--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtsw2_main.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,93 @@
+#include <unistd.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <math.h>
+#include "bwt.h"
+#include "bwtsw2.h"
+
+int bwa_bwtsw2(int argc, char *argv[])
+{
+	bsw2opt_t *opt;
+	bwt_t *target[2];
+	char buf[1024];
+	bntseq_t *bns;
+	int c;
+
+	opt = bsw2_init_opt();
+	srand48(11);
+	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:y:s:c:N:H:f:")) >= 0) {
+		switch (c) {
+		case 'q': opt->q = atoi(optarg); break;
+		case 'r': opt->r = atoi(optarg); break;
+		case 'a': opt->a = atoi(optarg); break;
+		case 'b': opt->b = atoi(optarg); break;
+		case 'w': opt->bw = atoi(optarg); break;
+		case 'T': opt->t = atoi(optarg); break;
+		case 't': opt->n_threads = atoi(optarg); break;
+		case 'z': opt->z = atoi(optarg); break;
+		case 'y': opt->yita = atof(optarg); break;
+		case 's': opt->is = atoi(optarg); break;
+		case 'm': opt->mask_level = atof(optarg); break;
+		case 'c': opt->coef = atof(optarg); break;
+		case 'N': opt->t_seeds = atoi(optarg); break;
+		case 'H': opt->hard_clip = 1; break;
+        case 'f': freopen(optarg, "w", stdout);
+		}
+	}
+	opt->qr = opt->q + opt->r;
+
+	if (optind + 2 > argc) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   bwa bwasw [options] <target.prefix> <query.fa>\n\n");
+		fprintf(stderr, "Options: -a INT   score for a match [%d]\n", opt->a);
+		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
+		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
+		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
+//		fprintf(stderr, "         -y FLOAT error recurrence coef. (4..16) [%.1f]\n", opt->yita);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -t INT   nmber of threads [%d]\n", opt->n_threads);
+		fprintf(stderr, "         -s INT   size of a chunk of reads [%d]\n", opt->chunk_size);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -w INT   band width [%d]\n", opt->bw);
+		fprintf(stderr, "         -m FLOAT mask level [%.2f]\n", opt->mask_level);
+		fprintf(stderr, "\n");
+		fprintf(stderr, "         -T INT   score threshold divided by a [%d]\n", opt->t);
+		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
+		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
+		fprintf(stderr, "         -N INT   # seeds to trigger reverse alignment [%d]\n", opt->t_seeds);
+		fprintf(stderr, "         -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
+		fprintf(stderr, "         -H       in SAM output, use hard clipping rather than soft\n");
+        fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n");
+		fprintf(stderr, "\n");
+
+		{
+			double c, theta, eps, delta;
+			c = opt->a / log(opt->yita);
+			theta = exp(-opt->b / c) / opt->yita;
+			eps = exp(-opt->q / c);
+			delta = exp(-opt->r / c);
+			fprintf(stderr, "mismatch: %lf, gap_open: %lf, gap_ext: %lf\n\n",
+					theta, eps, delta);
+		}
+		return 1;
+	}
+
+	// adjust opt for opt->a
+	opt->t *= opt->a;
+	opt->coef *= opt->a;
+
+	strcpy(buf, argv[optind]); target[0] = bwt_restore_bwt(strcat(buf, ".bwt"));
+	strcpy(buf, argv[optind]); bwt_restore_sa(strcat(buf, ".sa"), target[0]);
+	strcpy(buf, argv[optind]); target[1] = bwt_restore_bwt(strcat(buf, ".rbwt"));
+	strcpy(buf, argv[optind]); bwt_restore_sa(strcat(buf, ".rsa"), target[1]);
+	bns = bns_restore(argv[optind]);
+
+	bsw2_aln(opt, bns, target, argv[optind+1]);
+
+	bns_destroy(bns);
+	bwt_destroy(target[0]); bwt_destroy(target[1]);
+	free(opt);
+	
+	return 0;
+}