Clever.scala 561 Bytes
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers

import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.utils.config.Configurable

/** Script for sv caler Clever */
class Clever(val root: Configurable) extends SvCaller {
  def name = "clever"

  def biopetScript() {
    //TODO: check double directories
    for ((sample, bamFile) <- inputBams) {
      val cleverDir = new File(outputDir, sample)
      val clever = CleverCaller(this, bamFile, cleverDir)
      add(clever)
16

17
      addVCF(sample, clever.outputvcf)
Peter van 't Hof's avatar
Peter van 't Hof committed
18
19
20
    }
  }
}