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biopet.biopet
Commits
335cc12f
Commit
335cc12f
authored
Jun 10, 2015
by
Peter van 't Hof
Browse files
Adding versions of tools to summary
parent
1be5eeef
Changes
20
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
View file @
335cc12f
...
...
@@ -54,4 +54,8 @@ trait ToolCommand extends MainCommand with Logging {
protected
type
Args
<:
AbstractArgs
protected
type
OptParser
<:
AbstractOptParser
}
trait
ToolCommandFuntion
extends
BiopetJavaCommandLineFunction
{
override
def
getVersion
=
Some
(
"Biopet "
+
FullVersion
)
}
\ No newline at end of file
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
335cc12f
...
...
@@ -22,7 +22,7 @@ import htsjdk.tribble.bed.BEDCodec
import
htsjdk.variant.variantcontext.VariantContextBuilder
import
htsjdk.variant.variantcontext.writer.
{
VariantContextWriterBuilder
,
AsyncVariantContextWriter
}
import
htsjdk.variant.vcf.
{
VCFHeaderLineType
,
VCFHeaderLineCount
,
VCFInfoHeaderLine
,
VCFFileReader
}
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommand
Funtion
,
ToolCommand
}
import
scala.collection.JavaConverters.asScalaIteratorConverter
import
scala.collection.JavaConversions._
import
scala.collection.mutable
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
335cc12f
...
...
@@ -21,15 +21,14 @@ import htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.vcf.VCFFileReader
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.utils.VcfUtils._
import
scala.collection.mutable.ListBuffer
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input vcf file"
,
required
=
false
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
335cc12f
...
...
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.
{
SAMSequenceRecord
,
SamReaderFactory
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.PrintWriter
...
...
@@ -27,7 +26,7 @@ import scala.io.Source
/**
* @deprecated Use picard.util.BedToIntervalList instead
*/
class
BedToInterval
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
BedToInterval
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input Bed file"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
View file @
335cc12f
...
...
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
...
...
@@ -26,7 +25,7 @@ import scala.collection.SortedMap
import
scala.collection.mutable.Map
import
scala.io.Source
class
BedtoolsCoverageToCounts
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
BedtoolsCoverageToCounts
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
335cc12f
...
...
@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
import
htsjdk.samtools.
{
SAMRecord
,
SamReaderFactory
}
import
java.io.
{
PrintWriter
,
File
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
class
BiopetFlagstat
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
with
Summarizable
{
class
BiopetFlagstat
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
with
Summarizable
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input bam"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
View file @
335cc12f
...
...
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
FastqReader
,
BasicFastqWriter
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
...
...
@@ -27,7 +26,7 @@ import scala.collection.JavaConversions._
* Queue extension for the FastqSplitter
* @param root Parent object
*/
class
FastqSplitter
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
FastqSplitter
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fastq"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
View file @
335cc12f
...
...
@@ -27,7 +27,7 @@ import scala.collection.JavaConverters._
import
htsjdk.samtools.fastq.
{
AsyncFastqWriter
,
BasicFastqWriter
,
FastqReader
,
FastqRecord
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.
{
BiopetExecutable
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetExecutable
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
/**
...
...
@@ -35,7 +35,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*
* @param root Configuration object for the pipeline
*/
class
FastqSync
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
with
Summarizable
{
class
FastqSync
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
with
Summarizable
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
View file @
335cc12f
...
...
@@ -24,15 +24,14 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import
htsjdk.variant.vcf.VCFFileReader
import
htsjdk.variant.vcf.VCFHeader
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
scala.collection.SortedMap
import
scala.collection.mutable.
{
Map
,
Set
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
scala.collection.JavaConversions._
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
MergeAlleles
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
MergeAlleles
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input vcf files"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
View file @
335cc12f
...
...
@@ -19,8 +19,7 @@ import java.io.{ File, BufferedWriter, FileWriter, OutputStreamWriter }
import
scala.io.
{
BufferedSource
,
Source
}
import
scala.collection.mutable.
{
Set
=>
MutSet
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -29,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*
* @param root [[Configurable]] object
*/
class
MergeTables
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
MergeTables
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
335cc12f
...
...
@@ -18,8 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.utils.ConfigUtils
...
...
@@ -30,7 +29,7 @@ import scala.math.round
import
scala.math.floor
import
scala.collection.JavaConversions._
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input mpileup file"
,
shortName
=
"mpileup"
,
required
=
false
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
View file @
335cc12f
...
...
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
htsjdk.samtools.fastq.
{
FastqRecord
,
AsyncFastqWriter
,
FastqReader
,
BasicFastqWriter
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
,
Input
}
...
...
@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 1/13/15.
*/
class
PrefixFastq
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
PrefixFastq
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
override
val
defaultCoreMemory
=
1.0
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
View file @
335cc12f
...
...
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.biojava3.sequencing.io.fastq.
{
SangerFastqReader
,
StreamListener
,
Fastq
}
...
...
@@ -27,7 +26,7 @@ import scala.collection.SortedMap
import
scala.collection.mutable.Map
import
java.io.FileReader
class
SageCountFastq
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
SageCountFastq
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
View file @
335cc12f
...
...
@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.biojava3.core.sequence.DNASequence
import
org.biojava3.core.sequence.io.FastaReaderHelper
...
...
@@ -28,7 +27,7 @@ import scala.collection.mutable.{ Map, Set }
import
scala.collection.JavaConversions._
import
scala.util.matching.Regex
class
SageCreateLibrary
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
SageCreateLibrary
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
View file @
335cc12f
...
...
@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.io.Source
import
scala.collection.mutable.Map
import
scala.collection.SortedMap
class
SageCreateTagCounts
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
SageCreateTagCounts
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Raw count file"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/Seqstat.scala
View file @
335cc12f
...
...
@@ -29,8 +29,7 @@ import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
import
scalaz._
,
Scalaz
.
_
import
argonaut._
,
Argonaut
.
_
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.utils.ConfigUtils
...
...
@@ -39,7 +38,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
*
* @param root Configuration object for the pipeline
*/
class
Seqstat
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
with
Summarizable
{
class
Seqstat
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
with
Summarizable
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input FASTQ"
,
shortName
=
"input"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
View file @
335cc12f
...
...
@@ -20,14 +20,13 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
import
htsjdk.variant.vcf.VCFFileReader
import
htsjdk.variant.variantcontext.VariantContext
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
scala.collection.JavaConversions._
import
scala.io.Source
class
VcfFilter
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
VcfFilter
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input vcf"
,
shortName
=
"I"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
335cc12f
...
...
@@ -21,7 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.variant.variantcontext.
{
Allele
,
VariantContext
,
Genotype
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
scala.collection.JavaConversions._
...
...
@@ -35,7 +35,7 @@ import scala.util.Random
/**
* Created by pjvan_thof on 1/10/15.
*/
class
VcfStats
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
with
Summarizable
{
class
VcfStats
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
with
Summarizable
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fastq"
,
shortName
=
"I"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
View file @
335cc12f
...
...
@@ -25,7 +25,7 @@ import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, Variant
import
htsjdk.variant.vcf._
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
/**
...
...
@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
* Created by ahbbollen on 10/27/14.
*/
class
VepNormalizer
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
VepNormalizer
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input VCF, may be indexed"
,
shortName
=
"InputFile"
,
required
=
true
)
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala
View file @
335cc12f
...
...
@@ -34,8 +34,7 @@ import htsjdk.tribble.bed.BEDCodec
import
org.apache.commons.io.FilenameUtils.getExtension
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
// TODO: finish implementation for usage in pipelines
...
...
@@ -44,7 +43,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*
* @param root Configuration object for the pipeline
*/
class
WipeReads
(
val
root
:
Configurable
)
extends
BiopetJava
Command
Line
Fun
c
tion
{
class
WipeReads
(
val
root
:
Configurable
)
extends
Tool
CommandFuntion
{
javaMainClass
=
getClass
.
getName
...
...
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