From 47520134e784a9c3d6661a5de7e74e21a54fdbfb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 10 Apr 2013 11:04:32 -0400 Subject: [PATCH] r375: fixed compiling errors by the last change --- bwase.c | 4 ++-- bwtsw2_aux.c | 4 ++-- main.c | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/bwase.c b/bwase.c index fd06c7d..0d49739 100644 --- a/bwase.c +++ b/bwase.c @@ -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, >le, &gscore, 0); + ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, >le, &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, >le, &gscore, 0); + ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, 0, -1, len<<1, &qle, &tle, >le, &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 diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c index a84d7e0..d26d3fa 100644 --- a/bwtsw2_aux.c +++ b/bwtsw2_aux.c @@ -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; diff --git a/main.c b/main.c index b47c897..8a0542c 100644 --- a/main.c +++ b/main.c @@ -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[]);