/// <summary>
/// Parses NUCmer command line parameters.
/// </summary>
/// <param name="args">The arguments.</param>
private static void Alignment(string[] args)
{
NucmerArguments arguments = new NucmerArguments();
CommandLineArguments parser = new CommandLineArguments();
// Add Nucmer parameters
parser.Parameter(ArgumentType.DefaultArgument, "FilePath", ArgumentValueType.MultipleUniqueStrings, "", "File path");
parser.Parameter(ArgumentType.Optional, "Mum", ArgumentValueType.Bool, "m", "Use anchor matches that are unique in both the reference and query.");
parser.Parameter(ArgumentType.Optional, "MumReference", ArgumentValueType.Bool, "r", "Use anchor matches that are unique in the reference but not necessarily unique in the query (default behavior).");
parser.Parameter(ArgumentType.Optional, "MaxMatch", ArgumentValueType.Bool, "x", "Use all anchor matches regardless of their uniqueness.");
parser.Parameter(ArgumentType.Optional, "BreakLength", ArgumentValueType.Int, "b", "Distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200).");
parser.Parameter(ArgumentType.Optional, "MinCluster", ArgumentValueType.Int, "c", "Minimum cluster length (default 65).");
parser.Parameter(ArgumentType.Optional, "DiagFactor", ArgumentValueType.Int, "d", "Maximum diagonal difference factor for clustering, i.e. diagonal difference / match separation (default 0.12).");
parser.Parameter(ArgumentType.Optional, "Forward", ArgumentValueType.Bool, "f", "Use only the forward strand of the query sequence.");
parser.Parameter(ArgumentType.Optional, "MaxGap", ArgumentValueType.Int, "g", "Maximum gap between two adjacent matches in a cluster (default 90).");
parser.Parameter(ArgumentType.Optional, "Help", ArgumentValueType.Bool, "h", "Print the help information.");
parser.Parameter(ArgumentType.Optional, "MinMatch", ArgumentValueType.Int, "l", "Minimum length of an maximal exact match (default 20).");
parser.Parameter(ArgumentType.Optional, "OutputFile", ArgumentValueType.String, "o", "Output file");
parser.Parameter(ArgumentType.Optional, "Reverse", ArgumentValueType.Bool, "e", "Use only the reverse complement of the query sequence.");
parser.Parameter(ArgumentType.Optional, "NotExtend", ArgumentValueType.Bool, "n", "Toggle the outward extension of alignments from their anchoring clusters." +
"Setting this flag will prevent alignment extensions but still align the DNA between clustered matches and create the .delta file.");
parser.Parameter(ArgumentType.Optional, "Verbose", ArgumentValueType.Bool, "v", "Display verbose logging during processing.");
parser.Parameter(ArgumentType.Optional, "FixedSeparation", ArgumentValueType.Bool, "s", "Maximum fixed diagonal difference.");
if (args.Length > 1)
{
try
{
parser.Parse(args, arguments);
}
catch (ArgumentException ex)
{
DisplayErrorMessage(ex.Message);
DisplayErrorMessage(Resources.NUCmerUtilHelp);
}
if (arguments.Help)
{
DisplayErrorMessage(Resources.NUCmerUtilHelp);
}
else if (arguments.FilePath.Length == 2)
{
arguments.Align();
}
else
{
DisplayErrorMessage(Resources.NUCmerUtilHelp);
}
}
else
{
DisplayErrorMessage(Resources.NUCmerUtilHelp);
}
}