Simplify method

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{PrintWriter, File}
+import java.io.{ PrintWriter, File }
 
 import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -117,12 +117,12 @@ object SeqStat extends ToolCommand {
         |$commandName - Summarize FastQ
       """.stripMargin)
 
-    opt[File]('i', "fastq") required () unbounded() valueName "<fastq>" action { (x, c) =>
+    opt[File]('i', "fastq") required () unbounded () valueName "<fastq>" action { (x, c) =>
       c.copy(fastq = x)
     } validate {
       x => if (x.exists) success else failure("FASTQ file not found")
     } text "FastQ file to generate stats from"
-    opt[File]('o', "output") unbounded() valueName "<json>" action { (x, c) =>
+    opt[File]('o', "output") unbounded () valueName "<json>" action { (x, c) =>
       c.copy(fastq = x)
     } text "File to write output to, if not supplied output go to stdout"
   }

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

@@ -73,24 +73,11 @@ object VcfUtils {
     out
   }
 
+  //TODO: Add genotype comparing to this function
   def identicalVariantContext(var1: VariantContext, var2: VariantContext): Boolean = {
-    if (var1.getContig != var2.getContig) {
-      false
-    }
-    if (var1.getStart != var2.getStart) {
-      false
-    }
-    if (var1.getEnd != var2.getEnd) {
-      false
-    }
-    if (!var1.getAttributes.forall(x => var2.hasAttribute(x._1)) || !var2.getAttributes.forall(x => var1.hasAttribute(x._1))) {
-      false
-    }
-    if (!var1.getAttributes.forall(x => var2.getAttribute(x._1) == var1.getAttribute(x._1)) ||
-      !var2.getAttributes.forall(x => var1.getAttribute(x._1) == var2.getAttribute(x._1))) {
-      false
-    }
-
-    true
+    var1.getContig == var2.getContig &&
+      var1.getStart == var2.getStart &&
+      var1.getEnd == var2.getEnd &&
+      var1.getAttributes == var2.getAttributes
   }
 }