Breakdancer, scaliform reformat

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

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
   }