Switch to output classes for Arg parsing

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

@@ -22,7 +22,7 @@ import htsjdk.variant.variantcontext.writer.{
   VariantContextWriterBuilder
 }
 import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
 
 import scala.collection.JavaConversions._
@@ -51,9 +51,8 @@ object AnnotateVcfWithBed extends ToolCommand {
                   fieldName: String = null,
                   fieldDescription: String = "",
                   fieldType: String = "String")
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputFile") required () unbounded () valueName "<vcf file>" action { (x, c) =>
       c.copy(inputFile = x)
     } text "Input VCF file. Mandatory field"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{File, PrintWriter}
 
 import htsjdk.samtools.{SAMRecord, SamReaderFactory}
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ConfigUtils, ToolCommand}
 import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
 import picard.annotation.{Gene, GeneAnnotationReader}
 
@@ -35,9 +35,8 @@ object BaseCounter extends ToolCommand {
                   outputDir: File = null,
                   bamFile: File = null,
                   prefix: String = "output")
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('r', "refFlat") required () valueName "<file>" action { (x, c) =>
       c.copy(refFlat = x)
     } text "refFlat file. Mandatory"

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

@@ -20,7 +20,7 @@ import htsjdk.samtools.SamReaderFactory
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 import nl.lumc.sasc.biopet.utils.VcfUtils._
 
 import scala.collection.JavaConversions._
@@ -38,9 +38,8 @@ object BastyGenerateFasta extends ToolCommand {
                   minAD: Int = 8,
                   minDepth: Int = 8,
                   reference: File = null)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('V', "inputVcf") unbounded () valueName "<file>" action { (x, c) =>
       c.copy(inputVcf = x)
     } text "vcf file, needed for outputVariants and outputConsensusVariants" validate { x =>

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

@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{File, PrintWriter}
 
-import htsjdk.samtools.{SAMSequenceRecord, SamReaderFactory}
-import nl.lumc.sasc.biopet.utils.ToolCommand
-import scala.collection.JavaConversions._
+import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
+import scala.collection.JavaConversions._
 import scala.io.Source
 
 /**
@@ -28,9 +28,8 @@ import scala.io.Source
 object BedToInterval extends ToolCommand {
 
   case class Args(inputFile: File = null, outputFile: File = null, bamFile: File = null)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     }

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

@@ -16,15 +16,15 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{File, PrintWriter}
 
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.{SortedMap, mutable}
 import scala.io.Source
 
 object BedtoolsCoverageToCounts extends ToolCommand {
-  case class Args(input: File = null, output: File = null) extends AbstractArgs
+  case class Args(input: File = null, output: File = null)
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "input") required () valueName "<file>" action { (x, c) =>
       c.copy(input = x)
     } text "Coverage file produced with bedtools"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

@@ -23,7 +23,7 @@ import htsjdk.variant.variantcontext.writer.{
   VariantContextWriterBuilder
 }
 import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.JavaConversions._
 import scala.collection.mutable
@@ -49,9 +49,8 @@ object CheckAllelesVcfInBam extends ToolCommand {
                   samples: List[String] = Nil,
                   bamFiles: List[File] = Nil,
                   minMapQual: Int = 1)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     } text "VCF file"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{File, PrintWriter}
 
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.io.Source
 
@@ -31,9 +31,8 @@ object DownloadNcbiAssembly extends ToolCommand {
                   contigNameHeader: Option[String] = None,
                   mustHaveOne: List[(String, String)] = List(),
                   mustNotHave: List[(String, String)] = List())
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('a', "assembly_report") required () unbounded () valueName "<file>" action {
       (x, c) =>
         c.copy(assemblyReport = x)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

@@ -19,7 +19,7 @@ import java.io.File
 import htsjdk.samtools.{QueryInterval, SamReaderFactory, ValidationStringency}
 import htsjdk.samtools.fastq.{BasicFastqWriter, FastqReader, FastqRecord}
 import htsjdk.samtools.util.Interval
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.JavaConverters._
 import scala.collection.mutable.{Set => MSet}
@@ -181,10 +181,9 @@ object ExtractAlignedFastq extends ToolCommand {
                   outputFastq2: Option[File] = None,
                   minMapQ: Int = 0,
                   commonSuffixLength: Int = 0)
-      extends AbstractArgs
 
   /** Command line argument parser */
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
 
     head(s"""
         |$commandName - Select aligned FASTQ records

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractTagsFromGtf.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{File, PrintWriter}
 
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 import nl.lumc.sasc.biopet.utils.annotation.Feature
 
 import scala.io.Source
@@ -15,9 +15,8 @@ object ExtractTagsFromGtf extends ToolCommand {
                   gtfFile: File = null,
                   tags: List[String] = Nil,
                   feature: Option[String] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(outputFile = x)
     } text "Input refFlat file. Mandatory"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqFilter.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{AsyncFastqWriter, BasicFastqWriter, FastqReader}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.util.matching.Regex
 import scala.collection.JavaConversions._
@@ -33,9 +33,8 @@ object FastqFilter extends ToolCommand {
     * @param outputFile output fastq files
     */
   case class Args(inputFile: File = null, outputFile: File = null, idRegex: Option[Regex] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     } text "Path to input file"

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{AsyncFastqWriter, BasicFastqWriter, FastqReader}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 object FastqSplitter extends ToolCommand {
 
@@ -26,9 +26,9 @@ object FastqSplitter extends ToolCommand {
     * @param inputFile input fastq file
     * @param outputFile output fastq files
     */
-  case class Args(inputFile: File = null, outputFile: List[File] = Nil) extends AbstractArgs
+  case class Args(inputFile: File = null, outputFile: List[File] = Nil)
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputFile") required () valueName "<file>" action { (x, c) =>
       c.copy(inputFile = x)
     } text "Path to input file"

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 
 import htsjdk.samtools.fastq.{AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.annotation.tailrec
 import scala.collection.JavaConverters._
@@ -111,9 +111,8 @@ object FastqSync extends ToolCommand {
                   inputFastq2: File = new File(""),
                   outputFastq1: File = new File(""),
                   outputFastq2: File = new File(""))
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
 
     head(s"""
         |$commandName - Sync paired-end FASTQ files.

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindOverlapMatch.scala

@@ -16,7 +16,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{File, PrintStream}
 
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
@@ -35,9 +35,8 @@ object FindOverlapMatch extends ToolCommand {
                   filterSameNames: Boolean = true,
                   rowSampleRegex: Option[Regex] = None,
                   columnSampleRegex: Option[Regex] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('i', "input") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(inputMetrics = x)
     } text "Input should be a table where the first row and column have the ID's, those can be different"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

@@ -14,19 +14,18 @@
   */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{PrintWriter, File}
+import java.io.{File, PrintWriter}
 
 import htsjdk.samtools.{QueryInterval, SAMRecord, SamReaderFactory, ValidationStringency}
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.JavaConversions._
 import scala.io.Source
 
 object FindRepeatsPacBio extends ToolCommand {
   case class Args(inputBam: File = null, outputFile: Option[File] = None, inputBed: File = null)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputBam") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputBam = x)
     } text "Path to input file"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala

@@ -24,7 +24,7 @@ import htsjdk.variant.variantcontext.writer.{
 }
 import htsjdk.variant.variantcontext.{Allele, GenotypeBuilder, VariantContextBuilder}
 import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.utils.{FastaUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, FastaUtils, ToolCommand}
 
 import scala.collection.JavaConversions._
 import scala.io.Source
@@ -41,9 +41,8 @@ object GensToVcf extends ToolCommand {
                   referenceFasta: File = null,
                   contig: String = null,
                   sortInput: Boolean = false)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('g', "inputGenotypes") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputGenotypes = x)
     } text "Input genotypes"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GtfToRefflat.scala

 package nl.lumc.sasc.biopet.tools
 
-import nl.lumc.sasc.biopet.utils.{FastaUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, FastaUtils, ToolCommand}
 import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.annotation.{Exon, Feature, Gene, Transcript}
@@ -14,9 +14,8 @@ import scala.io.Source
 object GtfToRefflat extends ToolCommand {
 
   case class Args(refFlat: File = null, gtfFile: File = null, referenceFasta: Option[File] = None)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('r', "refFlat") required () unbounded () valueName "<file>" action { (x, c) =>
       c.copy(refFlat = x)
     } text "Input refFlat file. Mandatory"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala

@@ -18,7 +18,7 @@ import java.io.{File, PrintWriter}
 
 import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.utils.{VcfUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand, VcfUtils}
 import nl.lumc.sasc.biopet.utils.intervals.BedRecord
 
 import scala.collection.JavaConversions._
@@ -35,9 +35,8 @@ object GvcfToBed extends ToolCommand {
                   sample: Option[String] = None,
                   minGenomeQuality: Int = 0,
                   inverse: Boolean = false)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(inputVcf = x)
     } text "Input vcf file"

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.{File, PrintWriter}
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
@@ -60,9 +60,8 @@ object KrakenReportToJson extends ToolCommand {
   case class Args(krakenreport: File = null,
                   outputJson: Option[File] = None,
                   skipNames: Boolean = false)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
 
     head(s"""
          |$commandName - Convert Kraken-report (full) output to JSON

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

@@ -23,7 +23,7 @@ import htsjdk.variant.variantcontext.writer.{
 }
 import htsjdk.variant.variantcontext.{Allele, VariantContext, VariantContextBuilder}
 import htsjdk.variant.vcf.{VCFFileReader, VCFHeader}
-import nl.lumc.sasc.biopet.utils.{FastaUtils, ToolCommand}
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, FastaUtils, ToolCommand}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 import scala.collection.JavaConversions._
@@ -32,9 +32,8 @@ import scala.collection.{SortedMap, mutable}
 object MergeAlleles extends ToolCommand {
 
   case class Args(inputFiles: List[File] = Nil, outputFile: File = null, reference: File = null)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "inputVcf") minOccurs 2 required () unbounded () valueName "<file>" action {
       (x, c) =>
         c.copy(inputFiles = x :: c.inputFiles)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala

@@ -14,9 +14,9 @@
   */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{PrintWriter, File}
+import java.io.{File, PrintWriter}
 
-import nl.lumc.sasc.biopet.utils.ToolCommand
+import nl.lumc.sasc.biopet.utils.{AbstractOptParser, ToolCommand}
 
 import scala.io.Source
 
@@ -27,9 +27,8 @@ object MergeOtuMaps extends ToolCommand {
   case class Args(inputFiles: List[File] = Nil,
                   outputFile: File = null,
                   skipPrefix: List[String] = Nil)
-      extends AbstractArgs
 
-  class OptParser extends AbstractOptParser {
+  class OptParser extends AbstractOptParser[Args](commandName) {
     opt[File]('I', "input") minOccurs 2 required () unbounded () valueName "<file>" action {
       (x, c) =>
         c.copy(inputFiles = x :: c.inputFiles)