Merge branch 'fix-flexiprep_noext' into 'develop'

Update filename + extension retrieval in Flexiprep

Two changes:

* Refactored the uncompressed filename + extension retrieval. Also made sure now that extension trimming is case-insensitive (".gzip" and ".GZIP" are both trimmed).

* Added a clearer error message when the input file doesn't have any extension.

See merge request !256

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/IoUtils.scala

@@ -47,4 +47,26 @@ object IoUtils {
       }
     }
   }
+
+  /** Possible compression extensions to trim from input files. */
+  val zipExtensions = Set(".gz", ".gzip", ".bzip2", ".bz", ".xz", ".zip")
+
+  /**
+   * Given a file object and a set of compression extensions, return the filename without any of the compression
+   * extensions.
+   *
+   * Examples:
+   *  - my_file.fq.gz returns "my_file.fq"
+   *  - my_other_file.fastq returns "my_file.fastq"
+   *
+   * @param f Input file object.
+   * @param exts Possible compression extensions to trim.
+   * @return Filename without compression extension.
+   */
+  def getUncompressedFileName(f: File, exts: Set[String] = zipExtensions): String =
+    exts.foldLeft(f.getName) {
+      (fname, ext) =>
+        if (fname.toLowerCase.endsWith(ext)) fname.dropRight(ext.length)
+        else fname
+    }
 }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -19,7 +19,9 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
 import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.IoUtils._
 import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+
 import org.broadinstitute.gatk.queue.QScript
 
 class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -53,8 +55,6 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
   def summarySettings = Map("skip_trim" -> skipTrim, "skip_clip" -> skipClip, "paired" -> paired)
 
   var paired: Boolean = input_R2.isDefined
-  var R1_ext: String = _
-  var R2_ext: String = _
   var R1_name: String = _
   var R2_name: String = _
 
@@ -85,21 +85,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     inputFiles :+= new InputFile(input_R1)
     input_R2.foreach(inputFiles :+= new InputFile(_))
 
-    if (input_R1.endsWith(".gz")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gz"))
-    else if (input_R1.endsWith(".gzip")) R1_name = input_R1.getName.substring(0, input_R1.getName.lastIndexOf(".gzip"))
-    else R1_name = input_R1.getName
-    R1_ext = R1_name.substring(R1_name.lastIndexOf("."), R1_name.length)
-    R1_name = R1_name.substring(0, R1_name.lastIndexOf(R1_ext))
-
-    input_R2 match {
-      case Some(fileR2) =>
-        paired = true
-        if (fileR2.endsWith(".gz")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gz"))
-        else if (fileR2.endsWith(".gzip")) R2_name = fileR2.getName.substring(0, fileR2.getName.lastIndexOf(".gzip"))
-        else R2_name = fileR2.getName
-        R2_ext = R2_name.substring(R2_name.lastIndexOf("."), R2_name.length)
-        R2_name = R2_name.substring(0, R2_name.lastIndexOf(R2_ext))
-      case _ =>
+    R1_name = getUncompressedFileName(input_R1)
+    input_R2.foreach { fileR2 =>
+      paired = true
+      R2_name = getUncompressedFileName(fileR2)
     }
   }