makefile tweak

Makefile

@@ -78,6 +78,8 @@ all:
 		echo ""; \
 	done
 
+	echo "- Building main bedtools binary."
+	
 
 .PHONY: all
 

src/bedtools.cpp

+/*****************************************************************************
+  bedtools.cpp
+
+  (c) 2009 - Aaron Quinlan
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include <vector>
+#include <algorithm>    // for swap()
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "bedtools"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+
+int intersect_main(int argc, char* argv[]);
+int coverage_main(int argc, char* argv[]);
+int merge_main(int argc, char* argv[]);
+int substract_main(int argc, char* argv[]);
+
+static int help()
+{
+	cerr << "\n";
+	cerr << "Program: " << PROGRAM_NAME << " (Tools for genome arithmetic.)\n";
+	cerr << "Version: " << "2.15.5" << "\n";
+	cerr << "Author:  " << "Aaron Quinlan (aaronquinlan@gmail.com)" << "\n\n";
+	cerr << "Usage:   bedtools <tool> [options]\n";
+
+	cerr << "\n-Genome arithmetic tools:\n";	
+	cerr << "   intersect     Find overlapping/intersecting intervals b/w two files.\n";
+	cerr << "   coverage      Compute the coverage of one set of intervals over another.\n";
+	cerr << "   merge         Combine overlapping or nearby intervals into a single interval.\n";
+	cerr << "   subtract      Remove intervals based on overlaps b/w two files.\n";
+	
+	cerr << "\n-Format conversion tools:\n";	
+	cerr << "   intersect     Find overlapping/intersecting intervals b/w two files.\n";
+	
+	cerr << "\n-Fasta tools:\n";	
+	cerr << "   intersect     Find overlapping/intersecting intervals b/w two files.\n";
+	
+	cerr << "\n";
+	return 1;
+}
+
+int main(int argc, char *argv[])
+{
+    // make sure the user at least entered a sub_command
+	if (argc < 2) return help();
+
+    // spawn the proper tool.
+	if (strcmp(argv[1], "intersect") == 0)     return intersect_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "coverage") == 0) return coverage_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "merge") == 0)    return merge_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "subtract") == 0) return subtract_main(argc-1, argv+1);
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	return 0;	
+}