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an alternative strategy to fix for HPC 

it makes the result better, but still not quite right.
This commit is contained in:
Heng Li 2017-06-24 09:26:24 -04:00
parent 6088dc11ff
commit 2d8fda9586
2 changed files with 31 additions and 4 deletions
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33
align.c
View File

@ -81,6 +81,28 @@ static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) //
}
}
static inline void mm_adjust_minier(const mm_idx_t *mi, uint8_t *qseq0[2], uint8_t *tseq0, mm128_t *a, int32_t *r, int32_t *q)
{
if (mi->is_hpc && 1) {
int span, rev, i, r0, c;
rev = a->x >> 63;
*q = (int32_t)a->y;
for (i = *q - 1, c = qseq0[rev][*q]; i > 0; --i)
if (qseq0[rev][i] != c) break;
*q = i + 1;
span = a->y >> 32;
*r = (int32_t)a->x;
r0 = *r + 1 >= 256? *r + 1 - 256 : 0;
mm_idx_getseq(mi, a->x<<1>>33, r0, *r + 1, tseq0);
for (i = *r - 1 - r0, c = tseq0[*r - r0]; i > 0; --i)
if (tseq0[i] != c) break;
*r = i + r0 + 1;
} else {
*r = (int32_t)a->x + 1;
*q = (int32_t)a->y + 1;
}
}
static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
{
int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63;
@ -93,10 +115,16 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
ksw_gen_simple_mat(5, mat, opt->a, opt->b);
bw = (int)(opt->bw * 1.5 + 1.);
/*
rs = (int32_t)a[r->as].x + 1; // NB: this is the same as r->{rs,re}
re = (int32_t)a[r->as + r->cnt - 1].x + 1;
qs = (int32_t)a[r->as].y + 1; // NB: this is the coordinate on the reverse strand; r->{qs,qe} are on the reverse strand
qe = (int32_t)a[r->as + r->cnt - 1].y + 1;
*/
tseq = (uint8_t*)kmalloc(km, 256);
mm_adjust_minier(mi, qseq0, tseq, &a[r->as], &rs, &qs);
mm_adjust_minier(mi, qseq0, tseq, &a[r->as + r->cnt - 1], &re, &qe);
kfree(km, tseq);
if (qs > 0 && rs > 0) {
l = qs < opt->max_gap? qs : opt->max_gap;
@ -116,7 +144,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re0 = re + l;
} else re0 = re, qe0 = qe;
tseq = (uint8_t*)kmalloc(km, re0 - rs0); // TODO: we can allocate a smaller size
tseq = (uint8_t*)kmalloc(km, re0 - rs0 > 256? re0 - rs0 : 256); // TODO: we can allocate a smaller size
if (qs > 0 && rs > 0) { // left extension
uint32_t ql = qs - qs0, tl = rs - rs0;
@ -140,8 +168,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
assert(qs1 >= 0 && rs1 >= 0);
for (i = 1; i < r->cnt; ++i) { // gap filling
re = (int32_t)a[r->as + i].x + 1;
qe = (int32_t)a[r->as + i].y + 1;
mm_adjust_minier(mi, qseq0, tseq, &a[r->as + i], &re, &qe);
if (i == r->cnt - 1 || qe - qs >= opt->min_ksw_len || re - rs >= opt->min_ksw_len) {
qseq = &qseq0[rev][qs];
mm_idx_getseq(mi, rid, rs, re, tseq);

2
map.c
View File

@ -25,7 +25,7 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->a = 1, opt->b = 1, opt->q = 1, opt->e = 1;
opt->zdrop = 100;
opt->min_ksw_len = 100;
opt->min_ksw_len = 1000;
}
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)