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biopet.biopet
Commits
565cb85a
Commit
565cb85a
authored
Jul 25, 2017
by
Peter van 't Hof
Browse files
Fixing tests
parent
c46b3983
Changes
1
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Inline
Side-by-side
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
565cb85a
...
...
@@ -60,8 +60,6 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def
realignProvider
=
Array
(
false
,
true
)
def
baseRecalibrationProvider
=
Array
(
false
,
true
)
def
multisampleCalling
:
Boolean
=
true
def
sampleCalling
=
false
def
libraryCalling
=
false
def
dbsnp
=
true
def
svCalling
=
false
def
cnvCalling
=
false
...
...
@@ -86,8 +84,6 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_variantcalling"
->
multisampleCalling
,
"single_sample_variantcalling"
->
sampleCalling
,
"library_variantcalling"
->
libraryCalling
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
,
"sv_calling"
->
svCalling
,
...
...
@@ -133,26 +129,23 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline
.
samples
foreach
{
case
(
_
,
sample
)
=>
sample
.
summarySettings
.
get
(
"single_sample_variantcalling"
)
shouldBe
Some
(
sampleCalling
)
sample
.
summarySettings
.
get
(
"single_sample_variantcalling"
)
shouldBe
None
sample
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
Some
(
realign
)
sample
.
libraries
.
foreach
{
case
(
_
,
lib
)
=>
lib
.
summarySettings
.
get
(
"library_variantcalling"
)
shouldBe
Some
(
libraryCalling
)
lib
.
summarySettings
.
get
(
"library_variantcalling"
)
shouldBe
None
lib
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
None
// Should not exist anymore
lib
.
summarySettings
.
get
(
"use_base_recalibration"
)
shouldBe
Some
(
baseRecalibration
&&
dbsnp
)
}
}
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
((
if
(
multisampleCalling
)
2
else
0
)
+
(
if
(
sampleCalling
)
numberSamples
*
2
else
0
)
+
(
if
(
libraryCalling
)
numberLibs
*
2
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfStats
])
shouldBe
(
if
(
multisampleCalling
)
2
else
0
)
}
}
// remove temporary run directory all tests in the class have been run
@AfterClass
def
removeTempOutputDir
()
=
{
@AfterClass
def
removeTempOutputDir
()
:
Unit
=
{
dirs
.
filter
(
_
.
exists
()).
foreach
{
dir
=>
try
{
FileUtils
.
deleteDirectory
(
dir
)
...
...
@@ -175,20 +168,6 @@ class ShivaNoPrintReadsTest extends ShivaTestTrait {
override
def
realignProvider
=
Array
(
x
=
false
)
override
def
usePrintReads
=
false
}
class
ShivaLibraryCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
,
false
)
override
def
sample2
=
Array
(
false
,
true
)
override
def
realignProvider
=
Array
(
x
=
false
)
override
def
baseRecalibrationProvider
=
Array
(
x
=
false
)
override
def
libraryCalling
=
true
}
class
ShivaSampleCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
,
false
)
override
def
sample2
=
Array
(
false
,
true
)
override
def
realignProvider
=
Array
(
x
=
false
)
override
def
baseRecalibrationProvider
=
Array
(
x
=
false
)
override
def
sampleCalling
=
true
}
class
ShivaWithSvCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
x
=
true
)
override
def
sample2
=
Array
(
x
=
false
)
...
...
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