added a new tool to validate if paired end sequences are in sync

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckFastqPairs.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import htsjdk.samtools.fastq.FastqReader
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.collection.JavaConversions._
+
+/**
+ * Created by sajvanderzeeuw on 2-2-16.
+ */
+object CheckFastqPairs extends ToolCommand {
+  /**
+   * Args for commandline program
+   * @param input input first fastq file (R1) (can be zipped)
+   * @param input2 input second fastq file (R2) (can be zipped)
+   * @param output output fastq file (can be zipped)
+   */
+
+  case class Args(input: File = null, input2: Option[File] = None, output: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('i', "fastq1") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(input = x)
+    }
+    opt[File]('j', "fastq2") maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(input2 = Some(x))
+    }
+    opt[File]('o', "output") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(output = x)
+    }
+  }
+
+  def main(args: Array[String]): Unit = {
+    logger.info("Start")
+
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    val readFq1 = new FastqReader(cmdArgs.input)
+    val readFq2 = cmdArgs.input2.map(new FastqReader(_))
+
+    var counter = 0
+    var countline = 0
+
+    for (recordR1 <- readFq1.iterator()) {
+      if (readFq2.map(_.hasNext) == Some(false))
+        throw new IllegalStateException("R2 has less reads then R1")
+
+      //Getting R2 record, None if it's single end
+      val recordR2 = readFq2.map(_.next())
+
+      recordR2 match {
+        case Some(recordR2) => // Paired End
+          val readHeader = recordR1.getReadHeader
+          val readHeader2 = recordR2.getReadHeader
+          val id1 = readHeader.takeWhile(_ != ' ')
+          val id2 = readHeader2.takeWhile(_ != ' ')
+
+          if (counter % 1e5 == 0) logger.info(counter + " reads processed")
+
+          if (id1 == id2){
+
+          } else if (id1.stripSuffix("/1") == id2.stripSuffix("/2")) {
+
+          } else if (id1.stripSuffix(".1") == id2.stripSuffix(".2")) {
+
+          } else
+            throw new IllegalStateException(s"sequenceHeaders does not match at line '${(counter*4)-3}'. R1: '$readHeader', R2: '$readHeader2'")
+        case _ => // Single end
+      }
+      counter += 1
+    }
+
+    if (readFq2.map(_.hasNext) == Some(true))
+      throw new IllegalStateException("R2 has more reads then R1")
+
+    logger.info("Done processing the Fastq file(s) no errors found")
+    readFq1.close()
+    readFq2.foreach(_.close())
+  }
+
+}
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