Adding CleverFixVCF to add headers and fix the samplename in vcf output

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala

@@ -30,13 +30,13 @@ class BreakdancerVCF(val root: Configurable) extends PythonCommandLineFunction {
   @Output(doc = "Output VCF to PATH")
   var output: File = _
 
-  @Argument(doc="Samplename")
+  @Argument(doc = "Samplename")
   var sample: String = _
 
   def cmdLine = {
     getPythonCommand +
       "-i " + required(input) +
-      "-o " + required(output)+
+      "-o " + required(output) +
       "-s " + required(sample)
   }
 }

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions.clever
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ Version, Reference, BiopetCommandLineFunction }
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Reference, Version }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
   executable = config("exe", default = "clever")
@@ -39,17 +39,17 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
   @Input(doc = "Reference")
   var reference: File = _
 
-  protected def workDir: File = new File(cwd, "work")
-  var cwd: File = _
+  protected def cleverOutputDir: File = new File(cleverWorkDir, "work")
+  var cleverWorkDir: File = _
 
   @Output(doc = "Clever VCF output")
   lazy val outputvcf: File = {
-    new File(cwd, "predictions.vcf")
+    new File(cleverOutputDir, "predictions.vcf")
   }
 
   @Output(doc = "Clever raw output")
   lazy val outputraw: File = {
-    new File(workDir, "predictions.raw.txt")
+    new File(cleverOutputDir, "predictions.raw.txt")
   }
 
   //  var T: Option[Int] = config("T", default = defaultThreads)
@@ -61,7 +61,7 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
 
   override def beforeGraph() {
     super.beforeGraph()
-    if (workDir == null) throw new Exception("Clever :: Workdirectory is not defined")
+    if (cleverOutputDir == null) throw new Exception("Clever :: Workdirectory is not defined")
     if (reference == null) reference = referenceFasta()
   }
 
@@ -75,14 +75,14 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction wit
     conditional(r, "-r") +
     required(input) +
     required(reference) +
-    required(workDir)
+    required(cleverOutputDir)
 }
 
 object CleverCaller {
   def apply(root: Configurable, input: File, svDir: File): CleverCaller = {
     val clever = new CleverCaller(root)
     clever.input = input
-    clever.cwd = svDir
+    clever.cleverWorkDir = svDir
     clever
   }
 }
\ No newline at end of file

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala

+package nl.lumc.sasc.biopet.extensions.clever
+
+/**
+ * Created by wyleung on 4-4-16.
+ */
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.{ ToolCommand }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+import scala.io.Source
+
+class CleverFixVCF(val root: Configurable) extends BiopetJavaCommandLineFunction {
+  javaMainClass = getClass.getName
+  @Input(doc = "Input Clever VCF")
+  var input: File = _
+
+  @Output(doc = "Output fixed VCF")
+  var output: File = _
+
+  @Argument(doc = "Samplename")
+  var sampleName: String = _
+
+  override def cmdLine = super.cmdLine +
+    required("-i", input) +
+    required("-o", output) +
+    required("-s", sampleName)
+}
+
+object CleverFixVCF extends ToolCommand {
+  case class Args(inputVCF: File = null, sampleLabel: String = "",
+                  outputVCF: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('i', "inputvcf") required () valueName "<vcffile/path>" action { (x, c) =>
+      c.copy(inputVCF = x)
+    } text "Please specify the input Clever VCF file"
+    opt[String]('s', "samplelabel") valueName "<sample label>" action { (x, c) =>
+      c.copy(sampleLabel = x)
+    } text "Sample label is missing"
+    opt[File]('o', "outputvcf") valueName "<output>" action { (x, c) =>
+      c.copy(outputVCF = x)
+    } text "Output path is missing"
+  }
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    val input: File = commandArgs.inputVCF
+    val output: File = commandArgs.outputVCF
+
+    val vcfColHeader = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tdefault"
+    val vcfColReplacementHeader = s"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t${commandArgs.sampleLabel}"
+
+    val extraHeader = """##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
+##INFO=<ID=NOVEL,Number=0,Type=Flag,Description="Indicates a novel structural variation">
+##INFO=<ID=SVEND,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
+##INFO=<ID=MEINFO,Number=4,Type=String,Description="Mobile element info of the form NAME,START,END,POLARITY">
+##INFO=<ID=METRANS,Number=4,Type=String,Description="Mobile element transduction info of the form CHR,START,END,POLARITY">
+##INFO=<ID=DGVID,Number=1,Type=String,Description="ID of this element in Database of Genomic Variation">
+##INFO=<ID=DBVARID,Number=1,Type=String,Description="ID of this element in DBVAR">
+##INFO=<ID=DBRIPID,Number=1,Type=String,Description="ID of this element in DBRIP">
+##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
+##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
+##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
+##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
+##INFO=<ID=CN,Number=1,Type=Integer,Description="Copy number of segment containing breakend">
+##INFO=<ID=CNADJ,Number=.,Type=Integer,Description="Copy number of adjacency">
+##INFO=<ID=CICN,Number=2,Type=Integer,Description="Confidence interval around copy number for the segment">
+##INFO=<ID=CICNADJ,Number=.,Type=Integer,Description="Confidence interval around copy number for the adjacency">
+##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
+##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
+##FORMAT=<ID=CNL,Number=.,Type=Float,Description="Copy number genotype likelihood for imprecise events">
+##FORMAT=<ID=NQ,Number=1,Type=Integer,Description="Phred style probability score that the variant is novel">
+##FORMAT=<ID=HAP,Number=1,Type=Integer,Description="Unique haplotype identifier">
+##FORMAT=<ID=AHAP,Number=1,Type=Integer,Description="Unique identifier of ancestral haplotype">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">"""
+
+    val inputVCF = Source.fromFile(input)
+    val writer = new PrintWriter(output)
+    for (line <- inputVCF.getLines()) {
+      (line == vcfColHeader) match {
+        case true => {
+          writer.write(extraHeader+"\n")
+          writer.write(vcfColReplacementHeader + "\n")
+        }
+        case _ => writer.write(line + "\n")
+      }
+    }
+    writer.close()
+    inputVCF.close()
+  }
+}
+

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala

@@ -32,7 +32,7 @@ class Breakdancer(val root: Configurable) extends SvCaller {
       val bdcfg = BreakdancerConfig(this, bamFile, new File(breakdancerSampleDir, sample + ".breakdancer.cfg"))
       val breakdancer = BreakdancerCaller(this, bdcfg.output, new File(breakdancerSampleDir, sample + ".breakdancer.tsv"))
       val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
-        sample=sample)
+        sample = sample)
       add(bdcfg, breakdancer, bdvcf)
 
       addVCF(sample, bdvcf.output)

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

@@ -15,7 +15,7 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Script for sv caler Clever */
@@ -29,7 +29,13 @@ class Clever(val root: Configurable) extends SvCaller {
       val clever = CleverCaller(this, bamFile, cleverDir)
       add(clever)
 
-      addVCF(sample, clever.outputvcf)
+      val cleverVCF = new CleverFixVCF(this)
+      cleverVCF.input = clever.outputvcf
+      cleverVCF.output = new File(cleverDir, s"${sample}.clever.vcf")
+      cleverVCF.sampleName = sample
+      add(cleverVCF)
+
+      addVCF(sample, cleverVCF.output)
     }
   }
 }