• CommandLineOptionsParser
• FileOutputWriter
• GenePrioritizedOutputFormatWriterFactory
• OrderedGenesOutputFormatWriter
• OutputFormatWriter
• OutputWriter
• PrioritizedOutputFormatWriter
• PrioritizedOutputFormatWriterFactory
• ResultsPerGeneSeparatedValuesOutputFormatWriter
• ResultsPerGeneSeparatedValuesOutputFormatWriterUsingIds
• ResultsPerGeneSeparatedValuesOutputFormatWriterUsingUris
• RunMode
• StdoutOutputWriter
• ValuesSeparator
• VibeApplication
• VibeOptions
• VibeProperties
• VibePropertiesLoader