private static ExitCodes ProgramExecution()
{
if (_createIndex)
{
using (var indexCreator = new IndexCreator(_inputJson))
{
indexCreator.CreateIndex();
}
return(ExitCodes.Success);
}
string indexFileName = _inputJson + JasixCommons.FileExt;
ValidateIndexFile(indexFileName);
var writer = string.IsNullOrEmpty(_outputFile)
? null : GZipUtilities.GetStreamWriter(_outputFile);
using (var queryProcessor = new QueryProcessor(GZipUtilities.GetAppropriateStreamReader(_inputJson),
FileUtilities.GetReadStream(indexFileName), writer))
{
if (_list)
{
queryProcessor.ListChromosomesAndSections();
return(ExitCodes.Success);
}
if (_printHeaderOnly)
{
queryProcessor.PrintHeaderOnly();
return(ExitCodes.Success);
}
if (!string.IsNullOrEmpty(_section))
{
queryProcessor.PrintSection(_section);
return(ExitCodes.Success);
}
if (Queries == null)
{
Console.WriteLine("Please specify query region(s)");
return(ExitCodes.BadArguments);
}
queryProcessor.ProcessQuery(Queries, _printHeader);
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
if (ConfigurationSettings.CreateIndex)
{
using (var indexCreator = new IndexCreator(ConfigurationSettings.InputJson))
{
indexCreator.CreateIndex();
}
return(ExitCodes.Success);
}
var indexFileName = ConfigurationSettings.InputJson + JasixCommons.FileExt;
ValidateIndexFile(indexFileName);
var writer = string.IsNullOrEmpty(ConfigurationSettings.OutputFile)
? null : GZipUtilities.GetStreamWriter(ConfigurationSettings.OutputFile);
using (var queryProcessor = new QueryProcessor(GZipUtilities.GetAppropriateStreamReader(ConfigurationSettings.InputJson),
FileUtilities.GetReadStream(indexFileName), writer))
{
if (ConfigurationSettings.ListChromosomeName)
{
queryProcessor.PrintChromosomeList();
return(ExitCodes.Success);
}
if (ConfigurationSettings.PrintHeaderOnly)
{
queryProcessor.PrintHeader();
return(ExitCodes.Success);
}
if (ConfigurationSettings.Queries == null)
{
Console.WriteLine("Plese specify query region");
return(ExitCodes.BadArguments);
}
queryProcessor.ProcessQuery(ConfigurationSettings.Queries, ConfigurationSettings.PrintHeader);
}
return(ExitCodes.Success);
}