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biopet.biopet
Commits
02936179
Commit
02936179
authored
May 25, 2016
by
Peter van 't Hof
Browse files
Fix compile error
parent
0e6920a2
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
02936179
...
...
@@ -259,7 +259,7 @@ object VcfFilter extends ToolCommand {
/** Checks if all samples are a variant */
def
allSamplesVariant
(
record
:
VariantContext
)
:
Boolean
=
{
record
.
getGenotypes
.
forall
(
g
=>
!
g
.
isNonInformative
&&
g
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
record
.
getGenotypes
.
forall
(
g
=>
!
g
.
isNonInformative
&&
g
.
getAlleles
.
exists
(
a
=>
a
.
isNonReference
&&
!
a
.
isNoCall
))
}
/** returns true when DP INFO field is atleast the given value */
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
View file @
02936179
...
...
@@ -77,7 +77,7 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
"--mustHaveGenotype"
,
"Sample_101:HET"
)
main
(
arguments
)
val
size
=
new
VCFFileReader
(
new
File
(
tmpPath
)
,
false
).
size
val
size
=
new
VCFFileReader
(
tmp
,
false
).
size
size
shouldBe
1
val
tmp2
=
File
.
createTempFile
(
"VcfFilter"
,
".vcf.gz"
)
...
...
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