Commit de250d3f authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix pindel caller (fixing null error with Option[File] = None instead of _)

parent 8af58a0b
......@@ -20,7 +20,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.utils.Logging
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 }
/**
* Extension for pindel
......@@ -47,10 +47,10 @@ class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction wit
var input: File = _
@Argument(doc = "The pindel configuration file")
var pindel_file: Option[File] = _
var pindel_file: Option[File] = None
@Argument(doc = "Configuration file with: bam-location/insert size/name")
var config_file: Option[File] = _
var config_file: Option[File] = None
@Argument(doc = "Work directory")
var output_prefix: File = _
......
......@@ -32,7 +32,7 @@ class Pindel(val root: Configurable) extends SvCaller {
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(outputDir + "." + sample + ".pindel.cfg")
val cfg = new PindelConfig(this)
cfg.input = bamFile
......
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