From 8a9ad3324b9f306f58a1516457df7a428f7104ac Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 10 Feb 2015 21:01:22 +0100
Subject: [PATCH] Fix format
---
.../lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
.../biopet/pipelines/flexiprep/Fastqc.scala | 34 +++++++++----------
.../biopet/pipelines/flexiprep/SeqtkSeq.scala | 8 ++---
3 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index ba0dc2c6d..13dd46954 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -68,7 +68,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
f.checkExecutable
f.afterGraph
}
- case _ =>
+ case _ =>
}
if (new File(outputDir).canWrite) Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
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 6ef82870e..666ad7459 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
@@ -53,15 +53,15 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws IllegalStateException if the module lines have no content or mapping is empty.
*/
def qcModules: Map[String, FastQCModule] = {
- val fqModules = Source.fromFile(dataFile)
- // drop all the characters before the first module delimiter (i.e. '>>')
- .dropWhile(_ != '>')
- // pull everything into a string
- .mkString
- // split into modules
- .split(">>END_MODULE\n")
- // make map of module name -> module lines
- .map {
+ val fqModules = Source.fromFile(dataFile)
+ // drop all the characters before the first module delimiter (i.e. '>>')
+ .dropWhile(_ != '>')
+ // pull everything into a string
+ .mkString
+ // split into modules
+ .split(">>END_MODULE\n")
+ // make map of module name -> module lines
+ .map {
case (modString) =>
// module name is in the first line, without '>>' and before the tab character
val Array(firstLine, otherLines) = modString
@@ -77,10 +77,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
.slice(0, 2)
modName -> FastQCModule(modName, modStatus, otherLines.split("\n").toSeq)
}
- .toMap
+ .toMap
- if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
- else fqModules
+ if (fqModules.isEmpty) throw new IllegalStateException("Empty FastQC data file " + dataFile.toString)
+ else fqModules
}
/**
@@ -93,11 +93,11 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
def encoding: String = {
if (dataFile.exists())
qcModules("Basic Statistics") //FIXME: not save
- .lines
- .dropWhile(!_.startsWith("Encoding"))
- .head
- .stripPrefix("Encoding\t")
- .stripSuffix("\t")
+ .lines
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+ .stripSuffix("\t")
else ""
}
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index b89f3ebc8..05236e13c 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -27,11 +27,11 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
if (fastqc != null && Q == None) {
val encoding = fastqc.encoding
Q = encoding match {
- case null => None
+ case null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
- case s if (s.contains("Illumina <1.3")) => Option(64)
- case s if (s.contains("Illumina 1.3")) => Option(64)
- case s if (s.contains("Illumina 1.5")) => Option(64)
+ case s if (s.contains("Illumina <1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.5")) => Option(64)
case _ => None
}
if (Q != None) V = true
--
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