public bool Process(string[] args)
{
var options = new AnnovarSummaryBamDistillerOptions();
bool result = CommandLine.Parser.Default.ParseArguments(args, options);
if (result)
{
if (!options.PrepareOptions())
{
Console.Out.WriteLine(options.GetUsage());
result = false;
}
else
{
var files = new AnnovarSummaryBamDistiller(options.AffyAnnotationFile, options.BamFile, options.TargetDir, options.Suffix).Process(options.AnnovarFile);
Console.WriteLine("Run shell file to extract bam files:\n" + files.Merge("\n"));
}
}
return(result);
}
public bool Process(string[] args)
{
AnnovarSummaryBamDistillerOptions options;
bool result = true;
try
{
options = CommandLine.Parser.Default.ParseArguments<AnnovarSummaryBamDistillerOptions>(args,
() =>
{
result = false;
}
);
if (result)
{
if (!options.PrepareOptions())
{
Console.Out.WriteLine(options.GetUsage());
result = false;
}
else
{
var files = new AnnovarSummaryBamDistiller(options.AffyAnnotationFile, options.BamFile, options.TargetDir, options.Suffix).Process(options.AnnovarFile);
Console.WriteLine("Run shell file to extract bam files:\n" + files.Merge("\n"));
}
}
}
catch (Exception ex)
{
Console.Error.WriteLine(ex.ToString());
result = false;
}
return result;
}
