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intergration correctio

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chhylp123
2022-03-01 20:25:53 -05:00
parent 0ce5a7ba5b
commit 9c6a3607d1
8 changed files with 1263 additions and 77 deletions
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Process_Read.cpp
+132 -4
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@@ -7,6 +7,7 @@
#include "Correct.h"
#include "kalloc.h"
#define UL_FLANK 512
uint8_t seq_nt6_table[256] = {
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
@@ -749,7 +750,7 @@ void destory_Debug_reads(Debug_reads* x)
void init_all_ul_t(all_ul_t *x, All_reads *hR) {
memset(x, 0, sizeof(*x));
x->hR = hR; x->mm = 0x7fffffff;
x->hR = hR; x->mm = 0x40000000;
init_aux_table();
}
void destory_all_ul_t(all_ul_t *x) {
@@ -761,6 +762,7 @@ void destory_all_ul_t(all_ul_t *x) {
for (i = 0; i < x->nid.n; i++) free(x->nid.a[i].a);
free(x->nid.a);
free(x->ridx.idx.a); free(x->ridx.occ.a);
}
void ha_encode_base(uint8_t* dest, char* src, uint64_t src_l, N_t *nn, uint64_t nn_offset)
@@ -843,7 +845,7 @@ void push_subblock_original_bases(char* str, all_ul_t *x, ul_vec_t *p, uint32_t
}
}
void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on) {
void append_ul_t_compress_ovlp(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on) {
int64_t i, mine, maxs, ovlp, end;
ul_vec_t *p = NULL;
nid_t *np = NULL;
@@ -926,6 +928,132 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
}
}
void debug_append_ul_t(ul_ov_t *o, int64_t on, ul_vec_t *p)
{
int64_t k, l = 0;
uint32_t sp = (uint32_t)-1, ep = (uint32_t)-1, qss, qee, m;
for (k = on-1; k >= 0; k--) {
if(sp == (uint32_t)-1 || o[k].qe <= sp) {
if(sp != (uint32_t)-1) l += ep - sp;
if(sp == (uint32_t)-1) qss = o[k].qe, qee = p->rlen;
else qss = o[k].qe, qee = sp;
if(qee > qss) {
for (m = 0; m < p->bb.n; m++) {
if(qss == (p->bb.a[m].qs+((p->bb.a[m].hid>>15)&(0x7fffU))) &&
qee == (p->bb.a[m].qe-(p->bb.a[m].hid&(0x7fffU)))) {
break;
}
}
if(m >= p->bb.n) fprintf(stderr, "ERROR\n");
}
sp = o[k].qs;
ep = o[k].qe;
} else {
sp = MIN(sp, o[k].qs);
}
}
if(sp != (uint32_t)-1) l += ep - sp;
if(sp == (uint32_t)-1) qss = 0, qee = p->rlen;
else qss = 0, qee = sp;
if(qee > qss) {
for (m = 0; m < p->bb.n; m++) {
if(qss == (p->bb.a[m].qs+((p->bb.a[m].hid>>15)&(0x7fffU))) &&
qee == (p->bb.a[m].qe-(p->bb.a[m].hid&(0x7fffU)))) {
break;
}
}
if(m >= p->bb.n) fprintf(stderr, "ERROR\n");
}
}
void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on) {
int64_t i, mine, maxs, ovlp, st, et;
uint32_t o_l, o_r;
ul_vec_t *p = NULL;
nid_t *np = NULL;
ul_ov_t *z = NULL;
uc_block_t *b = NULL;
if(id) {
kv_pushp(nid_t, x->nid, &np);
np->n = id_l; MALLOC(np->a, np->n+1); memcpy(np->a, id, id_l); np->a[id_l] = '\0';
}
if(str) {
if(rid == NULL) {
kv_pushp(ul_vec_t, *x, &p);
memset(p, 0, sizeof(*p));
} else {
if((*rid) >= x->m) kv_resize(ul_vec_t, *x, (*rid) + 1);
if((*rid) >= x->n) {
memset(x->a+x->n, 0, sizeof(*p)*((*rid) + 1 - x->n));
x->n = (*rid) + 1;
}
p = &(x->a[(*rid)]);
}
p->bb.n = p->N_site.n = p->r_base.n = 0;
p->rlen = str_l;
if(o == NULL || on == 0) on = 0;
for (i = on-1, st = et = str_l; i >= 0; i--) {
z = &(o[i]);
mine = MIN(et, ((int64_t)z->qe)); maxs = MAX(st, ((int64_t)z->qs));
ovlp = mine - maxs;
if(ovlp < 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = x->mm; b->rev = 0;
b->qe = maxs; b->qs = b->qe + ovlp;
o_l = (b->qs >= UL_FLANK?UL_FLANK:b->qs);
o_r = ((str_l-b->qe)>=UL_FLANK?UL_FLANK:(str_l-b->qe));
b->hid |= (o_l<<15); b->hid |= o_r;
b->qs -= o_l; b->qe += o_r;
b->ts = p->r_base.n; b->te = b->ts + B4L(b->qe-b->qs);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
ha_encode_base(p->r_base.a+b->ts, str+b->qs, b->qe-b->qs, &(p->N_site), b->qs);
}
///push ovlp bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = z->tn; b->rev = z->rev;
b->qs = z->qs; b->qe = z->qe;
b->ts = z->ts; b->te = z->te;
st = MIN(st, z->qs);
}
if(st > 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = x->mm; b->rev = 0;
b->qe = st; b->qs = 0;
o_l = (b->qs >= UL_FLANK?UL_FLANK:b->qs);
o_r = ((str_l-b->qe)>=UL_FLANK?UL_FLANK:(str_l-b->qe));
b->hid |= (o_l<<15); b->hid |= o_r;
b->qs -= o_l; b->qe += o_r;
b->ts = p->r_base.n; b->te = b->ts + B4L(b->qe-b->qs);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
ha_encode_base(p->r_base.a+b->ts, str+b->qs, b->qe-b->qs, &(p->N_site), b->qs);
// push_subblock_original_bases(str, x, p, end, str_l, 321);//for debug
}
// debug_append_ul_t(o, on, p);
// char *sst = NULL; CALLOC(sst, str_l);//for debug
// retrieve_ul_t(NULL, sst, x, rid?*rid:x->n-1, 0, 0, -1);
// if(memcmp(sst, str, str_l)) {
// fprintf(stderr, "ap-Wrong read, id: %ld, [%d, %ld)\n", (int64_t)(rid?*rid:x->n-1), 0, str_l);
// for (i = 0; i < str_l; i++) {
// if(sst[i] != str[i]) fprintf(stderr, "[%ld] input:%c, decompress:%c\n", i, str[i], sst[i]);
// }
// }
// free(sst);
}
}
void retrieve_ul_t(UC_Read* i_r, char *i_s, all_ul_t *ref, uint64_t ID, uint8_t strand, int64_t s, int64_t l) {
ul_vec_t *p = &(ref->a[ID]);
if(l < 0) l = p->rlen;
@@ -956,7 +1084,7 @@ void retrieve_ul_t(UC_Read* i_r, char *i_s, all_ul_t *ref, uint64_t ID, uint8_t
sep = MIN(e, b->qe) - b->qs;
sl = sep - ssp;
if(b->hid == ref->mm){///original bases
if(b->hid&ref->mm){///original bases
offset = ssp&3;
begLen = 4-offset;
if(begLen > sl) begLen = sl;
@@ -1012,7 +1140,7 @@ void retrieve_ul_t(UC_Read* i_r, char *i_s, all_ul_t *ref, uint64_t ID, uint8_t
sl = sep - ssp;
///[ssp, sep)
if(b->hid == ref->mm){///original bases
if(b->hid&ref->mm){///original bases
begLen = sep&3;
offset = 4 - begLen;
if(begLen > sl) begLen = sl;