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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.
This commit is contained in:
John Marshall 2017-04-25 13:51:52 +01:00
parent f123871451
commit af87825525
4 changed files with 6 additions and 6 deletions
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2
bwt_lite.c
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@ -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;

2
bwtgap.c
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@ -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;

6
bwtgap.h
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@ -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;

2
bwtindex.c
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@ -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);