Commit 4639bd35 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added scala docs

parent faf89169
...@@ -22,6 +22,15 @@ class AnnotateVcfWithBed { ...@@ -22,6 +22,15 @@ class AnnotateVcfWithBed {
object AnnotateVcfWithBed extends ToolCommand { object AnnotateVcfWithBed extends ToolCommand {
/**
* Args for the commandline tool
* @param inputFile input vcf file
* @param bedFile bed file to annotate to vcf file
* @param outputFile output vcf file
* @param fieldName Info field that should be used
* @param fieldDescription Description at field if needed
* @param fieldType Type of filed, can be: "Integer", "Flag", "Character", "Float"
*/
case class Args(inputFile: File = null, case class Args(inputFile: File = null,
bedFile: File = null, bedFile: File = null,
outputFile: File = null, outputFile: File = null,
...@@ -50,6 +59,11 @@ object AnnotateVcfWithBed extends ToolCommand { ...@@ -50,6 +59,11 @@ object AnnotateVcfWithBed extends ToolCommand {
} text ("Description of field in new vcf file") } text ("Description of field in new vcf file")
} }
/**
* Program will Annotate a vcf file with the overlapping regions of a bed file, 4e column of the bed file we in a info tag in the vcf file
*
* @param args
*/
def main(args: Array[String]): Unit = { def main(args: Array[String]): Unit = {
val argsParser = new OptParser val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1) val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
......
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