Merge branch 'feature-prerelease_fixes' into 'develop'

Feature prerelease fixes

Commit messages should be clear enough :).

See merge request !61

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

@@ -19,9 +19,10 @@ import nl.lumc.sasc.biopet.core.ToolCommand
 
 object ExtractAlignedFastq extends ToolCommand {
 
+  /** type alias for Fastq input (may or may not be paired) */
   type FastqInput = (FastqRecord, Option[FastqRecord])
 
-  /** function to get FastqRecord ID */
+  /** Get the FastqRecord ID */
   def fastqId(rec: FastqRecord) = rec.getReadHeader.split(" ")(0)
 
   /**
@@ -54,14 +55,13 @@ object ExtractAlignedFastq extends ToolCommand {
     // by the Interval constructor only accepting ints
     def intFromCoord(s: String): Int = s.replaceAll(",", "").replaceAll("\\.", "").toInt
 
-    inStrings.map(x => x match {
+    inStrings.map {
       case ptn1(chr, start, end) => new Interval(chr, intFromCoord(start), intFromCoord(end))
       case ptn2(chr, start) =>
         val startCoord = intFromCoord(start)
         new Interval(chr, startCoord, startCoord)
       case _ => throw new IllegalArgumentException("Invalid interval string: " + x)
-    })
-      .toIterator
+    }.toIterator
   }
 
   /**
@@ -125,6 +125,13 @@ object ExtractAlignedFastq extends ToolCommand {
     }
   }
 
+  /**
+   * Extracts reads from the given input Fastq file and writes to a new output Fastq file
+   *
+   * @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
+   * @param inputFastq1 Input [[FastqReader]] object.
+   * @param outputFastq1 Output [[BasicFastqWriter]] object.
+   */
   def extractReads(memFunc: FastqInput => Boolean,
                    inputFastq1: FastqReader, outputFastq1: BasicFastqWriter): Unit =
     inputFastq1.iterator.asScala
@@ -132,6 +139,15 @@ object ExtractAlignedFastq extends ToolCommand {
       .filter(rec => memFunc(rec._1, rec._2))
       .foreach(rec => outputFastq1.write(rec._1))
 
+  /**
+   * Extracts reads from the given input Fastq pairs and writes to new output Fastq pair files
+   *
+   * @param memFunc Predicate for extracting reads. If evaluates to true, the read is extracted.
+   * @param inputFastq1 Input [[FastqReader]] object for pair 1.
+   * @param outputFastq1 Input [[FastqReader]] object for pair 2.
+   * @param inputFastq2 Output [[BasicFastqWriter]] object for pair 1.
+   * @param outputFastq2 Output [[BasicFastqWriter]] object for pair 2.
+   */
   def extractReads(memFunc: FastqInput => Boolean,
                    inputFastq1: FastqReader, outputFastq1: BasicFastqWriter,
                    inputFastq2: FastqReader, outputFastq2: BasicFastqWriter): Unit =
@@ -143,6 +159,7 @@ object ExtractAlignedFastq extends ToolCommand {
         outputFastq2.write(rec._2)
       })
 
+  /** Default arguments */
   case class Args(inputBam: File = new File(""),
                   intervals: List[String] = List.empty[String],
                   inputFastq1: File = new File(""),
@@ -152,6 +169,7 @@ object ExtractAlignedFastq extends ToolCommand {
                   minMapQ: Int = 0,
                   commonSuffixLength: Int = 0) extends AbstractArgs
 
+  /** Command line argument parser */
   class OptParser extends AbstractOptParser {
 
     head(
@@ -213,6 +231,7 @@ object ExtractAlignedFastq extends ToolCommand {
     }
   }
 
+  /** Parses the command line argument */
   def parseArgs(args: Array[String]): Args =
     new OptParser()
       .parse(args, Args())

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

@@ -47,12 +47,7 @@ class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
 
 object WipeReads extends ToolCommand {
 
-  /**
-   * Creates a SamReader object from an input BAM file, ensuring it is indexed
-   *
-   * @param inBam input BAM file
-   * @return
-   */
+  /** Creates a SamReader object from an input BAM file, ensuring it is indexed */
   private def prepInBam(inBam: File): SamReader = {
     val bam = SamReaderFactory
       .make()
@@ -62,6 +57,7 @@ object WipeReads extends ToolCommand {
     bam
   }
 
+  /** Creates a [[SAMFileWriter]] object for writing, indexed */
   private def prepOutBam(outBam: File, templateBam: File,
                          writeIndex: Boolean = true, async: Boolean = true): SAMFileWriter =
     new SAMFileWriterFactory()
@@ -336,6 +332,7 @@ object WipeReads extends ToolCommand {
     }
   }
 
+  /** Default arguments */
   case class Args(inputBam: File = new File(""),
                   targetRegions: File = new File(""),
                   outputBam: File = new File(""),
@@ -348,6 +345,7 @@ object WipeReads extends ToolCommand {
                   bloomSize: Long = 70000000,
                   bloomFp: Double = 4e-7) extends AbstractArgs
 
+  /** Command line argument parser */
   class OptParser extends AbstractOptParser {
 
     head(
@@ -418,12 +416,7 @@ object WipeReads extends ToolCommand {
 
   }
 
-  /**
-   * Parses the command line argument
-   *
-   * @param args Array of arguments
-   * @return
-   */
+  /** Parses the command line argument */
   def parseArgs(args: Array[String]): Args = new OptParser()
     .parse(args, Args())
     .getOrElse(sys.exit(1))

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnUnitTest.scala → public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/LnTest.scala

@@ -11,7 +11,7 @@ import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-class LnUnitTest extends TestNGSuite with Matchers {
+class LnTest extends TestNGSuite with Matchers {
 
   @Test(description = "Target and link in the same directory, relative set to true")
   def testSameLevelRelative() {

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqUnitTest.scala → public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastqTest.scala

@@ -17,7 +17,7 @@ import org.testng.annotations.{ DataProvider, Test }
 import htsjdk.samtools.util.Interval
 import htsjdk.samtools.fastq.{ BasicFastqWriter, FastqReader, FastqRecord }
 
-class ExtractAlignedFastqUnitTest extends TestNGSuite with MockitoSugar with Matchers {
+class ExtractAlignedFastqTest extends TestNGSuite with MockitoSugar with Matchers {
 
   import ExtractAlignedFastq._
 

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsUnitTest.scala → public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala

@@ -25,7 +25,7 @@ import org.scalatest.mock.MockitoSugar
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
 
-class WipeReadsUnitTest extends TestNGSuite with MockitoSugar with Matchers {
+class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
 
   import WipeReads._