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Mirrors
biopet.biopet
Commits
6c7f4701
Commit
6c7f4701
authored
Sep 18, 2015
by
Peter van 't Hof
Browse files
Fixed unit tests
parent
a87e2991
Changes
10
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
6c7f4701
...
...
@@ -93,6 +93,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
)
Files
.
touch
(
file
)
file
.
getAbsolutePath
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
@@ -136,8 +142,8 @@ object ShivaTest {
val
sample1
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"1_1_R1.fq"
,
"R2"
->
"1_1_R2.fq"
"R1"
->
inputTouch
(
"1_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"1_1_R2.fq"
)
)
)
)))
...
...
@@ -145,8 +151,8 @@ object ShivaTest {
val
sample2
=
Map
(
"samples"
->
Map
(
"sample2"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"2_1_R1.fq"
,
"R2"
->
"2_1_R2.fq"
"R1"
->
inputTouch
(
"2_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"2_1_R2.fq"
)
)
)
)))
...
...
@@ -154,12 +160,12 @@ object ShivaTest {
val
sample3
=
Map
(
"samples"
->
Map
(
"sample3"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"3_1_R1.fq"
,
"R2"
->
"3_1_R2.fq"
"R1"
->
inputTouch
(
"3_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_1_R2.fq"
)
),
"lib2"
->
Map
(
"R1"
->
"3_2_R1.fq"
,
"R2"
->
"3_2_R2.fq"
"R1"
->
inputTouch
(
"3_2_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_2_R2.fq"
)
)
)
)))
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
6c7f4701
...
...
@@ -73,7 +73,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
new
File
(
"bam_"
+
n
+
".bam"
)).
toList
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toList
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
...
...
@@ -107,6 +107,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
View file @
6c7f4701
...
...
@@ -69,7 +69,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
Map
(
"regions_of_interest"
->
(
1
to
rois
).
map
(
"roi_"
+
_
+
".bed"
).
toList
)
val
bammetrics
:
BamMetrics
=
initPipeline
(
map
)
bammetrics
.
inputBam
=
new
File
(
"inpu
t.bam
"
)
bammetrics
.
inputBam
=
BamMetricsTes
t
.
bam
bammetrics
.
sampleId
=
Some
(
"1"
)
bammetrics
.
libId
=
Some
(
"1"
)
bammetrics
.
script
()
...
...
@@ -98,6 +98,10 @@ class BamMetricsTest extends TestNGSuite with Matchers {
object
BamMetricsTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
val
bam
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"bla.bam"
)
Files
.
touch
(
bam
)
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
View file @
6c7f4701
...
...
@@ -57,7 +57,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Refer
}
override
def
beforeCmd
()
:
Unit
=
{
if
(
sample
==
null
&&
inputBam
.
exists
())
{
if
(
sample
==
null
&&
inputBam
.
exists
()
&&
inputBam
.
length
()
>
0
)
{
val
inputSam
=
SamReaderFactory
.
makeDefault
.
open
(
inputBam
)
val
readGroups
=
inputSam
.
getFileHeader
.
getReadGroups
val
samples
=
readGroups
.
map
(
readGroup
=>
readGroup
.
getSample
).
distinct
...
...
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
View file @
6c7f4701
...
...
@@ -97,6 +97,12 @@ class CarpTest extends TestNGSuite with Matchers {
object
CarpTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
)
Files
.
touch
(
file
)
file
.
getAbsolutePath
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
@@ -127,8 +133,8 @@ object CarpTest {
val
sample1
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"1_1_R1.fq"
,
"R2"
->
"1_1_R2.fq"
"R1"
->
inputTouch
(
"1_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"1_1_R2.fq"
)
)
)
)))
...
...
@@ -136,8 +142,8 @@ object CarpTest {
val
sample2
=
Map
(
"samples"
->
Map
(
"sample2"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"2_1_R1.fq"
,
"R2"
->
"2_1_R2.fq"
"R1"
->
inputTouch
(
"2_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"2_1_R2.fq"
)
)
)
)))
...
...
@@ -145,12 +151,12 @@ object CarpTest {
val
sample3
=
Map
(
"samples"
->
Map
(
"sample3"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"3_1_R1.fq"
,
"R2"
->
"3_1_R2.fq"
"R1"
->
inputTouch
(
"3_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_1_R2.fq"
)
),
"lib2"
->
Map
(
"R1"
->
"3_2_R1.fq"
,
"R2"
->
"3_2_R2.fq"
"R1"
->
inputTouch
(
"3_2_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_2_R2.fq"
)
)
)
)))
...
...
@@ -158,8 +164,8 @@ object CarpTest {
val
threatment1
=
Map
(
"samples"
->
Map
(
"threatment"
->
Map
(
"control"
->
"control1"
,
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"threatment_1_R1.fq"
,
"R2"
->
"threatment_1_R2.fq"
"R1"
->
inputTouch
(
"threatment_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"threatment_1_R2.fq"
)
)
)
)))
...
...
@@ -167,8 +173,8 @@ object CarpTest {
val
control1
=
Map
(
"samples"
->
Map
(
"control1"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"control_1_R1.fq"
,
"R2"
->
"control_1_R2.fq"
"R1"
->
inputTouch
(
"control_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"control_1_R2.fq"
)
)
)
)))
...
...
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
View file @
6c7f4701
...
...
@@ -67,8 +67,8 @@ class FlexiprepTest extends TestNGSuite with Matchers {
),
Map
(
FlexiprepTest
.
executables
.
toSeq
:
_
*
))
val
flexiprep
:
Flexiprep
=
initPipeline
(
map
)
flexiprep
.
input_R1
=
new
File
(
flexiprep
.
outputDir
,
"bla_R1.fq"
+
(
if
(
zipped
)
".gz"
else
""
)
)
if
(
paired
)
flexiprep
.
input_R2
=
Some
(
new
File
(
flexiprep
.
outputDir
,
"bla_R2.fq"
+
(
if
(
zipped
)
".gz"
else
""
)
))
flexiprep
.
input_R1
=
(
if
(
zipped
)
FlexiprepTest
.
r1Zipped
else
FlexiprepTest
.
r1
)
if
(
paired
)
flexiprep
.
input_R2
=
Some
(
(
if
(
zipped
)
FlexiprepTest
.
r2Zipped
else
FlexiprepTest
.
r2
))
flexiprep
.
sampleId
=
Some
(
"1"
)
flexiprep
.
libId
=
Some
(
"1"
)
flexiprep
.
script
()
...
...
@@ -95,6 +95,16 @@ class FlexiprepTest extends TestNGSuite with Matchers {
object
FlexiprepTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
val
r1
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq"
)
Files
.
touch
(
r1
)
val
r2
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq"
)
Files
.
touch
(
r2
)
val
r1Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
Files
.
touch
(
r1Zipped
)
val
r2Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq.gz"
)
Files
.
touch
(
r2Zipped
)
val
executables
=
Map
(
"seqstat"
->
Map
(
"exe"
->
"test"
),
...
...
public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
6c7f4701
...
...
@@ -43,8 +43,8 @@ class GentrapTest extends TestNGSuite with Matchers {
/** Convenience method for making library config */
private
def
makeLibConfig
(
idx
:
Int
,
paired
:
Boolean
=
true
)
=
{
val
files
=
Map
(
"R1"
->
"test_R1.fq"
)
if
(
paired
)
(
s
"lib_$idx"
,
files
++
Map
(
"R2"
->
"test_R2.fq"
))
val
files
=
Map
(
"R1"
->
GentrapTest
.
inputTouch
(
"test_R1.fq"
)
)
if
(
paired
)
(
s
"lib_$idx"
,
files
++
Map
(
"R2"
->
GentrapTest
.
inputTouch
(
"test_R2.fq"
))
)
else
(
s
"lib_$idx"
,
files
)
}
...
...
@@ -179,6 +179,12 @@ class GentrapTest extends TestNGSuite with Matchers {
object
GentrapTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
)
Files
.
touch
(
file
)
file
.
getAbsolutePath
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
6c7f4701
...
...
@@ -79,11 +79,11 @@ class MappingTest extends TestNGSuite with Matchers {
val
mapping
:
Mapping
=
initPipeline
(
map
)
if
(
zipped
)
{
mapping
.
input_R1
=
new
File
(
mapping
.
outputDir
,
"bla_R1.fq.gz"
)
if
(
paired
)
mapping
.
input_R2
=
Some
(
new
File
(
mapping
.
outputDir
,
"bla_R2.fq.gz"
)
)
mapping
.
input_R1
=
MappingTest
.
r1Zipped
if
(
paired
)
mapping
.
input_R2
=
Some
(
MappingTest
.
r2Zipped
)
}
else
{
mapping
.
input_R1
=
new
File
(
mapping
.
outputDir
,
"bla_R1.fq"
)
if
(
paired
)
mapping
.
input_R2
=
Some
(
new
File
(
mapping
.
outputDir
,
"bla_R2.fq"
)
)
mapping
.
input_R1
=
MappingTest
.
r1
if
(
paired
)
mapping
.
input_R2
=
Some
(
MappingTest
.
r2
)
}
mapping
.
sampleId
=
Some
(
"1"
)
mapping
.
libId
=
Some
(
"1"
)
...
...
@@ -131,6 +131,16 @@ class MappingTest extends TestNGSuite with Matchers {
object
MappingTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
val
r1
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq"
)
Files
.
touch
(
r1
)
val
r2
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq"
)
Files
.
touch
(
r2
)
val
r1Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R1.fq.gz"
)
Files
.
touch
(
r1Zipped
)
val
r2Zipped
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
"R2.fq.gz"
)
Files
.
touch
(
r2Zipped
)
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
6c7f4701
...
...
@@ -88,6 +88,12 @@ class ShivaTest extends TestNGSuite with Matchers {
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
String
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
)
Files
.
touch
(
file
)
file
.
getAbsolutePath
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
@@ -131,8 +137,8 @@ object ShivaTest {
val
sample1
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"1_1_R1.fq"
,
"R2"
->
"1_1_R2.fq"
"R1"
->
inputTouch
(
"1_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"1_1_R2.fq"
)
)
)
)))
...
...
@@ -140,8 +146,8 @@ object ShivaTest {
val
sample2
=
Map
(
"samples"
->
Map
(
"sample2"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"2_1_R1.fq"
,
"R2"
->
"2_1_R2.fq"
"R1"
->
inputTouch
(
"2_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"2_1_R2.fq"
)
)
)
)))
...
...
@@ -149,12 +155,12 @@ object ShivaTest {
val
sample3
=
Map
(
"samples"
->
Map
(
"sample3"
->
Map
(
"libraries"
->
Map
(
"lib1"
->
Map
(
"R1"
->
"3_1_R1.fq"
,
"R2"
->
"3_1_R2.fq"
"R1"
->
inputTouch
(
"3_1_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_1_R2.fq"
)
),
"lib2"
->
Map
(
"R1"
->
"3_2_R1.fq"
,
"R2"
->
"3_2_R2.fq"
"R1"
->
inputTouch
(
"3_2_R1.fq"
)
,
"R2"
->
inputTouch
(
"3_2_R2.fq"
)
)
)
)))
...
...
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
6c7f4701
...
...
@@ -61,7 +61,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val
map
=
Map
(
"variantcallers"
->
callers
.
toList
)
val
pipeline
=
initPipeline
(
map
)
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
new
File
(
"bam_"
+
n
+
".bam"
)).
toList
pipeline
.
inputBams
=
(
for
(
n
<-
1
to
bams
)
yield
ShivaVariantcallingTest
.
inputTouch
(
"bam_"
+
n
+
".bam"
)).
toList
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
freebayes
)
...
...
@@ -88,6 +88,12 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
object
ShivaVariantcallingTest
{
val
outputDir
=
Files
.
createTempDir
()
new
File
(
outputDir
,
"input"
).
mkdirs
()
def
inputTouch
(
name
:
String
)
:
File
=
{
val
file
=
new
File
(
outputDir
,
"input"
+
File
.
separator
+
name
).
getAbsoluteFile
Files
.
touch
(
file
)
file
}
private
def
copyFile
(
name
:
String
)
:
Unit
=
{
val
is
=
getClass
.
getResourceAsStream
(
"/"
+
name
)
...
...
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