From bf372d9a8b8517f9e9ddf1b89e3f04d479fbcc48 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Wed, 23 Jul 2014 14:24:42 +0200
Subject: [PATCH] Update imports style order

---
 .../lumc/sasc/biopet/function/fastq/Cutadapt.scala   | 10 ++++++----
 .../nl/lumc/sasc/biopet/function/fastq/Fastqc.scala  | 10 ++++++----
 .../nl/lumc/sasc/biopet/function/fastq/Sickle.scala  | 10 ++++++----
 .../sasc/biopet/pipelines/flexiprep/Flexiprep.scala  | 12 +++++++-----
 .../pipelines/flexiprep/scripts/FastqSync.scala      |  8 +++++---
 .../flexiprep/scripts/FastqcToContams.scala          |  8 +++++---
 .../flexiprep/scripts/FastqcToQualtype.scala         |  8 +++++---
 .../biopet/pipelines/flexiprep/scripts/Seqstat.scala |  6 ++++--
 .../pipelines/flexiprep/scripts/Summarize.scala      |  8 +++++---
 9 files changed, 49 insertions(+), 31 deletions(-)

diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
index 267650200..17df80bf4 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala
@@ -1,12 +1,14 @@
 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
-import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+
 class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input fastq file")
   var fastq_input: File = _
@@ -73,4 +75,4 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
       } else logger.warn("File : " + contams_file + " does not exist")
     }
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
index 7b87bbdc2..413defa02 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Fastqc.scala
@@ -1,11 +1,13 @@
 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.File
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
 class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
 
   @Input(doc = "Contaminants", required = false)
@@ -48,4 +50,4 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
       required(fastqfile) +
       required(" > ", output, escape = false)
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
index 40b5b9f31..d31ce0ffb 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Sickle.scala
@@ -1,12 +1,14 @@
 package nl.lumc.sasc.biopet.function.fastq
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.File
 import scala.io.Source._
 import scala.sys.process._
 
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+
 class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "R1 input")
   var input_R1: File = null
@@ -73,4 +75,4 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction {
     }
     return null
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index 222853ba9..38b9809da 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -1,15 +1,17 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep
 
-import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.config._
-import nl.lumc.sasc.biopet.function._
-import nl.lumc.sasc.biopet.function.fastq._
+import scala.util.parsing.json._
+
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.queue.extensions.gatk._
 import org.broadinstitute.gatk.queue.extensions.picard._
 import org.broadinstitute.gatk.queue.function._
-import scala.util.parsing.json._
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
+
+import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.config._
+import nl.lumc.sasc.biopet.function._
+import nl.lumc.sasc.biopet.function.fastq._
 import nl.lumc.sasc.biopet.pipelines.flexiprep.scripts._
 
 class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
index 56795a575..827a92f7c 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqSync.scala
@@ -1,9 +1,11 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("sync_paired_end_reads.py")
@@ -34,4 +36,4 @@ class FastqSync(val root: Configurable) extends PythonCommandLineFunction {
     required(output_R2) +
     " > " +
     required(output_stats)
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
index 843e890f2..d12073e3d 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToContams.scala
@@ -1,9 +1,11 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -25,4 +27,4 @@ class FastqcToContams(val root: Configurable) extends PythonCommandLineFunction
       " > " +
       required(out)
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
index f76cec1a9..c9aa8cd8f 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/FastqcToQualtype.scala
@@ -1,9 +1,11 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import nl.lumc.sasc.biopet.core.config.Configurable
+
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -21,4 +23,4 @@ class FastqcToQualtype(val root: Configurable) extends PythonCommandLineFunction
       " > " +
       required(out)
   }
-}
\ No newline at end of file
+}
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
index c5e03dbb3..fee321c7d 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Seqstat.scala
@@ -1,9 +1,11 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class Seqstat(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
index aa1db27ae..63f49191a 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/scripts/Summarize.scala
@@ -1,9 +1,11 @@
 package nl.lumc.sasc.biopet.pipelines.flexiprep.scripts
 
+import java.io.File
+
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.function.PythonCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
-import java.io.File
 
 class Summarize(val root: Configurable) extends PythonCommandLineFunction {
   setPythonScript("__init__.py", "pyfastqc/")
@@ -33,4 +35,4 @@ class Summarize(val root: Configurable) extends PythonCommandLineFunction {
       required(samplea) +
       required(out)
   }
-}
\ No newline at end of file
+}
-- 
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