Adding versions of tools to summary

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

@@ -54,4 +54,8 @@ trait ToolCommand extends MainCommand with Logging {
 
   protected type Args <: AbstractArgs
   protected type OptParser <: AbstractOptParser
+}
+
+trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
+  override def getVersion = Some("Biopet " + FullVersion)
 }
\ No newline at end of file

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

@@ -22,7 +22,7 @@ import htsjdk.tribble.bed.BEDCodec
 import htsjdk.variant.variantcontext.VariantContextBuilder
 import htsjdk.variant.variantcontext.writer.{ VariantContextWriterBuilder, AsyncVariantContextWriter }
 import htsjdk.variant.vcf.{ VCFHeaderLineType, VCFHeaderLineCount, VCFInfoHeaderLine, VCFFileReader }
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, ToolCommand }
 import scala.collection.JavaConverters.asScalaIteratorConverter
 import scala.collection.JavaConversions._
 import scala.collection.mutable

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

@@ -21,15 +21,14 @@ import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
 import nl.lumc.sasc.biopet.utils.VcfUtils._
 import scala.collection.mutable.ListBuffer
 
-class BastyGenerateFasta(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input vcf file", required = false)

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
 import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import java.io.PrintWriter
@@ -27,7 +26,7 @@ import scala.io.Source
 /**
  * @deprecated Use picard.util.BedToIntervalList instead
  */
-class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input Bed file", required = true)

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
@@ -26,7 +25,7 @@ import scala.collection.SortedMap
 import scala.collection.mutable.Map
 import scala.io.Source
 
-class BedtoolsCoverageToCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
 
 import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
 import java.io.{ PrintWriter, File }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
 
-class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input bam", shortName = "input", required = true)

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import htsjdk.samtools.fastq.{ AsyncFastqWriter, FastqReader, BasicFastqWriter }
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.collection.JavaConversions._
@@ -27,7 +26,7 @@ import scala.collection.JavaConversions._
  * Queue extension for the FastqSplitter
  * @param root Parent object
  */
-class FastqSplitter(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fastq", shortName = "input", required = true)

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

@@ -27,7 +27,7 @@ import scala.collection.JavaConverters._
 import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import nl.lumc.sasc.biopet.core.{ BiopetExecutable, BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetExecutable, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 /**
@@ -35,7 +35,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
  *
  * @param root Configuration object for the pipeline
  */
-class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
 
   javaMainClass = getClass.getName
 

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

@@ -24,15 +24,14 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 import htsjdk.variant.vcf.VCFFileReader
 import htsjdk.variant.vcf.VCFHeader
 import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import scala.collection.SortedMap
 import scala.collection.mutable.{ Map, Set }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import scala.collection.JavaConversions._
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class MergeAlleles(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input vcf files", shortName = "input", required = true)

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

@@ -19,8 +19,7 @@ import java.io.{ File, BufferedWriter, FileWriter, OutputStreamWriter }
 import scala.io.{ BufferedSource, Source }
 import scala.collection.mutable.{ Set => MutSet }
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -29,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
  *
  * @param root [[Configurable]] object
  */
-class MergeTables(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MergeTables(val root: Configurable) extends ToolCommandFuntion {
 
   javaMainClass = getClass.getName
 

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

@@ -18,8 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.io.PrintWriter
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.utils.ConfigUtils
@@ -30,7 +29,7 @@ import scala.math.round
 import scala.math.floor
 import scala.collection.JavaConversions._
 
-class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import htsjdk.samtools.fastq.{ FastqRecord, AsyncFastqWriter, FastqReader, BasicFastqWriter }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Output, Input }
@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
  *
  * Created by pjvan_thof on 1/13/15.
  */
-class PrefixFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   override val defaultCoreMemory = 1.0

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import org.biojava3.sequencing.io.fastq.{ SangerFastqReader, StreamListener, Fastq }
@@ -27,7 +26,7 @@ import scala.collection.SortedMap
 import scala.collection.mutable.Map
 import java.io.FileReader
 
-class SageCountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,8 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.biojava3.core.sequence.DNASequence
 import org.biojava3.core.sequence.io.FastaReaderHelper
@@ -28,7 +27,7 @@ import scala.collection.mutable.{ Map, Set }
 import scala.collection.JavaConversions._
 import scala.util.matching.Regex
 
-class SageCreateLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,15 +17,14 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 import scala.io.Source
 import scala.collection.mutable.Map
 import scala.collection.SortedMap
 
-class SageCreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Raw count file", shortName = "input", required = true)

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

@@ -29,8 +29,7 @@ import htsjdk.samtools.fastq.{ FastqReader, FastqRecord }
 import scalaz._, Scalaz._
 import argonaut._, Argonaut._
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 
@@ -39,7 +38,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils
  *
  * @param root Configuration object for the pipeline
  */
-class Seqstat(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class Seqstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)

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

@@ -20,14 +20,13 @@ import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
 import htsjdk.variant.vcf.VCFFileReader
 import htsjdk.variant.variantcontext.VariantContext
 import java.io.File
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 import scala.collection.JavaConversions._
 import scala.io.Source
 
-class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input vcf", shortName = "I", required = true)

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

@@ -21,7 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
 import htsjdk.variant.variantcontext.{ Allele, VariantContext, Genotype }
 import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 import scala.collection.JavaConversions._
@@ -35,7 +35,7 @@ import scala.util.Random
 /**
  * Created by pjvan_thof on 1/10/15.
  */
-class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction with Summarizable {
+class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input fastq", shortName = "I", required = true)

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

@@ -25,7 +25,7 @@ import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, Variant
 import htsjdk.variant.vcf._
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
-import nl.lumc.sasc.biopet.core.{ BiopetJavaCommandLineFunction, ToolCommand }
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 /**
@@ -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 ToolCommandFuntion {
   javaMainClass = getClass.getName
 
   @Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)

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

@@ -34,8 +34,7 @@ import htsjdk.tribble.bed.BEDCodec
 import org.apache.commons.io.FilenameUtils.getExtension
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
-import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
 import nl.lumc.sasc.biopet.core.config.Configurable
 
 // TODO: finish implementation for usage in pipelines
@@ -44,7 +43,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
  *
  * @param root Configuration object for the pipeline
  */
-class WipeReads(val root: Configurable) extends BiopetJavaCommandLineFunction {
+class WipeReads(val root: Configurable) extends ToolCommandFuntion {
 
   javaMainClass = getClass.getName