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biopet.biopet
Commits
6e163f45
Commit
6e163f45
authored
Oct 20, 2015
by
Sander van der Zeeuw
Browse files
added bcftools singlesample to the test
parent
f17e2175
Changes
1
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Inline
Side-by-side
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
6e163f45
...
...
@@ -44,12 +44,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
bams
<-
0
to
2
;
raw
<-
bool
;
bcftools
<-
bool
;
bcftools_singlesample
<-
bool
;
haplotypeCallerGvcf
<-
bool
;
haplotypeCallerAllele
<-
bool
;
unifiedGenotyperAllele
<-
bool
;
unifiedGenotyper
<-
bool
;
haplotypeCaller
<-
bool
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
)
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
)
).
toArray
}
...
...
@@ -57,6 +58,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
def
testShivaVariantcalling
(
bams
:
Int
,
raw
:
Boolean
,
bcftools
:
Boolean
,
bcftools_singlesample
:
Boolean
,
unifiedGenotyper
:
Boolean
,
haplotypeCaller
:
Boolean
,
haplotypeCallerGvcf
:
Boolean
,
...
...
@@ -65,6 +67,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val
callers
:
ListBuffer
[
String
]
=
ListBuffer
()
if
(
raw
)
callers
.
append
(
"raw"
)
if
(
bcftools
)
callers
.
append
(
"bcftools"
)
if
(
bcftools_singlesample
)
callers
.
append
(
"bcftools_singlesample"
)
if
(
unifiedGenotyper
)
callers
.
append
(
"unifiedgenotyper"
)
if
(
haplotypeCallerGvcf
)
callers
.
append
(
"haplotypecaller_gvcf"
)
if
(
haplotypeCallerAllele
)
callers
.
append
(
"haplotypecaller_allele"
)
...
...
@@ -78,7 +81,8 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
val
illegalArgumentException
=
pipeline
.
inputBams
.
isEmpty
||
(!
raw
&&
!
bcftools
&&
!
haplotypeCaller
&&
!
unifiedGenotyper
&&
!
haplotypeCallerGvcf
&&
!
haplotypeCallerAllele
&&
!
unifiedGenotyperAllele
)
!
haplotypeCallerGvcf
&&
!
haplotypeCallerAllele
&&
!
unifiedGenotyperAllele
&&
!
bcftools_singlesample
)
if
(
illegalArgumentException
)
intercept
[
IllegalArgumentException
]
{
pipeline
.
script
()
...
...
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