#include <vector>
#include "bamtools_convert.h"
+#include "bamtools_format.h"
#include "bamtools_options.h"
#include "BamReader.h"
#include "BamMultiReader.h"
using namespace std;
-using namespace BamTools;
+using namespace BamTools;
// ---------------------------------------------
// ConvertSettings implementation
ConvertSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
+ , InputFilename(Options::StandardIn())
, OutputFilename(Options::StandardOut())
- { }
+ { }
};
// ---------------------------------------------
, m_settings(new ConvertSettings)
{
// set program details
- Options::SetProgramInfo("bamtools convert", "converts between BAM and a number of other formats)", "-in <filename> [-in <filename> ... ] -out <filename> -format FORMAT");
+ Options::SetProgramInfo("bamtools convert", "converts between BAM and a number of other formats", "-in <filename> -out <filename> -format <FORMAT>");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
// open files
BamReader reader;
- reader.Open(m_settings->InputFilename, false);
+ reader.Open(m_settings->InputFilename);
// do conversion
+
+
+
// clean up & exit
reader.Close();
return 0;