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biopet.biopet
Commits
75ca4f74
Commit
75ca4f74
authored
Apr 19, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 19, 2017
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Merge branch 'develop' into fix-heatmap-margins
parents
361a7771
6f78cb16
Changes
1
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8 additions
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2 deletions
+8
-2
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+8
-2
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shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
75ca4f74
...
...
@@ -62,6 +62,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def
svCalling
=
false
def
cnvCalling
=
false
def
annotation
=
false
def
usePrintReads
=
true
private
var
dirs
:
List
[
File
]
=
Nil
...
...
@@ -83,7 +84,8 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
"use_base_recalibration"
->
baseRecalibration
,
"sv_calling"
->
svCalling
,
"cnv_calling"
->
cnvCalling
,
"annotation"
->
annotation
),
m
)
"annotation"
->
annotation
,
"use_printreads"
->
usePrintReads
),
m
)
}
...
...
@@ -105,7 +107,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
IndelRealigner
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
))
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
RealignerTargetCreator
])
shouldBe
(
numberLibs
*
(
if
(
realign
)
1
else
0
)
+
(
if
(
sample2
&&
realign
)
1
else
0
))
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
.
functions
.
count
(
_
.
isInstanceOf
[
PrintReads
])
shouldBe
(
if
(
dbsnp
&&
baseRecalibration
&&
usePrintReads
)
numberLibs
else
0
)
pipeline
.
summarySettings
.
get
(
"annotation"
)
shouldBe
Some
(
annotation
)
pipeline
.
summarySettings
.
get
(
"sv_calling"
)
shouldBe
Some
(
svCalling
)
...
...
@@ -143,6 +145,10 @@ class ShivaNoDbsnpTest extends ShivaTestTrait {
override
def
realignProvider
=
Array
(
true
)
override
def
dbsnp
=
false
}
class
ShivaNoPrintReadsTest
extends
ShivaTestTrait
{
override
def
realignProvider
=
Array
(
false
)
override
def
usePrintReads
=
false
}
class
ShivaLibraryCallingTest
extends
ShivaTestTrait
{
override
def
sample1
=
Array
(
true
,
false
)
override
def
sample2
=
Array
(
false
,
true
)
...
...
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