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biopet.biopet
Commits
1dae06f5
Commit
1dae06f5
authored
Sep 08, 2015
by
Sander Bollen
Browse files
create test stubs
parent
d5b713e0
Changes
2
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
1dae06f5
...
...
@@ -525,7 +525,7 @@ object VcfStats extends ToolCommand {
}
/** Function to check all general stats, all info expect sample/genotype specific stats */
protected
def
checkGeneral
(
record
:
VariantContext
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
protected
[
tools
]
def
checkGeneral
(
record
:
VariantContext
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
def
addToBuffer
(
key
:
String
,
value
:
Any
,
found
:
Boolean
)
:
Unit
=
{
...
...
@@ -581,7 +581,7 @@ object VcfStats extends ToolCommand {
}
/** Function to check sample/genotype specific stats */
protected
def
checkGenotype
(
record
:
VariantContext
,
genotype
:
Genotype
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
protected
[
tools
]
def
checkGenotype
(
record
:
VariantContext
,
genotype
:
Genotype
,
additionalTags
:
List
[
String
])
:
Map
[
String
,
Map
[
String
,
Map
[
Any
,
Int
]]]
=
{
val
buffer
=
mutable
.
Map
[
String
,
Map
[
Any
,
Int
]]()
def
addToBuffer
(
key
:
String
,
value
:
Any
,
found
:
Boolean
)
:
Unit
=
{
...
...
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
1dae06f5
...
...
@@ -116,4 +116,39 @@ class VcfStatsTest extends TestNGSuite with Matchers {
alleleOverlap
(
List
(
a1
,
a1
),
List
(
a2
,
a2
))
shouldBe
0
alleleOverlap
(
List
(
a2
,
a2
),
List
(
a1
,
a1
))
shouldBe
0
}
@Test
def
testMergeStatsMap
=
{
//stub
}
@Test
def
testMergeNestedStatsMap
=
{
//stub
}
@Test
def
testValueOfTsv
=
{
//stub
}
@Test
def
testMain
=
{
//stub
}
@Test
def
testSortAnyAny
=
{
//stub
}
@Test
def
testCheckGeneral
=
{
//stub
}
@Test
def
testCheckGenotype
=
{
//stub
}
}
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