Commit e42f7355 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix compile errors

parent d1384de8
......@@ -166,7 +166,7 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
optional("--MIN_DD_CLUSTER_SIZE", MIN_DD_CLUSTER_SIZE) +
optional("--MIN_DD_BREAKPOINT_SUPPORT", MIN_DD_BREAKPOINT_SUPPORT) +
optional("--MIN_DD_MAP_DISTANCE", MIN_DD_MAP_DISTANCE) +
optional("--DD_REPORT_DUPLICATION_READS", DD_REPORT_DUPLICATION_READS) +
optional("--DD_REPORT_DUPLICATION_READS", DD_REPORT_DUPLICATION_READS)
}
object PindelCaller {
......
......@@ -14,8 +14,8 @@
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.extensions.pindel
import java.io.{PrintWriter, File}
import collection.JavaConversions._
import java.io.{ PrintWriter, File }
import htsjdk.samtools.SamReaderFactory
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
......@@ -70,16 +70,13 @@ object PindelConfig extends ToolCommand {
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
val input: File = commandArgs.inputbam
val output: File = commandArgs.output.getOrElse( new File(input.getAbsoluteFile + ".pindel.cfg") )
val output: File = commandArgs.output.getOrElse(new File(input.getAbsoluteFile + ".pindel.cfg"))
val insertsize: Int = commandArgs.insertsize.getOrElse(0)
val bamReader = SamReaderFactory.makeDefault().open(input)
val writer = new PrintWriter(output)
var sampleName: String = ""
for( readgroup <- bamReader.getFileHeader.getReadGroups() ) {
val rg = bamReader.getFileHeader.getReadGroup( readgroup )
writer.write( s"${input.getAbsoluteFile}\t${insertsize}\t${rg.getSample}")
for (readgroup <- bamReader.getFileHeader.getReadGroups().toList) {
writer.write(s"${input.getAbsoluteFile}\t${insertsize}\t${readgroup.getSample}\n")
}
bamReader.close()
writer.close()
......
......@@ -17,8 +17,8 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelCaller$, PindelConfig}
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.pindel.{ PindelCaller, PindelCaller$, PindelConfig }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -27,35 +27,12 @@ class Pindel(val root: Configurable) extends SvCaller {
val name = "pindel"
def this() = this(null)
//
// @Input(doc = "Input file (bam)")
// var input: File = _
//
// @Input(doc = "Reference Fasta file")
// var reference: File = _
//
// @Argument(doc = "Work directory")
// var workdir: String = _
//
// // @Output(doc = "Pindel VCF output")
// // lazy val outputvcf: File = {
// // new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
// // }
//
// @Output(doc = "Pindel config")
// def configfile: File = {
// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
// }
// @Output(doc = "Pindel raw output")
// def outputvcf: File = {
// new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
// }
def biopetScript() {
for ((sample, bamFile) <- inputBams) {
val pindelDir = new File(outputDir, sample)
val config_file: File = new File( bamFile.getAbsolutePath + ".pindel.cfg" )
val config_file: File = new File(bamFile.getAbsolutePath + ".pindel.cfg")
val cfg = new PindelConfig(this)
cfg.input = bamFile
......
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