Merge branch 'fix-validator' into 'develop'

Fix validator

This looses the fastq validator

See merge request !344

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

@@ -10,6 +10,7 @@ import scala.collection.mutable.ListBuffer
 
 /**
  * Created by sajvanderzeeuw on 2-2-16.
+ * Modified by pjvan_thof
  */
 object ValidateFastq extends ToolCommand {
   /**
@@ -63,13 +64,13 @@ object ValidateFastq extends ToolCommand {
 
         //Here we check if the readnames of both files are concordant, and if the sequence content are correct DNA/RNA sequences
         recordR2 match {
-          case Some(recordR2) => // Paired End
-            validFastqRecord(recordR2)
-            duplicateCheck(recordR2, lastRecordR2)
-            checkMate(recordR1, recordR2)
+          case Some(r2) => // Paired End
+            validFastqRecord(r2)
+            duplicateCheck(r2, lastRecordR2)
+            checkMate(recordR1, r2)
           case _ => // Single end
         }
-        if (counter % 1e5 == 0) logger.info(counter + " reads processed")
+        if (counter % 1e5 == 0) logger.info(counter + (if (recordR2.isDefined) " pairs" else " reads") + " processed")
         lastRecordR1 = Some(recordR1)
         lastRecordR2 = recordR2
       }
@@ -78,9 +79,12 @@ object ValidateFastq extends ToolCommand {
       if (readFq2.map(_.hasNext) == Some(true))
         throw new IllegalStateException("R2 contains more reads then R1")
 
-      logger.info(s"Possible quality encodings found: ${getPossibleEncodings.mkString(", ")}")
+      getPossibleEncodings match {
+        case l if l.nonEmpty => logger.info(s"Possible quality encodings found: ${l.mkString(", ")}")
+        case _               => logger.warn(s"No possible quality encodings found")
+      }
 
-      logger.info(s"Done processing ${counter} fastq records, no errors found")
+      logger.info(s"Done processing $counter fastq records, no errors found")
     } catch {
       case e: IllegalStateException =>
         logger.error(s"Error found at readnumber: $counter, linenumber ${(counter * 4) - 3}")
@@ -96,9 +100,9 @@ object ValidateFastq extends ToolCommand {
   private[tools] var maxQual: Option[Char] = None
 
   /**
-   *
-   * @param record
-   * @throws IllegalStateException
+   * This method checks if the encoding in a fastq record is correct
+   * @param record The fastq record to check
+   * @throws IllegalStateException Throws this when an error is ofund during checking
    */
   private[tools] def checkQualEncoding(record: FastqRecord): Unit = {
     val min = record.getBaseQualityString.min
@@ -114,21 +118,21 @@ object ValidateFastq extends ToolCommand {
   }
 
   /**
-   *
-   * @return
-   * @throws IllegalStateException
+   * This method returns the possible encodings till now
+   * @return List of possible encodings
+   * @throws IllegalStateException Throws this when an error is ofund during checking
    */
   private[tools] def getPossibleEncodings: List[String] = {
     val buffer: ListBuffer[String] = ListBuffer()
     (minQual, maxQual) match {
       case (Some(min), Some(max)) =>
+        if (min < '!' || max > '~')
+          throw new IllegalStateException(s"Quality is out of ascii range 33-126.  minQual: '$min', maxQual: '$max'")
         if (min >= '!' && max <= 'I') buffer += "Sanger"
         if (min >= ';' && max <= 'h') buffer += "Solexa"
         if (min >= '@' && max <= 'h') buffer += "Illumina 1.3+"
         if (min >= 'C' && max <= 'h') buffer += "Illumina 1.5+"
         if (min >= '!' && max <= 'J') buffer += "Illumina 1.8+"
-        if (buffer.isEmpty)
-          throw new IllegalStateException(s"No possible quality encoding found.  minQual: '$min', maxQual: '$max'")
       case _ =>
     }
     buffer.toList
@@ -138,9 +142,9 @@ object ValidateFastq extends ToolCommand {
 
   /**
    * This function checks for duplicates.
-   * @param current
-   * @param before
-   * @throws IllegalStateException
+   * @param current currect fastq record
+   * @param before fastq record before the current record
+   * @throws IllegalStateException Throws this when an error is ofund during checking
    */
   def duplicateCheck(current: FastqRecord, before: Option[FastqRecord]): Unit = {
     if (before.exists(_.getReadHeader == current.getReadHeader))
@@ -148,9 +152,9 @@ object ValidateFastq extends ToolCommand {
   }
 
   /**
-   *
-   * @param record
-   * @throws IllegalStateException
+   * This method will check if fastq record is correct
+   * @param record Fastq record to check
+   * @throws IllegalStateException Throws this when an error is ofund during checking
    */
   def validFastqRecord(record: FastqRecord): Unit = {
     checkQualEncoding(record)
@@ -158,15 +162,15 @@ object ValidateFastq extends ToolCommand {
       case allowedBases(m) =>
       case _               => throw new IllegalStateException(s"Non IUPAC symbols identified")
     }
-    if (record.getReadString.size != record.getBaseQualityString.size)
+    if (record.getReadString.length != record.getBaseQualityString.length)
       throw new IllegalStateException(s"Sequence length does not match quality length")
   }
 
   /**
-   *
-   * @param r1
-   * @param r2
-   * @throws IllegalStateException
+   * This method checks if the pair is the same ID
+   * @param r1 R1 fastq record
+   * @param r2 R2 fastq record
+   * @throws IllegalStateException Throws this when an error is ofund during checking
    */
   def checkMate(r1: FastqRecord, r2: FastqRecord): Unit = {
     val id1 = r1.getReadHeader.takeWhile(_ != ' ')

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/ValidateFastqTest.scala

 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ OutputStream, PrintStream, ByteArrayOutputStream }
 import java.nio.file.Paths
 
 import htsjdk.samtools.fastq.FastqRecord
-import nl.lumc.sasc.biopet.utils.Logging
-import org.apache.log4j.{ FileAppender, Appender }
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.{ DataProvider, Test }
 
-import scala.collection.JavaConversions._
-
 /**
+ * This class test ValidateFatq
+ *
  * Created by pjvan_thof on 2/17/16.
  */
 class ValidateFastqTest extends TestNGSuite with Matchers {
 
   @Test
-  def testCheckMate: Unit = {
+  def testCheckMate(): Unit = {
     ValidateFastq.checkMate(new FastqRecord("read_1", "ATCG", "", "AAAA"), new FastqRecord("read_1", "ATCG", "", "AAAA"))
 
     intercept[IllegalStateException] {
@@ -27,7 +24,7 @@ class ValidateFastqTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testDuplicateCheck: Unit = {
+  def testDuplicateCheck(): Unit = {
     ValidateFastq.duplicateCheck(new FastqRecord("read_1", "ATCG", "", "AAAA"), None)
     ValidateFastq.duplicateCheck(new FastqRecord("read_1", "ATCG", "", "AAAA"), Some(new FastqRecord("read_2", "ATCG", "", "AAAA")))
 
@@ -58,38 +55,41 @@ class ValidateFastqTest extends TestNGSuite with Matchers {
   }
 
   @Test
-  def testGetPossibleEncodingsFail: Unit = {
-    intercept[IllegalStateException] {
-      ValidateFastq.minQual = Some('!')
-      ValidateFastq.maxQual = Some('h')
-      ValidateFastq.getPossibleEncodings
-    }
+  def testGetPossibleEncodingsFail(): Unit = {
+    ValidateFastq.minQual = Some('!')
+    ValidateFastq.maxQual = Some('h')
+    ValidateFastq.getPossibleEncodings shouldBe Nil
   }
 
   @Test
-  def testCheckQualEncoding: Unit = {
+  def testCheckQualEncoding(): Unit = {
     ValidateFastq.minQual = None
     ValidateFastq.maxQual = None
     ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "AAAA"))
+    ValidateFastq.getPossibleEncodings should not be Nil
 
-    intercept[IllegalStateException] {
-      ValidateFastq.minQual = None
-      ValidateFastq.maxQual = None
+    ValidateFastq.minQual = None
+    ValidateFastq.maxQual = None
 
-      ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "A!hA"))
-    }
+    ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "A!hA"))
+    ValidateFastq.getPossibleEncodings shouldBe Nil
+
+    ValidateFastq.minQual = None
+    ValidateFastq.maxQual = None
+
+    ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "hhhh"))
+    ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "!!!!"))
+    ValidateFastq.getPossibleEncodings shouldBe Nil
 
     intercept[IllegalStateException] {
       ValidateFastq.minQual = None
       ValidateFastq.maxQual = None
-
-      ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "hhhh"))
-      ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "!!!!"))
+      ValidateFastq.checkQualEncoding(new FastqRecord("read_1", "ATCG", "", "!! !!"))
     }
   }
 
   @Test
-  def testValidFastqRecord: Unit = {
+  def testValidFastqRecord(): Unit = {
     ValidateFastq.minQual = None
     ValidateFastq.maxQual = None
     ValidateFastq.validFastqRecord(new FastqRecord("read_1", "ATCG", "", "AAAA"))
@@ -107,7 +107,7 @@ class ValidateFastqTest extends TestNGSuite with Matchers {
     Paths.get(getClass.getResource(p).toURI).toString
 
   @Test
-  def testMain: Unit = {
+  def testMain(): Unit = {
     ValidateFastq.minQual = None
     ValidateFastq.maxQual = None
     val r1 = resourcePath("/paired01a.fq")