- Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
- Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
- Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts);
+ Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", listDesc, "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScript, m_settings->ScriptFilename, IO_Opts);