Commit 335cc12f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding versions of tools to summary

parent 1be5eeef
......@@ -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
......@@ -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
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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
......
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