diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala index 0379c36d9ace680b7833bf226912504bb619f8e2..4fb0a05fd7e04617c15a68c63763d7e60da322d4 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala @@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan { var vcfSampleList: Option[File] = config("vcf_sample_list") var variants: Option[Int] = config("variants") + override def defaultCoreMemory = 6.0 + override def beforeGraph(): Unit = { val validValues: Set[Int] = Set(0, 1) // check for boolean vars that are passed as ints diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala index f3d8585de87216b872bee7235e364df29514710a..76da0423cea32f599c978e852ca0aa35a740137e 100644 --- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala +++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala @@ -15,20 +15,15 @@ */ package nl.lumc.sasc.biopet.extensions.varscan -import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction +import nl.lumc.sasc.biopet.core.{ Version, BiopetJavaCommandLineFunction } -abstract class Varscan extends BiopetJavaCommandLineFunction { +abstract class Varscan extends BiopetJavaCommandLineFunction with Version { override def subPath = "varscan" :: super.subPath jarFile = config("varscan_jar") - /** - * TODO: test version - * override def versionCommand = super.commandLine - * override val versionRegex = """VarScan v(.*)""".r - */ - - override def defaultCoreMemory = 5.0 + def versionCommand = super.commandLine + def versionRegex = """VarScan v(.*)""".r } diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala index f13230534af0a61fa29f68daa8d48c81a55e1f23..d0c185cf1a837c816404c2c160bc8f6428e1cc19 100644 --- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala +++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala @@ -25,7 +25,8 @@ object BamUtils { val inputSam = SamReaderFactory.makeDefault.open(file) val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct if (samples.size == 1) samples.head -> file - else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file) + else if (samples.size > 1) throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file) + else throw new IllegalArgumentException("Bam does not contain sample ID or have no readgroups defined: " + file) } if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice") temp.toMap