Add a new tool

biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

@@ -31,6 +31,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
     nl.lumc.sasc.biopet.tools.ExtractAlignedFastq,
     nl.lumc.sasc.biopet.tools.FastqSplitter,
     nl.lumc.sasc.biopet.tools.FastqSync,
+    nl.lumc.sasc.biopet.tools.FastqFilter,
     nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
     nl.lumc.sasc.biopet.tools.FindOverlapMatch,
     nl.lumc.sasc.biopet.tools.GvcfToBed,

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader }
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.util.matching.Regex
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 28-10-16.
+ */
+object FastqFilter extends ToolCommand {
+  /**
+   * Arg for commandline program
+   * @param inputFile input fastq file
+   * @param outputFile output fastq files
+   */
+  case class Args(inputFile: File = null,
+                  outputFile: File = null,
+                  idRegex: Option[Regex] = None) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
+      c.copy(inputFile = x)
+    } text "Path to input file"
+    opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(outputFile = x)
+    } text "Path to output file"
+    opt[String]("idRegex") unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(idRegex = Some(x.r))
+    } text "Regex to match ID"
+  }
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
+
+    logger.info("Start")
+
+    val reader = new FastqReader(cmdArgs.inputFile)
+    val writer = new AsyncFastqWriter(new BasicFastqWriter(cmdArgs.outputFile), 10000)
+
+    var total = 0
+    var kept = 0
+    for (record <- reader.iterator()) {
+      if (cmdArgs.idRegex.map(_.findFirstIn(record.getReadHeader.takeWhile(_ != ' ')).isDefined).getOrElse(true)) {
+        writer.write(record)
+        kept += 1
+      }
+      total += 1
+      if (total % 100000 == 0) logger.info(s"Total reads: $total,  reads left: $kept")
+    }
+    logger.info(s"Total reads: $total,  reads left: $kept")
+
+    writer.close()
+    reader.close()
+
+    logger.info("Done")
+  }
+}