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debug cigar_offset

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chhylp123
2022-09-01 23:16:08 -04:00
parent 7b89478b2e
commit cc16626dfa
7 changed files with 407 additions and 211 deletions
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Hash_Table.cpp
+75 -8
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@@ -78,7 +78,54 @@ int get_fake_gap_shift(Fake_Cigar* x, int index)
return result;
}
int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int64_t yl, int64_t apend_be)
void gen_fake_cigar(Fake_Cigar* z, overlap_region *o, int64_t apend_be, k_mer_hit* hit, int64_t n_hit, int64_t print)
{
int64_t k, dq, dr, dd, pdd; z->length = 0;
if(apend_be == 1) add_fake_cigar(z, o->x_pos_s, 0, NULL);
for (k = 0, pdd = INT32_MAX; k < n_hit; k++) {
dq = hit[k].self_offset - o->x_pos_s;
dr = hit[k].offset - o->y_pos_s;
dd = dr - dq;
if(print) {
fprintf(stderr, "[M::k->%lu] x::%u, y::%u, cnt::%u, dd::%ld, pdd::%ld, z->n::%u\n",
k, hit[k].self_offset, hit[k].offset, hit[k].cnt&(0xffu), dd, pdd, z->length);
}
if(dd != pdd) {
pdd = dd;
add_fake_cigar(z, hit[k].self_offset, pdd, NULL);
}
}
if((apend_be == 1) && (get_fake_gap_pos(z, z->length-1)!=((int64_t)o->x_pos_e))) {
add_fake_cigar(z, o->x_pos_e, get_fake_gap_shift(z, z->length-1), NULL);
}
}
void debug_cigar(Fake_Cigar* z, overlap_region *o, int64_t apend_be, k_mer_hit* hit, uint64_t n_hit)
{
gen_fake_cigar(z, o, apend_be, hit, n_hit, 0);
if(!((z->length==o->f_cigar.length) &&
(!memcmp(z->buffer, o->f_cigar.buffer, sizeof((*(o->f_cigar.buffer)))*o->f_cigar.length)))) {
uint64_t k;
fprintf(stderr, "\n[M::%s] z->n::%u, o->n::%u, rev::%u\n", __func__, z->length, o->f_cigar.length, o->y_pos_strand);
for (k = 0; k < z->length; k++) {
fprintf(stderr, "[z::k->%lu] pos::%d, off::%d\n", k,
get_fake_gap_pos(z, k), get_fake_gap_shift(z, k));
}
for (k = 0; k < o->f_cigar.length; k++) {
fprintf(stderr, "[o::k->%lu] pos::%d, off::%d\n", k,
get_fake_gap_pos(&(o->f_cigar), k), get_fake_gap_shift(&(o->f_cigar), k));
}
gen_fake_cigar(z, o, apend_be, hit, n_hit, 1);
// for (k = 0; k < o->f_cigar.length; k++) {
// fprintf(stderr, "[M::k->%lu] x::%u, y::%u, cnt::%u\n",
// k, hit[k].self_offset, hit[k].offset, hit[k].cnt&(0xffu));
// }
}
}
int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int64_t yl, int64_t apend_be, k_mer_hit* hit, int64_t n_hit)
{
if (ol->length + 1 > ol->size) {
uint64_t sl = ol->size;
@@ -94,8 +141,7 @@ int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int6
((ol->list[ol->length-1].shared_seed == t->shared_seed) &&
(ol->list[ol->length-1].overlapLen <= t->overlapLen))) {
return 0;
}
else {
} else {
ol->length--;
}
}
@@ -126,7 +172,9 @@ int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int6
o->y_pos_strand = t->x_pos_strand;
resize_fake_cigar(&(o->f_cigar), (t->f_cigar.length + 2), NULL);
if(apend_be == 1) add_fake_cigar(&(o->f_cigar), o->x_pos_s, 0, NULL);
if(apend_be == 1) {
add_fake_cigar(&(o->f_cigar), ((t->x_pos_strand)?(xl-t->x_pos_e-1):(t->x_pos_s)), 0, NULL);
}
if (t->x_pos_strand == 1) {
o->x_pos_e = xl-t->x_pos_s-1; o->x_pos_s = xl-t->x_pos_e-1;
@@ -146,7 +194,7 @@ int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int6
dq = t->x_pos_e - t->x_pos_s;
dr = t->y_pos_e - t->y_pos_s;
id = dr - dq;
id = dr - dq;///indel size from left
pdd = INT32_MAX; fn = t->f_cigar.length;
for (i = fn-1; i >= 0; i--) {
@@ -159,10 +207,12 @@ int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int6
}
if((apend_be == 1) && (get_fake_gap_pos(&(o->f_cigar), o->f_cigar.length-1) != ((int64_t)o->x_pos_e))) {
add_fake_cigar(&(o->f_cigar), o->x_pos_e,
get_fake_gap_shift(&(o->f_cigar), o->f_cigar.length-1), NULL);
add_fake_cigar(&(o->f_cigar), o->x_pos_e, get_fake_gap_shift(&(o->f_cigar), o->f_cigar.length-1), NULL);
}
///debug
debug_cigar(&(t->f_cigar), o, apend_be, hit, n_hit);
return 1;
}
@@ -1407,5 +1457,22 @@ uint64_t lchain_dp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, ov
}
res->overlapLen = get_chainLen(a[msc_i].self_offset, a[i].self_offset, xl, a[msc_i].offset, a[i].offset, yl);
for (i = 0; i < cL; i++) des[i] = a[t[cL-i-1]];
if(res->x_pos_strand) {
int64_t hcl = cL>>1; k_mer_hit kp;
for (i = 0; i < hcl; i++) {
j = cL-i-1; kp = des[i]; des[i] = des[j]; des[j] = kp;
des[i].self_offset = xl-des[i].self_offset-1;
des[i].offset = yl-des[i].offset-1;
des[j].self_offset = xl-des[j].self_offset-1;
des[j].offset = yl-des[j].offset-1;
}
if(cL&1) {
des[i].self_offset = xl-des[i].self_offset-1;
des[i].offset = yl-des[i].offset-1;
}
}
return cL;
}