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Fix warnings about types passed to abs() functions #68

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Fix warnings about types passed to abs() functions #68

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1ca0485
Fix warnings about correct abs() functions.
leecbaker Jun 9, 2016
3e7102f
Fix warnings about abs() functions on mac
leecbaker Jun 10, 2016
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5 changes: 3 additions & 2 deletions bwa.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
#include <stdio.h>
#include <zlib.h>
#include <assert.h>
#include <inttypes.h>
#include "bntseq.h"
#include "bwa.h"
#include "ksw.h"
Expand Down Expand Up @@ -144,9 +145,9 @@ 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 + llabs(rlen - l_query) + 1) >> 1;
w = w < w_? w : w_;
min_w = abs(rlen - l_query) + 3;
min_w = llabs(rlen - l_query) + 3;
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But w and min_w are ints…

w = w > min_w? w : min_w;
// NW alignment
if (bwa_verbose >= 4) {
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2 changes: 1 addition & 1 deletion bwase.c
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Expand Up @@ -179,7 +179,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
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);
ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > llabs(rlen - len) * 1.5? SW_BW : llabs(rlen - len) * 1.5, 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
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2 changes: 1 addition & 1 deletion bwtsw2_pair.c
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Expand Up @@ -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 = abs(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
Expand Down