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biopet.biopet
Commits
68f99a4f
Commit
68f99a4f
authored
May 09, 2016
by
Peter van 't Hof
Browse files
Added more testing to shiva
parent
0db87187
Changes
1
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Inline
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
68f99a4f
...
...
@@ -58,7 +58,9 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def
multisampleCalling
:
Boolean
=
true
def
sampleCalling
=
false
def
libraryCalling
=
false
def
dbsnp
:
Boolean
=
true
def
dbsnp
=
true
def
svCalling
=
false
def
annotation
=
false
@Test
(
dataProvider
=
"shivaOptions"
)
def
testShiva
(
f
:
String
,
sample1
:
Boolean
,
sample2
:
Boolean
,
...
...
@@ -73,7 +75,9 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
"single_sample_variantcalling"
->
sampleCalling
,
"library_variantcalling"
->
libraryCalling
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
)
"use_base_recalibration"
->
baseRecalibration
,
"sv_calling"
->
svCalling
,
"annotation"
->
annotation
),
m
)
}
...
...
@@ -96,6 +100,19 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
BaseRecalibrator
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
(
numberLibs
*
2
)
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
)
numberLibs
else
0
)
pipeline
.
summarySettings
.
get
(
"annotation"
)
shouldBe
Some
(
annotation
)
pipeline
.
summarySettings
.
get
(
"sv_calling"
)
shouldBe
Some
(
svCalling
)
pipeline
.
samples
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
summarySettings
.
get
(
"single_sample_variantcalling"
)
shouldBe
Some
(
sampleCalling
)
sample
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
Some
(
realign
)
sample
.
libraries
.
foreach
{
case
(
libId
,
lib
)
=>
lib
.
summarySettings
.
get
(
"library_variantcalling"
)
shouldBe
Some
(
libraryCalling
)
lib
.
summarySettings
.
get
(
"use_indel_realigner"
)
shouldBe
Some
(
realign
)
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
)
+
...
...
@@ -125,6 +142,20 @@ class ShivaSampleCallingTest extends ShivaTestTrait {
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
sampleCalling
=
true
}
class
ShivaWithSvCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
realignProvider
=
Array
(
false
)
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
svCalling
=
true
}
class
ShivaWithAnnotationTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
)
override
def
sample2
=
Array
(
false
)
override
def
realignProvider
=
Array
(
false
)
override
def
baseRecalibrationProvider
=
Array
(
false
)
override
def
annotation
=
true
}
object
ShivaTest
{
val
outputDir
=
Files
.
createTempDir
()
...
...
@@ -170,7 +201,18 @@ object ShivaTest {
"wigtobigwig"
->
Map
(
"exe"
->
"test"
),
"md5sum"
->
Map
(
"exe"
->
"test"
),
"bgzip"
->
Map
(
"exe"
->
"test"
),
"tabix"
->
Map
(
"exe"
->
"test"
)
"tabix"
->
Map
(
"exe"
->
"test"
),
"breakdancerconfig"
->
Map
(
"exe"
->
"test"
),
"breakdancercaller"
->
Map
(
"exe"
->
"test"
),
"pindelconfig"
->
Map
(
"exe"
->
"test"
),
"pindelcaller"
->
Map
(
"exe"
->
"test"
),
"pindelvcf"
->
Map
(
"exe"
->
"test"
),
"clever"
->
Map
(
"exe"
->
"test"
),
"delly"
->
Map
(
"exe"
->
"test"
),
"pysvtools"
->
Map
(
"exe"
->
"test"
,
"exclusion_regions"
->
"test"
,
"translocations_only"
->
false
)
)
val
sample1
=
Map
(
...
...
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