diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala index 1c40d228d200623e56b618e279763f96304ceb99..3597d398c6bdff43dc61d6e177bbae7fd4822509 100644 --- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala +++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala @@ -40,22 +40,22 @@ object VcfToTsv extends ToolCommand { } text "output file, default to stdout" opt[String]('f', "field") unbounded () action { (x, c) => c.copy(fields = x :: c.fields) - } + } text "Genotype field to use" valueName "Genotype field name" opt[String]('i', "info_field") unbounded () action { (x, c) => c.copy(infoFields = x :: c.infoFields) - } + } text "Info field to use" valueName "Info field name" opt[Unit]("all_info") unbounded () action { (x, c) => c.copy(allInfo = true) - } + } text "Use all info fields in the vcf header" opt[Unit]("all_format") unbounded () action { (x, c) => c.copy(allFormat = true) - } + } text "Use all genotype fields in the vcf header" opt[String]('s', "sample_field") unbounded () action { (x, c) => c.copy(sampleFields = x :: c.sampleFields) - } + } text "Genotype fields to use in the tsv file" opt[Unit]('d', "disable_defaults") unbounded () action { (x, c) => c.copy(disableDefaults = true) - } + } text "Don't output the default columns from the vcf file" opt[String]("separator") maxOccurs 1 action { (x, c) => c.copy(separator = x) } text "Optional separator. Default is tab-delimited"