--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/bwtio.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,77 @@
+#include <string.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include "bwt.h"
+#include "utils.h"
+
+void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
+{
+	FILE *fp;
+	fp = xopen(fn, "wb");
+	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	fwrite(bwt->bwt, sizeof(bwtint_t), bwt->bwt_size, fp);
+	fclose(fp);
+}
+
+void bwt_dump_sa(const char *fn, const bwt_t *bwt)
+{
+	FILE *fp;
+	fp = xopen(fn, "wb");
+	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
+	fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
+	fclose(fp);
+}
+
+void bwt_restore_sa(const char *fn, bwt_t *bwt)
+{
+	char skipped[256];
+	FILE *fp;
+	bwtint_t primary;
+
+	fp = xopen(fn, "rb");
+	fread(&primary, sizeof(bwtint_t), 1, fp);
+	xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
+	fread(skipped, sizeof(bwtint_t), 4, fp); // skip
+	fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
+	fread(&primary, sizeof(bwtint_t), 1, fp);
+	xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");
+
+	bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
+	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
+	bwt->sa[0] = -1;
+
+	fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
+	fclose(fp);
+}
+
+bwt_t *bwt_restore_bwt(const char *fn)
+{
+	bwt_t *bwt;
+	FILE *fp;
+
+	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
+	fp = xopen(fn, "rb");
+	fseek(fp, 0, SEEK_END);
+	bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
+	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
+	fseek(fp, 0, SEEK_SET);
+	fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
+	fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
+	fread(bwt->bwt, 4, bwt->bwt_size, fp);
+	bwt->seq_len = bwt->L2[4];
+	fclose(fp);
+	bwt_gen_cnt_table(bwt);
+
+	return bwt;
+}
+
+void bwt_destroy(bwt_t *bwt)
+{
+	if (bwt == 0) return;
+	free(bwt->sa); free(bwt->bwt);
+	free(bwt);
+}