// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 7 September 2010
+// Last modified: 13 October 2010
// ---------------------------------------------------------------------------
// Merges multiple BAM files into one.
// ***************************************************************************
#include <iostream>
#include <string>
#include <vector>
-
#include "bamtools_merge.h"
#include "bamtools_options.h"
#include "bamtools_utilities.h"
#include "BamMultiReader.h"
#include "BamWriter.h"
-
using namespace std;
using namespace BamTools;
, m_settings(new MergeSettings)
{
// set program details
- Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename>]");
+ Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
-
- OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
- Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+ Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
}
MergeTool::~MergeTool(void) {