Add initial wrapper for seqtk

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/function/Seqtk.scala

+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 Seqtk extends BiopetCommandLineFunction {
+  executable = config("exe", default = "seqtk", submodule = "seqtk")
+  override def versionCommand = executable
+  override val versionRegex = """Version: (.*)""".r
+}
+
+class SeqtkSeq(val root: Configurable) extends Seqtk {
+  @Input(doc = "Input file (FASTQ or FASTA)")
+  var input: File = _
+
+  @Output(doc = "Output file")
+  var output: File = _
+
+  /* mask bases with quality lower than INT [0] */
+  var q: Option[Int] = config("q")
+
+  /* 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] */
+  var l: Option[Int] = config("l")
+
+  /* quality shift: ASCII-INT gives base quality [33] */
+  var Q: Option[Int] = config("Q")
+
+  /* random seed (effective with -f) [11] */
+  var s: Option[Int] = config("s")
+
+  /* sample FLOAT fraction of sequences [1] */
+  var f: Option[Int] = config("f")
+
+  /* mask regions in BED or name list FILE [null] */
+  var M: File = config("M")
+
+  /* drop sequences with length shorter than INT [0] */
+  var L: Option[Int] = config("L")
+
+  /* mask complement region (effective with -M) */
+  var c: Boolean = config("c")
+
+  /* reverse complement */
+  var r: Boolean = config("r")
+
+  /* force FASTA output (discard quality) */
+  var A: Boolean = config("A")
+
+  /* drop comments at the header lines */
+  var C: Boolean = config("C")
+
+  /* drop sequences containing ambiguous bases */
+  var N: Boolean = config("N")
+
+  /* output the 2n-1 reads only */
+  var flag1: Boolean = config("1")
+
+  /* output the 2n reads only */
+  var flag2: Boolean = config("2")
+
+  /* shift quality by '(-Q) - 33' */
+  var V: Boolean = config("V")
+
+  def cmdLine = {
+    required(executable) +
+      " seq " +
+      optional("-q", q) +
+      optional("-n", n) +
+      optional("-l", l) +
+      optional("-Q", Q) +
+      optional("-s", s) +
+      optional("-f", f) +
+      optional("-M", M) +
+      optional("-L", L) +
+      conditional(c, "-c") +
+      conditional(r, "-r") +
+      conditional(A, "-A") +
+      conditional(C, "-C") +
+      conditional(N, "-N") +
+      conditional(flag1, "-1") +
+      conditional(flag2, "-2") +
+      conditional(V, "-V") +
+      required(input) +
+      " > " + required(output)
+  }
+
+  /**
+   * Calculates the offset required for the -Q flag for format conversion (-V flag set).
+   * This is required since seqtk computes the encoding offset indirectly from the input
+   * and output offsets.
+   *
+   * @param  inQualOffset  ASCII offset of the input file encoding
+   * @param  outQualOffset ASCII offset of the output file encoding
+   * @return               the value to be used with the -Q flag with -V set
+   */
+  def calcQForV(inQualOffset: Int, outQualOffset: Int): Int = {
+    // For the input for the -Q flag for seqtk, together with -V
+    inQualOffset - (outQualOffset - 33)
+  }
+}