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smaller memory requirement

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chhylp123
2022-05-12 16:15:58 -04:00
parent dd8888aa90
commit a2198891e7
8 changed files with 1345 additions and 2581 deletions
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inter.cpp
+19 -24
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@@ -2295,9 +2295,9 @@ uint32_t overlap_statistics(overlap_region_alloc* olist, ma_ug_t *ug, int64_t *t
**/
if(tt){
uint32_t z;
for (z = 0; z < olist->list[k].w_list_length; z++) {
if(olist->list[k].w_list[z].y_end != -1) {
if(tt) *tt += olist->list[k].w_list[z].x_end+1-olist->list[k].w_list[z].x_start;
for (z = 0; z < olist->list[k].w_list.n; z++) {
if(olist->list[k].w_list.a[z].y_end != -1) {
if(tt) *tt += olist->list[k].w_list.a[z].x_end+1-olist->list[k].w_list.a[z].x_start;
}
}
}
@@ -2619,38 +2619,38 @@ double es_win_err(overlap_region* o, int64_t winLen, int64_t s, int64_t e)
os = (o->x_pos_s/winLen)*winLen;
si = (s-os)/winLen; ei = (e-os)/winLen;
for (k = si+1; k <= ei-1; k++) {
tLen += o->w_list[k].x_end+1-o->w_list[k].x_start;
if(o->w_list[k].y_end != -1) {
tErr += o->w_list[k].error;
tLen += o->w_list.a[k].x_end+1-o->w_list.a[k].x_start;
if(o->w_list.a[k].y_end != -1) {
tErr += o->w_list.a[k].error;
} else {
tErr += o->w_list[k].x_end+1-o->w_list[k].x_start;
tErr += o->w_list.a[k].x_end+1-o->w_list.a[k].x_start;
}
}
k = si;
maxS = MAX(s, (int64_t)(o->w_list[k].x_start)); minE = MIN(e, (int64_t)(o->w_list[k].x_end)) + 1;
maxS = MAX(s, (int64_t)(o->w_list.a[k].x_start)); minE = MIN(e, (int64_t)(o->w_list.a[k].x_end)) + 1;
ov = minE > maxS? minE - maxS:0;
if(ov == 0) {
fprintf(stderr, "WARNNING-1, o->w_list_length->%u, o->x_id->%u, s->%ld, e->%ld, w_list_s->%lu, w_list_e->%lu, winLen->%ld, o->x_pos_s->%u, o->x_pos_e->%u, si->%ld, flag->%d\n",
o->w_list_length, o->x_id, s, e, o->w_list[k].x_start, o->w_list[k].x_end, winLen, o->x_pos_s, o->x_pos_e, si, o->w_list[k].y_end);
fprintf(stderr, "WARNNING-1, o->w_list.n->%u, o->x_id->%u, s->%ld, e->%ld, w_list_s->%d, w_list_e->%d, winLen->%ld, o->x_pos_s->%u, o->x_pos_e->%u, si->%ld, flag->%d\n",
(uint32_t)o->w_list.n, o->x_id, s, e, o->w_list.a[k].x_start, o->w_list.a[k].x_end, winLen, o->x_pos_s, o->x_pos_e, si, o->w_list.a[k].y_end);
}
tLen += ov/**o->w_list[k].x_end+1-o->w_list[k].x_start**/;
if(o->w_list[k].y_end != -1) {
tErr += (ov*o->w_list[k].error)/(o->w_list[k].x_end+1-o->w_list[k].x_start);
if(o->w_list.a[k].y_end != -1) {
tErr += (ov*o->w_list.a[k].error)/(o->w_list.a[k].x_end+1-o->w_list.a[k].x_start);
} else {
tErr += ov/**o->w_list[k].x_end+1-o->w_list[k].x_start**/;
}
k = ei;
maxS = MAX(s, (int64_t)(o->w_list[k].x_start)); minE = MIN(e, (int64_t)(o->w_list[k].x_end)) + 1;
maxS = MAX(s, (int64_t)(o->w_list.a[k].x_start)); minE = MIN(e, (int64_t)(o->w_list.a[k].x_end)) + 1;
ov = minE > maxS? minE - maxS:0;
if(ov == 0) {
fprintf(stderr, "WARNNING-2, o->w_list_length->%u, o->x_id->%u, s->%ld, e->%ld, w_list_s->%lu, w_list_e->%lu, winLen->%ld, o->x_pos_s->%u, o->x_pos_e->%u, ei->%ld, flag->%d\n",
o->w_list_length, o->x_id, s, e, o->w_list[k].x_start, o->w_list[k].x_end, winLen, o->x_pos_s, o->x_pos_e, ei, o->w_list[k].y_end);
fprintf(stderr, "WARNNING-2, o->w_list.n->%u, o->x_id->%u, s->%ld, e->%ld, w_list_s->%d, w_list_e->%d, winLen->%ld, o->x_pos_s->%u, o->x_pos_e->%u, ei->%ld, flag->%d\n",
(uint32_t)o->w_list.n, o->x_id, s, e, o->w_list.a[k].x_start, o->w_list.a[k].x_end, winLen, o->x_pos_s, o->x_pos_e, ei, o->w_list.a[k].y_end);
}
tLen += ov/**o->w_list[k].x_end+1-o->w_list[k].x_start**/;
if(o->w_list[k].y_end != -1) {
tErr += (ov*o->w_list[k].error)/(o->w_list[k].x_end+1-o->w_list[k].x_start);
if(o->w_list.a[k].y_end != -1) {
tErr += (ov*o->w_list.a[k].error)/(o->w_list.a[k].x_end+1-o->w_list.a[k].x_start);
} else {
tErr += ov/**o->w_list[k].x_end+1-o->w_list[k].x_start**/;
}
@@ -5135,7 +5135,7 @@ static void worker_for_ul_scall_alignment(void *data, long i, int tid) // callba
b->self_read.seq = s->seq[i]; b->self_read.length = s->len[i]; b->self_read.size = 0;
correct_ul_overlap(&b->olist, s->uu, &b->self_read, &b->correct, &b->ovlp_read, &b->POA_Graph, &b->DAGCon,
&b->cigar1, &b->hap, &b->round2, 0, 1, &fully_cov, &abnormal, s->opt->diff_ec_ul, winLen, km);
&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 1, &fully_cov, &abnormal, s->opt->diff_ec_ul, winLen, km);
// uint64_t k;
// for (k = 0; k < b->olist.length; k++) {
@@ -5171,11 +5171,6 @@ static void worker_for_ul_scall_alignment(void *data, long i, int tid) // callba
//
// if(l1 == 0 && l2 > 0) fprintf(stderr, "[M::%s::%lu::no_match]\n", UL_INF.nid.a[s->id+i].a, s->len[i]);
// fprintf(stderr, "[M::%s::%lu::] l1->%u; l2->%u\n", UL_INF.nid.a[s->id+i].a, s->len[i], l1, l2);
if(km) {
destory_overlap_region_alloc_buf(km, &b->olist, 1);
destory_Correct_dumy_buf(km, &b->correct, 1);
destoryHaplotypeEvdience_buf(km, &b->hap, 1);
}
}
@@ -5203,7 +5198,7 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
b->self_read.seq = s->seq[i]; b->self_read.length = s->len[i]; b->self_read.size = 0;
correct_ul_overlap(&b->olist, s->uu, &b->self_read, &b->correct, &b->ovlp_read, &b->POA_Graph, &b->DAGCon,
&b->cigar1, &b->hap, &b->round2, 0, 1, &fully_cov, &abnormal, s->opt->diff_ec_ul, winLen, NULL);
&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 1, &fully_cov, &abnormal, s->opt->diff_ec_ul, winLen, NULL);
// uint64_t k;
// for (k = 0; k < b->olist.length; k++) {