Reorganized source tree & build system

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

diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp
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+// ***************************************************************************
+// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 22 July 2010
+// ---------------------------------------------------------------------------
+// Integrates a number of BamTools functionalities into a single executable.
+// ***************************************************************************
+
+// Std C/C++ includes
+#include <iostream>
+
+// BamTools includes
+#include "bamtools_convert.h"
+#include "bamtools_count.h"
+#include "bamtools_coverage.h"
+#include "bamtools_filter.h"
+#include "bamtools_header.h"
+#include "bamtools_index.h"
+#include "bamtools_merge.h"
+#include "bamtools_random.h"
+#include "bamtools_sort.h"
+#include "bamtools_stats.h"
+
+using namespace std;
+using namespace BamTools;
+
+// ------------------------------------------
+// bamtools subtool names
+static const string CONVERT  = "convert";
+static const string COUNT    = "count";
+static const string COVERAGE = "coverage";
+static const string FILTER   = "filter";
+static const string HEADER   = "header";
+static const string INDEX    = "index";
+static const string MERGE    = "merge";
+static const string RANDOM   = "random";
+static const string SORT     = "sort";
+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";
+
+static const string VERSION       = "version";
+static const string LONG_VERSION  = "--version";
+static const string SHORT_VERSION = "-v";
+
+// ------------------------------------------
+// Print help info
+int Help(int argc, char* argv[]) {
+  
+    // 'bamtools help COMMAND'
+    if (argc > 2) {
+        
+        AbstractTool* tool(0);
+        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] == STATS )    tool = new StatsTool;
+        
+        // if tool known, print its help screen
+        if ( tool ) return tool->Help();
+    }
+
+    // either 'bamtools help' or unrecognized argument after 'help'
+    cerr << endl;
+    cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
+    cerr << endl;
+    cerr << "Available bamtools commands:" << endl;
+    cerr << "\tconvert   Converts between BAM and a number of other formats" << endl;
+    cerr << "\tcount     Prints number of alignments in BAM file" << endl;
+    cerr << "\tcoverage  Prints coverage statistics from the input BAM file" << endl;
+    cerr << "\tfilter    Filters BAM file(s) by user-specified criteria" << endl;
+    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    Grab a random subset of alignments" << endl;
+    cerr << "\tsort      Sorts the BAM file according to some criteria" << endl;
+    cerr << "\tstats     Prints general alignment statistics" << endl;
+    cerr << endl;
+    cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
+    cerr << endl;
+    return 0;
+}
+
+// ------------------------------------------
+// Print version info
+int Version(void) {
+    cout << endl;
+    cout << "bamtools v0.8.xx" << 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 << endl;
+    return 0;
+}
+
+// ------------------------------------------
+// toolkit entry point
+int main(int argc, char* argv[]) {
+
+    // just 'bamtools'
+    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); 
+    
+    // 'bamtools version', 'bamtools --version', or 'bamtools -v'
+    if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version(); 
+        
+    // determine desired sub-tool
+    AbstractTool* tool(0);
+    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] == 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); 
+}