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correction done

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chhylp123
2022-06-18 22:42:01 -04:00
parent 7cf6d82115
commit a21bc8a336
2 changed files with 509 additions and 98 deletions
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inter.cpp
+31 -18
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@@ -8535,10 +8535,6 @@ static void update_ug_arch_ul(void *data, long i, int tid) // callback for kt_fo
uv = (((uint32_t)(p->hid))<<1)|((uint32_t)(p->rev));
if((uv == v) && (p->aidx != (uint32_t)-1)) {
n = &(UL_INF.a[a[k]>>32].bb.a[p->aidx]);
// if(!((!n->base)&&(n->el)&&(n->pchain)&&(n->pidx==((uint32_t)(a[k]))))) {
// fprintf(stderr, "k::%u, n->base::%u, n->el::%u, n->pchain::%u, n->pidx::%u, p->aidx::%u\n",
// k, n->base, n->el, n->pchain, n->pidx, p->aidx);
// }
assert((!n->base)&&(n->el)&&(n->pchain)&&(n->pidx==((uint32_t)(a[k]))));
uw = (((uint32_t)(n->hid))<<1)|((uint32_t)(n->rev));
if(uw == w) e->ou++;
@@ -8546,6 +8542,10 @@ static void update_ug_arch_ul(void *data, long i, int tid) // callback for kt_fo
if(((uv^1) == v) && (p->pidx != (uint32_t)-1)) {
n = &(UL_INF.a[a[k]>>32].bb.a[p->pidx]);
// if(!((!n->base)&&(n->el)&&(n->pchain)&&(n->aidx==((uint32_t)(a[k]))))) {
// fprintf(stderr, "ulid->%ld, n->base::%u, n->el::%u, n->pchain::%u, n->aidx::%u, ((uint32_t)(a[k]))::%u\n",
// i, n->base, n->el, n->pchain, n->aidx, ((uint32_t)(a[k])));
// }
assert((!n->base)&&(n->el)&&(n->pchain)&&(n->aidx==((uint32_t)(a[k]))));
uw = (((uint32_t)(n->hid))<<1)|((uint32_t)(n->rev)); uw ^= 1;
if(uw == w) e->ou++;
@@ -8558,14 +8558,25 @@ static void filter_short_ulalignments(void *data, long i, int tid) // callback f
const ma_ug_t *ug = (ma_ug_t *)data;
uc_block_t *a = NULL; uc_block_t *p; int64_t k, a_n; uint32_t z, fz, lz, l, bz;
a = UL_INF.a[i].bb.a; a_n = UL_INF.a[i].bb.n;
// if(i == 4) {
// fprintf(stderr, "[M::%s::i->%ld] a_n->%ld\n", __func__, i, a_n);
// }
for (k = a_n - 1; k >= 0; k--) {
p = &(a[k]);
// if(i == 4) {
// fprintf(stderr, "[M::%s::k->%ld] p->ts::%u, p->te::%u, p->pchain::%u, p->pidx::%u, p->aidx::%u\n",
// __func__, k, p->ts, p->te, p->pchain, p->pidx, p->aidx);
// }
if(p->base || (!p->el) || (!p->pchain)) continue;
if((p->pidx == (uint32_t)-1) && (p->aidx == (uint32_t)-1)) {
if(!ugl_cover_check(p->ts, p->te, &(ug->u.a[p->hid]))) p->pchain = 0;
if(p->pidx == (uint32_t)-1) {
if(!ugl_cover_check(p->ts, p->te, &(ug->u.a[p->hid]))) {
p->pchain = 0;
if(p->aidx != (uint32_t)-1) {
a[p->aidx].pidx = a[p->aidx].pdis = (uint32_t)-1; p->aidx = (uint32_t)-1;
}
}
continue;
}
if(p->pidx == (uint32_t)-1) continue;
if(ugl_cover_check(p->ts, p->te, &(ug->u.a[p->hid]))) continue;
for (z = p->pidx; z != (uint32_t)-1; z = a[z].pidx) {
if(ugl_cover_check(a[z].ts, a[z].te, &(ug->u.a[a[z].hid]))) break;
@@ -8585,16 +8596,18 @@ static void filter_short_ulalignments(void *data, long i, int tid) // callback f
}
}
// for (k = a_n - 1; k >= 0; k--) {
// p = &(a[k]);
// if(p->base || (!p->el) || (!p->pchain)) continue;
// if(p->pidx != (uint32_t)-1) {
// assert(a[p->pidx].aidx == (uint32_t)k);
// }
// if(p->aidx != (uint32_t)-1) {
// assert(a[p->aidx].pidx == (uint32_t)k);
// }
// }
for (k = a_n - 1; k >= 0; k--) {
p = &(a[k]);
if(p->base || (!p->el) || (!p->pchain)) continue;
if(p->pidx != (uint32_t)-1) {
assert(a[p->pidx].aidx == (uint32_t)k);
assert(a[p->pidx].pchain);
}
if(p->aidx != (uint32_t)-1) {
assert(a[p->aidx].pidx == (uint32_t)k);
assert(a[p->aidx].pchain);
}
}
}
@@ -10222,7 +10235,7 @@ void clear_all_ul_t(all_ul_t *x)
ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg)
{
fprintf(stderr, "[M::%s::] ==> UL\n", __func__);
fprintf(stderr, "[M::%s::] ==> starting UL\n", __func__);
mg_idxopt_t opt; uldat_t sl;
int32_t cutoff;
char* gfa_name = NULL; MALLOC(gfa_name, strlen(asm_opt.output_file_name)+50);