From af87825525e3eb203e2dd8a993c02cbfc8c777ad Mon Sep 17 00:00:00 2001
From: John Marshall <John.W.Marshall@glasgow.ac.uk>
Date: Tue, 25 Apr 2017 13:51:52 +0100
Subject: [PATCH] Replace u_int32_t by the more common uint32_t

The u_int32_t type comes from <sys/types.h>, which is often included
as a byproduct of other headers on glibc platforms, but not on FreeBSD
or Alpine Linux.  Use <stdint.h>'s uint32_t instead, which is used
elsewhere in bwa source code.
---
 bwt_lite.c | 2 +-
 bwtgap.c   | 2 +-
 bwtgap.h   | 6 +++---
 bwtindex.c | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bwt_lite.c b/bwt_lite.c
index f7946f5..eb16da6 100644
--- a/bwt_lite.c
+++ b/bwt_lite.c
@@ -48,7 +48,7 @@ bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
 	}
 	{ // 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;
diff --git a/bwtgap.c b/bwtgap.c
index 08bc1f4..7dde443 100644
--- a/bwtgap.c
+++ b/bwtgap.c
@@ -58,7 +58,7 @@ static inline void gap_push(gap_stack_t *stack, int i, bwtint_t k, bwtint_t l, i
 		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; 
diff --git a/bwtgap.h b/bwtgap.h
index 7dd6165..9085b62 100644
--- a/bwtgap.h
+++ b/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;
diff --git a/bwtindex.c b/bwtindex.c
index fb32231..571d087 100644
--- a/bwtindex.c
+++ b/bwtindex.c
@@ -119,7 +119,7 @@ bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is)
 		}
 		rope_destroy(r);
 	}
-	bwt->bwt = (u_int32_t*)calloc(bwt->bwt_size, 4);
+	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
 	for (i = 0; i < bwt->seq_len; ++i)
 		bwt->bwt[i>>4] |= buf[i] << ((15 - (i&15)) << 1);
 	free(buf);