varsd_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
varMIN_OBSERVATIONS:Option[Int]=config("min_observations",default=1000000)// Number of observation required to estimate mean and s.d. insert size [10_000]
varCOEFVAR_CUTOFF:Option[Int]=config("coef_cutoff",default=1)// Cutoff on coefficients of variation [1]
varHISTOGRAM_BINS:Option[Int]=config("histogram_bins",default=50)// Number of bins in the histogram [50]
varmin_observations:Option[Int]=config("min_observations",default=10000)// Number of observation required to estimate mean and s.d. insert size [10_000]
varcoefvar_cutoff:Option[Int]=config("coef_cutoff",default=1)// Cutoff on coefficients of variation [1]
varhistogram_bins:Option[Int]=config("histogram_bins",default=50)// Number of bins in the histogram [50]
defcmdLine=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)+" > "+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)
}
objectBreakdancerConfig{
...
...
@@ -74,18 +75,18 @@ class BreakdancerCaller(val root: Configurable) extends BiopetCommandLineFunctio