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r573: prepare to generalize index

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Heng Li
2017-11-11 19:54:06 -05:00
parent 3b518271ee
commit 2f463b1db0
6 changed files with 38 additions and 35 deletions
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8
align.c
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@@ -222,7 +222,7 @@ static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x
static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *const qseq0[2], mm128_t *a, int32_t *r, int32_t *q)
{
if (mi->is_hpc) {
if (mi->flag & MM_I_HPC) {
const uint8_t *qseq = qseq0[a->x>>63];
int i, c;
*q = (int32_t)a->y;
@@ -351,14 +351,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
int32_t rs1, qs1, re1, qe1;
int8_t mat[25];
if (is_sr) assert(!mi->is_hpc); // HPC won't work with SR because with HPC we can't easily tell if there is a gap
if (is_sr) assert(!(mi->flag & MM_I_HPC)); // HPC won't work with SR because with HPC we can't easily tell if there is a gap
r2->cnt = 0;
if (r->cnt == 0) return;
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
bw = (int)(opt->bw * 1.5 + 1.);
if (is_sr && !mi->is_hpc) {
if (is_sr && !(mi->flag & MM_I_HPC)) {
mm_max_stretch(opt, r, a, &as1, &cnt1);
rs = (int32_t)a[as1].x + 1 - (int32_t)(a[as1].y>>32&0xff);
qs = (int32_t)a[as1].y + 1 - (int32_t)(a[as1].y>>32&0xff);
@@ -470,7 +470,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
for (i = is_sr? cnt1 - 1 : 1; i < cnt1; ++i) { // gap filling
if ((a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) && i != cnt1 - 1) continue;
if (is_sr && !mi->is_hpc) {
if (is_sr && !(mi->flag & MM_I_HPC)) {
re = (int32_t)a[as1 + i].x + 1;
qe = (int32_t)a[as1 + i].y + 1;
} else mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);