From 90eaaf0925783c76283f172eed863a7f43e5917d Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 19 Oct 2015 13:31:01 +0200
Subject: [PATCH] Remove R1_ext and R2_ext from Flexiprep
---
.../pipelines/flexiprep/Flexiprep.scala | 26 ++++++++-----------
1 file changed, 11 insertions(+), 15 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 65a06dbf4..8b55b0856 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -21,7 +21,6 @@ import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
-import org.apache.commons.io.FilenameUtils.getExtension
import org.broadinstitute.gatk.queue.QScript
class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@@ -80,25 +79,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
/**
* Given a file object and a set of compression extensions, return the filename without any of the compression
- * extensions and the filename's extension.
+ * extensions.
*
* Examples:
- * - my_file.fq.gz returns ("my_file.fq", ".fq")
- * - my_other_file.fastq returns ("my_file.fastq", ".fastq")
+ * - 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 and its extension.
+ * @return Filename without compression extension.
*/
- private def getNameAndExt(f: File, exts: Set[String] = zipExtensions): (String, String) = {
- val unzippedFilename = zipExtensions
+ private def getUncompressedName(f: File, exts: Set[String] = zipExtensions): String =
+ zipExtensions
.foldLeft(f.toString) { case (fname, ext) =>
- if (fname.toLowerCase.endsWith(ext)) fname.dropRight(ext.length)
- else fname
- }
- val unzippedExt = "." + getExtension(unzippedFilename)
- (unzippedFilename, unzippedExt)
- } ensuring(_._2.length > 1, "Flexiprep input files must have an extension when uncompressed.")
+ if (fname.toLowerCase.endsWith(ext)) fname.dropRight(ext.length)
+ else fname
+ }
/** Function that's need to be executed before the script is accessed */
def init() {
@@ -112,10 +108,10 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
inputFiles :+= new InputFile(input_R1)
input_R2.foreach(inputFiles :+= new InputFile(_))
- (R1_ext, R1_name) = getNameAndExt(input_R1)
+ R1_name = getUncompressedName(input_R1)
input_R2.foreach { fileR2 =>
paired = true
- (R2_ext, R2_name) = getNameAndExt(fileR2)
+ R2_name = getUncompressedName(fileR2)
}
}
--
GitLab