Index: head/biology/bwa/files/patch-bwt_lite.c
===================================================================
--- head/biology/bwa/files/patch-bwt_lite.c
+++ head/biology/bwa/files/patch-bwt_lite.c
@@ -1,11 +0,0 @@
---- bwt_lite.c.orig	2014-05-19 13:11:41 UTC
-+++ bwt_lite.c
-@@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uin
- 	}
- 	{ // generate cnt_table
- 		for (i = 0; i != 256; ++i) {
--			u_int32_t j, x = 0;
-+			uint32_t j, x = 0;
- 			for (j = 0; j != 4; ++j)
- 				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
- 			b->cnt_table[i] = x;
Index: head/biology/bwa/files/patch-bwtgap.h
===================================================================
--- head/biology/bwa/files/patch-bwtgap.h
+++ head/biology/bwa/files/patch-bwtgap.h
@@ -1,15 +0,0 @@
---- bwtgap.h.orig	2014-02-25 21:20:01 UTC
-+++ bwtgap.h
-@@ -5,9 +5,9 @@
- #include "bwtaln.h"
- 
- typedef struct { // recursion stack
--	u_int32_t info; // score<<21 | i
--	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
--	u_int32_t n_ins:16, n_del:16;
-+	uint32_t info; // score<<21 | i
-+	uint32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
-+	uint32_t n_ins:16, n_del:16;
- 	int last_diff_pos;
- 	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
- } gap_entry_t;
Index: head/biology/bwa/files/patch-bwtgap.c
===================================================================
--- head/biology/bwa/files/patch-bwtgap.c
+++ head/biology/bwa/files/patch-bwtgap.c
@@ -1,11 +0,0 @@
---- bwtgap.c.orig	2014-02-25 21:20:01 UTC
-+++ bwtgap.c
-@@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t 
- 		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
- 	}
- 	p = q->stack + q->n_entries;
--	p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
-+	p->info = (uint32_t)score<<21 | i; p->k = k; p->l = l;
- 	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape;
- 	p->n_ins = n_ins; p->n_del = n_del;
- 	p->state = state;