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roughly right chaining

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chhylp123
2022-03-25 00:29:58 -04:00
parent 60236cd967
commit 95eb2de2b9
5 changed files with 305 additions and 100 deletions
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Process_Read.cpp
+34 -18
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@@ -750,7 +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 = 0x40000000;
x->hR = hR;
init_aux_table();
}
void destory_all_ul_t(all_ul_t *x) {
@@ -835,7 +835,7 @@ void push_subblock_original_bases(char* str, all_ul_t *x, ul_vec_t *p, uint32_t
while (qs < e) {
qe = qs + subLen; if(qe > e) qe = e;
kv_pushp(uc_block_t, p->bb, &b);
b->hid = x->mm; b->rev = 0;
b->hid = (uint32_t)-1; b->rev = 0;
b->qs = qs; b->qe = qe;
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;
@@ -887,7 +887,7 @@ void append_ul_t_compress_ovlp(all_ul_t *x, uint64_t *rid, char* id, int64_t id_
}
if(ovlp < 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = x->mm; b->rev = 0;
b->hid = (uint32_t)-1/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qs = end; b->qe = b->qs - ovlp;
b->ts = p->r_base.n; b->te = b->ts + B4L(-ovlp);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
@@ -896,7 +896,7 @@ void append_ul_t_compress_ovlp(all_ul_t *x, uint64_t *rid, char* id, int64_t id_
///push ovlp bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = z->tn; b->rev = z->rev;
b->hid = (z->tn<<1)>>1; b->rev = z->rev; b->base = 0; b->pchain = 0;
b->qs = z->qs + (ovlp>0?ovlp:0); b->qe = z->qe;
if(z->rev) {
b->ts = z->ts; b->te = z->ts + (b->qe - b->qs);
@@ -909,7 +909,7 @@ void append_ul_t_compress_ovlp(all_ul_t *x, uint64_t *rid, char* id, int64_t id_
if(end < str_l) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = x->mm; b->rev = 0;
b->hid = (uint32_t)-1/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qs = end; b->qe = str_l;
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;
@@ -969,13 +969,13 @@ void debug_append_ul_t(ul_ov_t *o, int64_t on, ul_vec_t *p)
}
}
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;
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, float p_chain_rate) {
int64_t i, mine, maxs, ovlp, st, et, bl = 0, pc = 0;
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;
uc_block_t *b = NULL, tt;
if(id) {
kv_pushp(nid_t, x->nid, &np);
@@ -996,7 +996,7 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
}
p->bb.n = p->N_site.n = p->r_base.n = 0; p->h = 0;
p->bb.n = p->N_site.n = p->r_base.n = 0; p->dd = 0;
p->rlen = str_l;
if(o == NULL || on == 0) on = 0;
@@ -1007,8 +1007,8 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
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;
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qe = maxs; b->qs = b->qe + ovlp; bl += (b->qe-b->qs);
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;
@@ -1020,17 +1020,19 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
///push ovlp bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (z->tn<<1)>>1; b->rev = z->rev;
b->hid = (z->tn<<1)>>1; b->rev = z->rev; b->base = 0;
b->pchain = ((z->tn&((uint32_t)(0x80000000)))?1:0);
b->qs = z->qs; b->qe = z->qe;
b->ts = z->ts; b->te = z->te;
if(b->pchain) pc++;
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;
b->hid = 0/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qe = st; b->qs = 0; bl += (b->qe-b->qs);
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;
@@ -1040,6 +1042,10 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
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
}
if(pc > 0) p->dd = 3;
if((pc == on) && ((str_l-bl) > (str_l*p_chain_rate))) p->dd = 2;
if((pc == on) && (bl == 0)) p->dd = 1;
// 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);
@@ -1050,6 +1056,13 @@ void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str,
// }
// }
// free(sst);
ovlp = p->bb.n>>1;
for (i = 0; i < ovlp; i++) {
tt = p->bb.a[i];
p->bb.a[i] = p->bb.a[p->bb.n-i-1];
p->bb.a[p->bb.n-i-1] = tt;
}
}
}
@@ -1084,7 +1097,7 @@ 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->base/**b->hid&ref->mm**/){///original bases
offset = ssp&3;
begLen = 4-offset;
if(begLen > sl) begLen = sl;
@@ -1140,7 +1153,7 @@ 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->base/**b->hid&ref->mm**/){///original bases
begLen = sep&3;
offset = 4 - begLen;
if(begLen > sl) begLen = sl;
@@ -1350,15 +1363,18 @@ uint64_t retrieve_r_cov_region(const ul_idx_t *ul, uint64_t id, uint8_t strand,
}
}
if(pi) *pi = k;
if(k + 1 >= a_n) return e>=s?e-s:0;
if(k < 0) k = 0;
///note: for unitig coverage, all
for (; k + 1 < a_n; k++) {
// fprintf(stderr, "[M::%s] k:%ld, a_n:%ld\n", __func__, k, a_n);
ts = a[k]>>32; te = a[k+1]>>32; cc = (uint32_t)a[k];
o = (MIN(e, te) > MAX(s, ts))?(MIN(e, te)-MAX(s, ts)):0;
tcc += o*cc;
// fprintf(stderr, ">>k:%ld, s:%lu, e:%lu, ts:%lu, te:%lu, o:%lu, cc:%lu\n", k, s, e, ts, te, o, cc);
if(e>=(a[k]>>32) && e<(a[k+1]>>32)) break;
if(e<=(a[k]>>32)) break;///if may happend when [s, e) does not overlap with the first region
}