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biopet.biopet
Commits
527d43b8
Commit
527d43b8
authored
Mar 09, 2017
by
Peter van 't Hof
Committed by
GitHub
Mar 09, 2017
Browse files
Merge pull request #34 from biopet/Fix_BIOPET_557
Changed VCFstats to check whether outputDir is a valid directory.
parents
5da52a7b
c55f3de2
Changes
2
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStats.scala
View file @
527d43b8
...
...
@@ -74,7 +74,7 @@ object VcfStats extends ToolCommand {
opt
[
File
](
'o'
,
"outputDir"
)
required
()
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputDir
=
x
)
}
validate
{
x
=>
if
(
x
==
null
)
failure
(
"
O
utput directory required"
)
else
success
x
=>
if
(
x
==
null
)
failure
(
"
Valid o
utput directory required"
)
else
if
(
x
.
exists
)
success
else
failure
(
s
"Output directory does not exist: $x"
)
}
text
"Path to directory for output (required)"
opt
[
File
](
'i'
,
"intervals"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
intervals
=
Some
(
x
))
...
...
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
527d43b8
...
...
@@ -15,15 +15,16 @@
package
nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.nio.file.
{
Files
,
Paths
}
import
java.nio.file.
{
Files
,
Paths
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.tools.vcfstats.
{
SampleStats
,
SampleToSampleStats
,
Stats
,
VcfStats
}
import
nl.lumc.sasc.biopet.tools.vcfstats.
{
SampleStats
,
SampleToSampleStats
,
Stats
,
VcfStats
}
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
import
nl.lumc.sasc.biopet.utils.sortAnyAny
import
org.apache.commons.io.FileUtils
import
scala.collection.mutable
...
...
@@ -162,6 +163,16 @@ class VcfStatsTest extends TestNGSuite with Matchers {
valueFromTsv
(
i
,
"Sample_ID_3"
,
"bam"
)
should
be
(
empty
)
}
@Test
def
testNoExistOutputDir
:
Unit
=
{
val
tmp
=
Files
.
createTempDirectory
(
"vcfStats"
)
FileUtils
.
deleteDirectory
(
new
File
(
tmp
.
toAbsolutePath
.
toString
))
val
vcf
=
resourcePath
(
"/chrQ.vcf.gz"
)
val
ref
=
resourcePath
(
"/fake_chrQ.fa"
)
an
[
IllegalArgumentException
]
should
be
thrownBy
main
(
Array
(
"-I"
,
vcf
,
"-R"
,
ref
,
"-o"
,
tmp
.
toAbsolutePath
.
toString
))
}
@Test
def
testMain
()
=
{
val
tmp
=
Files
.
createTempDirectory
(
"vcfStats"
)
...
...
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