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drop an unnecessary member from mem_aln_t

This commit is contained in:
Heng Li 2013-03-11 21:35:32 -04:00
parent 8f0d439913
commit 47952b6f3f
2 changed files with 14 additions and 4 deletions
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17
bwamem.c
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@ -714,6 +714,17 @@ void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, cons
#undef is_mapped #undef is_mapped
} }
static inline int get_rlen(int n_cigar, const uint32_t *cigar)
{
int k, l;
for (k = l = 0; k < n_cigar; ++k) {
int op = cigar[k]&0xf;
if (op == 0 || op == 2)
l += cigar[k]>>4;
}
return l;
}
void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m) void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m)
{ {
int i, copy_mate = 0; int i, copy_mate = 0;
@ -751,8 +762,8 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
kputc('\t', str); kputc('\t', str);
kputl(m->pos + 1, str); kputl(m->pos + 1, str);
if (p->rid == m->rid) { if (p->rid == m->rid) {
int64_t p0 = p->r5 < bns->l_pac? p->r5 : (bns->l_pac<<1) - 1 - p->r5; int64_t p0 = p->pos + (p->is_rev? get_rlen(p->n_cigar, p->cigar) : 0);
int64_t p1 = m->r5 < bns->l_pac? m->r5 : (bns->l_pac<<1) - 1 - m->r5; int64_t p1 = m->pos + (m->is_rev? get_rlen(m->n_cigar, m->cigar) : 0);
kputw(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str); kputw(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
} else kputc('0', str); } else kputc('0', str);
} else if (m && p->rid) { } else if (m && p->rid) {
@ -941,7 +952,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
} }
a.rid = bns_pos2rid(bns, pos); a.rid = bns_pos2rid(bns, pos);
a.pos = pos - bns->anns[a.rid].offset; a.pos = pos - bns->anns[a.rid].offset;
a.r5 = rb; a.score = ar->score; a.sub = ar->sub; a.score = ar->score; a.sub = ar->sub;
free(query); free(query);
return a; return a;
} }

1
bwamem.h
View File

@ -74,7 +74,6 @@ typedef struct { // This struct is only used for the convenience of API.
int n_cigar; // number of CIGAR operations int n_cigar; // number of CIGAR operations
uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234 uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234
int64_t r5; // position of the 5'-end of read (for computing TLEN)
int score, sub; int score, sub;
} mem_aln_t; } mem_aln_t;