Commit 48524cb0 authored by Peter van 't Hof's avatar Peter van 't Hof

Removed unused imports

parent b43fa492
......@@ -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
......
/*
* 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)
......
......@@ -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
......
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) {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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 {
......
......@@ -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
......
......@@ -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._
......
......@@ -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._
......
......@@ -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 {
......
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 }
......
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")
......
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)
......
......@@ -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._
......
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)
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment