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0.20.0-r631

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chhylp123
2024-10-09 17:09:10 -04:00
parent d5f8a8a6c0
commit e8b18560a5
14 changed files with 7710 additions and 356 deletions
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Hash_Table.cpp
+47 -4
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@@ -1512,6 +1512,34 @@ inline int32_t comput_sc_ch(const k_mer_hit *ai, const k_mer_hit *aj, double bw_
return sc;
}
inline int32_t comput_sc_ch_ec(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);
///for long gap
// if(lin_pen > a_pen) lin_pen = a_pen;
if(dd < 4) lin_pen = ((lin_pen > a_pen)?(a_pen):(lin_pen));
else lin_pen = ((lin_pen < a_pen)?(a_pen):(lin_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
@@ -1999,6 +2027,9 @@ int64_t *p, int64_t *t, int32_t *f, int32_t *ii, int64_t *plus, int64_t *msc, in
for (k = 1, l = 0; k <= a_n; k++) {
if(k == a_n || a[k].strand != a[l].strand) {
t[k-1] = 0; ii[k-1] = 0;
// if(a_n && a[0].readID == 3125488) {
// fprintf(stderr, "[M::%s::] ii::[%ld,%ld)(%c), is_srt::%ld, chn_pen_gap::%f, chn_pen_skip::%f, bw_rate::%f\n", __func__, l, k, "+-"[a[l].strand], is_srt, chn_pen_gap, chn_pen_skip, bw_rate);
// }
if(is_srt) {
plus0 = 0; msc0 = msc_i0 = INT32_MIN; movl0 = INT32_MAX; ddt = 0;
@@ -2016,6 +2047,9 @@ int64_t *p, int64_t *t, int32_t *f, int32_t *ii, int64_t *plus, int64_t *msc, in
dr = (int64_t)(ai->offset) - (int64_t)(aj->offset);
if(dr <= 0) break;
dd = dr > dq? dr - dq : dq - dr;//gap
// if(a_n && a[0].readID == 3125488) {
// fprintf(stderr, "%ld,", dd);
// }
if((dd > 16) && (dd > cal_bw(&(a[z]), &(a[z-1]), bw_rate, xl, yl))) break;
dg = dr < dq? dr : dq;//len
q_span = ai->cnt&(0xffu);
@@ -2024,7 +2058,10 @@ int64_t *p, int64_t *t, int32_t *f, int32_t *ii, int64_t *plus, int64_t *msc, in
if (dd || (dg > q_span && dg > 0)) {
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;
///for long gap
// if(lin_pen > a_pen) lin_pen = a_pen;
if(dd < 4) lin_pen = ((lin_pen > a_pen)?(a_pen):(lin_pen));
else lin_pen = ((lin_pen < a_pen)?(a_pen):(lin_pen));
lin_pen += (chn_pen_skip*(double)dg);
sc -= (int32_t)lin_pen;
}
@@ -2036,6 +2073,10 @@ int64_t *p, int64_t *t, int32_t *f, int32_t *ii, int64_t *plus, int64_t *msc, in
if(f[z] < plus0) plus0 = f[z];
}
// if(a_n && a[0].readID == 3125488) {
// fprintf(stderr, "\n");
// fprintf(stderr, "[M::%s::] msc0::%ld, msc_i0::%ld, (%c)\n", __func__, msc0, msc_i0, "+-"[a[l].strand]);
// }
if((z >= k) && (msc_i0 == (k - 1))) {
if((k - l >= 2) && (ddt > 16) && (ddt > cal_bw(&(a[k-1]), &(a[l]), bw_rate, xl, yl))) msc_i0 = INT32_MIN;
if(msc_i0 == (k - 1)) {
@@ -2087,7 +2128,9 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
msc = msc_i = INT32_MIN; movl = INT32_MAX; plus = 0; si = 0; ei = a_n;
memset(t, 0, (a_n*sizeof((*t))));
}
// if(a_n && a[0].readID == 3125488) {
// fprintf(stderr, "[M::%s::] si::%ld, ei::%ld, a_n::%ld\n", __func__, si, ei, a_n);
// }
for (i = st = si, max_ii = -1; i < ei; ++i) {
max_f = a[i].cnt&(0xffu);
n_skip = 0; max_j = end_j = -1;
@@ -2095,7 +2138,7 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
while (a[i].strand != a[st].strand) ++st;
for (j = i - 1; j >= st; --j) {
sc = comput_sc_ch(&a[i], &a[j], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
sc = comput_sc_ch_ec(&a[i], &a[j], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
if (sc == INT32_MIN) continue;
sc += f[j];
if (sc > max_f) {
@@ -2119,7 +2162,7 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
}
if ((max_ii >= 0) && (max_ii < end_j) && (a[i].strand == a[max_ii].strand)) {///just have a try with a[i]<->a[max_ii]
tmp = comput_sc_ch(&a[i], &a[max_ii], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
tmp = comput_sc_ch_ec(&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;
}