Commit ece3ce24 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added text to args

parent a36ce065
......@@ -73,37 +73,37 @@ object BastyGenerateFasta extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('V', "inputVcf") unbounded () valueName ("<file>") action { (x, c) =>
c.copy(inputVcf = x)
}
} text ("vcf file, needed for outputVariants and outputConsensusVariants")
opt[File]("bamFile") unbounded () valueName ("<file>") action { (x, c) =>
c.copy(bamFile = x)
}
opt[File]("outputVariants") unbounded () valueName ("<file>") action { (x, c) =>
} text ("bam file, needed for outputConsensus and outputConsensusVariants")
opt[File]("outputVariants") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
c.copy(outputVariants = x)
}
opt[File]("outputConsensus") unbounded () valueName ("<file>") action { (x, c) =>
} text ("fasta with only variants from vcf file")
opt[File]("outputConsensus") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
c.copy(outputConsensus = x)
}
opt[File]("outputConsensusVariants") unbounded () valueName ("<file>") action { (x, c) =>
} text ("Consensus fasta from bam, always reference bases else 'N'")
opt[File]("outputConsensusVariants") maxOccurs (1) unbounded () valueName ("<file>") action { (x, c) =>
c.copy(outputConsensusVariants = x)
}
} text ("Consensus fasta from bam with variants from vcf file, always reference bases else 'N'")
opt[Unit]("snpsOnly") unbounded () action { (x, c) =>
c.copy(snpsOnly = true)
}
} text ("Only use snps from vcf file")
opt[String]("sampleName") unbounded () action { (x, c) =>
c.copy(sampleName = x)
}
} text ("Sample name in vcf file")
opt[String]("outputName") required () unbounded () action { (x, c) =>
c.copy(outputName = x)
}
} text ("Output name in fasta file header")
opt[Int]("minAD") unbounded () action { (x, c) =>
c.copy(minAD = x)
}
} text ("min AD value in vcf file for sample")
opt[Int]("minDepth") unbounded () action { (x, c) =>
c.copy(minDepth = x)
}
} text ("min detp in bam file")
opt[File]("reference") unbounded () action { (x, c) =>
c.copy(reference = x)
}
} text ("Indexed reference fasta file")
}
protected var cmdArgs: Args = _
......
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