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chhylp123
2022-10-04 15:31:23 -04:00
parent 68a74fb16d
commit 8a4d6a5f24
4 changed files with 683 additions and 29 deletions
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Hash_Table.cpp
+262 -1
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@@ -1494,7 +1494,32 @@ inline int32_t comput_sc_ch(const k_mer_hit *ai, const k_mer_hit *aj, double bw_
q_span = ai->cnt&(0xffu);
sc = q_span < dg? q_span : dg;
sc = normal_w(sc, ((int32_t)(ai->cnt>>8)));
if (dd || dg > q_span) {
if (dd || (dg > q_span && dg > 0)) {
double lin_pen, a_pen;
lin_pen = (chn_pen_gap*(double)dd);
a_pen = ((double)(sc))*((((double)dd)/((double)dg))/bw_rate);
if(lin_pen > a_pen) lin_pen = a_pen;
lin_pen += (chn_pen_skip*(double)dg);
sc -= (int32_t)lin_pen;
}
return sc;
}
inline int32_t comput_sc_ff(const k_mer_hit *ai, const k_mer_hit *aj, double bw_rate, double chn_pen_gap, double chn_pen_skip, int64_t sl, int64_t ol)
{
///ai is the suffix of aj
int32_t dq, dr, dd, dg, q_span, sc;
dq = (int64_t)(ai->self_offset) - (int64_t)(aj->self_offset);
if(dq < 0) return INT32_MIN;
dr = (int64_t)(ai->offset) - (int64_t)(aj->offset);
if(dr < 0) return INT32_MIN;
dd = dr > dq? dr - dq : dq - dr;//gap
// if((dd > 16) && (dd > cal_bw(ai, aj, bw_rate, sl, ol))) return INT32_MIN;
dg = dr < dq? dr : dq;//len
q_span = ai->cnt&(0xffu);
sc = q_span < dg? q_span : dg;
sc = normal_w(sc, ((int32_t)(ai->cnt>>8)));
if (dd || (dg > q_span && dg > 0)) {
double lin_pen, a_pen;
lin_pen = (chn_pen_gap*(double)dd);
a_pen = ((double)(sc))*((((double)dd)/((double)dg))/bw_rate);
@@ -1816,6 +1841,178 @@ uint64_t lchain_qdp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, o
}
#define rev_khit(an, xl, yl) do { \
(an).self_offset = (xl)-1-((an).self_offset+1-((an).cnt&((uint32_t)(0xffu)))); \
(an).offset = (yl)-1-((an).offset+1-((an).cnt&((uint32_t)(0xffu))));\
} while (0)
///it is unpossibale that (left_fix == 0 && right_fix == 0)
uint64_t lchain_qdp_fix(k_mer_hit* a, int64_t a_n, Chain_Data* dp, int64_t max_skip,
int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip,
double bw_rate, int64_t xl, int64_t yl, int64_t quick_check,
int64_t left_fix, int64_t right_fix)
{
int64_t *p, *t, max_f, n_skip, st, max_j, end_j, sc, msc, msc_i, bw, max_ii, ovl, movl;
int32_t *f, max, tmp; int64_t i, j, ret, cL = 0, must_p = 1, is_reorder = 0; k_mer_hit z;
resize_Chain_Data(dp, a_n, NULL);
t = dp->tmp; f = dp->score; p = dp->pre;
bw = ((xl < yl)?xl:yl); bw *= bw_rate;
msc = msc_i = -1; movl = INT32_MAX;
if(quick_check) {
ret = lchain_qcheck(a, a_n, dp, bw_rate);
if (ret > 0) {
a_n = ret; msc_i = a_n-1; msc = f[msc_i];
goto skip_ldp;
}
}
memset(t, 0, (a_n*sizeof((*t))));
if((right_fix) && (!left_fix)) {
// fprintf(stderr, "\n[M::%s::] a_n::%ld\n", __func__, a_n);
// for (i = 0; i < a_n; ++i) {
// fprintf(stderr, "+[M::%s::] x::[%u, %u), y::[%u, %u)\n", __func__,
// a[i].self_offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].self_offset+1,
// a[i].offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].offset+1);
// }
n_skip = a_n>>1;
for (i=0; i<n_skip; ++i) {
z = a[i]; a[i] = a[a_n-i-1]; a[a_n-i-1] = z;
rev_khit(a[i], xl, yl); rev_khit(a[a_n-i-1], xl, yl);
}
if(a_n&1) rev_khit(a[i], xl, yl);
// for (i = 0; i < a_n; ++i) {
// fprintf(stderr, "-[M::%s::] x::[%u, %u), y::[%u, %u)\n", __func__,
// a[i].self_offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].self_offset+1,
// a[i].offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].offset+1);
// }
is_reorder = 1;
}
if((!right_fix) && (!left_fix)) must_p = 0;
for (i = st = 0, max_ii = -1; i < a_n; ++i) {
max_f = a[i].cnt&(0xffu); if(must_p) max_f = INT32_MIN;
n_skip = 0; max_j = end_j = -1;
if ((i-st) > max_iter) st = i-max_iter;
// if(a[0].self_offset == 171728) {
// fprintf(stderr, "i::%ld[M::%s::] x::[%u, %u), y::[%u, %u)\n", i, __func__,
// a[i].self_offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].self_offset+1,
// a[i].offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].offset+1);
// }
for (j = i - 1; j >= 0; --j) {
sc = comput_sc_ff(&a[i], &a[j], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
// if(a[0].self_offset == 171728) {
// fprintf(stderr, "j::%ld[M::%s::sc->%ld] x::[%u, %u), y::[%u, %u)\n", j, __func__, sc,
// a[j].self_offset+1-(a[j].cnt&((uint32_t)(0xffu))), a[j].self_offset+1,
// a[j].offset+1-(a[j].cnt&((uint32_t)(0xffu))), a[j].offset+1);
// }
if (sc == INT32_MIN) continue;
sc += f[j];
if (sc > max_f) {
max_f = sc, max_j = j;
if (n_skip > 0) --n_skip;
} else if (t[j] == (int32_t)i) {
if ((++n_skip) > max_skip) {
if((max_j != -1) || (must_p == 0)) break;
}
}
if (p[j] >= 0) t[p[j]] = i;
///put it here will allow at least one prefix no matter max_dis
///this is special for gap filling, not for chaining
if (a[i].self_offset > (max_dis + a[j].self_offset)) {
if((max_j != -1)) break;
}
if (j < st) {
if((max_j != -1) || (must_p == 0)) break;
}
}
end_j = j;
if (max_ii < 0 || ((int64_t)a[i].self_offset) - ((int64_t)a[max_ii].self_offset) > max_dis) {
max = INT32_MIN; max_ii = -1;
for (j = i - 1; (j >= st) && ((((int64_t)a[i].self_offset)-((int64_t)a[j].self_offset))<=max_dis); --j) {
if (max < f[j]) {
max = f[j], max_ii = j;
}
}
}
if (max_ii >= 0 && max_ii < end_j) {///just have a try with a[i]<->a[max_ii]
tmp = comput_sc_ff(&a[i], &a[max_ii], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
if (tmp != INT32_MIN && max_f < tmp + f[max_ii])
max_f = tmp + f[max_ii], max_j = max_ii;
}
if(max_j == -1) {
f[i] = 0; p[i] = max_j;
} else {
f[i] = max_f; p[i] = max_j;
}
if ((max_ii < 0) || (((((int64_t)a[i].self_offset)-((int64_t)a[max_ii].self_offset))<=max_dis) && (f[max_ii]<f[i]))) {
max_ii = i;
}
// if(a[0].self_offset == 171728) {
// fprintf(stderr, "i::%ld[M::%s::] f::%d, p::%ld\n", i, __func__, f[i], p[i]);
// }
if(f[i] >= msc) {
ovl = get_chainLen(a[i].self_offset, a[i].self_offset, xl, a[i].offset, a[i].offset, yl);
if(f[i] > msc || ovl < movl) {
msc = f[i]; msc_i = i; movl = ovl;
}
}
}
skip_ldp:
if(right_fix && left_fix) msc_i = a_n-1;
///a[] has been sorted by self_offset
i = msc_i; cL = 0;
while (i >= 0) {
t[cL++] = i; msc_i = i; i = p[i];
}
// if((right_fix) && (!left_fix)) {
// fprintf(stderr, "[M::%s::] cL::%ld\n", __func__, cL);
// }
if(is_reorder) {
n_skip = a_n>>1;
for (i=0; i<n_skip; ++i) {
z = a[i]; a[i] = a[a_n-i-1]; a[a_n-i-1] = z;
rev_khit(a[i], xl, yl); rev_khit(a[a_n-i-1], xl, yl);
}
if(a_n&1) rev_khit(a[i], xl, yl);
for (i = 0; i < cL; i++) {
t[i] = a_n - t[i] - 1;
// fprintf(stderr, ">[M::%s::] t[%ld]::%ld\n", __func__, i, t[i]);
}
// for (i = 0; i < a_n; ++i) {
// fprintf(stderr, ">[M::%s::] x::[%u, %u), y::[%u, %u)\n", __func__,
// a[i].self_offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].self_offset+1,
// a[i].offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].offset+1);
// }
} else {
n_skip = cL>>1;
for (i = 0; i < n_skip; i++) {
msc_i = t[i]; t[i] = t[cL-i-1]; t[cL-i-1] = msc_i;
}
}
// if(cL != a_n) {
// fprintf(stderr, "\n[M::%s::] a_n::%ld, left_fix::%ld, right_fix::%ld\n", __func__, a_n, left_fix, right_fix);
// for (i = 0; i < a_n; ++i) {
// fprintf(stderr, "+[M::%s::] x::[%u, %u), y::[%u, %u)\n", __func__,
// a[i].self_offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].self_offset+1,
// a[i].offset+1-(a[i].cnt&((uint32_t)(0xffu))), a[i].offset+1);
// }
// for (i = 0; i < cL; i++) {
// fprintf(stderr, ">[M::%s::] t[%ld]::%ld\n", __func__, i, t[i]);
// }
// }
return cL;
}
uint64_t lchain_refine(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp,
int64_t max_skip, int64_t max_iter, int64_t max_dis, int64_t long_gap)
{
@@ -1905,6 +2102,70 @@ uint64_t lchain_refine(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp
return cL;
}
uint64_t lchain_simple(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp,
int64_t max_skip, int64_t max_iter)
{
if(a_n <= 0) return 0;
int64_t *p, *t, max_f, n_skip, st, max_j, sc, msc, msc_i;
int32_t *f; int64_t i, j, cL = 0;
resize_Chain_Data(dp, a_n, NULL);
t = dp->tmp; f = dp->score; p = dp->pre; msc = msc_i = -1;
for (i=1, f[0]=a[0].cnt, p[0]=-1, msc_i=a_n-1; i<a_n; i++) {
j = i-1;
if((a[i].self_offset > a[j].self_offset)&&(a[i].offset > a[j].offset)) {
p[i] = j; f[i] = f[j]+a[i].cnt;
} else {
break;
}
}
if(i >= a_n) goto ss_kip;
memset(t, 0, (a_n*sizeof((*t))));
f[0]=a[0].cnt; p[0]=-1; msc = f[0]; msc_i = 0;
for (i = 1, st = 0; i < a_n; ++i) {
max_f = INT32_MIN; n_skip = 0; max_j = -1;
if ((i-st) > max_iter) st = i-max_iter;
///[st, i-2]
for (j=i-1; j >= st; --j) {
if((a[i].self_offset > a[j].self_offset)&&(a[i].offset > a[j].offset)) {
sc = f[j]+a[i].cnt;
if (sc > max_f) {
max_f = sc, max_j = j;
if (n_skip > 0) --n_skip;
} else if (t[j] == (int32_t)i) {
if (++n_skip > max_skip)
break;
}
if (p[j] >= 0) t[p[j]] = i;
}
}
f[i] = max_f; p[i] = max_j;
if(f[i] > msc) {
msc = f[i]; msc_i = i;
}
}
ss_kip:
///a[] has been sorted by self_offset
i = msc_i;
cL = 0;
while (i >= 0) {
t[cL++] = i; i = p[i];
}
n_skip = cL>>1;
for (i = 0; i < n_skip; i++) {
msc_i = t[i]; t[i] = t[cL-i-1]; t[cL-i-1] = msc_i;
}
if(des) {
for (i = 0; i < cL; i++) des[i] = a[t[i]];
}
return cL;
}
inline int64_t hit_long_gap(k_mer_hit *a, k_mer_hit *b, int64_t max_lgap, double small_bw_rate, int64_t min_small_bw)
{
int64_t dq, dr, dd, dm;