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collect contig alignment + renew_utg bug fixed

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chhylp123
2021-05-09 17:47:50 -04:00
parent 03adce6202
commit 7918396d21
7 changed files with 431 additions and 19 deletions
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hic.cpp
+12 -16
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@@ -14,6 +14,7 @@
#include "ksort.h"
#include "kseq.h" // FASTA/Q parser
#include "kdq.h"
#include "horder.h"
KSEQ_INIT(gzFile, gzread)
KDQ_INIT(uint64_t)
@@ -190,22 +191,10 @@ typedef struct {
uint64_t n_u;
} kvec_pe_hit_hap;
typedef struct {
uint64_t s, e, id, len;
} pe_hit;
typedef struct {
kvec_t(pe_hit) a;
kvec_t(uint64_t) idx;
kvec_t(uint64_t) occ;
} kvec_pe_hit;
typedef struct {
kvec_t(hc_edge) a;
}kvec_hc_edge;
#define pe_hit_an1_key(x) ((x).s)
KRADIX_SORT_INIT(pe_hit_an1, pe_hit, pe_hit_an1_key, member_size(pe_hit, s))
#define pe_hit_an2_key(x) ((x).e)
@@ -286,6 +275,11 @@ KRADIX_SORT_INIT(hc_s_hit_off_cnt, s_hit, hc_s_hit_off_cnt_key, 8)
KRADIX_SORT_INIT(hc_edge_u, hc_edge, hc_edge_key_u, 4)
#define hc_edge_key_d(a) ((a).dis)
KRADIX_SORT_INIT(hc_edge_d, hc_edge, hc_edge_key_d, member_size(hc_edge, dis))
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
typedef struct {
kvec_t(kvec_t_u64_warp) matrix;
@@ -302,7 +296,6 @@ typedef struct{
uint64_t max, med;
} trans_idx;
reads_t R1, R2;
ha_ug_index* ug_index;
@@ -15431,7 +15424,7 @@ void print_kv_u_trans_t(kv_u_trans_t *ta)
fprintf(stderr, "[M::%s::] \n", __func__);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt)
{
double index_time = yak_realtime();
sldat_t sl;
@@ -15503,6 +15496,8 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
verbose_het_stat(&bub);
horder_t *ho = init_horder_t(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, opt);
///print_hc_links(&link, 0, &hap);
// print_kv_u_trans(&k_trans, &link, s->s);
@@ -15514,6 +15509,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
///print_debug_bubble_graph(&bub, idx->ug, asm_opt.output_file_name);
// print_bubble_chain(&bub);
// destory_contig_partition(&hap);
destory_horder_t(&ho);
kv_destroy(back_hc_edge.a);
kv_destroy(sl.hits.a);
kv_destroy(sl.hits.idx);
@@ -15542,7 +15538,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
}
void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch)
void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt)
{
ug_index = NULL;
int exist = (asm_opt.load_index_from_disk?
@@ -15553,7 +15549,7 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch)
ug_index->read_g = read_g;
ug_index->t_ch = t_ch;
///test_unitig_index(ug_index, ug);
hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index);
hic_short_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt);
destory_hc_pt_index(ug_index);
}