample
2
"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
inputTouch
(
"2_1_R1.fq"
),
"R2"
->
inputTouch
(
"2_1_R2.fq"
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment