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r766: removed useless code

This commit is contained in:
Heng Li 2014-05-13 13:09:29 -04:00
parent 0168f39eeb
commit 061c63f36a
3 changed files with 4 additions and 9 deletions
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2
Makefile
View File

@ -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)

9
bwamem.c
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@ -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;

2
main.c
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@ -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[]);