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#[] Scaffolder::ToolIndex
description Scaffolder::Tool::Sequence
description Scaffolder::Tool::Validate
description Scaffolder::Tool::Help
#determine_tool Scaffolder::BinaryHelper
#errors Scaffolder::Tool::Validate
#execute Scaffolder::Tool::Help
#execute Scaffolder::Tool::Sequence
#execute Scaffolder::Tool::Validate
#get_tool Scaffolder::ToolIndex
#initialize Scaffolder::Tool
inserts_overlap? Scaffolder::Tool::Validate
#remove_first_argument Scaffolder::BinaryHelper
#run Scaffolder::Tool
#scaffold Scaffolder::Tool
#scaffold_file Scaffolder::Tool
#select_tool Scaffolder::BinaryHelper
sequence_errors Scaffolder::Tool::Validate
#sequence_file Scaffolder::Tool
#settings Scaffolder::Tool
#tool_exists? Scaffolder::ToolIndex