Commit 0c1c8db6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs for bwa

parent e98f7409
......@@ -3,6 +3,8 @@ package nl.lumc.sasc.biopet.extensions.bwa
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
/**
* General bwa extension
*
* Created by pjvan_thof on 1/16/15.
*/
abstract class Bwa extends BiopetCommandLineFunction {
......
......@@ -6,6 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Extension for bwa aln
*
* Based on version 0.7.12-r1039
*
* Created by pjvan_thof on 1/16/15.
*/
class BwaAln(val root: Configurable) extends Bwa {
......@@ -44,6 +48,7 @@ class BwaAln(val root: Configurable) extends Bwa {
override val defaultVmem = "5G"
override val defaultThreads = 8
/** Returns command to execute */
def cmdLine = required(executable) +
required("aln") +
optional("-n", n) +
......
......@@ -22,6 +22,11 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.summary.Summarizable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for bwa mem
*
* Based on version 0.7.12-r1039
*/
class BwaMem(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = _
......
......@@ -10,7 +10,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
*
* based on executable version 0.7.10-r789
*
* @param root Configurable
*/
class BwaSampe(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", required = true)
......
......@@ -6,7 +6,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 1/16/15.
* BWA samse wrapper
*
* based on executable version 0.7.10-r789
*
*/
class BwaSamse(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file", required = true)
......@@ -24,6 +27,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var n: Option[Int] = config("n")
var r: String = _
/** Returns command to execute */
def cmdLine = required(executable) +
required("samse") +
optional("-n", n) +
......
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