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Assembly.cpp
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Assembly.cpp
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#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <zlib.h>
#include "Assembly.h"
#include "Process_Read.h"
#include "CommandLines.h"
#include "Hash_Table.h"
#include "POA.h"
#include "Correct.h"
#include "htab.h"
#include "kthread.h"
#include "rcut.h"
#include "kalloc.h"
#include "ecovlp.h"
void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, 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, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp);
void ha_get_ug_candidates(ha_abuf_t *ab, int64_t rid, ma_utg_t *u, ma_utg_v *ua, overlap_region_alloc *overlap_list, 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, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, double chain_match_rate);
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
All_reads R_INF;
Debug_reads R_INF_FLAG;
all_ul_t UL_INF, ULG_INF;
uint32_t *het_cnt = NULL;
// uint32_t debug_out = 0;
void get_corrected_read_from_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int* new_length)
{
int i, j;
int pre_i, new_i;
int operation, operation_length;
pre_i = new_i = 0;
int diff_char_i = 0;
for (i = 0; i < (long long)cigar->length; i++)
{
operation = Get_Cigar_Type(cigar->record[i]);
operation_length = Get_Cigar_Length(cigar->record[i]);
if (operation == 0)
{
memcpy(new_read + new_i, pre_read + pre_i, operation_length);
pre_i = pre_i + operation_length;
new_i = new_i + operation_length;
}
else if (operation == 1)
{
for (j = 0; j < operation_length; j++)
{
new_read[new_i] = Get_MisMatch_Base(cigar->lost_base[diff_char_i]);
new_i++;
diff_char_i++;
}
pre_i = pre_i + operation_length;
}
else if (operation == 3)
{
pre_i = pre_i + operation_length;
diff_char_i = diff_char_i + operation_length;
}
else if (operation == 2)
{
memcpy(new_read + new_i, cigar->lost_base + diff_char_i, operation_length);
new_i = new_i + operation_length;
diff_char_i = diff_char_i + operation_length;
}
}
*new_length = new_i;
}
void get_uncorrected_read_from_cigar(Cigar_record* cigar, char* new_read, int new_length, char* pre_read, int* pre_length)
{
int i, j;
int pre_i, new_i;
int operation, operation_length;
pre_i = new_i = 0;
int diff_char_i = 0;
for (i = 0; i < (long long)cigar->length; i++)
{
operation = Get_Cigar_Type(cigar->record[i]);
operation_length = Get_Cigar_Length(cigar->record[i]);
if (operation == 0)
{
memcpy(pre_read + pre_i, new_read + new_i, operation_length);
pre_i = pre_i + operation_length;
new_i = new_i + operation_length;
}
else if (operation == 1)
{
for (j = 0; j < operation_length; j++)
{
pre_read[pre_i] = Get_Match_Base(cigar->lost_base[diff_char_i]);
pre_i++;
diff_char_i++;
}
new_i = new_i + operation_length;
}
else if (operation == 3)
{
memcpy(pre_read + pre_i, cigar->lost_base + diff_char_i, operation_length);
pre_i = pre_i + operation_length;
diff_char_i = diff_char_i + operation_length;
}
else if (operation == 2)
{
new_i = new_i + operation_length;
diff_char_i = diff_char_i + operation_length;
}
}
*pre_length = pre_i;
}
inline int get_cigar_errors(Cigar_record* cigar)
{
int i;
int total_errors = 0;
for (i = 0; i < (long long)cigar->length; i++)
{
if (Get_Cigar_Type(cigar->record[i]) > 0)
{
total_errors = total_errors + Get_Cigar_Length(cigar->record[i]);
}
}
return total_errors;
}
int debug_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int new_length, int correct_base)
{
int i;
int total_errors = 0;
for (i = 0; i < (long long)cigar->length; i++)
{
if (Get_Cigar_Type(cigar->record[i]) > 0)
{
total_errors = total_errors + Get_Cigar_Length(cigar->record[i]);
}
}
if(total_errors!=correct_base)
{
fprintf(stderr, "total_errors: %d, correct_base: %d\n", total_errors, correct_base);
}
int pre_i, new_i;
int operation, operation_length;
pre_i = new_i = 0;
for (i = 0; i < (long long)cigar->length; i++)
{
operation = Get_Cigar_Type(cigar->record[i]);
operation_length = Get_Cigar_Length(cigar->record[i]);
if (operation == 0)
{
pre_i = pre_i + operation_length;
new_i = new_i + operation_length;
}
if (operation == 1)
{
pre_i = pre_i + operation_length;
new_i = new_i + operation_length;
}
if (operation == 3)
{
pre_i = pre_i + operation_length;
}
if (operation == 2)
{
new_i = new_i + operation_length;
}
}
if (pre_i != pre_length)
{
fprintf(stderr, "pre_i: %d, pre_length: %d\n", pre_i, pre_length);
}
if(new_i != new_length)
{
fprintf(stderr, "new_i: %d, new_length: %d\n", new_i, new_length);
}
return 1;
char* tmp_seq = (char*)malloc(new_length + pre_length);
int tmp_length;
get_corrected_read_from_cigar(cigar, pre_read, pre_length, tmp_seq, &tmp_length);
if(tmp_length != new_length)
{
fprintf(stderr, "tmp_length: %d, new_length: %d\n", tmp_length, new_length);
}
if(memcmp(new_read, tmp_seq, new_length)!=0)
{
fprintf(stderr, "error new string\n");
}
get_uncorrected_read_from_cigar(cigar, new_read, new_length, tmp_seq, &tmp_length);
if(tmp_length != pre_length)
{
fprintf(stderr, "tmp_length: %d, pre_length: %d\n", tmp_length, pre_length);
}
if(memcmp(pre_read, tmp_seq, pre_length)!=0)
{
fprintf(stderr, "error pre string\n");
}
free(tmp_seq);
if((int)cigar->new_read_length != new_length)
{
fprintf(stderr, "cigar->new_read_length: %d, new_length: %d\n", cigar->new_read_length, new_length);
}
}
inline void push_cigar(Compressed_Cigar_record* records, long long ID, Cigar_record* input)
{
if (input->length > records[ID].size)
{
records[ID].size = input->length;
records[ID].record = (uint32_t*)realloc(records[ID].record, records[ID].size*sizeof(uint32_t));
}
records[ID].length = input->length;
memcpy(records[ID].record, input->record, input->length*sizeof(uint32_t));
if (input->lost_base_length > records[ID].lost_base_size)
{
records[ID].lost_base_size = input->lost_base_length;
records[ID].lost_base = (char*)realloc(records[ID].lost_base, records[ID].lost_base_size);
}
records[ID].lost_base_length = input->lost_base_length;
memcpy(records[ID].lost_base, input->lost_base, input->lost_base_length);
records[ID].new_length = input->new_read_length;
}
void push_overlaps(ma_hit_t_alloc* paf, overlap_region_alloc* overlap_list, int flag, All_reads* R_INF, int if_reverse)
{
long long i = 0, xLen, yLen;
int32_t size = 0;
ma_hit_t tmp;
for (i = 0; i < (long long)overlap_list->length; ++i)
if (overlap_list->list[i].is_match == flag)
++size;
resize_ma_hit_t_alloc(paf, size);
clear_ma_hit_t_alloc(paf);
for (i = 0; i < (long long)overlap_list->length; i++)
{
if (overlap_list->list[i].is_match == flag)
{
xLen = Get_READ_LENGTH((*R_INF), overlap_list->list[i].x_id);
yLen = Get_READ_LENGTH((*R_INF), overlap_list->list[i].y_id);
tmp.qns = overlap_list->list[i].x_id;
tmp.qns = tmp.qns << 32;
tmp.tn = overlap_list->list[i].y_id;
if(if_reverse != 0)
{
tmp.qns = tmp.qns | (uint64_t)(xLen - overlap_list->list[i].x_pos_s - 1);
tmp.qe = xLen - overlap_list->list[i].x_pos_e - 1;
tmp.ts = yLen - overlap_list->list[i].y_pos_s - 1;
tmp.te = yLen - overlap_list->list[i].y_pos_e - 1;
}
else
{
tmp.qns = tmp.qns | (uint64_t)(overlap_list->list[i].x_pos_s);
tmp.qe = overlap_list->list[i].x_pos_e;
tmp.ts = overlap_list->list[i].y_pos_s;
tmp.te = overlap_list->list[i].y_pos_e;
}
///for overlap_list, the x_strand of all overlaps are 0, so the tmp.rev is the same as the y_strand
tmp.rev = overlap_list->list[i].y_pos_strand;
///tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
tmp.bl = Get_READ_LENGTH((*R_INF), overlap_list->list[i].y_id);
tmp.ml = overlap_list->list[i].strong;
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
add_ma_hit_t_alloc(paf, &tmp);
}
}
}
long long push_final_overlaps(ma_hit_t_alloc* paf, ma_hit_t_alloc* reverse_paf_list, overlap_region_alloc* overlap_list, int flag)
{
long long i = 0;
long long available_overlaps = 0;
ma_hit_t tmp;
clear_ma_hit_t_alloc(paf); // paf has been preallocated, so we don't need preallocation
for (i = 0; i < (long long)overlap_list->length; i++)
{
if (overlap_list->list[i].is_match == flag)
{
available_overlaps++;
/**********************query***************************/
//the interval of overlap is half-open [start, end)
tmp.qns = overlap_list->list[i].x_id;
tmp.qns = tmp.qns << 32;
tmp.qns = tmp.qns | (uint64_t)(overlap_list->list[i].x_pos_s);
///the end pos is open
tmp.qe = overlap_list->list[i].x_pos_e + 1;
/**********************query***************************/
///for overlap_list, the x_strand of all overlaps are 0, so the tmp.rev is the same as the y_strand
tmp.rev = overlap_list->list[i].y_pos_strand;
/**********************target***************************/
tmp.tn = overlap_list->list[i].y_id;
if(tmp.rev == 1)
{
long long y_readLen = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ts = y_readLen - overlap_list->list[i].y_pos_e - 1;
tmp.te = y_readLen - overlap_list->list[i].y_pos_s - 1;
}
else
{
tmp.ts = overlap_list->list[i].y_pos_s;
tmp.te = overlap_list->list[i].y_pos_e;
}
///the end pos is open
tmp.te++;
/**********************target***************************/
tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ml = overlap_list->list[i].strong;
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
tmp.el = overlap_list->list[i].shared_seed;
add_ma_hit_t_alloc(paf, &tmp);
}
}
return available_overlaps;
}
long long push_final_overlaps_increment(ma_hit_t_alloc* paf, ma_hit_t_alloc* reverse_paf_list, overlap_region_alloc* overlap_list, int flag)
{
long long i = 0;
long long available_overlaps = paf->length;
ma_hit_t tmp;
///clear_ma_hit_t_alloc(paf); // paf has been preallocated, so we don't need preallocation
for (i = 0; i < (long long)overlap_list->length; i++)
{
if (overlap_list->list[i].is_match == flag)
{
available_overlaps++;
/**********************query***************************/
//the interval of overlap is half-open [start, end)
tmp.qns = overlap_list->list[i].x_id;
tmp.qns = tmp.qns << 32;
tmp.qns = tmp.qns | (uint64_t)(overlap_list->list[i].x_pos_s);
///the end pos is open
tmp.qe = overlap_list->list[i].x_pos_e + 1;
/**********************query***************************/
///for overlap_list, the x_strand of all overlaps are 0, so the tmp.rev is the same as the y_strand
tmp.rev = overlap_list->list[i].y_pos_strand;
/**********************target***************************/
tmp.tn = overlap_list->list[i].y_id;
if(tmp.rev == 1)
{
long long y_readLen = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ts = y_readLen - overlap_list->list[i].y_pos_e - 1;
tmp.te = y_readLen - overlap_list->list[i].y_pos_s - 1;
}
else
{
tmp.ts = overlap_list->list[i].y_pos_s;
tmp.te = overlap_list->list[i].y_pos_e;
}
///the end pos is open
tmp.te++;
/**********************target***************************/
tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ml = overlap_list->list[i].strong;
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
tmp.el = overlap_list->list[i].shared_seed;
add_ma_hit_t_alloc(paf, &tmp);
}
}
return available_overlaps;
}
ha_ovec_buf_t *ha_ovec_buf_init(void *km, int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;
KCALLOC(km, b, 1);
b->is_final = !!is_final, b->save_ov = !!save_ov;
init_UC_Read(&b->self_read);//set 0
init_UC_Read(&b->ovlp_read);//set 0
init_Candidates_list(&b->clist);//set 0
memset(&b->olist, 0, sizeof(overlap_region_alloc));
memset(&b->olist_hp, 0, sizeof(overlap_region_alloc));
// init_overlap_region_alloc(&b->olist);
// init_overlap_region_alloc(&b->olist_hp);
init_fake_cigar(&(b->tmp_region.f_cigar));//set 0
kv_init(b->b_buf.a);//set 0
kv_init(b->r_buf.a);//set 0
kv_init(b->k_flag.a);//set 0
kv_init(b->sp);//set 0
if(!is_ug) b->ab = ha_abuf_init_buf(km);
else b->abl = ha_abufl_init_buf(km);
if (!b->is_final) {
init_Cigar_record_buf(&b->cigar1, km);
// init_Graph(&b->POA_Graph);
// init_Graph(&b->DAGCon);
init_Correct_dumy_buf(&b->correct, km);//set 0
InitHaplotypeEvdience_buf(&b->hap, km);
init_Round2_alignment_buf(&b->round2, km);
}
return b;
}
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;
CALLOC(b, 1);
b->is_final = !!is_final, b->save_ov = !!save_ov;
init_UC_Read(&b->self_read);
init_UC_Read(&b->ovlp_read);
init_Candidates_list(&b->clist);
init_overlap_region_alloc(&b->olist);
init_overlap_region_alloc(&b->olist_hp);
init_fake_cigar(&(b->tmp_region.f_cigar));
memset(&(b->tmp_region.w_list), 0, sizeof(b->tmp_region.w_list));
CALLOC(b->tmp_region.w_list.a, 1); b->tmp_region.w_list.n = b->tmp_region.w_list.m = 1;
kv_init(b->b_buf.a);
kv_init(b->r_buf.a);
kv_init(b->k_flag.a);
kv_init(b->sp);
init_bit_extz_t(&(b->exz), 31);
if(!is_ug) b->ab = ha_abuf_init();
else b->abl = ha_abufl_init();
if (!b->is_final) {
init_Cigar_record(&b->cigar1);
init_Graph(&b->POA_Graph);
init_Graph(&b->DAGCon);
init_Correct_dumy(&b->correct);
InitHaplotypeEvdience(&b->hap);
init_Round2_alignment(&b->round2);
}
return b;
}
void ha_ovec_destroy(ha_ovec_buf_t *b)
{
destory_UC_Read(&b->self_read);
destory_UC_Read(&b->ovlp_read);
destory_Candidates_list(&b->clist);
destory_overlap_region_alloc(&b->olist);
destory_overlap_region_alloc(&b->olist_hp);
ha_abuf_destroy(b->ab);
ha_abufl_destroy(b->abl);
destory_fake_cigar(&(b->tmp_region.f_cigar));
free(b->tmp_region.w_list.a); free(b->tmp_region.w_list.c.a);
kv_destroy(b->b_buf.a);
kv_destroy(b->r_buf.a);
kv_destroy(b->k_flag.a);
kv_destroy(b->sp);
destroy_bit_extz_t(&(b->exz));
if (!b->is_final) {
destory_Cigar_record(&b->cigar1);
destory_Graph(&b->POA_Graph);
destory_Graph(&b->DAGCon);
destory_Correct_dumy(&b->correct);
destoryHaplotypeEvdience(&b->hap);
destory_Round2_alignment(&b->round2);
}
free(b);
}
static int64_t ha_Graph_mem(const Graph *g)
{
int64_t i, mem = 0;
mem = sizeof(Graph) + g->node_q.size * 8 + g->g_nodes.size * sizeof(Node);
for (i = 0; i < (int64_t)g->g_nodes.size; ++i) {
Node *n = &g->g_nodes.list[i];
mem += n->mismatch_edges.size * sizeof(Edge);
mem += n->deletion_edges.size * sizeof(Edge);
mem += n->insertion_edges.size * sizeof(Edge);
}
mem += g->g_nodes.sort.size * 9;
return mem;
}
int64_t ha_ovec_mem(const ha_ovec_buf_t *b, int64_t *mem_a)
{
int64_t i, mem_ab = 0, mem_clist, mem_olist, mem_hap = 0, mem_aux = 0;
// mem_clist = b->clist.size * sizeof(k_mer_hit) + b->clist.chainDP.size * 7 * 4;
mem_clist = (b->clist.size * sizeof(k_mer_hit)) + ((sizeof((*b->clist.chainDP.score)) + sizeof((*b->clist.chainDP.pre))
+ sizeof((*b->clist.chainDP.indels)) + sizeof((*b->clist.chainDP.self_length))
+ sizeof((*b->clist.chainDP.occ)) + sizeof((*b->clist.chainDP.tmp))) * b->clist.chainDP.size);
mem_clist += sizeof(*(b->b_buf.a.a)) * b->b_buf.a.m;
mem_clist += sizeof(*(b->r_buf.a.a)) * b->r_buf.a.m;
mem_clist += sizeof(*(b->k_flag.a.a)) * b->k_flag.a.m;
mem_clist += sizeof(*(b->sp.a)) * b->sp.m;
mem_clist += sizeof(*(b->tmp_region.f_cigar.buffer)) * b->tmp_region.f_cigar.size;
mem_clist += sizeof(*(b->tmp_region.w_list.a)) * b->tmp_region.w_list.n;
mem_clist += sizeof(*(b->tmp_region.w_list.c.a)) * b->tmp_region.w_list.c.n;
mem_olist = b->olist.size * sizeof(overlap_region);
for (i = 0; i < (int64_t)b->olist.size; ++i) {
const overlap_region *r = &b->olist.list[i];
mem_olist += (r->w_list.n*sizeof(*(r->w_list.a))) + (r->w_list.c.n*sizeof(*(r->w_list.c.a)));
mem_olist += r->f_cigar.size * 8;
mem_olist += (r->boundary_cigars.n*sizeof(*(r->boundary_cigars.a)))
+ (r->boundary_cigars.c.n*sizeof(*(r->boundary_cigars.c.a)));
}
mem_olist += b->olist_hp.size * sizeof(overlap_region);
for (i = 0; i < (int64_t)b->olist_hp.size; ++i) {
const overlap_region *r = &b->olist_hp.list[i];
mem_olist += (r->w_list.n*sizeof(*(r->w_list.a))) + (r->w_list.c.n*sizeof(*(r->w_list.c.a)));
mem_olist += r->f_cigar.size * 8;
mem_olist += (r->boundary_cigars.n*sizeof(*(r->boundary_cigars.a)))
+ (r->boundary_cigars.c.n*sizeof(*(r->boundary_cigars.c.a)));
}
if(b->ab) mem_ab += ha_abuf_mem(b->ab);
if(b->abl) mem_ab += ha_abufl_mem(b->abl);
if (!b->is_final) {
mem_hap += sizeof(Cigar_record) + b->cigar1.lost_base_size + b->cigar1.size * 4;
mem_hap += sizeof(Correct_dumy) + b->correct.size * 8;
mem_hap += sizeof(Round2_alignment) + b->round2.cigar.size * 4 + b->round2.tmp_cigar.size * 4;
mem_hap += sizeof(haplotype_evdience_alloc) + b->hap.size * sizeof(haplotype_evdience) + b->hap.snp_matrix_size + b->hap.r_snp_size + b->hap.snp_stat.m * sizeof(SnpStats) + b->hap.snp_srt.m * sizeof(uint64_t);
mem_hap += ha_Graph_mem(&b->POA_Graph);
mem_hap += ha_Graph_mem(&b->DAGCon);
}
mem_aux += sizeof(*(b->self_read.seq)) * b->self_read.size;
mem_aux += sizeof(*(b->ovlp_read.seq)) * b->ovlp_read.size;
if(mem_a) {
mem_a[0] = mem_ab; mem_a[1] = mem_clist; mem_a[2] = mem_olist;
mem_a[3] = mem_hap; mem_a[4] = mem_aux;
}
return mem_ab + mem_clist + mem_olist + mem_hap + mem_aux;
}
uint32_t get_het_cnt(haplotype_evdience_alloc *hap)
{
uint32_t i, cnt;
for (i = cnt = 0; i < hap->snp_stat.n; i++) {
if(hap->snp_stat.a[i].score == 1 && (!(hap->snp_stat.a[i].occ_0 < 2 || hap->snp_stat.a[i].occ_1 < 2))) {
cnt++;
}
}
return cnt;
}
static void worker_ovec(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
int fully_cov, abnormal;
// if(i != 12578) return;
// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
// if (memcmp("7897e875-76e5-42c8-bc37-94b370c4cc8d", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
// } else {
// return;
// }
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, NULL/**&(b->k_flag)**/, &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
// prt_chain(&b->olist);
// return;
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
correct_overlap(&b->olist, &R_INF, &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);
b->num_read_base += b->self_read.length;
b->num_correct_base += b->correct.corrected_base;
b->num_recorrect_base += b->round2.dumy.corrected_base;
push_cigar(R_INF.cigars, i, &b->cigar1);
push_cigar(R_INF.second_round_cigar, i, &b->round2.cigar);
R_INF.paf[i].is_fully_corrected = 0;
if (fully_cov) {
if (get_cigar_errors(&b->cigar1) == 0 && get_cigar_errors(&b->round2.cigar) == 0)
R_INF.paf[i].is_fully_corrected = 1;
}
R_INF.paf[i].is_abnormal = abnormal;
R_INF.trio_flag[i] = AMBIGU;
///need to be fixed in r305
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), NULL);
// }
if (R_INF.trio_flag[i] != AMBIGU || b->save_ov) {
int is_rev = (asm_opt.number_of_round % 2 == 0);
push_overlaps(&(R_INF.paf[i]), &b->olist, 1, &R_INF, is_rev);
push_overlaps(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, is_rev);
}
if(het_cnt) het_cnt[i] = get_het_cnt(&b->hap);
// fprintf(stderr, "[M::%s-end] rid->%ld\n", __func__, i);
}
static void worker_ovec_cal0(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
int fully_cov, abnormal;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, NULL/**&(b->k_flag)**/, &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
correct_overlap(&b->olist, &R_INF, &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, 0/**1***/, &fully_cov, &abnormal);
b->num_read_base += b->self_read.length;
b->num_correct_base += b->correct.corrected_base;
b->num_recorrect_base += b->round2.dumy.corrected_base;
// R_INF.paf[i].is_fully_corrected = 0;
// R_INF.paf[i].is_abnormal = abnormal;
R_INF.trio_flag[i] = AMBIGU;
// R_INF.paf[i].is_fully_corrected = 0;
// if (fully_cov) {
// if (get_cigar_errors(&b->cigar1) == 0 && get_cigar_errors(&b->round2.cigar) == 0)
// R_INF.paf[i].is_fully_corrected = 1;
// }
// R_INF.paf[i].is_abnormal = abnormal;
// R_INF.trio_flag[i] = AMBIGU;
push_final_overlaps(&(R_INF.paf[i]), R_INF.reverse_paf, &b->olist, 1);
push_final_overlaps(&(R_INF.reverse_paf[i]), R_INF.reverse_paf, &b->olist, 2);
if(het_cnt) het_cnt[i] = get_het_cnt(&b->hap);
}
static void worker_ovec_related_reads(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
uint64_t k, queryNameLen;
for (k = 0; k < R_INF_FLAG.query_num; k++)
{
queryNameLen = strlen(R_INF_FLAG.read_name[k]);
if (queryNameLen != Get_NAME_LENGTH((R_INF),i)) continue;
if (memcmp(R_INF_FLAG.read_name[k], Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0)
{
break;
}
}
if(k < R_INF_FLAG.query_num)
{
R_INF_FLAG.read_id[k] = i;
int fully_cov, abnormal, q_idx = k;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, NULL/**&(b->k_flag)**/, &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), &(R_INF_FLAG.candidate_count[q_idx]), &(b->sp));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
correct_overlap(&b->olist, &R_INF, &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);
b->num_read_base += b->self_read.length;
b->num_correct_base += b->correct.corrected_base;
b->num_recorrect_base += b->round2.dumy.corrected_base;
push_cigar(R_INF.cigars, i, &b->cigar1);
push_cigar(R_INF.second_round_cigar, i, &b->round2.cigar);
R_INF.paf[i].is_fully_corrected = 0;
if (fully_cov) {
if (get_cigar_errors(&b->cigar1) == 0 && get_cigar_errors(&b->round2.cigar) == 0)
R_INF.paf[i].is_fully_corrected = 1;
}
R_INF.paf[i].is_abnormal = abnormal;
pthread_mutex_lock(&R_INF_FLAG.OutputMutex);
fprintf(R_INF_FLAG.fp, "\n>%.*s, rid: %ld\n", (int)Get_NAME_LENGTH((R_INF), i), Get_NAME((R_INF), i), i);
fprintf(R_INF_FLAG.fp, "%d-th round, len: %lu, hom_cov: %d, max_n_chain: %d\n",
asm_opt.number_of_round, Get_READ_LENGTH(R_INF, i), asm_opt.hom_cov, asm_opt.max_n_chain);
fprintf(R_INF_FLAG.fp, "***************************k-mer counts (%d)***************************\n", (int)(R_INF_FLAG.candidate_count[q_idx].a.n));
sort_kvec_t_u64_warp(&(R_INF_FLAG.candidate_count[q_idx]), 0);
for (k = 0; k < R_INF_FLAG.candidate_count[q_idx].a.n; k++)
{
fprintf(R_INF_FLAG.fp, "[%lu] Count(%u): %lu, filtered: %lu\n", k,
(uint32_t)R_INF_FLAG.candidate_count[q_idx].a.a[k], R_INF_FLAG.candidate_count[q_idx].a.a[k]>>33,
(R_INF_FLAG.candidate_count[q_idx].a.a[k]>>32)&(uint64_t)1);
}
fprintf(R_INF_FLAG.fp, "***************************forward ovlp***************************\n");
for (k = 0; k < b->olist.length; k++)
{
if(b->olist.list[k].is_match != 1) continue;
fprintf(R_INF_FLAG.fp, "%.*s\n", (int)Get_NAME_LENGTH((R_INF), b->olist.list[k].y_id), Get_NAME((R_INF), b->olist.list[k].y_id));
fprintf(R_INF_FLAG.fp, "qs: %u, qe: %u, ts: %u, te: %u, rev: %u, strong: %u, no_l_indel: %u, len: %lu\n",
b->olist.list[k].x_pos_s, b->olist.list[k].x_pos_e, b->olist.list[k].y_pos_s, b->olist.list[k].y_pos_e,
b->olist.list[k].y_pos_strand, b->olist.list[k].strong, b->olist.list[k].without_large_indel,
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
fprintf(R_INF_FLAG.fp, "***************************reverse ovlp***************************\n");
for (k = 0; k < b->olist.length; k++)
{
if(b->olist.list[k].is_match != 2) continue;
fprintf(R_INF_FLAG.fp, "%.*s\n", (int)Get_NAME_LENGTH((R_INF), b->olist.list[k].y_id), Get_NAME((R_INF), b->olist.list[k].y_id));
fprintf(R_INF_FLAG.fp, "qs: %u, qe: %u, ts: %u, te: %u, rev: %u, strong: %u, no_l_indel: %u, len: %lu\n",
b->olist.list[k].x_pos_s, b->olist.list[k].x_pos_e, b->olist.list[k].y_pos_s, b->olist.list[k].y_pos_e,
b->olist.list[k].y_pos_strand, b->olist.list[k].strong, b->olist.list[k].without_large_indel,
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
/**
fprintf(R_INF_FLAG.fp, "***************************unmatched ovlp***************************\n");
for (k = 0; k < b->olist.length; k++)
{
if(b->olist.list[k].is_match == 1) continue;
if(b->olist.list[k].is_match == 2) continue;
fprintf(R_INF_FLAG.fp, "%.*s\n", (int)Get_NAME_LENGTH((R_INF), b->olist.list[k].y_id), Get_NAME((R_INF), b->olist.list[k].y_id));
fprintf(R_INF_FLAG.fp, "qs: %u, qe: %u, ts: %u, te: %u, rev: %u, strong: %u, no_l_indel: %u, len: %lu\n",
b->olist.list[k].x_pos_s, b->olist.list[k].x_pos_e, b->olist.list[k].y_pos_s, b->olist.list[k].y_pos_e,
b->olist.list[k].y_pos_strand, b->olist.list[k].strong, b->olist.list[k].without_large_indel,
Get_READ_LENGTH(R_INF, b->olist.list[k].y_id));
}
**/
R_INF.trio_flag[i] = AMBIGU;
///need to be fixed in r305
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), R_INF_FLAG.fp);
// }
fprintf(R_INF_FLAG.fp, "R_INF.trio_flag[%ld]: %u\n", i, R_INF.trio_flag[i]);
pthread_mutex_unlock(&R_INF_FLAG.OutputMutex);
}
}
static inline long long get_N_occ(char* seq, long long length)
{
long long j, N_occ = 0;
for (j = 0; j < length; j++)
if(seq_nt6_table[(uint8_t)seq[j]] >= 4)
N_occ++;
return N_occ;
}
typedef struct {
UC_Read g_read;
int first_round_read_size;
int second_round_read_size;
char *first_round_read;
char *second_round_read;
} ha_ecsave_buf_t;
static void worker_ec_save(void *data, long i, int tid)
{
ha_ecsave_buf_t *e = (ha_ecsave_buf_t*)data + tid;
Cigar_record cigar;
int first_round_read_length;
int second_round_read_length;
uint64_t N_occ;
char *new_read;
int new_read_length;
recover_UC_Read(&e->g_read, &R_INF, i);
// round 1
if ((long long)R_INF.cigars[i].new_length > e->first_round_read_size) {
e->first_round_read_size = R_INF.cigars[i].new_length;
REALLOC(e->first_round_read, e->first_round_read_size);
}
cigar.length = R_INF.cigars[i].length;
cigar.lost_base_length = R_INF.cigars[i].lost_base_length;
cigar.record = R_INF.cigars[i].record;
cigar.lost_base = R_INF.cigars[i].lost_base;
get_corrected_read_from_cigar(&cigar, e->g_read.seq, e->g_read.length, e->first_round_read, &first_round_read_length);
// round 2
if ((long long)R_INF.second_round_cigar[i].new_length > e->second_round_read_size) {
e->second_round_read_size = R_INF.second_round_cigar[i].new_length;
REALLOC(e->second_round_read, e->second_round_read_size);
}
cigar.length = R_INF.second_round_cigar[i].length;
cigar.lost_base_length = R_INF.second_round_cigar[i].lost_base_length;
cigar.record = R_INF.second_round_cigar[i].record;
cigar.lost_base = R_INF.second_round_cigar[i].lost_base;
get_corrected_read_from_cigar(&cigar, e->first_round_read, first_round_read_length, e->second_round_read, &second_round_read_length);
new_read = e->second_round_read;
new_read_length = second_round_read_length;
if (asm_opt.roundID != asm_opt.number_of_round - 1)
{
///need modification
reverse_complement(new_read, new_read_length);
}
else if(asm_opt.number_of_round % 2 == 0)
{
///need modification
reverse_complement(new_read, new_read_length);
}
N_occ = get_N_occ(new_read, new_read_length);
if ((long long)R_INF.read_size[i] < new_read_length) {
R_INF.read_size[i] = new_read_length;
REALLOC(R_INF.read_sperate[i], R_INF.read_size[i]/4+1);
}
R_INF.read_length[i] = new_read_length;
ha_compress_base(Get_READ(R_INF, i), new_read, new_read_length, &R_INF.N_site[i], N_occ);
}
void Output_corrected_reads()
{
long long i;
UC_Read g_read;
init_UC_Read(&g_read);
char* gfa_name = (char*)malloc(strlen(asm_opt.output_file_name)+35);
sprintf(gfa_name, "%s.ec.fa", asm_opt.output_file_name);
FILE* output_file = fopen(gfa_name, "w");
free(gfa_name);
for (i = 0; i < (long long)R_INF.total_reads; i++)
{
recover_UC_Read(&g_read, &R_INF, i);
fwrite(">", 1, 1, output_file);
fwrite(Get_NAME(R_INF, i), 1, Get_NAME_LENGTH(R_INF, i), output_file);
fwrite("\n", 1, 1, output_file);
fwrite(g_read.seq, 1, g_read.length, output_file);
fwrite("\n", 1, 1, output_file);
}
destory_UC_Read(&g_read);
fclose(output_file);
}
void debug_print_pob_regions()
{
uint64_t i, total = 0;
for (i = 0; i < R_INF.total_reads; i++)
{
if(R_INF.trio_flag[i]!=AMBIGU)
{
total++;
fprintf(stderr, "(%lu) %.*s\n", i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
}
}
fprintf(stderr, "total hp reads: %lu, R_INF.total_reads: %lu\n", total, R_INF.total_reads);
exit(1);
}
void rescue_hp_reads(ha_ovec_buf_t **b)
{
int hom_cov, het_cov;
ha_flt_tab_hp = ha_idx_hp = NULL;
if (!(asm_opt.flag & HA_F_NO_KMER_FLT)) {
ha_flt_tab_hp = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 1, 0);
}
ha_idx_hp = ha_pt_gen(&asm_opt, ha_flt_tab, 1, 1, &R_INF, &hom_cov, &het_cov);
if (asm_opt.required_read_name)
kt_for(asm_opt.thread_num, worker_ovec_related_reads, b, R_INF.total_reads);
else
kt_for(asm_opt.thread_num, worker_ovec, b, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab_hp); ha_flt_tab_hp = NULL;
ha_pt_destroy(ha_idx_hp); ha_idx_hp = NULL;
}
void print_het_cnt_log(uint32_t *het_cnt)
{
if(!het_cnt) return;
char* gfa_name = (char*)malloc(strlen(asm_opt.output_file_name)+35);
sprintf(gfa_name, "%s.het_cnt.log", asm_opt.output_file_name);
FILE* output_file = fopen(gfa_name, "w");
fprintf(stderr, "[M::%s::] ==> print cnt of het sites to %s...\n", __func__, gfa_name);
free(gfa_name);
uint64_t i;
for (i = 0; i < R_INF.total_reads; i++){
fprintf(output_file, ">%.*s\t%u\n", (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i), het_cnt[i]);
}
fclose(output_file);
}
void prt_dbg_rs(FILE *fp, Debug_reads* x, uint64_t round)
{
uint64_t k, id; UC_Read g_read; init_UC_Read(&g_read);
for (k = 0; k < R_INF_FLAG.query_num; k++) {
id = x->read_id[k];
if(id == ((uint64_t)-1)) continue;
recover_UC_Read(&g_read, &R_INF, id);
fprintf(fp, ">%.*s_r%lu\n", (int)Get_NAME_LENGTH((R_INF), id), Get_NAME((R_INF), id), round);
fprintf(fp, "%.*s\n", (int)g_read.length, g_read.seq);
}
destory_UC_Read(&g_read);
}
void ha_ec(int64_t round, int num_pround, int des_idx, uint64_t *tot_b, uint64_t *tot_e)
{
int hom_cov, het_cov, r_out = 0;
ha_flt_tab_hp = ha_idx_hp = NULL; (*tot_b) = (*tot_e) = 0;
if((ha_idx == NULL)&&(asm_opt.flag & HA_F_VERBOSE_GFA)&&(round == asm_opt.number_of_round - 1)) r_out = 1;
if(asm_opt.required_read_name) init_Debug_reads(&R_INF_FLAG, asm_opt.required_read_name); // for debugging only
if(ha_idx) hom_cov = asm_opt.hom_cov;
if(ha_idx == NULL) {
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, 0, &R_INF, &hom_cov, &het_cov); // build the index
asm_opt.hom_cov = hom_cov; asm_opt.het_cov = het_cov;
}
///debug_adapter(&asm_opt, &R_INF);
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
het_cnt = NULL;
if(round == asm_opt.number_of_round-1 && asm_opt.is_dbg_het_cnt) CALLOC(het_cnt, R_INF.total_reads);
if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
cal_ec_r(asm_opt.thread_num, round, num_pround, R_INF.total_reads, (round == (asm_opt.number_of_round-1))?1:0, tot_b, tot_e);
// exit(1);
// if (r_out) write_pt_index(ha_flt_tab, ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name);
if(des_idx) {