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r375: fixed compiling errors by the last change

This commit is contained in:
Heng Li 2013-04-10 11:04:32 -04:00
parent 3d8a8c1e37
commit 47520134e7
3 changed files with 5 additions and 5 deletions
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4
bwase.c
View File

@ -176,7 +176,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
seq_reverse(len, seq, 0); // as we need to do left extension, we have to reverse both query and reference sequences
seq_reverse(rlen, rseq, 0);
ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
if (gscore > 0) tle = gtle, qle = len;
rb = re - tle; rlen = tle;
seq_reverse(len, seq, 0);
@ -192,7 +192,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
rb = *_pos; re = rb + len + SW_BW;
if (re > l_pac) re = l_pac;
rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
if (gscore > 0) tle = gtle, qle = len;
re = rb + tle; rlen = tle;
ksw_global(qle, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension

4
bwtsw2_aux.c
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@ -125,7 +125,7 @@ void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq
for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
lt = j;
score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, p->G, &qle, &tle, 0, 0, 0);
score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, p->G, &qle, &tle, 0, 0, 0);
if (score > p->G) { // extensible
p->G = score;
p->k -= tle;
@ -153,7 +153,7 @@ void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq,
for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
lt = j;
score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0) - 1;
score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, 1, &qle, &tle, 0, 0, 0) - 1;
// if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
if (score >= p->G) {
p->G = score;

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3-r374-beta"
#define PACKAGE_VERSION "0.7.3-r375-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);