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hifiasm/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"
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain);
All_reads R_INF;
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;
ma_hit_t tmp;
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);
}
}
}
int if_exact_match(char* x, long long xLen, char* y, long long yLen, long long xBeg, long long xEnd, long long yBeg, long long yEnd)
{
long long overlapLen = xEnd - xBeg + 1;
if(yEnd - yBeg + 1 == overlapLen)
{
long long i;
for (i = 0; i < overlapLen; i++)
{
if(x[xBeg + i] != y[yBeg + i])
{
break;
}
}
if(i == overlapLen)
{
return 1;
}
}
return 0;
}
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);
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;
}
typedef struct {
int is_final;
// chaining and overlapping related buffers
UC_Read self_read, ovlp_read;
Candidates_list clist;
overlap_region_alloc olist;
ha_abuf_t *ab;
// error correction related buffers
int64_t num_read_base, num_correct_base, num_recorrect_base;
Cigar_record cigar1;
Graph POA_Graph;
Graph DAGCon;
Correct_dumy correct;
haplotype_evdience_alloc hap;
Round2_alignment round2;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final)
{
ha_ovec_buf_t *b;
CALLOC(b, 1);
b->is_final = !!is_final;
init_UC_Read(&b->self_read);
init_UC_Read(&b->ovlp_read);
init_Candidates_list(&b->clist);
init_overlap_region_alloc(&b->olist);
b->ab = ha_abuf_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);
ha_abuf_destroy(b->ab);
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 i, mem = 0, mem_clist, mem_olist;
mem_clist = b->clist.size * sizeof(k_mer_hit) + b->clist.chainDP.size * 7 * 4;
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_size * sizeof(window_list);
mem_olist += r->f_cigar.size * 8;
mem_olist += r->boundary_cigars.size * sizeof(window_list);
}
mem = ha_abuf_mem(b->ab) + mem_clist + mem_olist;
if (!b->is_final) {
mem += sizeof(Cigar_record) + b->cigar1.lost_base_size + b->cigar1.size * 4;
mem += sizeof(Correct_dumy) + b->correct.size * 8;
mem += sizeof(Round2_alignment) + b->round2.cigar.size * 4 + b->round2.tmp_cigar.size * 4;
mem += sizeof(haplotype_evdience_alloc) + b->hap.size * sizeof(haplotype_evdience) + b->hap.snp_matrix_size + b->hap.snp_stat_size * sizeof(SnpStats);
mem += ha_Graph_mem(&b->POA_Graph);
mem += ha_Graph_mem(&b->DAGCon);
}
return mem;
}
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;
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1);
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, 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;
push_overlaps(&(R_INF.paf[i]), &b->olist, 1, &R_INF, asm_opt.roundID%2);
push_overlaps(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, asm_opt.roundID%2);
}
static void worker_ovec_related_reads(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
int required_read_name_length = strlen(asm_opt.required_read_name);
uint64_t k;
if (required_read_name_length == (int)Get_NAME_LENGTH((R_INF),i)
&&
memcmp(asm_opt.required_read_name, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0)
{
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1);
fprintf(stderr, ">%.*s\n", (int)Get_NAME_LENGTH((R_INF), i), Get_NAME((R_INF), i));
recover_UC_Read(&b->self_read, &R_INF, i);
fprintf(stderr, "%.*s\n", (int)b->self_read.length, b->self_read.seq);
for (k = 0; k < b->olist.length; k++) {
fprintf(stderr, ">%.*s\n", (int)Get_NAME_LENGTH((R_INF), b->olist.list[k].y_id), Get_NAME((R_INF), b->olist.list[k].y_id));
recover_UC_Read(&b->self_read, &R_INF, b->olist.list[k].y_id);
fprintf(stderr, "%.*s\n", (int)b->self_read.length, b->self_read.seq);
}
}
}
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 ha_overlap_and_correct(int round)
{
int i, hom_cov;
ha_ovec_buf_t **b;
ha_ecsave_buf_t *e;
// overlap and correct reads
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(0);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, round == 0? 0 : 1, &R_INF, &hom_cov); // build the index
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_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_pt_destroy(ha_idx);
ha_idx = 0;
// collect statistics
for (i = 0; i < asm_opt.thread_num; ++i) {
asm_opt.num_bases += b[i]->num_read_base;
asm_opt.num_corrected_bases += b[i]->num_correct_base;
asm_opt.num_recorrected_bases += b[i]->num_recorrect_base;
asm_opt.mem_buf += ha_ovec_mem(b[i]);
ha_ovec_destroy(b[i]);
}
free(b);
if (asm_opt.required_read_name) exit(0); // for debugging only
// save corrected reads to R_INF
CALLOC(e, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i) {
init_UC_Read(&e[i].g_read);
e[i].first_round_read_size = e[i].second_round_read_size = 50000;
CALLOC(e[i].first_round_read, e[i].first_round_read_size);
CALLOC(e[i].second_round_read, e[i].second_round_read_size);
}
kt_for(asm_opt.thread_num, worker_ec_save, e, R_INF.total_reads);
for (i = 0; i < asm_opt.thread_num; ++i) {
destory_UC_Read(&e[i].g_read);
free(e[i].first_round_read);
free(e[i].second_round_read);
}
free(e);
}
void update_overlaps(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf,
UC_Read* g_read, UC_Read* overlap_read, int is_match, int is_exact)
{
uint64_t inner_j = 0;
uint64_t j = 0;
long long x_overlapLen, y_overlapLen;
while (j < overlap_list->length && inner_j < paf->length)
{
if(overlap_list->list[j].y_id < paf->buffer[inner_j].tn)
{
j++;
}
else if(overlap_list->list[j].y_id > paf->buffer[inner_j].tn)
{
inner_j++;
}
else
{
if(overlap_list->list[j].y_pos_strand == paf->buffer[inner_j].rev)
{
x_overlapLen = Get_qe(paf->buffer[inner_j]) - Get_qs(paf->buffer[inner_j]) + 1;
y_overlapLen = Get_te(paf->buffer[inner_j]) - Get_ts(paf->buffer[inner_j]) + 1;
if(x_overlapLen < y_overlapLen) x_overlapLen = y_overlapLen;
x_overlapLen = x_overlapLen * 0.1;
// if(
// ((DIFF(overlap_list->list[j].x_pos_s, Get_qs(paf->buffer[inner_j])) < x_overlapLen)
// && (DIFF(overlap_list->list[j].x_pos_e, Get_qe(paf->buffer[inner_j])) < x_overlapLen))
// ||
// ((DIFF(overlap_list->list[j].y_pos_s, Get_ts(paf->buffer[inner_j])) < x_overlapLen)
// && (DIFF(overlap_list->list[j].y_pos_e, Get_te(paf->buffer[inner_j])) < x_overlapLen)))
if(
((DIFF(overlap_list->list[j].x_pos_s, Get_qs(paf->buffer[inner_j])) < (uint64_t)x_overlapLen)
&& (DIFF(overlap_list->list[j].x_pos_e, Get_qe(paf->buffer[inner_j])) < (uint64_t)x_overlapLen))
||
((DIFF(overlap_list->list[j].y_pos_s, Get_ts(paf->buffer[inner_j])) < (uint64_t)x_overlapLen)
&& (DIFF(overlap_list->list[j].y_pos_e, Get_te(paf->buffer[inner_j])) < (uint64_t)x_overlapLen))
)
{
overlap_list->list[j].is_match = is_match;
overlap_list->list[j].strong = paf->buffer[inner_j].ml;
overlap_list->list[j].without_large_indel = paf->buffer[inner_j].no_l_indel;
if(is_exact == 1)
{
if(overlap_list->list[j].y_pos_strand == 0)
{
recover_UC_Read(overlap_read, &R_INF, overlap_list->list[j].y_id);
}
else
{
recover_UC_Read_RC(overlap_read, &R_INF, overlap_list->list[j].y_id);
}
if(if_exact_match(g_read->seq, g_read->length, overlap_read->seq, overlap_read->length,
overlap_list->list[j].x_pos_s, overlap_list->list[j].x_pos_e,
overlap_list->list[j].y_pos_s, overlap_list->list[j].y_pos_e))
{
overlap_list->list[j].shared_seed = 1;
}
else
{
overlap_list->list[j].shared_seed = 0;
}
}
}
else
{
overlap_list->list[j].is_match = 3;
}
}
else
{
overlap_list->list[j].is_match = 3;
}
j++;
inner_j++;
}
}
}
void update_exact_overlaps(overlap_region_alloc* overlap_list, UC_Read* g_read, UC_Read* overlap_read)
{
uint64_t j;
for (j = 0; j < overlap_list->length; j++)
{
if (overlap_list->list[j].is_match != 1)
{
if(overlap_list->list[j].y_pos_strand == 0)
{
recover_UC_Read(overlap_read, &R_INF, overlap_list->list[j].y_id);
}
else
{
recover_UC_Read_RC(overlap_read, &R_INF, overlap_list->list[j].y_id);
}
if(if_exact_match(g_read->seq, g_read->length, overlap_read->seq, overlap_read->length,
overlap_list->list[j].x_pos_s, overlap_list->list[j].x_pos_e,
overlap_list->list[j].y_pos_s, overlap_list->list[j].y_pos_e))
{
overlap_list->list[j].is_match = 1;
overlap_list->list[j].strong = 0;
overlap_list->list[j].without_large_indel = 1;
overlap_list->list[j].shared_seed = 1;
}
}
}
}
void ha_print_ovlp_stat(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, long long readNum)
{
long long forward, reverse, strong, weak, exact, no_l_indel;
long long i, j;
no_l_indel = forward = reverse = exact = strong = weak = 0;
for (i = 0; i < readNum; i++) {
forward += paf[i].length;
reverse += rev_paf[i].length;
for (j = 0; j < paf[i].length; j++) {
if (paf[i].buffer[j].el == 1) exact++;
if (paf[i].buffer[j].ml == 1) strong++;
if (paf[i].buffer[j].ml == 0) weak++;
if (paf[i].buffer[j].no_l_indel == 1) no_l_indel++;
}
}
fprintf(stderr, "[M::%s] # overlaps: %lld\n", __func__, forward);
fprintf(stderr, "[M::%s] # strong overlaps: %lld\n", __func__, strong);
fprintf(stderr, "[M::%s] # weak overlaps: %lld\n", __func__, weak);
fprintf(stderr, "[M::%s] # exact overlaps: %lld\n", __func__, exact); // this seems not right
fprintf(stderr, "[M::%s] # inexact overlaps: %lld\n", __func__, forward - exact);
fprintf(stderr, "[M::%s] # overlaps without large indels: %lld\n", __func__, no_l_indel);
fprintf(stderr, "[M::%s] # reverse overlaps: %lld\n", __func__, reverse);
}
void fill_chain(Fake_Cigar* chain, char* x_string, char* y_string, long long xBeg, long long yBeg,
long long x_readLen, long long y_readLen, Cigar_record* cigar, uint8_t* c2n)
{
long long i, xOffset, yOffset, xRegionLen, yRegionLen, /**bandLen,**/ maxXpos, maxYpos, mapScore, zdroped;
///float band_rate = 0.08;
int endbouns;
if(chain->length <= 0) return;
kvec_t(uint8_t) x_num;
kvec_t(uint8_t) y_num;
kv_init(x_num);
kv_init(y_num);
///deal with region 0 backward
i = 0;
endbouns = 0;
xOffset = get_fake_gap_pos(chain, 0);
xOffset = xOffset - 1;
yOffset = (xOffset - xBeg) + yBeg + get_fake_gap_shift(chain, 0);
if(xOffset >= 0 && yOffset >= 0)
{
xRegionLen = xOffset + 1;
yRegionLen = yOffset + 1;
//note here cannot use DIFF(xRegionLen, yRegionLen)
// bandLen = (MIN(xRegionLen, yRegionLen))*band_rate;
// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
///do alignment backward
kv_resize(uint8_t, x_num, (uint64_t)xRegionLen);
kv_resize(uint8_t, y_num, (uint64_t)yRegionLen);
///text is x, query is y
afine_gap_alignment(x_string, x_num.a, xRegionLen, y_string, y_num.a, yRegionLen,
c2n, BACKWARD_KSW, MATCH_SCORE_KSW, MISMATCH_SCORE_KSW, GAP_OPEN_KSW, GAP_EXT_KSW,
/**bandLen,**/BAND_KSW, Z_DROP_KSW, endbouns, &maxXpos, &maxYpos, &mapScore, &zdroped);
// fprintf(stderr, "* xOffset: %lld, yOffset: %lld, xRegionLen: %lld, yRegionLen: %lld, bandLen: %lld, maxXpos: %lld, maxYpos: %lld, zdroped: %lld\n",
// xOffset, yOffset, xRegionLen, yRegionLen, BAND_KSW, maxXpos, maxYpos, zdroped);
}
///align forward
for (i = 0; i < (long long)chain->length; i++)
{
// xOffset = get_fake_gap_pos(chain, i);
// yOffset = xOffset + get_fake_gap_shift(chain, i);
xOffset = get_fake_gap_pos(chain, i);
yOffset = (xOffset - xBeg) + yBeg + get_fake_gap_shift(chain, i);
///last region
if(i == (long long)(chain->length - 1))
{
endbouns = 0;
xRegionLen = x_readLen - xOffset;
yRegionLen = y_readLen - yOffset;
//note here cannot use DIFF(xRegionLen, yRegionLen)
// bandLen = (MIN(xRegionLen, yRegionLen))*band_rate;
// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
}
else
{
///higher endbouns for middle regions
endbouns = MATCH_SCORE_KSW;
xRegionLen = get_fake_gap_pos(chain, i+1) - xOffset;
yRegionLen = (get_fake_gap_pos(chain, i+1) + get_fake_gap_shift(chain, i+1)) -
(get_fake_gap_pos(chain, i) + get_fake_gap_shift(chain, i));
// bandLen = MAX((MIN(xRegionLen, yRegionLen))*band_rate, DIFF(xRegionLen, yRegionLen));
// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
}
///do alignment forward
kv_resize(uint8_t, x_num, (uint64_t)xRegionLen);
kv_resize(uint8_t, y_num, (uint64_t)yRegionLen);
///text is x, query is y
afine_gap_alignment(x_string+xOffset, x_num.a, xRegionLen, y_string+yOffset, y_num.a, yRegionLen,
c2n, FORWARD_KSW, MATCH_SCORE_KSW, MISMATCH_SCORE_KSW, GAP_OPEN_KSW, GAP_EXT_KSW,
/**bandLen,**/BAND_KSW, Z_DROP_KSW, endbouns, &maxXpos, &maxYpos, &mapScore, &zdroped);
// fprintf(stderr, "# xOffset: %lld, yOffset: %lld, xRegionLen: %lld, yRegionLen: %lld, bandLen: %lld, maxXpos: %lld, maxYpos: %lld, zdroped: %lld\n",
// xOffset, yOffset, xRegionLen, yRegionLen, BAND_KSW, maxXpos, maxYpos, zdroped);
}
kv_destroy(x_num);
kv_destroy(y_num);
}
void Final_phasing(overlap_region_alloc* overlap_list, Cigar_record_alloc* cigarline,
UC_Read* g_read, UC_Read* overlap_read, uint8_t* c2n)
{
uint64_t i, xLen, yStrand;
char* x_string;
char* y_string;
Cigar_record* cigar;
resize_Cigar_record_alloc(cigarline, overlap_list->length);
for (i = 0; i < overlap_list->length; i++)
{
if(overlap_list->list[i].is_match == 1 ||
overlap_list->list[i].is_match == 2 ||
overlap_list->list[i].is_match == 3)
{
xLen = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
yStrand = overlap_list->list[i].y_pos_strand;
cigar = &(cigarline->buffer[i]);
///has already been matched exactly
if(overlap_list->list[i].is_match == 1 && overlap_list->list[i].shared_seed == 1)
{
add_cigar_record(g_read->seq + overlap_list->list[i].x_pos_s, xLen, cigar, 0);
}
else
{
if(yStrand == 0)
{
recover_UC_Read(overlap_read, &R_INF, overlap_list->list[i].y_id);
}
else
{
recover_UC_Read_RC(overlap_read, &R_INF, overlap_list->list[i].y_id);
}
x_string = g_read->seq;
y_string = overlap_read->seq;
fill_chain(&(overlap_list->list[i].f_cigar), x_string, y_string,
overlap_list->list[i].x_pos_s, overlap_list->list[i].y_pos_s,
Get_READ_LENGTH(R_INF, overlap_list->list[i].x_id),
Get_READ_LENGTH(R_INF, overlap_list->list[i].y_id), cigar, c2n);
}
}
}
}
static void worker_ov_final(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
uint8_t c2n[256]; // this may be moved to ha_ovec_buf_t, but it should be fast to populate anyway
memset(c2n, 4, 256);
c2n[(uint8_t)'A'] = c2n[(uint8_t)'a'] = 0; c2n[(uint8_t)'C'] = c2n[(uint8_t)'c'] = 1;
c2n[(uint8_t)'G'] = c2n[(uint8_t)'g'] = 2; c2n[(uint8_t)'T'] = c2n[(uint8_t)'t'] = 3; // build the encoding table
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
ha_get_new_candidates(b->ab, i, &b->self_read, &b->olist, &b->clist, 0.001, asm_opt.max_n_chain, 0);
/**
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
&current_cigar, &hap, &second_round, 0, 0);
push_final_overlaps(&(R_INF.paf[i]), &overlap_list);
**/
overlap_region_sort_y_id(b->olist.list, b->olist.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);
ma_hit_sort_tn(R_INF.reverse_paf[i].buffer, R_INF.reverse_paf[i].length);
update_overlaps(&b->olist, &(R_INF.paf[i]), &b->self_read, &b->ovlp_read, 1, 1);
update_overlaps(&b->olist, &(R_INF.reverse_paf[i]), &b->self_read, &b->ovlp_read, 2, 0);
///recover missing exact overlaps
update_exact_overlaps(&b->olist, &b->self_read, &b->ovlp_read);
///Final_phasing(&overlap_list, &cigarline, &g_read, &overlap_read, c2n);
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);
}
void Output_PAF()
{
fprintf(stderr, "Writing PAF to disk ...... \n");
char* paf_name = (char*)malloc(strlen(asm_opt.output_file_name)+50);
sprintf(paf_name, "%s.ovlp.paf", asm_opt.output_file_name);
FILE* output_file = fopen(paf_name, "w");
uint64_t i, j;
ma_hit_t_alloc* sources = R_INF.paf;
for (i = 0; i < R_INF.total_reads; i++)
{
for (j = 0; j < sources[i].length; j++)
{
fwrite(Get_NAME(R_INF, Get_qn(sources[i].buffer[j])), 1,
Get_NAME_LENGTH(R_INF, Get_qn(sources[i].buffer[j])), output_file);
fwrite("\t", 1, 1, output_file);
fprintf(output_file, "%lu\t", (unsigned long)Get_READ_LENGTH(R_INF, Get_qn(sources[i].buffer[j])));
fprintf(output_file, "%d\t", Get_qs(sources[i].buffer[j]));
fprintf(output_file, "%d\t", Get_qe(sources[i].buffer[j]));
if(sources[i].buffer[j].rev)
{
fprintf(output_file, "-\t");
}
else
{
fprintf(output_file, "+\t");
}
fwrite(Get_NAME(R_INF, Get_tn(sources[i].buffer[j])), 1,
Get_NAME_LENGTH(R_INF, Get_tn(sources[i].buffer[j])), output_file);
fwrite("\t", 1, 1, output_file);
fprintf(output_file, "%lu\t", (unsigned long)Get_READ_LENGTH(R_INF, Get_tn(sources[i].buffer[j])));
fprintf(output_file, "%d\t", Get_ts(sources[i].buffer[j]));
fprintf(output_file, "%d\t", Get_te(sources[i].buffer[j]));
fprintf(output_file, "%d\t", sources[i].buffer[j].ml);
fprintf(output_file, "%d\t", sources[i].buffer[j].bl);
fprintf(output_file, "255\n");
}
}
free(paf_name);
fclose(output_file);
fprintf(stderr, "PAF has been written.\n");
}
int check_cluster(uint64_t* list, long long listLen, ma_hit_t_alloc* paf, float threshold)
{
long long i, k;
uint32_t qn, tn;
long long T_edges, A_edges;
T_edges = A_edges = 0;
for (i = 0; i < listLen; i++)
{
qn = (uint32_t)list[i];
for (k = i + 1; k < listLen; k++)
{
tn = (uint32_t)list[k];
if(get_specific_overlap(&(paf[qn]), qn, tn) != -1)
{
A_edges++;
}
if(get_specific_overlap(&(paf[tn]), tn, qn) != -1)
{
A_edges++;
}
T_edges = T_edges + 2;
}
}
if(A_edges >= (T_edges*threshold))
{
return 1;
}
else
{
return 0;
}
}
void rescue_edges(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf,
long long readNum, long long rescue_threshold, float cluster_threshold)
{
double startTime = Get_T();
long long i, j, revises = 0;
uint32_t qn, tn;
kvec_t(uint64_t) edge_vector;
kv_init(edge_vector);
kvec_t(uint64_t) edge_vector_index;
kv_init(edge_vector_index);
uint64_t flag;
int index;
for (i = 0; i < readNum; i++)
{
edge_vector.n = 0;
edge_vector_index.n = 0;
for (j = 0; j < paf[i].length; j++)
{
qn = Get_qn(paf[i].buffer[j]);
tn = Get_tn(paf[i].buffer[j]);
index = get_specific_overlap(&(rev_paf[tn]), tn, qn);
if(index != -1)
{
flag = tn;
flag = flag << 32;
flag = flag | (uint64_t)(index);
kv_push(uint64_t, edge_vector, flag);
kv_push(uint64_t, edge_vector_index, j);
}
}
///the read itself has these overlaps, but all related reads do not have
///we need to remove all overlaps from paf[i], and then add all overlaps to rev_paf[i]
if((long long)edge_vector.n >= rescue_threshold &&
check_cluster(edge_vector.a, edge_vector.n, paf, cluster_threshold) == 1)
{
add_overlaps(&(paf[i]), &(rev_paf[i]), edge_vector_index.a, edge_vector_index.n);
remove_overlaps(&(paf[i]), edge_vector_index.a, edge_vector_index.n);
revises = revises + edge_vector.n;
}
edge_vector.n = 0;
edge_vector_index.n = 0;
for (j = 0; j < rev_paf[i].length; j++)
{
qn = Get_qn(rev_paf[i].buffer[j]);
tn = Get_tn(rev_paf[i].buffer[j]);
index = get_specific_overlap(&(paf[tn]), tn, qn);
if(index != -1)
{
flag = tn;
flag = flag << 32;
flag = flag | (uint64_t)(index);
kv_push(uint64_t, edge_vector, flag);
kv_push(uint64_t, edge_vector_index, j);
}
}
///the read itself do not have these overlaps, but all related reads have
///we need to remove all overlaps from rev_paf[i], and then add all overlaps to paf[i]
if((long long)edge_vector.n >= rescue_threshold &&
check_cluster(edge_vector.a, edge_vector.n, paf, cluster_threshold) == 1)
{
remove_overlaps(&(rev_paf[i]), edge_vector_index.a, edge_vector_index.n);
add_overlaps_from_different_sources(paf, &(paf[i]), edge_vector.a, edge_vector.n);
revises = revises + edge_vector.n;
}
}
kv_destroy(edge_vector);
kv_destroy(edge_vector_index);
fprintf(stderr, "[M::%s] took %0.2fs, revise edges #: %lld\n\n", __func__, Get_T()-startTime, revises);
}
void ha_overlap_final(void)
{
int i, hom_cov;
ha_ovec_buf_t **b;
CALLOC(b, asm_opt.thread_num);
for (i = 0; i < asm_opt.thread_num; ++i)
b[i] = ha_ovec_init(1);
ha_idx = ha_pt_gen(&asm_opt, ha_flt_tab, 1, &R_INF, &hom_cov); // build the index
kt_for(asm_opt.thread_num, worker_ov_final, b, R_INF.total_reads);
ha_pt_destroy(ha_idx);
ha_idx = 0;
for (i = 0; i < asm_opt.thread_num; ++i)
ha_ovec_destroy(b[i]);
free(b);
}
int ha_assemble(void)
{
int r, hom_cov = -1, ovlp_loaded = 0;
if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
ovlp_loaded = 1;
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
trio_partition();
}
if (!ovlp_loaded) {
// construct hash table for high occurrence k-mers
if (!asm_opt.no_kmer_flt) {
ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov);
ha_opt_update_cov(&asm_opt, hom_cov);
}
// error correction
assert(asm_opt.number_of_round > 0);
for (r = 0; r < asm_opt.number_of_round; ++r) {
ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
ha_overlap_and_correct(r);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> corrected reads for round %d\n", __func__, yak_realtime(),
yak_cpu_usage(), yak_peakrss_in_gb(), r + 1);
fprintf(stderr, "[M::%s] # bases: %lld; # corrected bases: %lld; # recorrected bases: %lld\n", __func__,
asm_opt.num_bases, asm_opt.num_corrected_bases, asm_opt.num_recorrected_bases);
fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
}
//Output_corrected_reads();
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> written corrected reads to disk\n", __func__, yak_realtime(), yak_cpu_usage());
// overlap between corrected reads
ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
ha_overlap_final();
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(),
yak_cpu_usage(), yak_peakrss_in_gb());
ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
ha_ft_destroy(ha_flt_tab);
//Output_PAF();
trio_partition();
}
build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf,
R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round,
asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
if (asm_opt.verbose_gfa) R_INF.paf = R_INF.reverse_paf = 0; // with --dbg-gfa, R_INF.paf and R_INF.reverse_paf are freed in load_debug_graph()
destory_All_reads(&R_INF);
return 0;
}
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