Commit aefd3a63 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Split into separated files

parent d97202a8
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Breakdancer */
class Breakdancer(val root: Configurable) extends SvCaller {
def name = "breakdancer"
def biopetScript() {
//TODO: move minipipeline of breakdancer to here
for ((sample, bamFile) <- inputBams) {
val breakdancerDir = new File(outputDir, sample)
val breakdancer = Breakdancer(this, bamFile, breakdancerDir)
addAll(breakdancer.functions)
}
}
}
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)
}
}
}
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler delly */
class Delly(val root: Configurable) extends SvCaller {
def name = "delly"
def biopetScript() {
//TODO: Move mini delly pipeline to here
for ((sample, bamFile) <- inputBams) {
val dellyDir = new File(outputDir, sample)
val delly = Delly(this, bamFile, dellyDir)
delly.outputName = sample
addAll(delly.functions)
}
}
}
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import java.io.File
import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import nl.lumc.sasc.biopet.extensions.delly.Delly
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
......@@ -24,44 +18,8 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
def init() = {}
}
class Breakdancer(val root: Configurable) extends SvCaller {
def name = "breakdancer"
def biopetScript() {
//TODO: move minipipeline of breakdancer to here
for ((sample, bamFile) <- inputBams) {
val breakdancerDir = new File(outputDir, sample)
val breakdancer = Breakdancer(this, bamFile, breakdancerDir)
addAll(breakdancer.functions)
}
}
}
/** default mode of bcftools */
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)
}
}
}
/** Makes a vcf file from a mpileup without statistics */
class Delly(val root: Configurable) extends SvCaller {
def name = "delly"
def biopetScript() {
//TODO: Move mini delly pipeline to here
for ((sample, bamFile) <- inputBams) {
val dellyDir = new File(outputDir, sample)
val delly = Delly(this, bamFile, dellyDir)
delly.outputName = sample
addAll(delly.functions)
}
}
}
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