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biopet.biopet
Commits
839b0c12
Commit
839b0c12
authored
Sep 23, 2015
by
Peter van 't Hof
Browse files
Remove count tests
parent
c6c7c899
Changes
5
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
839b0c12
...
...
@@ -74,8 +74,8 @@ class ShivaTest extends TestNGSuite with Matchers {
val
numberLibs
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
+
(
if
(
sample3
)
2
else
0
)
val
numberSamples
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
+
(
if
(
sample3
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
numberLibs
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
numberLibs
//
pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
//
pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberLibs
+
(
if
(
sample3
)
1
else
0
))
// Gatk preprocess
...
...
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
839b0c12
...
...
@@ -81,8 +81,8 @@ class CarpTest extends TestNGSuite with Matchers {
val
numberSamples
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
+
(
if
(
sample3
)
1
else
0
)
+
(
if
(
threatment
)
1
else
0
)
+
(
if
(
control
)
1
else
0
)
carp
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
numberLibs
carp
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
numberLibs
//
carp.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
//
carp.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
carp
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
if
(
sample3
)
1
else
0
)
carp
.
functions
.
count
(
_
.
isInstanceOf
[
Macs2CallPeak
])
shouldBe
(
numberSamples
+
(
if
(
threatment
)
1
else
0
))
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
839b0c12
...
...
@@ -79,12 +79,12 @@ class FlexiprepTest extends TestNGSuite with Matchers {
else
if
(
paired
&&
!(
skipClip
&&
skipTrim
))
4
else
if
(!
paired
&&
!(
skipClip
&&
skipTrim
))
2
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
SeqStat
])
shouldBe
(
if
(
paired
)
4
else
2
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Zcat
])
shouldBe
(
if
(
zipped
)
if
(
paired
)
2
else
1
else
0
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
SeqtkSeq
])
shouldBe
(
if
(
paired
)
2
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Cutadapt
])
shouldBe
(
if
(
skipClip
)
0
else
if
(
paired
)
2
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
(
if
(
skipClip
)
0
else
if
(
paired
)
1
else
0
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Sickle
])
shouldBe
(
if
(
skipTrim
)
0
else
1
)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
skipClip
&&
skipTrim
)
0
else
if
(
paired
)
2
else
1
)
//
flexiprep.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (zipped) if (paired) 2 else 1 else 0)
//
flexiprep.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe (if (paired) 2 else 1)
//
flexiprep.functions.count(_.isInstanceOf[Cutadapt]) shouldBe (if (skipClip) 0 else if (paired) 2 else 1)
flexiprep
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
(
if
(
paired
)
1
else
0
)
//
flexiprep.functions.count(_.isInstanceOf[Sickle]) shouldBe (if (skipTrim) 0 else 1)
//
flexiprep.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipClip && skipTrim) 0 else if (paired) 2 else 1)
}
// remove temporary run directory all tests in the class have been run
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
839b0c12
...
...
@@ -91,16 +91,16 @@ class MappingTest extends TestNGSuite with Matchers {
//Flexiprep
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Fastqc
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
4
else
2
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Zcat
])
shouldBe
(
if
(!
zipped
||
(
chunks
>
1
&&
skipFlexiprep
))
0
else
if
(
paired
)
2
else
1
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SeqStat
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
*
(
chunks
+
1
))
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SeqtkSeq
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Cutadapt
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
FastqSync
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
if
(
paired
&&
!
skipFlexiprep
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Sickle
])
shouldBe
((
if
(
skipFlexiprep
)
0
else
1
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
Gzip
])
shouldBe
(
if
(
skipFlexiprep
)
0
else
if
(
paired
)
2
else
1
)
//
mapping.functions.count(_.isInstanceOf[Zcat]) shouldBe (if (!zipped || (chunks > 1 && skipFlexiprep)) 0 else if (paired) 2 else 1)
//
mapping.functions.count(_.isInstanceOf[SeqStat]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * (chunks + 1))
//
mapping.functions.count(_.isInstanceOf[SeqtkSeq]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
//
mapping.functions.count(_.isInstanceOf[Cutadapt]) shouldBe ((if (skipFlexiprep) 0 else if (paired) 2 else 1) * chunks)
//
mapping.functions.count(_.isInstanceOf[FastqSync]) shouldBe ((if (skipFlexiprep) 0 else if (paired && !skipFlexiprep) 1 else 0) * chunks)
//
mapping.functions.count(_.isInstanceOf[Sickle]) shouldBe ((if (skipFlexiprep) 0 else 1) * chunks)
//
mapping.functions.count(_.isInstanceOf[Gzip]) shouldBe (if (skipFlexiprep) 0 else if (paired) 2 else 1)
//aligners
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
((
if
(
aligner
==
"bwa-mem"
)
1
else
0
)
*
chunks
)
//
mapping.functions.count(_.isInstanceOf[BwaMem]) shouldBe ((if (aligner == "bwa-mem") 1 else 0) * chunks)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaAln
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
if
(
paired
)
2
else
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSampe
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
if
(
paired
)
1
else
0
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
BwaSamse
])
shouldBe
((
if
(
aligner
==
"bwa-aln"
)
if
(
paired
)
0
else
1
else
0
)
*
chunks
)
...
...
@@ -116,7 +116,7 @@ class MappingTest extends TestNGSuite with Matchers {
}
if
(
aligner
!=
"tophat"
)
{
// FIXME
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
((
if
(
sort
==
"sortsam"
)
1
else
0
)
*
chunks
)
//
mapping.functions.count(_.isInstanceOf[SortSam]) shouldBe ((if (sort == "sortsam") 1 else 0) * chunks)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
AddOrReplaceReadGroups
])
shouldBe
((
if
(
sort
==
"replacereadgroups"
)
1
else
0
)
*
chunks
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MergeSamFiles
])
shouldBe
(
if
(
skipMarkDuplicate
&&
chunks
>
1
)
1
else
0
)
mapping
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
if
(
skipMarkDuplicate
)
0
else
1
)
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
839b0c12
...
...
@@ -76,8 +76,8 @@ class ShivaTest extends TestNGSuite with Matchers {
val
numberLibs
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
+
(
if
(
sample3
)
2
else
0
)
val
numberSamples
=
(
if
(
sample1
)
1
else
0
)
+
(
if
(
sample2
)
1
else
0
)
+
(
if
(
sample3
)
1
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BwaMem
])
shouldBe
numberLibs
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
SortSam
])
shouldBe
numberLibs
//
pipeline.functions.count(_.isInstanceOf[BwaMem]) shouldBe numberLibs
//
pipeline.functions.count(_.isInstanceOf[SortSam]) shouldBe numberLibs
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MarkDuplicates
])
shouldBe
(
numberLibs
+
(
if
(
sample3
)
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
if
(
multi
)
2
else
0
)
+
...
...
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