Reorganize tools

Fix for #29

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

@@ -18,9 +18,9 @@ object BiopetExecutable {
       nl.lumc.sasc.biopet.pipelines.basty.Basty,
       nl.lumc.sasc.biopet.pipelines.yamsvp.Yamsvp),
     "tool" -> List(
-      nl.lumc.sasc.biopet.core.apps.WipeReads,
-      nl.lumc.sasc.biopet.core.apps.BiopetFlagstat,
-      nl.lumc.sasc.biopet.core.apps.CheckAllelesVcfInBam)
+      nl.lumc.sasc.biopet.tools.WipeReads,
+      nl.lumc.sasc.biopet.tools.BiopetFlagstat,
+      nl.lumc.sasc.biopet.tools.CheckAllelesVcfInBam)
   )
   
   /**

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.scripts.CoverageStats
 import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
-import nl.lumc.sasc.biopet.core.apps.{ BedToInterval, BiopetFlagstat }
+import nl.lumc.sasc.biopet.tools.{ BedToInterval, BiopetFlagstat }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
 import nl.lumc.sasc.biopet.extensions.picard.{ CollectInsertSizeMetrics, CollectGcBiasMetrics, CalculateHsMetrics, CollectAlignmentSummaryMetrics }

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand}
 import java.io.File
-import nl.lumc.sasc.biopet.core.apps.{ MpileupToVcf, VcfFilter }
+import nl.lumc.sasc.biopet.tools.{ MpileupToVcf, VcfFilter }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.{AnalyzeCovariates,BaseRecalibrator,GenotypeGVCFs,HaplotypeCaller,IndelRealigner,PrintReads,RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper}
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -4,7 +4,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
 import java.io.File
 import java.util.Date
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
-import nl.lumc.sasc.biopet.core.apps.FastqSplitter
+import nl.lumc.sasc.biopet.tools.FastqSplitter
 import nl.lumc.sasc.biopet.extensions.aligners.{ Bwa, Star , Bowtie, Stampy}
 import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups}
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BedToInterval.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.SAMFileReader
 import htsjdk.samtools.SAMSequenceRecord

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/BiopetFlagstat.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.SAMFileReader
 import htsjdk.samtools.SAMRecord

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/CheckAllelesVcfInBam.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.SAMFileReader
 import htsjdk.samtools.SAMRecord

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/FastqSplitter.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import java.io.{ BufferedInputStream, File, FileInputStream, PrintWriter }
 import java.util.zip.GZIPInputStream

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/MpileupToVcf.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/VcfFilter.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala → biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/WipeReads.scala

@@ -2,7 +2,7 @@
  * Copyright (c) 2014 Leiden University Medical Center - Sequencing Analysis Support Core <sasc@lumc.nl>
  * @author Wibowo Arindrarto <w.arindrarto@lumc.nl>
  */
-package nl.lumc.sasc.biopet.core.apps
+package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, IOException }