Rename VEPNormalizer -> VepNormalizer for consistency

docs/pipelines/toucan.md

@@ -7,7 +7,7 @@ The Toucan pipeline is a VEP-based annotation pipeline.
 Currently, it comprises just two steps:
 
 * Variant Effect Predictor run
-* [VEP Normalizer on the VEP output](../tools/VEPNormalizer.md)
+* [VEP Normalizer on the VEP output](../tools/VepNormalizer.md)
 
 Example
 -----------
@@ -34,7 +34,7 @@ It is wise to set the `cache_version` field as well.
 Furthermore, the `fork` field will be overwritten by `threads` in case that one exists in the config. 
 Therefore, it is recommended not to use `fork`, but to rather use `threads`. 
 
-With that in mind, an example configuration using mode `standard` of the VEPNormalizer would thus be:
+With that in mind, an example configuration using mode `standard` of the VepNormalizer would thus be:
 ~~~~
 {
     "varianteffectpredictor": {

docs/release_notes_0.3.0.md

@@ -24,7 +24,7 @@ Also a impressive list of tools have been added to the updated framework:
 - MergeTables
 - SamplesTsvToJson
 - Seqstat ( this is a lift over tool based on our previous python implementation of seqstat )
-- VEPNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of [VCF 4.1](https://samtools.github.io/hts-specs/VCFv4.1.pdf) )
+- VepNormalizer ( This normalizer enables a user to parse VEP output VCFs to the exact specs of [VCF 4.1](https://samtools.github.io/hts-specs/VCFv4.1.pdf) )
 - VcfStats
 
 Some tools have a new version for better compatibility with our latest pipelines. The tools that have a changed version are:

docs/tools/VEPNormalizer.md → docs/tools/VepNormalizer.md

-VEPNormalizer
+VepNormalizer
 ============
 
 Introduction
@@ -22,9 +22,9 @@ Example
 ---------
 
 ~~~~bash
-java -jar Biopet-0.3.0.jar tool VEPNormalizer -h
-|VEPNormalizer - Parse VEP-annotated VCF to standard VCF format 
-Usage: VEPNormalizer [options]
+java -jar Biopet-0.3.0.jar tool VepNormalizer -h
+|VepNormalizer - Parse VEP-annotated VCF to standard VCF format 
+Usage: VepNormalizer [options]
 
   -l <value> | --log_level <value>
         Log level

mkdocs.yml

@@ -21,7 +21,7 @@ pages:
 - ['tools/VcfFilter.md','Tools','VcfFilter']
 - ['tools/MpileupToVcf.md', 'Tools', 'MpileupToVcf']
 - ['tools/sagetools.md', 'Tools', 'Sagetools']
-- ['tools/VEPNormalizer.md', 'Tools', 'VEPNormalizer']
+- ['tools/VepNormalizer.md', 'Tools', 'VepNormalizer']
 - ['tools/WipeReads.md', 'Tools', 'WipeReads']
 #- ['developing/Setup.md', 'Developing', 'Setting up your local development environment']
 - ['about.md', 'About']

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VEPNormalizer.scala → public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala

@@ -38,7 +38,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
  * Created by ahbbollen on 10/27/14.
  */
 
-class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class VepNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunction {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
@@ -60,7 +60,7 @@ class VEPNormalizer(val root: Configurable) extends BiopetJavaCommandLineFunctio
     conditional(doNotRemove, "--do-not-remove")
 }
 
-object VEPNormalizer extends ToolCommand {
+object VepNormalizer extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val commandArgs: Args = new OptParser()

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VEPNormalizerTest.scala → public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala

@@ -30,8 +30,8 @@ import htsjdk.variant.variantcontext.VariantContext
  * This class tests the VEPNormalizer
  * Created by ahbbollen on 11/24/14.
  */
-class VEPNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
-  import VEPNormalizer._
+class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
+  import VepNormalizer._
 
   private def resourcePath(p: String): String = {
     Paths.get(getClass.getResource(p).toURI).toString

public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

@@ -54,6 +54,6 @@ object BiopetExecutablePublic extends BiopetExecutable {
     nl.lumc.sasc.biopet.tools.MergeAlleles,
     nl.lumc.sasc.biopet.tools.SamplesTsvToJson,
     nl.lumc.sasc.biopet.tools.Seqstat,
-    nl.lumc.sasc.biopet.tools.VEPNormalizer,
+    nl.lumc.sasc.biopet.tools.VepNormalizer,
     nl.lumc.sasc.biopet.tools.AnnotateVcfWithBed)
 }

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.toucan
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, BiopetQScript }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.VariantEffectPredictor
-import nl.lumc.sasc.biopet.tools.VEPNormalizer
+import nl.lumc.sasc.biopet.tools.VepNormalizer
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.queue.QScript
 import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
@@ -49,7 +49,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript {
     vep.isIntermediate = true
     add(vep)
 
-    val normalizer = new VEPNormalizer(this)
+    val normalizer = new VepNormalizer(this)
     normalizer.inputVCF = vep.output
     normalizer.outputVCF = swapExt(vep.output, ".vcf", ".normalized.vcf.gz")
     add(normalizer)