From 63bd608235b081171f5521415e4fc2ca7a757b6c Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 3 Mar 2012 10:49:58 -0500 Subject: [PATCH] kill errors and warnings by g++ -Wall --- kseq.h | 4 ++-- ksw.c | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/kseq.h b/kseq.h index 437fefb..9b4b001 100644 --- a/kseq.h +++ b/kseq.h @@ -51,7 +51,7 @@ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ - ks->buf = malloc(__bufsize); \ + ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ @@ -113,7 +113,7 @@ typedef struct __kstring_t { for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ - if (str->m - str->l < i - ks->begin + 1) { \ + if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ diff --git a/ksw.c b/ksw.c index dd8c803..8f5a534 100644 --- a/ksw.c +++ b/ksw.c @@ -63,7 +63,7 @@ kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t size = size > 1? 2 : 1; p = 8 * (3 - size); // # values per __m128i slen = (qlen + p - 1) / p; // segmented length - q = malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory + q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory q->H0 = q->qp + slen * m; q->H1 = q->H0 + slen; @@ -185,7 +185,7 @@ end_loop16: if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append if (n_b == m_b) { m_b = m_b? m_b<<1 : 8; - b = realloc(b, 8 * m_b); + b = (uint64_t*)realloc(b, 8 * m_b); } b[n_b++] = (uint64_t)imax<<32 | i; } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last @@ -287,7 +287,7 @@ end_loop8: if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { if (n_b == m_b) { m_b = m_b? m_b<<1 : 8; - b = realloc(b, 8 * m_b); + b = (uint64_t*)realloc(b, 8 * m_b); } b[n_b++] = (uint64_t)imax<<32 | i; } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last @@ -421,18 +421,18 @@ int main(int argc, char *argv[]) while (kseq_read(ksq) > 0) { kswq_t *q[2] = {0, 0}; kswr_t r; - for (i = 0; i < ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]]; + for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]]; if (!forward_only) { // reverse - if (ksq->seq.m > max_rseq) { + if ((int)ksq->seq.m > max_rseq) { max_rseq = ksq->seq.m; - rseq = realloc(rseq, max_rseq); + rseq = (uint8_t*)realloc(rseq, max_rseq); } - for (i = 0, j = ksq->seq.l - 1; i < ksq->seq.l; ++i, --j) + for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j) rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i]; } gzrewind(fpt); kseq_rewind(kst); while (kseq_read(kst) > 0) { - for (i = 0; i < kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]]; + for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]]; r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]); if (r.score >= minsc) printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2); -- 2.47.3