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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;
}
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;
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';
}
}
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(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';
}
}
}
#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) {
qe = qs + subLen; if(qe > e) qe = e;
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (uint32_t)-1; b->rev = 0;
b->qs = qs; b->qe = qe;
b->ts = p->r_base.n; b->te = b->ts + B4L(b->qe - b->qs);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
ha_encode_base(p->r_base.a+b->ts, str+b->qs, b->qe-b->qs, &(p->N_site), b->qs);
qs = qe;
}
}
void append_ul_t_compress_ovlp(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on) {
int64_t i, mine, maxs, ovlp, end;
ul_vec_t *p = NULL;
nid_t *np = NULL;
ul_ov_t *z = NULL, *zp = NULL;
uc_block_t *b = NULL;
if(id) {
kv_pushp(nid_t, x->nid, &np);
np->n = id_l; MALLOC(np->a, np->n+1); memcpy(np->a, id, id_l); np->a[id_l] = '\0';
}
if(str) {
if(rid == NULL) {
kv_pushp(ul_vec_t, *x, &p);
memset(p, 0, sizeof(*p));
} else {
if((*rid) >= x->m) kv_resize(ul_vec_t, *x, (*rid) + 1);
if((*rid) >= x->n) {
memset(x->a+x->n, 0, sizeof(*p)*((*rid) + 1 - x->n));
x->n = (*rid) + 1;
}
p = &(x->a[(*rid)]);
}
p->bb.n = p->N_site.n = p->r_base.n = 0;
p->rlen = str_l;
if(o == NULL || on == 0) on = 0;
for (i = end = 0, zp = NULL; i < on; i++) {
z = &(o[i]);
if(!z->el) continue;
if(zp) {
mine = MIN(zp->qe, z->qe); maxs = MAX(zp->qs, z->qs);
ovlp = mine - maxs;
if(zp->qe >= z->qe && zp->qs <= z->qs) continue;
} else {
ovlp = -z->qs;
}
if(ovlp < 0) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (uint32_t)-1/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qs = end; b->qe = b->qs - ovlp;
b->ts = p->r_base.n; b->te = b->ts + B4L(-ovlp);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
ha_encode_base(p->r_base.a+b->ts, str+b->qs, b->qe-b->qs, &(p->N_site), b->qs);
}
///push ovlp bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (z->tn<<1)>>1; b->rev = z->rev; b->base = 0; b->pchain = 0;
b->qs = z->qs + (ovlp>0?ovlp:0); b->qe = z->qe;
if(z->rev) {
b->ts = z->ts; b->te = z->ts + (b->qe - b->qs);
} else {
b->ts = z->te - (b->qe - b->qs); b->te = z->te;
}
end = MAX(zp?zp->qe:0, z->qe);
}
if(end < str_l) {///push original bases
kv_pushp(uc_block_t, p->bb, &b);
b->hid = (uint32_t)-1/**x->mm**/; b->rev = 0; b->base = 1; b->pchain = 0;
b->qs = end; b->qe = str_l;
b->ts = p->r_base.n; b->te = b->ts + B4L(b->qe - b->qs);
kv_resize(uint8_t, p->r_base, b->te); p->r_base.n = b->te;
ha_encode_base(p->r_base.a+b->ts, str+b->qs, b->qe-b->qs, &(p->N_site), b->qs);
// push_subblock_original_bases(str, x, p, end, str_l, 321);//for debug
}
// char *sst = NULL; CALLOC(sst, str_l);//for debug
// retrieve_ul_t(NULL, sst, x, rid?*rid:x->n-1, 0, 0, -1);
// if(memcmp(sst, str, str_l)) {
// fprintf(stderr, "ap-Wrong read, id: %ld, [%d, %ld)\n", (int64_t)(rid?*rid:x->n-1), 0, str_l);
// for (i = 0; i < str_l; i++) {
// if(sst[i] != str[i]) fprintf(stderr, "[%ld] input:%c, decompress:%c\n", i, str[i], sst[i]);
// }
// }
// free(sst);
}
}
void debug_append_ul_t(ul_ov_t *o, int64_t on, ul_vec_t *p)
{
int64_t k, l = 0;
uint32_t sp = (uint32_t)-1, ep = (uint32_t)-1, qss, qee, m;
for (k = on-1; k >= 0; k--) {
if(sp == (uint32_t)-1 || o[k].qe <= sp) {
if(sp != (uint32_t)-1) l += ep - sp;
if(sp == (uint32_t)-1) qss = o[k].qe, qee = p->rlen;
else qss = o[k].qe, qee = sp;
if(qee > qss) {
for (m = 0; m < p->bb.n; m++) {
if(qss == (p->bb.a[m].qs+((p->bb.a[m].hid>>15)&(0x7fffU))) &&
qee == (p->bb.a[m].qe-(p->bb.a[m].hid&(0x7fffU)))) {
break;
}
}
if(m >= p->bb.n) fprintf(stderr, "ERROR\n");
}
sp = o[k].qs;
ep = o[k].qe;
} else {
sp = MIN(sp, o[k].qs);
}
}
if(sp != (uint32_t)-1) l += ep - sp;
if(sp == (uint32_t)-1) qss = 0, qee = p->rlen;
else qss = 0, qee = sp;
if(qee > qss) {
for (m = 0; m < p->bb.n; m++) {
if(qss == (p->bb.a[m].qs+((p->bb.a[m].hid>>15)&(0x7fffU))) &&
qee == (p->bb.a[m].qe-(p->bb.a[m].hid&(0x7fffU)))) {
break;
}
}
if(m >= p->bb.n) fprintf(stderr, "ERROR\n");
}
}
void append_ul_t_back(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on, float p_chain_rate) {
int64_t i, mine, maxs, ovlp, st, et, bl = 0, pc = 0;
uint32_t o_l, o_r;
ul_vec_t *p = NULL;
nid_t *np = NULL;
ul_ov_t *z = NULL;
uc_block_t *b = NULL, tt;
if(id) {
kv_pushp(nid_t, x->nid, &np);
np->n = id_l; MALLOC(np->a, np->n+1); memcpy(np->a, id, id_l); np->a[id_l] = '\0';
}