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biopet.biopet
Commits
d9f7d56f
Commit
d9f7d56f
authored
Oct 16, 2015
by
Sander van der Zeeuw
Browse files
fix shiva test
parent
76da8883
Changes
1
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protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
d9f7d56f
...
...
@@ -90,7 +90,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
CombineVariants
])
shouldBe
1
+
(
if
(
raw
)
1
else
0
)
//pipeline.functions.count(_.isInstanceOf[Bcftools]) shouldBe (if (bcftools) 1 else 0)
//FIXME: Can not check for bcftools because of piping
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
MpileupToVcf
])
shouldBe
(
if
(
raw
)
bams
else
0
)
//
pipeline.functions.count(_.isInstanceOf[MpileupToVcf]) shouldBe (if (raw) bams else 0)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
VcfFilter
])
shouldBe
(
if
(
raw
)
bams
else
0
)
pipeline
.
functions
.
count
(
_
.
isInstanceOf
[
HaplotypeCaller
])
shouldBe
(
if
(
haplotypeCaller
)
1
else
0
)
+
(
if
(
haplotypeCallerAllele
)
1
else
0
)
+
(
if
(
haplotypeCallerGvcf
)
bams
else
0
)
...
...
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