From bc2a511c917d7ea98da8a6db095007c283b8c92e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 28 Jul 2015 17:03:14 +0200
Subject: [PATCH] Remove some defaults
---
.../breakdancer/BreakdancerCaller.scala | 16 ++++++++--------
.../breakdancer/BreakdancerConfig.scala | 10 +++++-----
2 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
index 14f8f0495..4b2efd150 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerCaller.scala
+++ b/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() {
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
index 72ef2e268..6a67b3714 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerConfig.scala
+++ b/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) +
--
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