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Prevent Clang warnings on abs() and fabs() calls 

In the bwa.c and bwase.c calls, rlen is an int64_t returned from
bns_get_seq() and is the number of reference bases covered by the
alignment; l_query/len is an int and the query length of the alignment;
and the result is an int given to an int parameter of ksw_global[2]().

As even the result is int and as rlen is effectively bounded by the
maximum length of a reference sequence, we maintain the status quo in
this code and simply cast rlen to int to silence Clang's "use llabs()"
(llabs() would not be a great answer given an int64_t anyway).

The bwtsw2_pair.c call needs to remain fabs() so both divisions are
done in floating point; cast to double to prevent Clang suggesting
changing the call to integer abs().
This commit is contained in:
John Marshall 2017-06-26 10:45:13 +01:00
parent 6a5caf764f
commit ab3a92bc73
3 changed files with 6 additions and 4 deletions
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4
bwa.c
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@ -144,9 +144,9 @@ uint32_t *bwa_gen_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins,
max_del = (int)((double)(((l_query+1)>>1) * mat[0] - o_del) / e_del + 1.);
max_gap = max_ins > max_del? max_ins : max_del;
max_gap = max_gap > 1? max_gap : 1;
w = (max_gap + abs(rlen - l_query) + 1) >> 1;
w = (max_gap + abs((int)rlen - l_query) + 1) >> 1;
w = w < w_? w : w_;
min_w = abs(rlen - l_query) + 3;
min_w = abs((int)rlen - l_query) + 3;
w = w > min_w? w : min_w;
// NW alignment
if (bwa_verbose >= 4) {

4
bwase.c
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@ -173,13 +173,15 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
ubyte_t *rseq;
int64_t k, rb, re, rlen;
int8_t mat[25];
int w;
bwa_fill_scmat(1, 3, mat);
rb = *_rb; re = rb + len + ref_shift;
assert(re <= l_pac);
rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
assert(re - rb == rlen);
ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32);
w = abs((int)rlen - len) * 1.5;
ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > w? SW_BW : w, n_cigar, &cigar32);
assert(*n_cigar > 0);
if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; // change endding ins to soft clipping
if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 3; // change beginning ins to soft clipping

2
bwtsw2_pair.c
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@ -236,7 +236,7 @@ void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, b
double diff;
G[0] = hits[i]->hits[0].G + a[1].G;
G[1] = hits[i+1]->hits[0].G + a[0].G;
diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.);
diff = fabs((double)(G[0] - G[1])) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.);
if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0;
}
if (a[0].G == 0 || a[1].G == 0) { // one proper pair only