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r770: matching N bases not working properly (#155)

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This commit is contained in:
Heng Li
2018-04-30 19:55:23 -04:00
parent aef7b0744c
commit 734ac379bb
9 changed files with 19 additions and 10 deletions
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align.c
+6 -5
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@@ -6,18 +6,19 @@
#include "mmpriv.h"
#include "ksw2.h"
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc_ambi)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
sc_ambi = sc_ambi > 0? -sc_ambi : sc_ambi;
for (i = 0; i < m - 1; ++i) {
for (j = 0; j < m - 1; ++j)
mat[i * m + j] = i == j? a : b;
mat[i * m + m - 1] = 0;
mat[i * m + m - 1] = sc_ambi;
}
for (j = 0; j < m; ++j)
mat[(m - 1) * m + j] = 0;
mat[(m - 1) * m + j] = sc_ambi;
}
static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
@@ -434,7 +435,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
r2->cnt = 0;
if (r->cnt == 0) return;
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
ksw_gen_simple_mat(5, mat, opt->a, opt->b, opt->sc_ambi);
bw = (int)(opt->bw * 1.5 + 1.);
if (is_sr && !(mi->flag & MM_I_HPC)) {
@@ -652,7 +653,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
if (ql < opt->min_chain_score || ql > opt->max_gap) return 0;
if (tl < opt->min_chain_score || tl > opt->max_gap) return 0;
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
ksw_gen_simple_mat(5, mat, opt->a, opt->b, opt->sc_ambi);
tseq = (uint8_t*)kmalloc(km, tl);
mm_idx_getseq(mi, r1->rid, r1->re, r2->rs, tseq);
qseq = r1->rev? &qseq0[0][r2->qe] : &qseq0[1][qlen - r2->qs];