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chhylp123
2022-08-28 02:39:05 -04:00
parent 8b7ca5f0c3
commit 7b89478b2e
10 changed files with 1206 additions and 93 deletions
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inter.cpp
+3 -87
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@@ -20,22 +20,6 @@ KSEQ_INIT(gzFile, gzread)
void ha_get_ul_candidates_interface(ha_abufl_t *ab, int64_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t high_occ, void *km);
#define G_CHAIN_BW 16//128
#define FLANK_M (0x7fffU)
#define P_CHAIN_COV 0.985
#define P_FRAGEMENT_CHAIN_COV 0.20
#define P_FRAGEMENT_PRIMARY_CHAIN_COV 0.70
#define P_FRAGEMENT_PRIMARY_SECOND_COV 0.25
#define P_CHAIN_SCORE 0.6
#define G_CHAIN_GAP 0.1
#define UG_SKIP 5
#define RG_SKIP 25
#define G_CHAIN_TRANS_RATE 0.25
#define G_CHAIN_TRANS_WEIGHT -1
#define G_CHAIN_INDEL 128
#define W_CHN_PEN_GAP 0.1
#define N_GCHAIN_RATE 0.04
#define PRIMARY_UL_CHAIN_MIN 75000
#define MG_SEED_IGNORE (1ULL<<41)
#define MG_SEED_TANDEM (1ULL<<42)
@@ -85,13 +69,6 @@ KRADIX_SORT_INIT(hap_ev_cov_srt, haplotype_evdience, hap_ev_cov_key, member_size
#define uc_block_t_qe_key(x) ((x).qe)
KRADIX_SORT_INIT(uc_block_t_qe_srt, uc_block_t, uc_block_t_qe_key, member_size(uc_block_t, qe));
struct mg_tbuf_s {
void *km;
int frag_gap;
};
typedef struct mg_tbuf_s mg_tbuf_t;
mg_tbuf_t *mg_tbuf_init(void)
{
mg_tbuf_t *b;
@@ -112,15 +89,6 @@ void *mg_tbuf_get_km(mg_tbuf_t *b)
return b->km;
}
typedef struct {
int w, k, bw, max_gap, is_HPC, hap_n, occ_weight, max_gap_pre, max_gc_seq_ext, seed;
int max_lc_skip, max_lc_iter, min_lc_cnt, min_lc_score, max_gc_skip, ref_bonus;
int min_gc_cnt, min_gc_score, sub_diff, best_n;
float chn_pen_gap, mask_level, pri_ratio;
///base-alignment
double bw_thres, diff_ec_ul, diff_ec_ul_low; int max_n_chain, ec_ul_round;
} mg_idxopt_t;
typedef struct {
///off: start idx in mg128_t * a[];
///cnt: how many eles in this chain
@@ -159,58 +127,6 @@ KRADIX_SORT_INIT(mg_pathv_t_v_srt, mg_pathv_t, mg_pathv_t_v_srt_key, member_size
KRADIX_SORT_INIT(mg_pathv_t_d_srt, mg_pathv_t, mg_pathv_t_d_srt_key, member_size(mg_pathv_t, d))
typedef struct {
int32_t off, cnt;
uint32_t v;
int32_t score;
} mg_llchain_t;
typedef struct {
int32_t id, parent;
int32_t off, cnt;
int32_t n_anchor, score;
int32_t qs, qe;
int32_t plen, ps, pe;
int32_t blen, mlen;
float div;
uint32_t hash;
int32_t subsc, n_sub;
uint32_t mapq:8, flt:1, dummy:23;
} mg_gchain_t;
typedef struct {
size_t n,m;
uint64_t *a, tl;
kvec_t(char) cc;
} mg_dbn_t;
typedef struct {
int32_t cnt;
uint32_t v;
int32_t score;
uint32_t qs, qe, ts, te;
} mg_lres_t;
typedef struct {
int32_t n_gc, n_lc;
mg_gchain_t *gc;///g_chain; idx in l_chains
mg_lres_t *lc;///l_chain
uint64_t qid, qlen;
} mg_gres_t;
typedef struct {
size_t n,m;
mg_gres_t *a;
uint64_t total_base;
uint64_t total_pair;
} mg_gres_a;
typedef struct {
FILE *fp;
ul_vec_t u;
uint64_t flag;
} ucr_file_t;
typedef struct { // global data structure for kt_pipeline()
const void *ha_flt_tab;
const ha_pt_t *ha_idx;
@@ -5309,7 +5225,7 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
// if(s->id+i!=41927 && s->id+i!=47072 && s->id+i!=67641 && s->id+i!=90305 && s->id+i!=698342 && s->id+i!=329421) {
// return;
// }
// if(s->id+i!=43) return;
// if(s->id+i!=97) return;
// fprintf(stderr, "\n[M::%s] rid::%ld, len::%lu, name::%.*s\n", __func__, s->id+i, s->len[i],
// (int32_t)UL_INF.nid.a[s->id+i].n, UL_INF.nid.a[s->id+i].a);
@@ -5326,7 +5242,7 @@ static void worker_for_ul_rescall_alignment(void *data, long i, int tid) // call
b->self_read.seq = s->seq[i]; b->self_read.length = s->len[i]; b->self_read.size = 0;
correct_ul_overlap(&b->olist, s->uu, &b->self_read, &b->correct, &b->ovlp_read, &b->POA_Graph, &b->DAGCon,
&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 1, &fully_cov, &abnormal, s->opt->diff_ec_ul, winLen, NULL);
// exit(1);
// uint64_t k;
// for (k = 0; k < b->olist.length; k++) {
// if(b->olist.list[k].is_match == 1) b->num_correct_base += b->olist.list[k].x_pos_e+1-b->olist.list[k].x_pos_s;
@@ -10688,7 +10604,7 @@ ma_ug_t *ul_realignment(const ug_opt_t *uopt, asg_t *sg, uint32_t double_check_c
if(!load_all_ul_t(&UL_INF, gfa_name, &R_INF, ug)/**1**/) {
gen_UL_reovlps(&sl, ug, sg, gfa_name, cutoff);
// exit(1);
write_all_ul_t(&UL_INF, gfa_name, ug);
// write_all_ul_t(&UL_INF, gfa_name, ug);
} else if(double_check_cache){
if(drenew_UL_reovlps(&sl, ug, sg, gfa_name, cutoff)) {
write_all_ul_t(&UL_INF, gfa_name, ug);