Commit 12da2fa8 authored by akaljuvee's avatar akaljuvee

gatk.tools.CatVariants outputs an empty file when input files don't contain...

gatk.tools.CatVariants outputs an empty file when input files don't contain anything, added a script that writes 2 VCF-file header lines to that empty output file
parent 1b34e7ea
......@@ -37,6 +37,9 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var outputFile: File = _
/** When Gatk's CatVariants has been called with empty VCF-files, then it also outputs an empty file. When this parameter is set to true, then the empty file gets added a valid VCF-file header.*/
var writeHeaderToEmptyOutput: Boolean = false
/** assumeSorted should be true if the input files are already sorted (based on the position of the variants) */
@Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if the input files are already sorted (based on the position of the variants)", required = false, exclusiveOf = "", validation = "")
var assumeSorted: Boolean = _
......@@ -73,5 +76,14 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
optional("--variant_index_type", variant_index_type, spaceSeparated = true, escape = true, format = "%s") +
optional("--variant_index_parameter", variant_index_parameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-l", logging_level, spaceSeparated = true, escape = true, format = "%s") +
optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s")
optional("-log", log_to_file, spaceSeparated = true, escape = true, format = "%s") +
(if (writeHeaderToEmptyOutput) s"""
|c=$$?
|if [ $$c -eq 0 ] && [ ! -s $outputFile ]; then
| echo '##fileformat=VCFv4.2' > $outputFile
| echo '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO' >> $outputFile
|fi
|exit $$c""".stripMargin
else "")
}
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