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Process_Read.cpp
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Process_Read.cpp
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#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <fcntl.h>
#include "Process_Read.h"
#include "htab.h"
#include "Correct.h"
#include "kalloc.h"
#include <assert.h>
#define UL_FLANK 512
uint8_t seq_nt6_table[256] = {
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 0, 5, 1, 5, 5, 5, 2, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
};
char bit_t_seq_table[256][4] = {{0}};
char bit_t_seq_table_rc[256][4] = {{0}};
char s_H[5] = {'A', 'C', 'G', 'T', 'N'};
char rc_Table[6] = {'T', 'G', 'C', 'A', 'N', 'N'};
void init_All_reads(All_reads* r)
{
memset(r, 0, sizeof(All_reads));
r->index_size = READ_INIT_NUMBER;
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
r->name_index_size = READ_INIT_NUMBER;
r->name_index = (uint64_t*)malloc(sizeof(uint64_t)*r->name_index_size);
r->name_index[0] = 0;
}
void destory_All_reads(All_reads* r)
{
uint64_t i = 0;
for (i = 0; i < r->total_reads; i++) {
if (r->N_site[i]) free(r->N_site[i]);
if (r->read_sperate[i]) free(r->read_sperate[i]);
if (r->paf && r->paf[i].buffer) free(r->paf[i].buffer);
if (r->reverse_paf && r->reverse_paf[i].buffer) free(r->reverse_paf[i].buffer);
///if (r->pb_regions) kv_destroy(r->pb_regions[i].a);
}
free(r->paf);
free(r->reverse_paf);
free(r->N_site);
free(r->read_sperate);
free(r->name);
free(r->name_index);
free(r->read_length);
free(r->trio_flag);
///if (r->pb_regions) free(r->pb_regions);
}
void write_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stderr, "Writing reads to disk... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+15);
sprintf(index_name, "%s.bin", read_file_name);
FILE* fp = fopen(index_name, "w");
fwrite(&asm_opt.adapterLen, sizeof(asm_opt.adapterLen), 1, fp);
fwrite(&r->index_size, sizeof(r->index_size), 1, fp);
fwrite(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
fwrite(&r->total_reads, sizeof(r->total_reads), 1, fp);
fwrite(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
fwrite(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
uint64_t i = 0;
uint64_t zero = 0;
for (i = 0; i < r->total_reads; i++)
{
if (r->N_site[i] != NULL)
{
///number of Ns
fwrite(&r->N_site[i][0], sizeof(r->N_site[i][0]), 1, fp);
if (r->N_site[i][0])
{
fwrite(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
else
{
fwrite(&zero, sizeof(zero), 1, fp);
}
}
fwrite(r->read_length, sizeof(uint64_t), r->total_reads, fp);
for (i = 0; i < r->total_reads; i++)
{
fwrite(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
fwrite(r->name, sizeof(char), r->total_name_length, fp);
fwrite(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
fwrite(r->trio_flag, sizeof(uint8_t), r->total_reads, fp);
fwrite(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp);
fwrite(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp);
free(index_name);
fflush(fp);
fclose(fp);
fprintf(stderr, "Reads has been written.\n");
}
int load_All_reads(All_reads* r, char* read_file_name)
{
char* index_name = (char*)malloc(strlen(read_file_name)+15);
sprintf(index_name, "%s.bin", read_file_name);
FILE* fp = fopen(index_name, "r");
if (!fp) {
free(index_name);
return 0;
}
int local_adapterLen;
int f_flag;
f_flag = fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != asm_opt.adapterLen)
{
fprintf(stderr, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, asm_opt.adapterLen);
exit(1);
}
f_flag += fread(&r->index_size, sizeof(r->index_size), 1, fp);
f_flag += fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
f_flag += fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
f_flag += fread(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
f_flag += fread(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
uint64_t i = 0;
uint64_t zero = 0;
r->N_site = (uint64_t**)malloc(sizeof(uint64_t*)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
f_flag += fread(&zero, sizeof(zero), 1, fp);
if (zero)
{
r->N_site[i] = (uint64_t*)malloc(sizeof(uint64_t)*(zero + 1));
r->N_site[i][0] = zero;
if (r->N_site[i][0])
{
f_flag += fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
else
{
r->N_site[i] = NULL;
}
}
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
f_flag += fread(r->read_length, sizeof(uint64_t), r->total_reads, fp);
r->read_size = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
memcpy (r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
f_flag += fread(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
f_flag += fread(r->name, sizeof(char), r->total_name_length, fp);
r->name_index = (uint64_t*)malloc(sizeof(uint64_t)*r->name_index_size);
f_flag += fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
/****************************may have bugs********************************/
r->trio_flag = (uint8_t*)malloc(sizeof(uint8_t)*r->total_reads);
f_flag += fread(r->trio_flag, sizeof(uint8_t), r->total_reads, fp);
f_flag += fread(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp);
f_flag += fread(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp);
/****************************may have bugs********************************/
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->second_round_cigar = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
for (i = 0; i < r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
r->second_round_cigar[i].length = r->cigars[i].length = 0;
r->second_round_cigar[i].record = r->cigars[i].record = NULL;
r->second_round_cigar[i].lost_base_size = r->cigars[i].lost_base_size = 0;
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
}
///r->pb_regions = NULL;
free(index_name);
fclose(fp);
fprintf(stderr, "Reads has been loaded.\n");
return 1;
}
void read_ma(ma_hit_t* x, FILE* fp)
{
int f_flag;
f_flag = fread(&(x->qns), sizeof(x->qns), 1, fp);
f_flag += fread(&(x->qe), sizeof(x->qe), 1, fp);
f_flag += fread(&(x->tn), sizeof(x->tn), 1, fp);
f_flag += fread(&(x->ts), sizeof(x->ts), 1, fp);
f_flag += fread(&(x->te), sizeof(x->te), 1, fp);
f_flag += fread(&(x->el), sizeof(x->el), 1, fp);
f_flag += fread(&(x->no_l_indel), sizeof(x->no_l_indel), 1, fp);
uint32_t t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->ml = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->rev = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->bl = t;
f_flag += fread(&(t), sizeof(t), 1, fp);
x->del = t;
}
int append_All_reads(All_reads* r, char *idx, uint32_t id)
{
char *gfa_name = NULL; MALLOC(gfa_name, (strlen(idx)+100));
FILE *fp = NULL, *fpo = NULL;
sprintf(gfa_name, "%s.ec%u.bin", idx, id);
fp = fopen(gfa_name, "r");
if (!fp) {free(gfa_name); return 0;}
sprintf(gfa_name, "%s.ovlp%u.source.bin", idx, id);
fpo = fopen(gfa_name, "r");
if (!fpo) {free(gfa_name); fclose(fp); return 0;}
free(gfa_name);
int local_adapterLen, f_flag;
f_flag = fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != asm_opt.adapterLen) {
fprintf(stderr, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, asm_opt.adapterLen);
exit(1);
}
uint64_t index_size0, name_index_size0, total_reads0, total_reads_bases0, total_name_length0;
index_size0 = r->index_size;
total_reads0 = r->total_reads;
total_reads_bases0 = r->total_reads_bases;
total_name_length0 = r->total_name_length;
name_index_size0 = ((total_reads0)?(total_reads0+1):(0));///r->name_index_size;
f_flag += fread(&r->index_size, sizeof(r->index_size), 1, fp);
f_flag += fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
f_flag += fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
f_flag += fread(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
f_flag += fread(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
r->index_size += index_size0;
r->name_index_size += name_index_size0; if(name_index_size0) r->name_index_size--;
r->total_reads += total_reads0;
r->total_reads_bases += total_reads_bases0;
r->total_name_length += total_name_length0;
uint64_t i = 0, zero = 0, k;
REALLOC(r->N_site, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
f_flag += fread(&zero, sizeof(zero), 1, fp);
if (zero) {
r->N_site[i] = (uint64_t*)malloc(sizeof(uint64_t)*(zero + 1));
r->N_site[i][0] = zero;
if (r->N_site[i][0]) {
f_flag += fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
} else {
r->N_site[i] = NULL;
}
}
REALLOC(r->read_length, r->total_reads);
f_flag += fread(r->read_length + total_reads0, sizeof(uint64_t), r->total_reads-total_reads0, fp);
REALLOC(r->read_size, r->total_reads);
memcpy (r->read_size + total_reads0, r->read_length + total_reads0, sizeof(uint64_t)*(r->total_reads-total_reads0));
REALLOC(r->read_sperate, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
f_flag += fread(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
}
REALLOC(r->name, r->total_name_length);
f_flag += fread(r->name + total_name_length0, sizeof(char), r->total_name_length - total_name_length0, fp);
REALLOC(r->name_index, r->name_index_size); uint64_t sft = 0;
if(name_index_size0) sft = r->name_index[--name_index_size0];
// fprintf(stderr, "name_index_size0::%lu, total_reads0::%lu, sft::%lu\n", name_index_size0, total_reads0, sft);
f_flag += fread(r->name_index + name_index_size0, sizeof(uint64_t), r->name_index_size-name_index_size0, fp);
if(sft) {
for (i = name_index_size0; i < r->name_index_size; i++) r->name_index[i] += sft;
}
/****************************may have bugs********************************/
REALLOC(r->trio_flag, r->total_reads);
f_flag += fread(r->trio_flag + total_reads0, sizeof(uint8_t), r->total_reads - total_reads0, fp);
int hom_cov0 = asm_opt.hom_cov, het_cov0 = asm_opt.het_cov;
f_flag += fread(&(asm_opt.hom_cov), sizeof(asm_opt.hom_cov), 1, fp); asm_opt.hom_cov += hom_cov0;
f_flag += fread(&(asm_opt.het_cov), sizeof(asm_opt.het_cov), 1, fp); asm_opt.het_cov += het_cov0;
/****************************may have bugs********************************/
REALLOC(r->cigars, r->total_reads);
REALLOC(r->second_round_cigar, r->total_reads);
for (i = total_reads0; i < r->total_reads; i++) {
r->second_round_cigar[i].size = r->cigars[i].size = 0;
r->second_round_cigar[i].length = r->cigars[i].length = 0;
r->second_round_cigar[i].record = r->cigars[i].record = NULL;
r->second_round_cigar[i].lost_base_size = r->cigars[i].lost_base_size = 0;
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
}
///r->pb_regions = NULL;
REALLOC(r->paf, r->total_reads);
memset(r->paf+total_reads0, 0, sizeof((*(r->paf)))*(r->total_reads - total_reads0));
long long n_read; f_flag = fread(&n_read, sizeof(n_read), 1, fpo); ma_hit_t t;
for (i = total_reads0; i < r->total_reads; i++) {
f_flag += fread(&(r->paf[i].is_fully_corrected), sizeof(r->paf[i].is_fully_corrected), 1, fpo);
f_flag += fread(&(r->paf[i].is_abnormal), sizeof(r->paf[i].is_abnormal), 1, fpo);
f_flag += fread(&(r->paf[i].length), sizeof(r->paf[i].length), 1, fpo);
if(r->paf[i].length == 0) continue;
for (k = 0; k < r->paf[i].length; k++) read_ma(&t, fpo);
r->paf[i].length = 0;
}
REALLOC(r->reverse_paf, r->total_reads);
memset(r->reverse_paf+total_reads0, 0, sizeof((*(r->reverse_paf)))*(r->total_reads - total_reads0));
fclose(fp); fclose(fpo);
fprintf(stderr, "Reads has been loaded.\n");
return 1;
}
int destory_read_bin(All_reads* r)
{
uint64_t i = 0;
for (i = 0; i < r->total_reads; i++)
{
if (r->N_site[i]) free(r->N_site[i]);
if (r->read_sperate[i]) free(r->read_sperate[i]);
if (r->cigars[i].record) free(r->cigars[i].record);
if (r->cigars[i].lost_base) free(r->cigars[i].lost_base);
if (r->second_round_cigar[i].record) free(r->second_round_cigar[i].record);
if (r->second_round_cigar[i].lost_base) free(r->second_round_cigar[i].lost_base);
}
free(r->N_site);
free(r->read_length);
free(r->read_size);
free(r->read_sperate);
free(r->name);
free(r->name_index);
free(r->trio_flag);
free(r->cigars);
free(r->second_round_cigar);
return 1;
}
void ha_insert_read_len(All_reads *r, int read_len, int name_len)
{
r->total_reads++;
r->total_reads_bases += (uint64_t)read_len;
r->total_name_length += (uint64_t)name_len;
// must +1
if (r->index_size < r->total_reads + 2) {
r->index_size = r->index_size * 2 + 2;
r->read_length = (uint64_t*)realloc(r->read_length, sizeof(uint64_t) * r->index_size);
r->name_index_size = r->name_index_size * 2 + 2;
r->name_index = (uint64_t*)realloc(r->name_index, sizeof(uint64_t) * r->name_index_size);
}
r->read_length[r->total_reads - 1] = read_len;
r->name_index[r->total_reads] = r->name_index[r->total_reads - 1] + name_len;
}
void malloc_All_reads(All_reads* r)
{
r->read_size = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
memcpy(r->read_size, r->read_length, sizeof(uint64_t)*r->total_reads);
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
long long i = 0;
for (i = 0; i < (long long)r->total_reads; i++)
{
r->read_sperate[i] = (uint8_t*)malloc(sizeof(uint8_t)*(r->read_length[i]/4+1));
}
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->second_round_cigar = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
r->paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
r->reverse_paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
///r->pb_regions = (kvec_t_u64_warp*)malloc(r->total_reads*sizeof(kvec_t_u64_warp));
for (i = 0; i < (long long)r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
r->second_round_cigar[i].length = r->cigars[i].length = 0;
r->second_round_cigar[i].record = r->cigars[i].record = NULL;
r->second_round_cigar[i].lost_base_size = r->cigars[i].lost_base_size = 0;
r->second_round_cigar[i].lost_base_length = r->cigars[i].lost_base_length = 0;
r->second_round_cigar[i].lost_base = r->cigars[i].lost_base = NULL;
init_ma_hit_t_alloc(&(r->paf[i]));
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
///kv_init(r->pb_regions[i].a);
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
r->trio_flag = (uint8_t*)malloc(r->total_reads*sizeof(uint8_t));
memset(r->trio_flag, AMBIGU, r->total_reads*sizeof(uint8_t));
}
void destory_UC_Read(UC_Read* r)
{
free(r->seq);
}
void init_aux_table()
{
if (bit_t_seq_table[0][0] == 0)
{
uint64_t i = 0;
for (i = 0; i < 256; i++)
{
bit_t_seq_table[i][0] = s_H[((i >> 6)&(uint64_t)3)];
bit_t_seq_table[i][1] = s_H[((i >> 4)&(uint64_t)3)];
bit_t_seq_table[i][2] = s_H[((i >> 2)&(uint64_t)3)];
bit_t_seq_table[i][3] = s_H[(i&(uint64_t)3)];
bit_t_seq_table_rc[i][0] = RC_CHAR(bit_t_seq_table[i][3]);
bit_t_seq_table_rc[i][1] = RC_CHAR(bit_t_seq_table[i][2]);
bit_t_seq_table_rc[i][2] = RC_CHAR(bit_t_seq_table[i][1]);
bit_t_seq_table_rc[i][3] = RC_CHAR(bit_t_seq_table[i][0]);
}
}
}
void init_UC_Read(UC_Read* r)
{
r->length = 0;
r->size = 0;
r->seq = NULL;
if (bit_t_seq_table[0][0] == 0)
{
uint64_t i = 0;
for (i = 0; i < 256; i++)
{
bit_t_seq_table[i][0] = s_H[((i >> 6)&(uint64_t)3)];
bit_t_seq_table[i][1] = s_H[((i >> 4)&(uint64_t)3)];
bit_t_seq_table[i][2] = s_H[((i >> 2)&(uint64_t)3)];
bit_t_seq_table[i][3] = s_H[(i&(uint64_t)3)];
bit_t_seq_table_rc[i][0] = RC_CHAR(bit_t_seq_table[i][3]);
bit_t_seq_table_rc[i][1] = RC_CHAR(bit_t_seq_table[i][2]);
bit_t_seq_table_rc[i][2] = RC_CHAR(bit_t_seq_table[i][1]);
bit_t_seq_table_rc[i][3] = RC_CHAR(bit_t_seq_table[i][0]);
}
}
}
void recover_UC_Read_sub_region(char* r, int64_t start_pos, int64_t length, uint8_t strand, All_reads* R_INF, int64_t ID)
{
int64_t readLen = Get_READ_LENGTH((*R_INF), ID);
int64_t end_pos = start_pos + length - 1, begLen, tailLen, offset, mn, src_i, des_i, i;
uint8_t* src = Get_READ((*R_INF), ID);
if(strand == 0) {
offset = start_pos&3;
begLen = 4-offset;
if(begLen > length) begLen = length;
tailLen = (length-begLen)&3;
mn = (length - begLen - tailLen)>>2;
src_i = start_pos; des_i = 0; i = 0;
if(begLen > 0) {
memcpy(r+des_i, bit_t_seq_table[src[src_i>>2]]+offset, begLen);
des_i += begLen; src_i += begLen;
}
for (i = 0; i < mn; i++) {
memcpy(r+des_i, bit_t_seq_table[src[src_i>>2]], 4);
des_i += 4; src_i += 4;
}
if(tailLen > 0) {
memcpy(r+des_i, bit_t_seq_table[src[src_i>>2]], tailLen);
des_i += tailLen; src_i += tailLen;
}
if (R_INF->N_site[ID]) {
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++) {
if ((long long)R_INF->N_site[ID][i] >= start_pos && (long long)R_INF->N_site[ID][i] <= end_pos) {
r[R_INF->N_site[ID][i] - start_pos] = 'N';
}
else if((long long)R_INF->N_site[ID][i] > end_pos) {
break;
}
}
}
}
else {
start_pos = readLen - start_pos - 1;
end_pos = readLen - end_pos - 1;
begLen = (start_pos+1)&3;
offset = 4 - begLen;
if(begLen > length) begLen = length;
tailLen = (length-begLen)&3;
mn = (length - begLen - tailLen)>>2;
src_i = start_pos; des_i = 0; i = 0;
if(begLen > 0) {
memcpy(r+des_i, bit_t_seq_table_rc[src[src_i>>2]]+offset, begLen);
des_i += begLen; src_i -= begLen;
}
for (i = 0; i < mn; i++) {
memcpy(r+des_i, bit_t_seq_table_rc[src[src_i>>2]], 4);
des_i += 4; src_i -= 4;
}
if(tailLen > 0) {
memcpy(r+des_i, bit_t_seq_table_rc[src[src_i>>2]], tailLen);
des_i += tailLen; src_i -= tailLen;
}
/**
if (R_INF->N_site[ID]) {
offset = readLen - start_pos - 1;
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++) {
if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos) {
r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
}
else if((long long)R_INF->N_site[ID][i] > start_pos) {
break;
}
}
}
**/
if (R_INF->N_site[ID]) {
start_pos = readLen - start_pos - 1; end_pos = readLen - end_pos - 1;
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++) {
offset = readLen - R_INF->N_site[ID][i] - 1;
if(offset >= start_pos && offset <= end_pos) {
r[offset - start_pos] = 'N';
} else if(offset < start_pos) {
break;
}
}
}
}
}
void recover_UC_sub_Read(UC_Read* i_r, long long start_pos, long long length, uint8_t strand, All_reads* R_INF, long long ID)
{
i_r->length = length;i_r->RID = ID;
if (i_r->length + 8 > i_r->size)
{
i_r->size = i_r->length + 4;
i_r->seq = (char*)realloc(i_r->seq,sizeof(char)*(i_r->size));
}
char* r = i_r->seq;
long long readLen = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
long long i;
long long copyLen;
long long end_pos = start_pos + length - 1;
if (strand == 0)
{
i = start_pos;
copyLen = 0;
long long initLen = start_pos % 4;
if (initLen != 0)
{
memcpy(r, bit_t_seq_table[src[i>>2]] + initLen, 4 - initLen);
copyLen = copyLen + 4 - initLen;
i = i + copyLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table[src[i>>2]], 4);
copyLen = copyLen + 4;
i = i + 4;
}
if (R_INF->N_site[ID])
{
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if ((long long)R_INF->N_site[ID][i] >= start_pos && (long long)R_INF->N_site[ID][i] <= end_pos)
{
r[R_INF->N_site[ID][i] - start_pos] = 'N';
}
else if((long long)R_INF->N_site[ID][i] > end_pos)
{
break;
}
}
}
}
else
{
start_pos = readLen - start_pos - 1;
end_pos = readLen - end_pos - 1;
///start_pos > end_pos
i = start_pos;
copyLen = 0;
long long initLen = (start_pos + 1) % 4;
if (initLen != 0)
{
memcpy(r, bit_t_seq_table_rc[src[i>>2]] + 4 - initLen, initLen);
copyLen = copyLen + initLen;
i = i - initLen;
}
while (copyLen < length)
{
memcpy(r+copyLen, bit_t_seq_table_rc[src[i>>2]], 4);
copyLen = copyLen + 4;
i = i - 4;
}
if (R_INF->N_site[ID])
{
long long offset = readLen - start_pos - 1;
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if ((long long)R_INF->N_site[ID][i] >= end_pos && (long long)R_INF->N_site[ID][i] <= start_pos)
{
r[readLen - R_INF->N_site[ID][i] - 1 - offset] = 'N';
}
else if((long long)R_INF->N_site[ID][i] > start_pos)
{
break;
}
}
}
}
}
void recover_UC_Read(UC_Read* r, const All_reads *R_INF, uint64_t ID)
{
r->length = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
if (r->length + 4 > r->size) {
r->size = r->length + 4;
r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
}
uint64_t i = 0;
if(src) {
while ((long long)i < r->length) {
memcpy(r->seq+i, bit_t_seq_table[src[i>>2]], 4);
i = i + 4;
}
if (R_INF->N_site[ID]) {
for (i = 1; i <= R_INF->N_site[ID][0]; i++) r->seq[R_INF->N_site[ID][i]] = 'N';
}
} else {///N
memset(r->seq, 'N', r->length);
}
r->RID = ID;
}
void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
{
r->length = Get_READ_LENGTH((*R_INF), ID);
uint8_t* src = Get_READ((*R_INF), ID);
if (r->length + 4 > r->size) {
r->size = r->length + 4;
r->seq = (char*)realloc(r->seq,sizeof(char)*(r->size));
}
long long last_chr = r->length % 4;
long long i = r->length / 4 - 1 + (last_chr != 0);
long long index = 0;
if(src) {
if(last_chr!=0) {
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]] + 4 - last_chr, last_chr);
index = last_chr;
i--;
}
while (i >= 0) {
memcpy(r->seq + index, bit_t_seq_table_rc[src[i]], 4);
i--;
index = index + 4;
}
if (R_INF->N_site[ID]) {
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++) {
r->seq[r->length - R_INF->N_site[ID][i] - 1] = 'N';
}
}
} else {///N
memset(r->seq, 'N', r->length);
}
}
#define COMPRESS_BASE {c = seq_nt6_table[(uint8_t)src[i]];\
if (c >= 4)\
{\
c = 0;\
(*N_site_lis)[N_site_i] = i;\
N_site_i++;\
}\
i++;}\
void ha_compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_lis, uint64_t N_site_occ)
{
///N_site_lis saves the pos of all Ns in this read
///N_site_lis[0] is the number of Ns
free((*N_site_lis));
if (N_site_occ)
{
(*N_site_lis) = (uint64_t*)malloc(sizeof(uint64_t)*(N_site_occ + 1));
(*N_site_lis)[0] = N_site_occ;
}
else
{
(*N_site_lis) = NULL;
}
uint64_t i = 0;
uint64_t N_site_i = 1;
uint64_t dest_i = 0;
uint8_t tmp = 0;
uint8_t c = 0;
while (i + 4 <= src_l)
{
tmp = 0;
COMPRESS_BASE;
tmp = tmp | (c<<6);
COMPRESS_BASE;
tmp = tmp | (c<<4);
COMPRESS_BASE;
tmp = tmp | (c<<2);
COMPRESS_BASE;
tmp = tmp | c;
dest[dest_i] = tmp;
dest_i++;
}
//at most 3 bases here
uint64_t shift = 6;
if (i < src_l)
{
tmp = 0;
while (i < src_l)
{
COMPRESS_BASE;
tmp = tmp | (c << shift);
shift = shift -2;
}
dest[dest_i] = tmp;
dest_i++;
}
}
void reverse_complement(char* pattern, uint64_t length)
{
uint64_t i = 0;
uint64_t end = length / 2;
char k;
uint64_t index;
for (i = 0; i < end; i++)
{
index = length - i - 1;
k = pattern[index];
pattern[index] = RC_CHAR(pattern[i]);
pattern[i] = RC_CHAR(k);
}
if(length&(uint64_t)1)
{
pattern[end] = RC_CHAR(pattern[end]);
}
}
void init_Debug_reads(Debug_reads* x, const char* file)
{
int nameLen, i, bufLen = 1000;
if((uint64_t)(bufLen) < strlen(file) + 50) bufLen = strlen(file) + 50;
char* Name_Buffer = (char*)malloc(sizeof(char)*bufLen);
fprintf(stderr, "Queried debugging reads at: %s\n", file);
x->fp = fopen(file,"r");
x->query_num = 0;
while(fgets(Name_Buffer, bufLen, x->fp))
{
x->query_num++;
}
x->read_name = (char**)malloc(sizeof(char*)*x->query_num);
x->candidate_count = (kvec_t_u64_warp*)malloc(sizeof(kvec_t_u64_warp)*x->query_num);
x->read_id = NULL; MALLOC(x->read_id, x->query_num);
memset(x->read_id, -1, sizeof((*(x->read_id)))*x->query_num);
fseek(x->fp, 0, SEEK_SET);
i = 0;
while(fgets(Name_Buffer, bufLen, x->fp))
{
nameLen = strlen(Name_Buffer) - 1;
x->read_name[i] = (char*)malloc(sizeof(char)*(nameLen+1));
memcpy(x->read_name[i], Name_Buffer, sizeof(char)*nameLen);
x->read_name[i][nameLen] = '\0';
kv_init(x->candidate_count[i].a);
i++;
}
fclose(x->fp);
sprintf(Name_Buffer, "%s.debug.stdout", file);
x->fp = fopen(Name_Buffer,"w");
fprintf(stderr, "Print debugging information to: %s\n", Name_Buffer);
sprintf(Name_Buffer, "%s.debug.r0.fa", file);
x->fp_r0 = fopen(Name_Buffer,"w");
fprintf(stderr, "Print raw reads to: %s\n", Name_Buffer);
sprintf(Name_Buffer, "%s.debug.r1.fa", file);
x->fp_r1 = fopen(Name_Buffer,"w");
fprintf(stderr, "Print corrected reads to: %s\n", Name_Buffer);
free(Name_Buffer);
}
void destory_Debug_reads(Debug_reads* x)
{
uint64_t i;
for (i = 0; i < x->query_num; i++)
{
free(x->read_name[i]);
kv_destroy(x->candidate_count[i].a);
}
free(x->read_name); free(x->read_id);
fclose(x->fp); fclose(x->fp_r0); fclose(x->fp_r1);
}
void init_all_ul_t(all_ul_t *x, All_reads *hR) {
memset(x, 0, sizeof(*x));
x->hR = hR;
init_aux_table();
}
void destory_all_ul_t(all_ul_t *x) {
uint64_t i;
for (i = 0; i < x->n; i++) {
free(x->a[i].N_site.a); free(x->a[i].r_base.a); free(x->a[i].bb.a);
}
free(x->a);
for (i = 0; i < x->nid.n; i++) free(x->nid.a[i].a);
free(x->nid.a);
free(x->ridx.idx.a); free(x->ridx.occ.a);
// if(x->mm) {
// for (i = 0; i < x->mm->n; i++) free(x->mm->a[i].a);
// free(x->mm->a); free(x->mm); x->mm = NULL;
// }
}
void ha_encode_base(uint8_t* dest, char* src, uint64_t src_l, N_t *nn, uint64_t nn_offset)
{
uint64_t i = 0;
uint64_t dest_i = 0;
uint8_t tmp = 0;
uint8_t c = 0;
while (i + 4 <= src_l) {
tmp = 0;
// fprintf(stderr, "i->%lu, src_l->%ld, src[i]->%c, (uint8_t)src[i]->%u\n", i, src_l, src[i], (uint8_t)src[i]);
c = seq_nt6_table[(uint8_t)src[i]];
if (c >= 4) {
c = 0; kv_push(uint32_t, *nn, i+nn_offset);
}
i++;
tmp = tmp | (c<<6);
c = seq_nt6_table[(uint8_t)src[i]];
if (c >= 4) {
c = 0; kv_push(uint32_t, *nn, i+nn_offset);
}
i++;
tmp = tmp | (c<<4);
c = seq_nt6_table[(uint8_t)src[i]];
if (c >= 4) {
c = 0; kv_push(uint32_t, *nn, i+nn_offset);
}
i++;
tmp = tmp | (c<<2);
c = seq_nt6_table[(uint8_t)src[i]];
if (c >= 4) {
c = 0; kv_push(uint32_t, *nn, i+nn_offset);
}
i++;
tmp = tmp | c;
dest[dest_i] = tmp;
dest_i++;
}
//at most 3 bases here
uint64_t shift = 6;
if (i < src_l) {
tmp = 0;
while (i < src_l) {
c = seq_nt6_table[(uint8_t)src[i]];
if (c >= 4) {
c = 0; kv_push(uint32_t, *nn, i+nn_offset);
}
i++;
tmp = tmp | (c << shift);
shift = shift -2;
}
dest[dest_i] = tmp;
dest_i++;
}
}
#define B4L(x) (((x)>>2)+(((x)&3)?1:0))
void push_subblock_original_bases(char* str, all_ul_t *x, ul_vec_t *p, uint32_t s, uint32_t e, uint32_t subLen)//for debug
{
uc_block_t *b = NULL;
uint32_t qs = s, qe = e;
while (qs < e) {