Commit 2c14276c authored by bow's avatar bow
Browse files

Update seqtk wrapper docs and formatting

parent a7522c76
/**
* Copyright (c) 2014 Leiden University Medical Center
*
* @author Wibowo Arindrarto
*/
package nl.lumc.sasc.biopet.function
import java.io.File
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import nl.lumc.sasc.biopet.core.config.Configurable
/**
* Abstract class for all seqtk wrappers.
*/
abstract class Seqtk extends BiopetCommandLineFunction {
executable = config("exe", default = "seqtk", submodule = "seqtk")
override def versionCommand = executable
override val versionRegex = """Version: (.*)""".r
}
/**
* Wrapper for the seqtk seq subcommand.
* Written based on seqtk version 1.0-r63-dirty.
*/
class SeqtkSeq(val root: Configurable) extends Seqtk {
/** input file */
@Input(doc = "Input file (FASTQ or FASTA)")
var input: File = _
/** output file */
@Output(doc = "Output file")
var output: File = _
/* mask bases with quality lower than INT [0] */
/** mask bases with quality lower than INT [0] */
var q: Option[Int] = config("q")
/* masked bases converted to CHAR; 0 for lowercase [0] */
/** masked bases converted to CHAR; 0 for lowercase [0] */
var n: String = config("n")
/* number of residues per line; 0 for 2^32-1 [0] */
/** number of residues per line; 0 for 2^32-1 [0] */
var l: Option[Int] = config("l")
/* quality shift: ASCII-INT gives base quality [33] */
/** quality shift: ASCII-INT gives base quality [33] */
var Q: Option[Int] = config("Q")
/* random seed (effective with -f) [11] */
/** random seed (effective with -f) [11] */
var s: Option[Int] = config("s")
/* sample FLOAT fraction of sequences [1] */
/** sample FLOAT fraction of sequences [1] */
var f: Option[Int] = config("f")
/* mask regions in BED or name list FILE [null] */
/** mask regions in BED or name list FILE [null] */
var M: File = config("M")
/* drop sequences with length shorter than INT [0] */
/** drop sequences with length shorter than INT [0] */
var L: Option[Int] = config("L")
/* mask complement region (effective with -M) */
/** mask complement region (effective with -M) */
var c: Boolean = config("c")
/* reverse complement */
/** reverse complement */
var r: Boolean = config("r")
/* force FASTA output (discard quality) */
/** force FASTA output (discard quality) */
var A: Boolean = config("A")
/* drop comments at the header lines */
/** drop comments at the header lines */
var C: Boolean = config("C")
/* drop sequences containing ambiguous bases */
/** drop sequences containing ambiguous bases */
var N: Boolean = config("N")
/* output the 2n-1 reads only */
/** output the 2n-1 reads only */
var flag1: Boolean = config("1")
/* output the 2n reads only */
/** output the 2n reads only */
var flag2: Boolean = config("2")
/* shift quality by '(-Q) - 33' */
/** shift quality by '(-Q) - 33' */
var V: Boolean = config("V")
def cmdLine = {
......
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