diff --git a/Makefile b/Makefile index 7f9f975..60c2104 100644 --- a/Makefile +++ b/Makefile @@ -1,6 +1,6 @@ CC= gcc #CC= clang --analyze -CFLAGS= -g -Wall -Wextra -Wno-unused-function -O2 +CFLAGS= -g -Wall -Wno-unused-function -O2 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS AR= ar DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) diff --git a/bwamem.c b/bwamem.c index 582b809..8a9af3b 100644 --- a/bwamem.c +++ b/bwamem.c @@ -973,7 +973,7 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue; if (p->secondary >= 0 && p->score < a->a[p->secondary].score * opt->drop_ratio) continue; q = kv_pushp(mem_aln_t, aa); - *q = mem_reg2aln2(opt, bns, pac, s->l_seq, s->seq, p, s->name); + *q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p); assert(q->rid >= 0); // this should not happen with the new code q->XA = XA? XA[k] : 0; q->flag |= extra_flag; // flag secondary @@ -1038,7 +1038,7 @@ mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntse return regs; } -mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar, const char *name) +mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar) { mem_aln_t a; int i, w2, tmp, qb, qe, NM, score, is_rev, last_sc = -(1<<30), l_MD; @@ -1109,11 +1109,6 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t return a; } -mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar) -{ - return mem_reg2aln2(opt, bns, pac, l_query, query_, ar, 0); -} - typedef struct { const mem_opt_t *opt; const bwt_t *bwt; diff --git a/main.c b/main.c index 9b65696..324dd5d 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.8-r765-dirty" +#define PACKAGE_VERSION "0.7.8-r766-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);