Major update to BamTools version 1.0

[bamtools.git] / src / toolkit / bamtools.cpp

diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp
index c7491d71d90ed899a85de274a236ac7b5a77f4d1..4875a9a10bdb3ba1dbfdc9ac50d1f5ccfc0ebe07 100644 (file)
--- a/src/toolkit/bamtools.cpp
+++ b/src/toolkit/bamtools.cpp
@@ -3,21 +3,11 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 5 December 2010
+// Last modified: 21 March 2011 (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 <sstream>
-#include <string>
 #include "bamtools_convert.h"
 #include "bamtools_count.h"
 #include "bamtools_coverage.h"
@@ -31,8 +21,13 @@
 #include "bamtools_split.h"
 #include "bamtools_stats.h"
 #include "bamtools_version.h"
-using namespace std;
+#include <cstdio>
+#include <cstdlib>
+#include <iostream>
+#include <sstream>
+#include <string>
 using namespace BamTools;
+using namespace std;
 
 // bamtools subtool names
 static const string CONVERT  = "convert";
@@ -117,13 +112,14 @@ int Help(int argc, char* argv[]) {
     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
@@ -131,16 +127,16 @@ int Version(void) {
 
     stringstream versionStream("");
     versionStream << BAMTOOLS_VERSION_MAJOR << "."
-                 << BAMTOOLS_VERSION_MINOR << "."
-                 << BAMTOOLS_VERSION_BUILD;
+                  << BAMTOOLS_VERSION_MINOR << "."
+                  << BAMTOOLS_VERSION_BUILD;
 
     cout << 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
@@ -155,10 +151,10 @@ int main(int argc, char* argv[]) {
     // '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);
 }