Commit bc2a511c authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove some defaults

parent f634582b
......@@ -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() {
}
......
......@@ -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) +
......
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