From 2c14276c6e3a8f0b7b96f51c17bc3d9df9dfc264 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 23 Jul 2014 18:43:40 +0200
Subject: [PATCH] Update seqtk wrapper docs and formatting
---
.../nl/lumc/sasc/biopet/function/Seqtk.scala | 50 ++++++++++++-------
1 file changed, 32 insertions(+), 18 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
index 5cc3d8cab..286b7235b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala
@@ -1,71 +1,85 @@
+/**
+ * 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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