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biopet.biopet
Commits
92a3a1b7
Commit
92a3a1b7
authored
Jun 02, 2016
by
Sander Bollen
Browse files
autostyle fixes
parent
33c611e0
Changes
5
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
92a3a1b7
...
...
@@ -18,17 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.File
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedCheck
import
org.broadinstitute.gatk.queue.QScript
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala
View file @
92a3a1b7
...
...
@@ -84,9 +84,9 @@ object BedtoolsCoverage {
}
/**
* Creates the genome file. i.e. the first two columns of the fasta index
* @return
*/
* Creates the genome file. i.e. the first two columns of the fasta index
* @return
*/
def
createGenomeFile
(
fai
:
File
,
dir
:
File
)
:
File
=
{
val
tmp
=
File
.
createTempFile
(
fai
.
getName
,
".genome"
,
dir
)
tmp
.
deleteOnExit
()
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala
View file @
92a3a1b7
...
...
@@ -4,12 +4,11 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 26-5-16.
*/
* Created by Sander Bollen on 26-5-16.
*/
class
BedtoolsSort
(
val
root
:
Configurable
)
extends
Bedtools
with
Reference
{
@Input
...
...
@@ -21,9 +20,8 @@ class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
@Argument
(
required
=
false
)
var
faidx
:
File
=
referenceFai
def
cmdLine
=
required
(
executable
)
+
required
(
"sort"
)
+
required
(
"-i"
,
input
)
+
optional
(
"-faidx"
,
faidx
)
+
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
(
if
(
outputAsStsout
)
""
else
" > "
+
required
(
output
))
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
View file @
92a3a1b7
...
...
@@ -118,7 +118,7 @@ object CleverFixVCF extends ToolCommand {
*/
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
val
argsParser
=
new
OptParser
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
commandArgs
:
Args
=
argsParser
.
parse
(
args
,
Args
())
getOrElse
(
throw
new
IllegalArgumentException
)
val
input
:
File
=
commandArgs
.
inputVCF
val
output
:
File
=
commandArgs
.
outputVCF
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala
View file @
92a3a1b7
...
...
@@ -4,7 +4,7 @@ import java.io.File
import
java.nio.file.Paths
import
nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
...
...
@@ -21,7 +21,7 @@ class BedToolsTest extends TestNGSuite with Matchers {
val
file
=
new
File
(
Paths
.
get
(
this
.
getClass
.
getResource
(
"/ref.fa.fai"
).
toURI
).
toString
)
val
tmp
=
File
.
createTempFile
(
"test"
,
".bed"
)
tmp
.
deleteOnExit
()
class
TestCov
(
override
val
root
:
Configurable
)
extends
BedtoolsCoverage
(
root
)
{
class
TestCov
(
override
val
root
:
Configurable
)
extends
BedtoolsCoverage
(
root
)
{
jobTempDir
=
tmp
override
def
referenceFai
=
file
...
...
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