Commit cb684be5 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Style reformat after compiling

parent c7d7faa8
......@@ -2,15 +2,15 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for bowtie 2
*
* Based on version 2.2.6
*/
* Extension for bowtie 2
*
* Based on version 2.2.6
*/
class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = null
......@@ -33,18 +33,18 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var bowtieIndex: String = config("bowtie_index")
/* Input options */
var q: Boolean = config("q", default=true)
var qseq: Boolean = config("qseq", default=false)
var f: Boolean = config("f", default=false)
var r: Boolean = config("r", default=false)
var c: Boolean = config("c", default=false)
var q: Boolean = config("q", default = true)
var qseq: Boolean = config("qseq", default = false)
var f: Boolean = config("f", default = false)
var r: Boolean = config("r", default = false)
var c: Boolean = config("c", default = false)
var skip: Option[Int] = config("skip")
var upto: Option[Int] = config("upto")
var trim5: Option[Int] = config("trim5")
var trim3: Option[Int] = config("trim3")
var phred33: Boolean = config("phred33", default=false)
var phred64: Boolean = config("phred64", default=false)
var int_quals: Boolean = config("int_quals", default=false)
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")
......@@ -53,12 +53,12 @@ class Bowtie2(val root: Configurable) extends BiopetCommandLineFunction with Ref
var n_ceil: Option[String] = config("n_ceil")
var dpad: Option[Int] = config("dpad")
var gbar: Option[Int] = config("gbar")
var ignore_quals: Boolean = config("ignore_quals", default=false)
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)
var ignore_quals: Boolean = config("ignore_quals", default = false)
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", 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)
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", default=false)
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", default=true)
var quiet: Boolean = config("quiet", default = true)
var met_file: Option[String] = config("met_file")
var met_stderr: Boolean = config("met_stderr", default=false)
var met_stderr: Boolean = config("met_stderr", default = false)
var met: Option[Int] = config("met")
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 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", default=false)
var omit_sec_seq: Boolean = config("omit_sec_seq", default = false)
/* Performance */
var reorder: Boolean = config("reorder", default=false)
var mm: Boolean = config("mm", default=true)
var reorder: Boolean = config("reorder", default = false)
var mm: Boolean = config("mm", default = true)
/* Other */
var qc_filter: Boolean = config("qc_filter", default=false)
var qc_filter: Boolean = config("qc_filter", default = false)
var seed: Option[Int] = config("seed")
var non_deterministic: Boolean = config("non_deterministic", default=false)
var non_deterministic: Boolean = config("non_deterministic", default = false)
/** return commandline to execute */
def cmdLine = required(executable) +
......
......@@ -219,7 +219,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
case "bwa-mem" => addBwaMem(R1, R2, outputBam)
case "bwa-aln" => addBwaAln(R1, R2, outputBam)
case "bowtie" => addBowtie(R1, R2, outputBam)
case "bowtie2" => addBowtie2(R1, R2, outputBam)
case "bowtie2" => addBowtie2(R1, R2, outputBam)
case "gsnap" => addGsnap(R1, R2, outputBam)
// TODO: make TopHat here accept multiple input files
case "tophat" => addTophat(R1, R2, outputBam)
......
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