--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/main.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,58 @@
+#include <stdio.h>
+#include <string.h>
+#include "main.h"
+
+#ifndef PACKAGE_VERSION
+#define PACKAGE_VERSION "0.5.7 (r1310)"
+#endif
+
+static int usage()
+{
+	fprintf(stderr, "\n");
+	fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
+	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+	fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
+	fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
+	fprintf(stderr, "Command: index         index sequences in the FASTA format\n");
+	fprintf(stderr, "         aln           gapped/ungapped alignment\n");
+	fprintf(stderr, "         samse         generate alignment (single ended)\n");
+	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
+	fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
+	fprintf(stderr, "\n");
+	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
+	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
+	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
+	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
+	fprintf(stderr, "         pac_rev       generate reverse PAC\n");
+	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
+	fprintf(stderr, "         pac2cspac     convert PAC to color-space PAC\n");
+	fprintf(stderr, "         stdsw         standard SW/NW alignment\n");
+	fprintf(stderr, "\n");
+	return 1;
+}
+
+int main(int argc, char *argv[])
+{
+	if (argc < 2) return usage();
+	if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1);
+	else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1);
+	else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1);
+	else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1);
+	else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1);
+	else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1);
+	else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1);
+	else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1);
+	else {
+		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+		return 1;
+	}
+	return 0;
+}