From c3de5e12afc25a026692fe6ac89b0584c240562a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 11 Feb 2015 16:44:45 +0100
Subject: [PATCH] Add comment
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 666ad7459..21cb069d6 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -91,7 +91,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* when a line starting with "Encoding" does not exist.
*/
def encoding: String = {
- if (dataFile.exists())
+ if (dataFile.exists) // On a dry run this file does not yet exist
qcModules("Basic Statistics") //FIXME: not save
.lines
.dropWhile(!_.startsWith("Encoding"))
@@ -110,7 +110,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @return a [[Set]] of [[AdapterSequence]] objects.
*/
def foundAdapters: Set[AdapterSequence] = {
- if (dataFile.exists()) {
+ if (dataFile.exists) { // On a dry run this file does not yet exist
/** Returns a list of adapter and/or contaminant sequences known to FastQC */
def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
case None => Set.empty[AdapterSequence]
--
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