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biopet.biopet
Commits
9a9f6f66
Commit
9a9f6f66
authored
Sep 08, 2015
by
Sander Bollen
Browse files
testing main and valuefromtsv
parent
6a21310f
Changes
1
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public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
9a9f6f66
...
...
@@ -15,6 +15,9 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.nio.file.
{
Files
,
Paths
}
import
htsjdk.variant.variantcontext.Allele
import
nl.lumc.sasc.biopet.tools.VcfStats._
import
org.scalatest.Matchers
...
...
@@ -29,6 +32,10 @@ import scala.collection.mutable
* Created by pjvan_thof on 2/5/15.
*/
class
VcfStatsTest
extends
TestNGSuite
with
Matchers
{
private
def
resourcePath
(
p
:
String
)
:
String
=
{
Paths
.
get
(
getClass
.
getResource
(
p
).
toURI
).
toString
}
@Test
def
testSampleToSampleStats
()
:
Unit
=
{
...
...
@@ -168,12 +175,53 @@ class VcfStatsTest extends TestNGSuite with Matchers {
@Test
def
testValueOfTsv
=
{
//stub
val
i
=
new
File
(
resourcePath
(
"/sample.tsv"
))
valueFromTsv
(
i
,
"Sample_ID_1"
,
"library"
)
should
be
(
Some
(
"Lib_ID_1"
))
valueFromTsv
(
i
,
"Sample_ID_2"
,
"library"
)
should
be
(
Some
(
"Lib_ID_2"
))
valueFromTsv
(
i
,
"Sample_ID_1"
,
"bam"
)
should
be
(
Some
(
"MyFirst.bam"
))
valueFromTsv
(
i
,
"Sample_ID_2"
,
"bam"
)
should
be
(
Some
(
"MySecond.bam"
))
valueFromTsv
(
i
,
"Sample_ID_3"
,
"bam"
)
should
be
(
empty
)
}
@Test
def
testMain
=
{
//stub
val
tmp
=
Files
.
createTempDirectory
(
"vcfStats"
)
val
vcf
=
resourcePath
(
"/chrQ.vcf.gz"
)
val
ref
=
resourcePath
(
"/fake_chrQ.fa"
)
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
))
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--allInfoTags"
))
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--allInfoTags"
,
"--allGenotypeTags"
))
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--binSize"
,
"50"
,
"--writeBinStats"
))
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--binSize"
,
"50"
,
"--writeBinStats"
,
"--generalWiggle"
,
"Total"
))
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--binSize"
,
"50"
,
"--writeBinStats"
,
"--genotypeWiggle"
,
"Total"
))
val
genotypes
=
List
(
"Het"
,
"HetNonRef"
,
"Hom"
,
"HomRef"
,
"HomVar"
,
"Mixed"
,
"NoCall"
,
"NonInformative"
,
"Available"
,
"Called"
,
"Filtered"
,
"Variant"
)
genotypes
.
foreach
(
x
=>
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--binSize"
,
"50"
,
"--writeBinStats"
,
"--genotypeWiggle"
,
x
))
)
val
general
=
List
(
"Biallelic"
,
"ComplexIndel"
,
"Filtered"
,
"FullyDecoded"
,
"Indel"
,
"Mixed"
,
"MNP"
,
"MonomorphicInSamples"
,
"NotFiltered"
,
"PointEvent"
,
"PolymorphicInSamples"
,
"SimpleDeletion"
,
"SimpleInsertion"
,
"SNP"
,
"StructuralIndel"
,
"Symbolic"
,
"SymbolicOrSV"
,
"Variant"
)
general
.
foreach
(
x
=>
noException
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
,
"--binSize"
,
"50"
,
"--writeBinStats"
,
"--generalWiggle"
,
x
))
)
}
@Test
...
...
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