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implemented chain splitting; NOT tested!!!

This commit is contained in:
Heng Li 2017-06-24 22:57:43 -04:00
parent aa5881e7bb
commit ef5dd318ca
3 changed files with 14 additions and 6 deletions
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16
align.c
View File

@ -224,10 +224,10 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
kfree(km, tseq);
}
void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a)
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
{
extern unsigned char seq_nt4_table[256];
int i, reg;
int i, r, n_regs = *n_regs_;
uint8_t *qseq0[2];
ksw_extz_t ez;
@ -239,10 +239,18 @@ void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
qseq0[1][qlen - 1 - i] = qseq0[0][i] < 4? 3 - qseq0[0][i] : 4;
}
for (reg = 0; reg < n_regs; ++reg) {
for (r = 0; r < n_regs; ++r) {
mm_reg1_t r2;
mm_align1(km, opt, mi, qlen, qseq0, &regs[reg], &r2, a, &ez);
mm_align1(km, opt, mi, qlen, qseq0, &regs[r], &r2, a, &ez);
if (r2.cnt > 0) {
regs = (mm_reg1_t*)realloc(regs, n_regs + 1); // this should be very rare
if (r + 1 != n_regs)
memmove(&regs[r + 2], &regs[r + 1], sizeof(mm_reg1_t) * (n_regs - r - 1));
regs[r + 1] = r2;
++n_regs;
}
}
kfree(km, qseq0[0]); kfree(km, qseq0[1]); kfree(km, ez.cigar);
return regs;
}

2
map.c
View File

@ -291,7 +291,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
regs = mm_gen_reg(qlen, n_u, u, a);
*n_regs = n_u;
mm_select_sub(opt->mask_level, opt->pri_ratio, n_regs, regs, b->km);
mm_align_skeleton(b->km, opt, mi, qlen, seq, *n_regs, regs, a);
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a);
// free
kfree(b->km, a);

2
mmpriv.h
View File

@ -16,7 +16,7 @@ uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
void mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int n_regs, mm_reg1_t *regs, mm128_t *a);
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
#ifdef __cplusplus
}