Remove some defaults

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala

@@ -58,20 +58,20 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio
        -y INT          output score filter [30]
    */
 
-  var s: Option[Int] = config("s", default = 7)
-  var c: Option[Int] = config("c", default = 3)
-  var m: Option[Int] = config("m", default = 1000000000)
-  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 s: Option[Int] = config("s")
+  var c: Option[Int] = config("c")
+  var m: Option[Int] = config("m")
+  var q: Option[Int] = config("qs")
+  var r: Option[Int] = config("r")
+  var x: Option[Int] = config("x")
+  var b: Option[Int] = config("b")
   var t: Boolean = config("t", default = false)
   var d: Option[String] = config("d")
   var g: Option[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")
 
   override def beforeCmd() {
   }

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala

@@ -32,14 +32,14 @@ class BreakdancerConfig(val root: Configurable) extends BiopetCommandLineFunctio
 
   var min_mq: Option[Int] = config("min_mq", default = 20) // minimum of MQ to consider for taking read into histogram
   var use_mq: Boolean = config("use_mq", default = false)
-  var min_insertsize: Option[Int] = config("min_insertsize", default = 450)
+  var min_insertsize: Option[Int] = config("min_insertsize")
   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]
+  var sd_cutoff: Option[Int] = config("sd_cutoff") // 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]
+  var min_observations: Option[Int] = config("min_observations") //  Number of observation required to estimate mean and s.d. insert size [10_000]
+  var coefvar_cutoff: Option[Int] = config("coef_cutoff") // Cutoff on coefficients of variation [1]
+  var histogram_bins: Option[Int] = config("histogram_bins") // Number of bins in the histogram [50]
 
   def cmdLine = required(executable) +
     optional("-q", min_mq) +