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data/ext/bamtools/src/toolkit/bamtools.cpp

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+// ***************************************************************************
+// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 18 May 2011 (DB)
+// ---------------------------------------------------------------------------
+// Integrates a number of BamTools functionalities into a single executable.
+// ***************************************************************************
+
+#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_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;
+
+// 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 RESOLVE  = "resolve";
+static const string REVERT   = "revert";
+static const string SORT     = "sort";
+static const string SPLIT    = "split";
+static const string STATS    = "stats";
+
+// 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";
+
+// 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 == CONVERT )  return new ConvertTool;
+    if ( arg == COUNT )    return new CountTool;
+    if ( arg == COVERAGE ) return new CoverageTool;
+    if ( arg == FILTER )   return new FilterTool;
+    if ( arg == HEADER )   return new HeaderTool;
+    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;
+
+    // unknown arg
+    return 0;
+}
+
+// print help info
+int Help(int argc, char* argv[]) {
+  
+    // check for 'bamtools help COMMAND' to print tool-specific help message
+    if (argc > 2) {
+        
+	// determine desired sub-tool
+        AbstractTool* tool = CreateTool( argv[2] );
+
+        // if tool known, print its help screen
+        if ( tool ) return tool->Help();
+    }
+
+    // print general BamTools help message
+    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(s)" << 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          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 EXIT_SUCCESS;
+}
+
+// print version info
+int Version(void) {
+
+    stringstream versionStream("");
+    versionStream << BAMTOOLS_VERSION_MAJOR << "."
+                  << 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) 2009-2011 Marth Lab, Biology Dept., Boston College" << endl;
+    cout << endl;
+    return EXIT_SUCCESS;
+}
+
+// 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 ( IsHelp(argv[1]) ) return Help(argc, argv); 
+    
+    // 'bamtools version', 'bamtools --version', or 'bamtools -v'
+    if ( IsVersion(argv[1]) ) return Version(); 
+        
+    // determine desired sub-tool, run if found
+    AbstractTool* tool = CreateTool( argv[1] );
+    if ( tool ) return tool->Run(argc, argv);
+
+    // no tool matched, show help
+    return Help(argc, argv);
+}