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fix filter_short_ulalignments

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chhylp123
2023-07-19 19:11:37 -04:00
parent adeb2c603d
commit 64091a76a5
2 changed files with 36 additions and 8 deletions
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CommandLines.h
+1 -1
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@@ -5,7 +5,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.19.5-r592" #define HA_VERSION "0.19.5-r593"
#define VERBOSE 0 #define VERBOSE 0
inter.cpp
+35 -7
View File
@@ -17891,11 +17891,12 @@ static void filter_short_ulalignments(void *data, long i, int tid) // callback f
a = UL_INF.a[i].bb.a; a_n = UL_INF.a[i].bb.n; a = UL_INF.a[i].bb.a; a_n = UL_INF.a[i].bb.n;
for (k = a_n - 1; k >= 0; k--) { for (k = a_n - 1; k >= 0; k--) {
// if(i == 1126) {
// fprintf(stderr, "[M::%s::id->%ld::rlen->%u] (%ld) utg%.6dl, q::[%u, %u), t::[%u, %u), pidx::%u, aidx::%u, pdis::%u\n",
// __func__, i, UL_INF.a[i].rlen, k, (int32_t)a[k].hid+1, a[k].qs, a[k].qe, a[k].ts, a[k].te, a[k].pidx, a[k].aidx, a[k].pdis);
// }
p = &(a[k]); p = &(a[k]);
// if(i == 338344) {
// fprintf(stderr, "+[M::%s::id->%ld::rlen->%u::glen->%u] (%ld) utg%.6dl, q::[%u, %u), t::[%u, %u), pidx::%u, aidx::%u, pdis::%u, a[k].base::%u, a[k].el::%u, a[k].pchain::%u\n",
// __func__, i, UL_INF.a[i].rlen, ug->u.a[p->hid].len, k, (int32_t)a[k].hid+1, a[k].qs, a[k].qe, a[k].ts, a[k].te, a[k].pidx, a[k].aidx, a[k].pdis,
// a[k].base, a[k].el, a[k].pchain);
// }
if(p->base || (!p->el) || (!p->pchain)) continue; if(p->base || (!p->el) || (!p->pchain)) continue;
if(p->pidx == (uint32_t)-1) { if(p->pidx == (uint32_t)-1) {
if(!ugl_cover_check(p->ts, p->te, &(ug->u.a[p->hid]))) { if(!ugl_cover_check(p->ts, p->te, &(ug->u.a[p->hid]))) {
@@ -17928,9 +17929,32 @@ static void filter_short_ulalignments(void *data, long i, int tid) // callback f
for (k = a_n - 1; k >= 0; k--) { for (k = a_n - 1; k >= 0; k--) {
p = &(a[k]); p = &(a[k]);
if(p->base || (!p->el) || (!p->pchain)) continue; if(p->base || (!p->el) || (!p->pchain)) continue;
// if(i == 1126) { if(p->pidx != (uint32_t)-1) {
// fprintf(stderr, "-[M::%s::id->%ld::rlen->%u] (%ld) utg%.6dl, q::[%u, %u), t::[%u, %u), pidx::%u, aidx::%u, pdis::%u\n", if((a[p->pidx].aidx != ((uint32_t)k)) && (a[p->pidx].aidx == ((uint32_t)-1))) {
// __func__, i, UL_INF.a[i].rlen, k, (int32_t)a[k].hid+1, a[k].qs, a[k].qe, a[k].ts, a[k].te, a[k].pidx, a[k].aidx, a[k].pdis); p->pidx = (uint32_t)-1;
} else {
assert(a[p->pidx].aidx == (uint32_t)k);
assert(a[p->pidx].pchain);
}
}
if(p->aidx != (uint32_t)-1) {
if((a[p->aidx].pidx != (uint32_t)k) && (a[p->aidx].pidx == ((uint32_t)-1))) {
p->aidx = (uint32_t)-1;
} else {
assert(a[p->aidx].pidx == (uint32_t)k);
assert(a[p->aidx].pchain);
}
}
}
for (k = a_n - 1; k >= 0; k--) {
p = &(a[k]);
if(p->base || (!p->el) || (!p->pchain)) continue;
// if(i == 338344) {
// fprintf(stderr, "-[M::%s::id->%ld::rlen->%u::glen->%u] (%ld) utg%.6dl, q::[%u, %u), t::[%u, %u), pidx::%u, aidx::%u, pdis::%u, a[k].base::%u, a[k].el::%u, a[k].pchain::%u\n",
// __func__, i, UL_INF.a[i].rlen, ug->u.a[p->hid].len, k, (int32_t)a[k].hid+1, a[k].qs, a[k].qe, a[k].ts, a[k].te, a[k].pidx, a[k].aidx, a[k].pdis,
// a[k].base, a[k].el, a[k].pchain);
// } // }
if(p->pidx != (uint32_t)-1) { if(p->pidx != (uint32_t)-1) {
// if(!(a[p->pidx].aidx == (uint32_t)k)) { // if(!(a[p->pidx].aidx == (uint32_t)k)) {
@@ -17941,6 +17965,10 @@ static void filter_short_ulalignments(void *data, long i, int tid) // callback f
assert(a[p->pidx].pchain); assert(a[p->pidx].pchain);
} }
if(p->aidx != (uint32_t)-1) { if(p->aidx != (uint32_t)-1) {
// if(a[p->aidx].pidx != (uint32_t)k) {
// fprintf(stderr, "[M::%s::id->%ld] name::%.*s, a_n::%ld, p->aidx::%u, p->pidx::%u, a[p->aidx].pidx::%u\n", __func__, i, (int32_t)UL_INF.nid.a[i].n, UL_INF.nid.a[i].a, a_n,
// p->aidx, p->pidx, a[p->aidx].pidx);
// }
assert(a[p->aidx].pidx == (uint32_t)k); assert(a[p->aidx].pidx == (uint32_t)k);
assert(a[p->aidx].pchain); assert(a[p->aidx].pchain);
} }