diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
index 631e9d33b564d4a22b5ed79a93e893fd4d27f30f..8c6cbb13b730f4ad12e9db86aa310f5dbb0af76c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
@@ -22,22 +22,22 @@ class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunctio
var min_insertsize: Option[Int] = config("min_insertsize", default = 450)
var solid_data: Boolean = config("solid", default = false)
var sd_cutoff: Option[Int] = config("sd_cutoff", default = 4) // Cutoff in unit of standard deviation [4]
-
+
// we set this to a higher number to avoid biases in small numbers in sorted bams
var min_observations: Option[Int] = config("min_observations", default = 10000) // Number of observation required to estimate mean and s.d. insert size [10_000]
var coefvar_cutoff: Option[Int] = config("coef_cutoff", default = 1) // Cutoff on coefficients of variation [1]
var histogram_bins: Option[Int] = config("histogram_bins", default = 50) // Number of bins in the histogram [50]
-
+
def cmdLine = required(executable) +
- optional("-q", min_mq) +
- conditional(use_mq, "-m") +
- optional("-s", min_insertsize) +
- conditional(solid_data, "-s") +
- optional("-c", sd_cutoff) +
- optional("-n", min_observations) +
- optional("-v", coefvar_cutoff) +
- optional("-b", histogram_bins) +
- required(input) + " 1> " + required(output)
+ optional("-q", min_mq) +
+ conditional(use_mq, "-m") +
+ optional("-s", min_insertsize) +
+ conditional(solid_data, "-s") +
+ optional("-c", sd_cutoff) +
+ optional("-n", min_observations) +
+ optional("-v", coefvar_cutoff) +
+ optional("-b", histogram_bins) +
+ required(input) + " 1> " + required(output)
}
object BreakdancerConfig {
@@ -61,35 +61,30 @@ object BreakdancerConfig {
private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".breakdancer.cfg"
}
-
-
-
/*
* The caller
*
**/
-
-class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
+class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "breakdancer-max", freeVar = false)
-
+
override val defaultVmem = "6G"
override val defaultThreads = 1 // breakdancer can only work on 1 single thread
-
+
override val versionRegex = """.*[Vv]ersion:? (.*)""".r
override val versionExitcode = List(1)
override def versionCommand = executable
-
-
+
@Input(doc = "The breakdancer configuration file")
var input: File = _
-
-// @Argument(doc = "Work directory")
-// var workdir: String = _
-
- @Output(doc = "Breakdancer VCF output")
+
+ // @Argument(doc = "Work directory")
+ // var workdir: String = _
+
+ @Output(doc = "Breakdancer TSV output")
var output: File = _
-
+
/*
Options:
-o STRING operate on a single chromosome [all chromosome]
@@ -115,36 +110,36 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
var q: Option[Int] = config("qs", default = 35)
var r: Option[Int] = config("r", default = 2)
var x: Option[Int] = config("x", default = 1000)
- var b: Option[Int] = config("b", default = 100)
+ var b: Option[Int] = config("b", default = 100)
var t: Boolean = config("t", default = false)
var d: String = config("d")
var g: String = config("g")
var l: Boolean = config("l", default = false)
var a: Boolean = config("a", default = false)
var h: Boolean = config("h", default = false)
- var y: Option[Int] = config("y", default = 30)
-
+ var y: Option[Int] = config("y", default = 30)
+
override def beforeCmd {
}
- def cmdLine = required(executable) +
- optional("-s", s) +
- optional("-c", c) +
- optional("-m", m) +
- optional("-q", q) +
- optional("-r", r) +
- optional("-x", x) +
- optional("-b", b) +
- conditional(t ,"-t") +
- optional("-d", d) +
- optional("-g", g) +
- conditional(l ,"-l") +
- conditional(a ,"-a") +
- conditional(h ,"-h") +
- optional("-y", y) +
- required(input) +
- ">" +
- required(output)
+ def cmdLine = required(executable) +
+ optional("-s", s) +
+ optional("-c", c) +
+ optional("-m", m) +
+ optional("-q", q) +
+ optional("-r", r) +
+ optional("-x", x) +
+ optional("-b", b) +
+ conditional(t, "-t") +
+ optional("-d", d) +
+ optional("-g", g) +
+ conditional(l, "-l") +
+ conditional(a, "-a") +
+ conditional(h, "-h") +
+ optional("-y", y) +
+ required(input) +
+ ">" +
+ required(output)
}
object BreakdancerCaller {
@@ -159,23 +154,18 @@ object BreakdancerCaller {
/// Breakdancer is actually a mini pipeline executing binaries from the breakdancer package
class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
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 = _
-
- var deps : List[File] = Nil
-
- @Output(doc = "Breakdancer VCF output")
- lazy val outputvcf: File = {
- new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.vcf")
- }
-
+
+ var deps: List[File] = Nil
+
@Output(doc = "Breakdancer config")
lazy val configfile: File = {
new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.cfg")
@@ -184,32 +174,35 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
lazy val outputraw: File = {
new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.tsv")
}
-
+ @Output(doc = "Breakdancer VCF output")
+ lazy val outputvcf: File = {
+ new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".breakdancer.vcf")
+ }
+
override def init() {
}
def biopetScript() {
// read config and set all parameters for the pipeline
logger.info("Starting Breakdancer configuration")
-
+
val bdcfg = BreakdancerConfig(this, input, this.configfile)
bdcfg.deps = this.deps
- outputFiles += ("cfg" -> bdcfg.output )
- add( bdcfg )
-
- val output_tsv: File = this.outputraw
- val breakdancer = BreakdancerCaller( this, bdcfg.output, output_tsv )
- add( breakdancer )
- outputFiles += ("tsv" -> breakdancer.output )
-
- val bdvcf = BreakdancerVCF( this, breakdancer.output, this.outputvcf )
- add( bdvcf )
- outputFiles += ("vcf" -> bdvcf.output )
+ outputFiles += ("cfg" -> bdcfg.output)
+ add(bdcfg)
+
+ val breakdancer = BreakdancerCaller(this, bdcfg.output, this.outputraw)
+ add(breakdancer)
+ outputFiles += ("tsv" -> breakdancer.output)
+
+ val bdvcf = BreakdancerVCF(this, breakdancer.output, this.outputvcf)
+ add(bdvcf)
+ outputFiles += ("vcf" -> bdvcf.output)
}
}
object Breakdancer extends PipelineCommand {
- def apply(root: Configurable, input: File, reference: File, runDir: String): Breakdancer = {
+ def apply(root: Configurable, input: File, reference: File, runDir: String): Breakdancer = {
val breakdancer = new Breakdancer(root)
breakdancer.input = input
breakdancer.reference = reference
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
index 731b0f8292102218a856b6aa21da72a86261f7db..d23299ab800b0209f66bb3957261e76d5073f4be 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/BreakdancerVCF.scala
@@ -37,15 +37,15 @@ class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
def cmdLine = {
getPythonCommand +
- "-i " + required(input) +
- "-o " + required(output)
+ "-i " + required(input) +
+ "-o " + required(output)
}
}
object BreakdancerVCF {
- def apply(root: Configurable, input:File, output:File): BreakdancerVCF = {
+ def apply(root: Configurable, input: File, output: File): BreakdancerVCF = {
val bd = new BreakdancerVCF(root)
- bd.input =input
+ bd.input = input
bd.output = output
return bd
}
diff --git a/biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/extension/svcallers/breakdancer2vcf.py b/biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py
similarity index 100%
rename from biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/extension/svcallers/breakdancer2vcf.py
rename to biopet-framework/src/main/scripts/nl/lumc/sasc/biopet/extensions/svcallers/breakdancer2vcf.py