Minor cleanup

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

diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp
index 2f91e2def6c4e3a11b97818476517711259d853b..97c032f6f70586382e10955de24f4bbf8d270e5d 100644 (file)
--- a/src/toolkit/bamtools.cpp
+++ b/src/toolkit/bamtools.cpp
@@ -1,14 +1,12 @@
 // ***************************************************************************
 // bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 13 December 2010
+// Last modified: 18 May 2011 (DB)
 // ---------------------------------------------------------------------------
 // Integrates a number of BamTools functionalities into a single executable.
 // ***************************************************************************
 
-// includes
 #include "bamtools_convert.h"
 #include "bamtools_count.h"
 #include "bamtools_coverage.h"
@@ -17,17 +15,17 @@
 #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"
 #include "bamtools_version.h"
-
 #include <cstdio>
+#include <cstdlib>
 #include <iostream>
 #include <sstream>
 #include <string>
-
 using namespace BamTools;
 using namespace std;
 
@@ -40,6 +38,7 @@ static const string HEADER   = "header";
 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";
@@ -79,6 +78,7 @@ AbstractTool* CreateTool(const string& arg) {
     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;
@@ -113,7 +113,8 @@ int Help(int argc, char* argv[]) {
     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;
@@ -121,7 +122,7 @@ int Help(int argc, char* argv[]) {
     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
@@ -136,9 +137,9 @@ int Version(void) {
     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
@@ -153,10 +154,10 @@ 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);
 }