// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 19 September 2010
+// Last modified: 21 March 2011 (DB)
// ---------------------------------------------------------------------------
// Integrates a number of BamTools functionalities into a single executable.
// ***************************************************************************
-#include <iostream>
#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_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 COUNT = "count";
static const string INDEX = "index";
static const string MERGE = "merge";
static const string RANDOM = "random";
+static const string REVERT = "revert";
static const string SORT = "sort";
static const string SPLIT = "split";
static const string STATS = "stats";
-// ------------------------------------------
-// bamtools help/version names
-static const string HELP = "help";
-static const string LONG_HELP = "--help";
-static const string SHORT_HELP = "-h";
-
+// bamtools help/version constants
+static const string HELP = "help";
+static const string LONG_HELP = "--help";
+static const string SHORT_HELP = "-h";
static const string VERSION = "version";
static const string LONG_VERSION = "--version";
static const string SHORT_VERSION = "-v";
-// ------------------------------------------
-// Subtool factory method
+// determine if string is a help constant
+static bool IsHelp(char* str) {
+ return ( str == HELP ||
+ str == LONG_HELP ||
+ str == SHORT_HELP );
+}
+
+// determine if string is a version constant
+static bool IsVersion(char* str) {
+ return ( str == VERSION ||
+ str == LONG_VERSION ||
+ str == SHORT_VERSION );
+}
+
+// subtool factory method
AbstractTool* CreateTool(const string& arg) {
// determine tool type based on arg
if ( arg == INDEX ) return new IndexTool;
if ( arg == MERGE ) return new MergeTool;
if ( arg == RANDOM ) return new RandomTool;
+ if ( arg == REVERT ) return new RevertTool;
if ( arg == SORT ) return new SortTool;
if ( arg == SPLIT ) return new SplitTool;
if ( arg == STATS ) return new StatsTool;
return 0;
}
-// ------------------------------------------
-// Print help info
+// print help info
int Help(int argc, char* argv[]) {
- // 'bamtools help COMMAND'
+ // check for 'bamtools help COMMAND' to print tool-specific help message
if (argc > 2) {
+ // determine desired sub-tool
AbstractTool* tool = CreateTool( argv[2] );
-// if ( argv[2] == CONVERT ) tool = new ConvertTool;
-// if ( argv[2] == COUNT ) tool = new CountTool;
-// if ( argv[2] == COVERAGE ) tool = new CoverageTool;
-// if ( argv[2] == FILTER ) tool = new FilterTool;
-// if ( argv[2] == HEADER ) tool = new HeaderTool;
-// if ( argv[2] == INDEX ) tool = new IndexTool;
-// if ( argv[2] == MERGE ) tool = new MergeTool;
-// if ( argv[2] == RANDOM ) tool = new RandomTool;
-// if ( argv[2] == SORT ) tool = new SortTool;
-// if ( argv[2] == SPLIT ) tool = new SplitTool;
-// if ( argv[2] == STATS ) tool = new StatsTool;
-
+
// if tool known, print its help screen
if ( tool ) return tool->Help();
}
- // either 'bamtools help' or unrecognized argument after 'help'
+ // print general BamTools help message
cerr << endl;
cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
cerr << 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 << "\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
+// print version info
int Version(void) {
+
+ stringstream versionStream("");
+ versionStream << BAMTOOLS_VERSION_MAJOR << "."
+ << BAMTOOLS_VERSION_MINOR << "."
+ << BAMTOOLS_VERSION_BUILD;
+
cout << endl;
- cout << "bamtools v0.8.xx" << 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) 2009-2011 Marth Lab, Biology Dept., Boston College" << endl;
cout << endl;
- return 0;
+ return EXIT_SUCCESS;
}
-// ------------------------------------------
// toolkit entry point
int main(int argc, char* argv[]) {
if ( (argc == 1) ) return Help(argc, argv);
// 'bamtools help', 'bamtools --help', or 'bamtools -h'
- if ( (argv[1] == HELP) || (argv[1] == LONG_HELP) || (argv[1] == SHORT_HELP) ) return Help(argc, argv);
+ if ( IsHelp(argv[1]) ) return Help(argc, argv);
// 'bamtools version', 'bamtools --version', or 'bamtools -v'
- if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version();
+ if ( IsVersion(argv[1]) ) return Version();
- // determine desired sub-tool
+ // determine desired sub-tool, run if found
AbstractTool* tool = CreateTool( argv[1] );
-// if ( argv[1] == CONVERT ) tool = new ConvertTool;
-// if ( argv[1] == COUNT ) tool = new CountTool;
-// if ( argv[1] == COVERAGE ) tool = new CoverageTool;
-// if ( argv[1] == FILTER ) tool = new FilterTool;
-// if ( argv[1] == HEADER ) tool = new HeaderTool;
-// if ( argv[1] == INDEX ) tool = new IndexTool;
-// if ( argv[1] == MERGE ) tool = new MergeTool;
-// if ( argv[1] == RANDOM ) tool = new RandomTool;
-// if ( argv[1] == SORT ) tool = new SortTool;
-// if ( argv[1] == SPLIT ) tool = new SplitTool;
-// if ( argv[1] == STATS ) tool = new StatsTool;
-
- // if found, run tool
if ( tool ) return tool->Run(argc, argv);
- // no match found, show help
- else return Help(argc, argv);
+
+ // no tool matched, show help
+ return Help(argc, argv);
}
projects / bamtools.git / blobdiff