Commit 1a27786b authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Set defaults for Boolean values

parent 6c3cd444
......@@ -42,9 +42,9 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var upto: Option[Int] = config("upto")
var trim5: Option[Int] = config("trim5")
var trim3: Option[Int] = config("trim3")
var phred33: Boolean = config("phred33")
var phred64: Boolean = config("phred64")
var int_quals: Boolean = config("int_quals")
var phred33: Boolean = config("phred33", default=false)
var phred64: Boolean = config("phred64", default=false)
var int_quals: Boolean = config("int_quals", default=false)
/* Alignment options */
var N: Option[Int] = config("N")
......@@ -54,11 +54,11 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var dpad: Option[Int] = config("dpad")
var gbar: Option[Int] = config("gbar")
var ignore_quals: Boolean = config("ignore_quals")
var nofw: Boolean = config("nofw")
var norc: Boolean = config("norc")
var no_1mm_upfront: Boolean = config("no_1mm_upfront")
var end_to_end: Boolean = config("end_to_end")
var local: Boolean = config("local")
var nofw: Boolean = config("nofw", default=false)
var norc: Boolean = config("norc", default=false)
var no_1mm_upfront: Boolean = config("no_1mm_upfront", default=false)
var end_to_end: Boolean = config("end_to_end", default=false)
var local: Boolean = config("local", default=false)
/* Scoring */
var ma: Option[Int] = config("ma")
......@@ -79,17 +79,17 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
/* Paired-end */
var minins: Option[Int] = config("minins")
var maxins: Option[Int] = config("maxins")
var fr: Boolean = config("fr")
var rf: Boolean = config("rf")
var ff: Boolean = config("ff")
var no_mixed: Boolean = config("no_mixed")
var no_discordant: Boolean = config("no_discordant")
var no_dovetail: Boolean = config("no_dovetail")
var no_contain: Boolean = config("no_contain")
var no_overlap: Boolean = config("no_overlap")
var fr: Boolean = config("fr", default=false)
var rf: Boolean = config("rf", default=false)
var ff: Boolean = config("ff", default=false)
var no_mixed: Boolean = config("no_mixed", default=false)
var no_discordant: Boolean = config("no_discordant", default=false)
var no_dovetail: Boolean = config("no_dovetail", default=false)
var no_contain: Boolean = config("no_contain", default=false)
var no_overlap: Boolean = config("no_overlap", default=false)
/* Output */
var time: Boolean = config("no_overlap")
var time: Boolean = config("no_overlap", default=false)
var un: Option[String] = config("un")
var al: Option[String] = config("al")
......@@ -106,28 +106,28 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var un_conc_bz2: Option[String] = config("un_conc_bz2")
var al_conc_bz2: Option[String] = config("al_conc_bz2")
var quiet: Boolean = config("quiet")
var quiet: Boolean = config("quiet", default=true)
var met_file: Option[String] = config("met_file")
var met_stderr: Boolean = config("met_stderr")
var met_stderr: Boolean = config("met_stderr", default=false)
var met: Option[Int] = config("met")
var no_unal: Boolean = config("no_unal")
var no_head: Boolean = config("no_head")
var no_sq: Boolean = config("no_sq")
var no_unal: Boolean = config("no_unal", default=false)
var no_head: Boolean = config("no_head", default=false)
var no_sq: Boolean = config("no_sq", default=false)
var rg_id: Option[String] = config("rg_id")
var rg: Option[String] = config("rg")
var omit_sec_seq: Boolean = config("omit_sec_seq")
var omit_sec_seq: Boolean = config("omit_sec_seq", default=false)
/* Performance */
var reorder: Boolean = config("reorder")
var mm: Boolean = config("mm")
var reorder: Boolean = config("reorder", default=false)
var mm: Boolean = config("mm", default=true)
/* Other */
var qc_filter: Boolean = config("qc_filter")
var qc_filter: Boolean = config("qc_filter", default=false)
var seed: Option[Int] = config("seed")
var non_deterministic: Boolean = config("non_deterministic")
var non_deterministic: Boolean = config("non_deterministic", default=false)
/** return commandline to execute */
def cmdLine = required(executable) +
......
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