Added contig

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

@@ -129,7 +129,7 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
       conditional(fullParameterEstimates, "-full_parameter_estimates") +
       optional("-method", method) +
       optional("-pheno", pheno)
-      conditional(summaryStatsOnly, "-summary_stats_only") +
+    conditional(summaryStatsOnly, "-summary_stats_only") +
       conditional(covAll, "-cov_all") +
       conditional(covAllContinuous, "-cov_all_continuous") +
       conditional(covAllDiscrete, "-cov_all_discrete") +

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala

@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{Input, Output}
 
@@ -43,7 +44,7 @@ class SnptestToVcf(val root: Configurable) extends ToolCommandFunction with Refe
   override def beforeGraph(): Unit = {
     super.beforeGraph()
     if (reference == null) reference = referenceFasta()
-    if (contig == null) throw new IllegalStateException
+    if (contig == null) Logging.addError("SnptestToVcf is missing a contig")
     //if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
   }
 

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

@@ -3,9 +3,9 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.util
 
-import htsjdk.samtools.reference.{FastaSequenceFile, ReferenceSequenceFileFactory}
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, Options, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{Allele, GenotypeBuilder, VariantContextBuilder}
+import htsjdk.samtools.reference.{ FastaSequenceFile, ReferenceSequenceFileFactory }
+import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, Options, VariantContextWriterBuilder }
+import htsjdk.variant.variantcontext.{ Allele, GenotypeBuilder, VariantContextBuilder }
 import htsjdk.variant.vcf._
 import nl.lumc.sasc.biopet.utils.ToolCommand
 
@@ -48,7 +48,7 @@ object SnptestToVcf extends ToolCommand {
 
     infoHeader match {
       case Some(header) => parseLines(header, infoIt, cmdArgs)
-      case _ => logger.info("No header and records found in file")
+      case _            => logger.info("No header and records found in file")
     }
 
     logger.info("Done")
@@ -59,9 +59,9 @@ object SnptestToVcf extends ToolCommand {
     val headerMap = headerKeys.zipWithIndex.toMap
     require(headerKeys.size == headerMap.size, "Duplicates header keys found")
     val metaLines = new util.HashSet[VCFHeaderLine]()
-    for (key <- headerKeys if key != "rsid" if key != "chromosome" if key != "position"
-         if key != "alleleA" if key != "alleleB" if key != "alleleA")
-      metaLines.add(new VCFInfoHeaderLine(s"ST_$key", 1, VCFHeaderLineType.String, ""))
+    for (
+      key <- headerKeys if key != "rsid" if key != "chromosome" if key != "position" if key != "alleleA" if key != "alleleB" if key != "alleleA"
+    ) metaLines.add(new VCFInfoHeaderLine(s"ST_$key", 1, VCFHeaderLineType.String, ""))
 
     val reference = new FastaSequenceFile(cmdArgs.referenceFasta, true)
     require(reference.getSequenceDictionary.getSequence(cmdArgs.contig) != null,
@@ -76,8 +76,9 @@ object SnptestToVcf extends ToolCommand {
       .build)
     writer.writeHeader(vcfHeader)
 
-    val infoKeys = for (key <- headerKeys if key != "rsid" if key != "chromosome" if key != "position"
-                        if key != "alleleA" if key != "alleleB" if key != "alleleA") yield key
+    val infoKeys = for (
+      key <- headerKeys if key != "rsid" if key != "chromosome" if key != "position" if key != "alleleA" if key != "alleleB" if key != "alleleA"
+    ) yield key
 
     var counter = 0
     for (line <- lineIt if !line.startsWith("#")) {
@@ -94,7 +95,7 @@ object SnptestToVcf extends ToolCommand {
         .stop(end)
         .noGenotypes()
 
-      val infoBuilder = infoKeys.foldLeft(builder) { case (a,b) => a.attribute("ST_" + b, values(headerMap(b))) }
+      val infoBuilder = infoKeys.foldLeft(builder) { case (a, b) => a.attribute("ST_" + b, values(headerMap(b))) }
 
       writer.add(builder.id(rsid).make())
 

public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala

@@ -4,10 +4,10 @@ import java.io.File
 import java.util
 
 import htsjdk.samtools.reference.FastaSequenceFile
-import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand, Reference}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Snptest
-import nl.lumc.sasc.biopet.extensions.gatk.{CatVariants, SelectVariants}
-import nl.lumc.sasc.biopet.extensions.tools.{GensToVcf, SnptestToVcf}
+import nl.lumc.sasc.biopet.extensions.gatk.{ CatVariants, SelectVariants }
+import nl.lumc.sasc.biopet.extensions.tools.{ GensToVcf, SnptestToVcf }
 import nl.lumc.sasc.biopet.pipelines.gwastest.impute.ImputeOutput
 import nl.lumc.sasc.biopet.utils.Logging
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -107,8 +107,6 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
         sv.isIntermediate = true
         add(sv)
 
-        //TODO: snptest
-
         val snptest = new Snptest(this)
         snptest.inputGenotypes :+= sv.outputFile
         snptest.inputSampleFiles :+= phenotypeFile
@@ -118,6 +116,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
         val snptestToVcf = new SnptestToVcf(this)
         snptestToVcf.inputInfo = snptest.outputFile.get
         snptestToVcf.outputVcf = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest.vcf.gz")
+        snptestToVcf.contig = region.chr
         add(snptestToVcf)
 
         region -> snptestToVcf.outputVcf