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biopet.biopet
Commits
5f0512b5
Commit
5f0512b5
authored
Aug 13, 2015
by
Sander Bollen
Browse files
VcfFilter tests. See #188.
parent
02e5f5ec
Changes
3
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
5f0512b5
...
...
@@ -56,7 +56,7 @@ class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
object
VcfFilter
extends
ToolCommand
{
/** Container class for a trio */
protected
case
class
Trio
(
child
:
String
,
father
:
String
,
mother
:
String
)
{
protected
[
tools
]
case
class
Trio
(
child
:
String
,
father
:
String
,
mother
:
String
)
{
def
this
(
arg
:
String
)
=
{
this
(
arg
.
split
(
":"
)(
0
),
arg
.
split
(
":"
)(
1
),
arg
.
split
(
":"
)(
2
))
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
View file @
5f0512b5
...
...
@@ -50,7 +50,7 @@ class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
var
mode
:
String
=
config
(
"mode"
,
default
=
"explode"
)
var
doNotRemove
:
Boolean
=
config
(
"donotremove"
,
default
=
false
)
override
def
defaultCoreMemory
=
1
.0
override
def
defaultCoreMemory
=
4
.0
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
inputVCF
)
+
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
View file @
5f0512b5
...
...
@@ -147,4 +147,63 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
mustHaveVariant
(
record
,
List
(
"Child_7006504"
,
"Father_7006506"
,
"Mother_7006508"
))
shouldBe
false
}
@Test
def
testSameGenotype
()
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
notSameGenotype
(
record
,
"Child_7006504"
,
"Father_7006506"
)
shouldBe
false
notSameGenotype
(
record
,
"Child_7006504"
,
"Mother_7006508"
)
shouldBe
true
notSameGenotype
(
record
,
"Father_7006506"
,
"Mother_7006508"
)
shouldBe
true
}
@Test
def
testfilterHetVarToHomVar
()
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
filterHetVarToHomVar
(
record
,
"Child_7006504"
,
"Father_7006506"
)
shouldBe
true
filterHetVarToHomVar
(
record
,
"Child_7006504"
,
"Mother_7006508"
)
shouldBe
true
filterHetVarToHomVar
(
record
,
"Father_7006506"
,
"Mother_7006508"
)
shouldBe
true
}
@Test
def
testDeNovo
()
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
denovoInSample
(
record
,
"Child_7006504"
)
shouldBe
false
denovoInSample
(
record
,
"Father_7006506"
)
shouldBe
false
denovoInSample
(
record
,
"Mother_7006508"
)
shouldBe
false
}
@Test
def
testResToDom
()
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
val
trio
=
new
Trio
(
"Child_7006504"
,
"Father_7006506"
,
"Mother_7006508"
)
resToDom
(
record
,
List
(
trio
))
shouldBe
false
}
@Test
def
testTrioCompound
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
val
trio
=
new
Trio
(
"Child_7006504"
,
"Father_7006506"
,
"Mother_7006508"
)
trioCompound
(
record
,
List
(
trio
))
}
@Test
def
testDeNovoTrio
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
val
trio
=
new
Trio
(
"Child_7006504"
,
"Father_7006506"
,
"Mother_7006508"
)
denovoTrio
(
record
,
List
(
trio
))
}
@Test
def
testInIDSet
()
=
{
val
reader
=
new
VCFFileReader
(
vepped
,
false
)
val
record
=
reader
.
iterator
().
next
()
inIdSet
(
record
,
Set
(
"rs199537431"
))
shouldBe
true
inIdSet
(
record
,
Set
(
"dummy"
))
shouldBe
false
}
}
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