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This commit is contained in:
Heng Li 2017-07-29 11:01:49 -04:00
parent 5e3eecd6d4
commit 120bebc290
1 changed files with 22 additions and 0 deletions
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22
align.c
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@ -355,6 +355,25 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
kfree(km, tseq);
}
static void mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, uint8_t *qseq0[2], const mm_reg1_t *r1, const mm_reg1_t *r2, mm_reg1_t *r_inv, ksw_extz_t *ez)
{
int tlen, qlen;
uint8_t *tseq, *qseq;
int8_t mat[25];
memset(r_inv, 0, sizeof(mm_reg1_t));
if (r1->rid != r2->rid || r1->rev != r2->rev) return;
qlen = r2->qs - r1->qe;
tlen = r2->rs - r1->re;
if (qlen < 0 || qlen > opt->max_gap) return;
if (tlen < 0 || tlen > opt->max_gap) return;
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
tseq = (uint8_t*)kmalloc(km, tlen);
mm_idx_getseq(mi, r1->rid, r1->re, r2->rs, tseq);
qseq = &qseq0[!r1->rev][r1->qe];
mm_align_pair(km, opt, qlen, qseq, tlen, tseq, mat, -1, KSW_EZ_APPROX_MAX, ez);
fprintf(stderr, "%d; (%d,%d); (%d,%d)\n", ez->score, r1->re, r2->rs, r1->qe, r2->qs);
}
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];
@ -382,6 +401,9 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
regs[i + 1] = r2;
++n_regs;
}
if (i > 0 && (regs[i].split&2) && (regs[i-1].split&1)) {
mm_align1_inv(km, opt, mi, qseq0, &regs[i-1], &regs[i], &r2, &ez);
}
}
*n_regs_ = n_regs;
kfree(km, qseq0[0]); kfree(km, qseq0[1]);