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biopet.biopet
Commits
48524cb0
Commit
48524cb0
authored
Aug 11, 2014
by
Peter van 't Hof
Browse files
Removed unused imports
parent
b43fa492
Changes
16
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biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
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48524cb0
...
...
@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.config.
_
import
org.broadinstitute.gatk.utils.commandline.
_
import
nl.lumc.sasc.biopet.core.config.
Configurable
import
org.broadinstitute.gatk.utils.commandline.
Argument
import
org.broadinstitute.gatk.queue.QSettings
import
org.broadinstitute.gatk.queue.function.QFunction
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala
View file @
48524cb0
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package
nl.lumc.sasc.biopet.core
import
java.io.FileOutputStream
//import org.broadinstitute.sting.queue.QCommandLine
import
org.broadinstitute.gatk.queue.util.Logging
trait
PipelineCommand
extends
Logging
{
// val src = ""
// val extension = ".scala"
val
pipeline
=
""
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
// val tempFile = java.io.File.createTempFile(src + ".", extension)
// val is = getClass.getResourceAsStream(src + extension)
// val os = new FileOutputStream(tempFile)
// org.apache.commons.io.IOUtils.copy(is, os)
// os.close()
var
argv
:
Array
[
String
]
=
Array
()
//argv ++= Array("-S", tempFile.getAbsolutePath)
argv
++=
Array
(
"-S"
,
pipeline
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala
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48524cb0
...
...
@@ -2,9 +2,8 @@ package nl.lumc.sasc.biopet.core.apps
import
htsjdk.samtools.SAMFileReader
import
htsjdk.samtools.SAMRecord
import
java.io.
{
BufferedInputStream
,
File
,
FileInputStream
,
PrintWriter
}
import
java.io.
File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
scala.io.Source
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.queue.util.Logging
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
View file @
48524cb0
package
nl.lumc.sasc.biopet.core.config
import
nl.lumc.sasc.biopet.core._
import
java.io.File
import
org.broadinstitute.gatk.queue.util.Logging
import
argonaut._
,
Argonaut
.
_
...
...
@@ -131,15 +130,6 @@ class Config(var map: Map[String, Any]) extends Logging {
}
}
// def apply(module: String, path: List[String], key: String, freeVar:Boolean = true): ConfigValue = {
// val requestedIndex = ConfigValueIndex(module, path, key)
// if (contains(requestedIndex, freeVar)) return foundCache(requestedIndex)
// else {
// logger.error("Value in config could not be found but it seems required, index: " + requestedIndex)
// throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
// }
// }
private
def
getMapFromPath
(
path
:
List
[
String
])
:
Map
[
String
,
Any
]
=
{
var
returnMap
:
Map
[
String
,
Any
]
=
map
for
(
m
<-
path
)
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala
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48524cb0
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
_
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
class
Cat
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
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48524cb0
...
...
@@ -4,8 +4,8 @@ import java.io.File
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.core.config.
_
import
nl.lumc.sasc.biopet.core.
BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.
Configurable
class
Fastqc
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gzip.scala
View file @
48524cb0
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
_
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
class
Gzip
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala
View file @
48524cb0
...
...
@@ -2,7 +2,6 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
scala.sys.process.Process
import
org.apache.commons.io.FilenameUtils
;
import
org.broadinstitute.gatk.queue.function.InProcessFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.config.Configurable
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Md5sum.scala
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48524cb0
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
_
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala
View file @
48524cb0
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
_
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
import
argonaut._
,
Argonaut
.
_
import
scalaz._
,
Scalaz
.
_
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
View file @
48524cb0
...
...
@@ -5,7 +5,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Ln
,
Pbzip2
,
Md5sum
,
Zcat
}
import
nl.lumc.sasc.biopet.extensions.
{
Gzip
,
Pbzip2
,
Md5sum
,
Zcat
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
class
Flexiprep
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
...
...
gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
48524cb0
package
nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.core.config.
_
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.
Configurable
import
nl.lumc.sasc.biopet.extensions._
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
BaseRecalibrator
,
CommandLineGATK
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
GenotypeGVCFs
,
AnalyzeCovariates
}
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Bwa.scala
View file @
48524cb0
package
nl.lumc.sasc.biopet.extensions.aligners
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.core.config.
_
import
nl.lumc.sasc.biopet.core.
BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.
Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
import
scala.sys.process._
class
Bwa
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Fastq file R1"
,
shortName
=
"R1"
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/extensions/aligners/Star.scala
View file @
48524cb0
package
nl.lumc.sasc.biopet.extensions.aligners
import
nl.lumc.sasc.biopet.core.
_
import
nl.lumc.sasc.biopet.core.config.
_
import
nl.lumc.sasc.biopet.core.
BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.
Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
import
java.io.File
import
scala.sys.process._
class
Star
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"The reference file for the bam files."
,
required
=
false
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
48524cb0
...
...
@@ -10,7 +10,7 @@ import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
,
ClassType
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Argument
,
ClassType
}
import
org.broadinstitute.gatk.queue.extensions.picard.
{
MergeSamFiles
,
SortSam
,
AddOrReplaceReadGroups
}
import
scala.math._
...
...
pipeline-template/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/PipelineTemplate.scala
View file @
48524cb0
package
nl.lumc.sasc.biopet.pipelines.pipelinetemplate
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.config._
import
nl.lumc.sasc.biopet.extensions._
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
import
org.broadinstitute.gatk.queue.function._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
,
Argument
}
class
PipelineTemplate
(
val
root
:
Configurable
)
extends
QScript
with
BiopetQScript
{
def
this
()
=
this
(
null
)
...
...
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