// ***************************************************************************
// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 25 October 2010
+// Last modified: 12 October 2012 (DB)
// ---------------------------------------------------------------------------
// Integrates a number of BamTools functionalities into a single executable.
// ***************************************************************************
-// stringify version information
-#define BAMTOOLS_VER1_(x) #x
-#define BAMTOOLS_VER_(x) BAMTOOLS_VER1_(x)
-#define BAMTOOLS_VERSION BAMTOOLS_VER_(BT_VERSION)
-
-// includes
-#include <cstdio>
-#include <iostream>
-#include <string>
#include "bamtools_convert.h"
#include "bamtools_count.h"
#include "bamtools_coverage.h"
#include "bamtools_index.h"
#include "bamtools_merge.h"
#include "bamtools_random.h"
+#include "bamtools_resolve.h"
+#include "bamtools_revert.h"
#include "bamtools_sort.h"
#include "bamtools_split.h"
#include "bamtools_stats.h"
-using namespace std;
+#include "bamtools_version.h"
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <sstream>
+#include <string>
using namespace BamTools;
+using namespace std;
// bamtools subtool names
static const string CONVERT = "convert";
static const string INDEX = "index";
static const string MERGE = "merge";
static const string RANDOM = "random";
+static const string RESOLVE = "resolve";
+static const string REVERT = "revert";
static const string SORT = "sort";
static const string SPLIT = "split";
static const string STATS = "stats";
if ( arg == INDEX ) return new IndexTool;
if ( arg == MERGE ) return new MergeTool;
if ( arg == RANDOM ) return new RandomTool;
+ if ( arg == RESOLVE ) return new ResolveTool;
+ if ( arg == REVERT ) return new RevertTool;
if ( arg == SORT ) return new SortTool;
if ( arg == SPLIT ) return new SplitTool;
if ( arg == STATS ) return new StatsTool;
cerr << "\theader Prints BAM header information" << endl;
cerr << "\tindex Generates index for BAM file" << endl;
cerr << "\tmerge Merge multiple BAM files into single file" << endl;
- cerr << "\trandom Select random alignments from existing BAM file(s)" << endl;
+ cerr << "\trandom Select random alignments from existing BAM file(s), intended more as a testing tool." << endl;
+ cerr << "\tresolve Resolves paired-end reads (marking the IsProperPair flag as needed)" << endl;
+ cerr << "\trevert Removes duplicate marks and restores original base qualities" << endl;
cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
cerr << "\tsplit Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;
cerr << "\tstats Prints some basic statistics from input BAM file(s)" << endl;
cerr << endl;
cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
cerr << endl;
- return 0;
+ return EXIT_SUCCESS;
}
// print version info
int Version(void) {
+
+ stringstream versionStream("");
+ versionStream << BAMTOOLS_VERSION_MAJOR << "."
+ << BAMTOOLS_VERSION_MINOR << "."
+ << BAMTOOLS_VERSION_BUILD;
+
cout << endl;
- cout << "bamtools " << BAMTOOLS_VERSION << endl;
+ cout << "bamtools " << versionStream.str() << endl;
cout << "Part of BamTools API and toolkit" << endl;
cout << "Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg" << endl;
- cout << "(c) 2009-2010 Marth Lab, Biology Dept., Boston College" << endl;
+ cout << "(c) 2009-2012 Marth Lab, Biology Dept., Boston College" << endl;
cout << endl;
- return 0;
+ return EXIT_SUCCESS;
}
// toolkit entry point
// 'bamtools version', 'bamtools --version', or 'bamtools -v'
if ( IsVersion(argv[1]) ) return Version();
- // determine desired sub-tool
+ // determine desired sub-tool, run if found
AbstractTool* tool = CreateTool( argv[1] );
-
- // if found, run tool... otherwise show help
if ( tool ) return tool->Run(argc, argv);
- else return Help(argc, argv);
+
+ // no tool matched, show help
+ return Help(argc, argv);
}