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r792: fixed -Wextra warnings and resolved #184

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This commit is contained in:
Heng Li
2018-06-19 15:26:58 -04:00
parent 408e098859
commit 7e6e8ca73f
15 changed files with 67 additions and 58 deletions
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index.c
+13 -13
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@@ -45,10 +45,10 @@ mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
void mm_idx_destroy(mm_idx_t *mi)
{
int i;
uint32_t i;
if (mi == 0) return;
if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
for (i = 0; i < 1<<mi->b; ++i) {
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
@@ -82,14 +82,15 @@ const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
void mm_idx_stat(const mm_idx_t *mi)
{
int i, n = 0, n1 = 0;
int n = 0, n1 = 0;
uint32_t i;
uint64_t sum = 0, len = 0;
fprintf(stderr, "[M::%s] kmer size: %d; skip: %d; is_hpc: %d; #seq: %d\n", __func__, mi->k, mi->w, mi->flag&MM_I_HPC, mi->n_seq);
for (i = 0; i < mi->n_seq; ++i)
len += mi->seq[i].len;
for (i = 0; i < 1<<mi->b; ++i)
for (i = 0; i < 1U<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
for (i = 0; i < 1<<mi->b; ++i) {
for (i = 0; i < 1U<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
khint_t k;
if (h == 0) continue;
@@ -172,7 +173,8 @@ int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
static void worker_post(void *g, long i, int tid)
{
int j, start_a, start_p, n, n_keys;
int n, n_keys;
size_t j, start_a, start_p;
idxhash_t *h;
mm_idx_t *mi = (mm_idx_t*)g;
mm_idx_bucket_t *b = &mi->B[i];
@@ -200,7 +202,7 @@ static void worker_post(void *g, long i, int tid)
int absent;
mm128_t *p = &b->a.a[j-1];
itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
assert(absent && j - start_a == n);
assert(absent && j == start_a + n);
if (n == 1) {
kh_key(h, itr) |= 1;
kh_val(h, itr) = p->y;
@@ -216,7 +218,7 @@ static void worker_post(void *g, long i, int tid)
} else ++n;
}
b->h = h;
assert(b->n == start_p);
assert(b->n == (int32_t)start_p);
// deallocate and clear b->a
kfree(0, b->a.a);
@@ -336,7 +338,7 @@ mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini
pipeline_t pl;
if (fp == 0 || mm_bseq_eof(fp)) return 0;
memset(&pl, 0, sizeof(pipeline_t));
pl.mini_batch_size = mini_batch_size < batch_size? mini_batch_size : batch_size;
pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
pl.batch_size = batch_size;
pl.fp = fp;
pl.mi = mm_idx_init(w, k, b, flag);
@@ -413,8 +415,7 @@ mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const cha
void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
{
uint64_t sum_len = 0;
uint32_t x[5];
int i;
uint32_t x[5], i;
x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->flag;
fwrite(MM_IDX_MAGIC, 1, 4, fp);
@@ -454,9 +455,8 @@ void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
mm_idx_t *mm_idx_load(FILE *fp)
{
int i;
char magic[4];
uint32_t x[5];
uint32_t x[5], i;
uint64_t sum_len = 0;
mm_idx_t *mi;