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seed_ali_core.c
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#include <time.h>
#include <ctype.h>
#include <inttypes.h>
#include <omp.h>
#include <math.h>
//#include "global.h"
#include "binarys_qsort.h"
#include "LandauVishkin.h"
#include "seed_ali_p.h"
#include "bit_operation.h"
#include "ksw.h"
#ifdef PTHREAD_USE
#include <pthread.h>
#ifdef R_W_LOCK
static void *worker(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
int _read_seq;
while (1)
{
pthread_rwlock_wrlock(&rwlock);
_read_seq = read_seq++;
pthread_rwlock_unlock(&rwlock);
if (_read_seq < d->seqn)
{
seed_ali_core(_read_seq, d->tid);
}
else break;
}
return 0;
}
static void *worker_single_end(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
int _read_seq;
while (1)
{
pthread_rwlock_wrlock(&rwlock);
_read_seq = read_seq++;
pthread_rwlock_unlock(&rwlock);
if (_read_seq < d->seqn)
{
seed_ali_core_single_end(_read_seq, d->tid);
}
else break;
}
return 0;
}
#else
static void *worker(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
seed_ali_core(d->seqn, d->tid);
return 0;
}
static void *worker_single_end(void *data)
{
thread_ali_t *d = (thread_ali_t*)data;
seed_ali_core_single_end(d->seqn, d->tid);
return 0;
}
#endif
#endif
int seed_ali()
{
fprintf(stderr, "pair end reads mapping\n\n");
double t = 0.00;
clock_t start = 0, end = 0;
uint8_t readlen_name = 200;
uint16_t v_cnt_i = 0;
//uint16_t read_bit_char = 0;
uint32_t r_i = 0;
uint32_t seqi = 0;
uint32_t seqii = 0;
uint32_t read_in = 0X10000;
int32_t l, m, k1;//maybe changed here
int64_t kr1 = 1;
int64_t kr2 = 1;
char h_chars[6];
#ifdef PAIR_RANDOM_SEED
uint32_t r_dup_i = 0;
uint32_t pos_r_ir = 0;
int pos_r_nr = 0;
#endif
start = clock();
load_index_file();
end = clock();
t = (double)(end - start) / CLOCKS_PER_SEC;
fp1 = gzopen(read_fastq1, "r");
seq1 = kseq_init(fp1);
fp2 = gzopen(read_fastq2, "r");
seq2 = kseq_init(fp2);
if((fp1 == NULL) || (fp2 == NULL))
{
fprintf(stderr, "wrong input file route or name: %s %s\n", read_fastq1, read_fastq2);
exit(1);
}
if(flag_std == 0)
{
fp_sam = fopen(sam_result, "w");
if(fp_sam == NULL)
{
fprintf(stderr, "wrong output file route or name: %s\n", sam_result);
exit(1);
}
}
seed_l_max = seed_step * cir_fix_n;
insert_dis = (upper_ins + floor_ins) >> 1;
devi = (upper_ins - floor_ins) >> 1;
pair_ran_intvp = seed_l_max;
#ifdef SEED_FILTER_POS
seed_filter_pos_num = seed_filter_pos_numn >> 2;
#endif
//fprintf(stderr, "number of threads: %u\nkmer size: %u\ninsert size: %u\nstandard varaiance: %"PRId64"\nseed interval: %u\nthe max read length: %u\nmax lv error rate: %.2f\nmax pair error rate: %.2f\nthe minimum seed interval: %u\nthe number of seed circulation: %u\nlv rate on anchor: %.2f\nthe max rate of mismatch alignment on anchor: %.2f\n", thread_n, k_t, insert_dis, (devi / 3), pair_ran_intvp, readlen_max, lv_rate, max_pair_score_r, seed_step, cir_fix_n, lv_rate_anchor, mis_match_r_single);
fprintf(stderr, "number of threads: %u\nkmer size: %u\nseed interval: %u\nthe max read length: %u\nmax lv error rate: %.2f\nmax pair error rate: %.2f\nthe minimum seed interval: %u\nthe number of seed circulation: %u\nlv rate on anchor: %.2f\nthe max rate of mismatch alignment on anchor: %.2f\n", thread_n, k_t, pair_ran_intvp, readlen_max, lv_rate, max_pair_score_r, seed_step, cir_fix_n, lv_rate_anchor, mis_match_r_single);
fprintf(stderr, "local alignment score match: %d mismatch: %d gap open: %d gap extension: %d\n", mat_score, mis_score, gapo_score, gape_score);
fprintf(stderr, "%lf seconds is used for loading index\n", t);
if(local_ksw) fprintf(stderr, "use local sw alignment\n");
if(last_circle_rate) fprintf(stderr, "use last circle end-to-end alignment and the max rate of alignment score is %.2f\n", last_circle_rate);
if(!mgn_flag) fprintf(stderr, "use the mode of multi-genomes\n");
#ifdef LV_MP
fprintf(stderr, "cal mapping quality on LV\n");
#endif
#ifdef QUAL_ANCHOR
fprintf(stderr, "use quality in anchor\n");
#endif
if(flag_std)
fprintf(stderr, "output alignments by stdout\n");
k_r = k_t - k;
re_b = 32 - k_t;
re_bt = (re_b << 1);
re_2bt = 64 - k_t;
//should allocate at beginning
seed_num = ((readlen_max - k_t) / seed_l_l) + 1;
new_seed_cnt = seed_num * pos_n_max;
uint16_t cigar_max_n = MAX_LV_CIGARCOM;
#ifdef STA_SEED
fp_read = fopen(file_read, "w");
fp_seed = fopen(file_seed, "w");
#endif
//allocation
start = clock();
#ifdef PTHREAD_USE
#ifdef ANCHOR_HASH_ALI
anchor_hash = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_hash[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_hash[r_i][m] = (uint16_t* )calloc(1 << 16, 2);
}
anchor_array = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_array[r_i] = (uint8_t** )calloc(4, sizeof(uint8_t* ));
for(m = 0; m < 4; m++) anchor_array[r_i][m] = (uint8_t* )calloc(readlen_max - k_anchor + 1, 1);
}
anchor_point = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_point[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_point[r_i][m] = (uint16_t* )calloc(readlen_max - k_anchor + 1, 2);
}
anchor_pos = (uint16_t*** )calloc(thread_n, sizeof(uint16_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
anchor_pos[r_i] = (uint16_t** )calloc(4, sizeof(uint16_t* ));
for(m = 0; m < 4; m++) anchor_pos[r_i][m] = (uint16_t* )calloc(readlen_max - k_anchor + 1, 2);
}
rh = (read_h** )calloc(thread_n, sizeof(read_h* ));
for(r_i = 0; r_i < thread_n; r_i++)
rh[r_i] = (read_h* )calloc(readlen_max - k_anchor + 1, sizeof(read_h));
anchor_seed_buffer = (anchor_seed** )calloc(thread_n, sizeof(anchor_seed* ));
for(r_i = 0; r_i < thread_n; r_i++)
anchor_seed_buffer[r_i] = (anchor_seed* )calloc((readlen_max - k_anchor + 1) * insert_dis, sizeof(anchor_seed));
#endif
g_low = (int64_t* )calloc(thread_n, 8);
r_low = (int64_t* )calloc(thread_n, 8);
seedm = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedm[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedu = (seed_m** )calloc(thread_n, sizeof(seed_m* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedu[r_i] = (seed_m* )calloc(seed_num, sizeof(seed_m));
seedsets = (seed_sets** )calloc(thread_n, sizeof(seed_sets* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedsets[r_i] = (seed_sets* )calloc(new_seed_cnt, sizeof(seed_sets));
seed_set_off = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_off[r_i] = (uint32_t* )calloc(new_seed_cnt, sizeof(uint32_t ));
#ifdef UNPIPATH_OFF_K20
seed_set_pos[0][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][0][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[0][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][1][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[1][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][0][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
seed_set_pos[1][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][1][r_i] = (uint64_t* )calloc(new_seed_cnt, 8);
#else
seed_set_pos[0][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][0][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[0][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[0][1][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[1][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][0][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
seed_set_pos[1][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_set_pos[1][1][r_i] = (uint32_t* )calloc(new_seed_cnt, 4);
#endif
seedpa1[0] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa1[0][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa1[1] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa1[1][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa2[0] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa2[0][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
seedpa2[1] = (seed_pa** )calloc(thread_n, sizeof(seed_pa* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpa2[1][r_i] = (seed_pa* )calloc(new_seed_cnt, sizeof(seed_pa ));
fprintf(stderr, "Load seed reduction allocation\n");
#ifdef ALTER_DEBUG
seed_length_arr = (seed_length_array** )calloc(thread_n, sizeof(seed_length_array* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_length_arr[r_i] = (seed_length_array* )calloc(cus_max_output_ali, sizeof(seed_length_array));
rep_go = (uint8_t* )calloc(thread_n, 1);
#endif
#ifdef UNPIPATH_OFF_K20
#ifdef REDUCE_ANCHOR
poses1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses1[r_i] = (uint64_t* )calloc(cus_max_output_ali << 1, 8);
poses2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses2[r_i] = (uint64_t* )calloc(cus_max_output_ali << 1, 8);
#endif
op_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
op_vector_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos2[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
ops_vector_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
ops_vector_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos2[r_i] = (uint64_t* )calloc(cus_max_output_ali, 8);
#else
#ifdef REDUCE_ANCHOR
poses1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses1[r_i] = (uint32_t* )calloc(cus_max_output_ali << 1, 4);
poses2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
poses2[r_i] = (uint32_t* )calloc(cus_max_output_ali << 1, 4);
#endif
op_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
op_vector_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_vector_pos2[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
ops_vector_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos1[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
ops_vector_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_vector_pos2[r_i] = (uint32_t* )calloc(cus_max_output_ali, 4);
#endif
#ifdef REDUCE_ANCHOR
ls1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
rs1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
rs1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
ls2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
rs2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
rs2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
#endif
op_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_l2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_l2[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_r2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_r2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_l1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_l1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_r1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_r1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_l2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_l2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_r2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_r2[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_ex1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_ex1[r_i] = (int* )calloc(cus_max_output_ali, 4);
op_dm_ex2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_dm_ex2[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_ex1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_ex1[r_i] = (int* )calloc(cus_max_output_ali, 4);
ops_dm_ex2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_dm_ex2[r_i] = (int* )calloc(cus_max_output_ali, 4);
//for S
#ifdef QUALS_CHECK
op_err = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_err[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ops_err = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_err[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
#endif
op_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
op_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((op_vector_seq1[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
op_vector_seq2 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
op_vector_seq2[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((op_vector_seq2[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
ops_vector_seq1 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
ops_vector_seq1[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((ops_vector_seq1[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
ops_vector_seq2 = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
ops_vector_seq2[r_i] = (uint64_t** )calloc(cus_max_output_ali, sizeof(uint64_t* ));
for(m = 0; m < cus_max_output_ali; m++)
if((ops_vector_seq2[r_i][m] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8)) == NULL)
exit(1);
}
fprintf(stderr, "Load alignment allocation\n");
#ifdef ALT_ALL
chr_res = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
chr_res[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, 4);
sam_pos1s = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
if((sam_pos1s[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(uint32_t ))) == NULL)
exit(1);
sam_pos2s = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
if((sam_pos2s[r_i] = (uint32_t* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(uint32_t ))) == NULL)
exit(1);
cigar_p1s = (char*** )calloc(thread_n, sizeof(char** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
cigar_p1s[r_i] = (char** )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(char* ));
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if((cigar_p1s[r_i][m] = (char* )calloc(cigar_max_n, 1)) == NULL)
exit(1);
}
cigar_p2s = (char*** )calloc(thread_n, sizeof(char** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
cigar_p2s[r_i] = (char** )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(char* ));
for(m = 0; m < CUS_MAX_OUTPUT_ALI2; m++)
if((cigar_p2s[r_i][m] = (char* )calloc(cigar_max_n, 1)) == NULL)
exit(1);
}
xa_d1s = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
xa_d1s[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
xa_d2s = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
xa_d2s[r_i] = (char* )calloc(CUS_MAX_OUTPUT_ALI2, 1);
lv_re1s = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
lv_re1s[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(int));
lv_re2s = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
lv_re2s[r_i] = (int* )calloc(CUS_MAX_OUTPUT_ALI2, sizeof(int));
#endif
fprintf(stderr, "Load output allocation\n");
#ifdef REDUCE_ANCHOR
rcs1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
rcs1[r_i] = (uint8_t* )calloc(cus_max_output_ali << 1, 1);
rcs2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
rcs2[r_i] = (uint8_t* )calloc(cus_max_output_ali << 1, 1);
#endif
op_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
op_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ops_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ops_rc[r_i] = (uint8_t* )calloc(cus_max_output_ali, 1);
ref_seq_tmp1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ref_seq_tmp1[r_i] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8);
ref_seq_tmp2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ref_seq_tmp2[r_i] = (uint64_t* )calloc(MAX_REF_SEQ_C, 8);
#ifdef UNPIPATH_OFF_K20
mat_pos1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos1[r_i] = (uint64_t* )calloc(CUS_SEED_SET, 8);
mat_pos2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos2[r_i] = (uint64_t* )calloc(CUS_SEED_SET, 8);
#else
mat_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos1[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
mat_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_pos2[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
#endif
mat_rc = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
mat_rc[r_i] = (uint8_t* )calloc(CUS_SEED_SET, 1);
seed_no1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_no1[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
seed_no2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_no2[r_i] = (uint32_t* )calloc(CUS_SEED_SET, 4);
fprintf(stderr, "Load alignment more allocation\n");
#ifdef PAIR_RANDOM
#ifdef UNPIPATH_OFF_K20
seedpos[0][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[0][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[1][0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seedpos[1][1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_single_pos[0] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[0][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_single_pos[1] = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[1][r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
seed_k_pos = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++) //2000
{
seed_k_pos[r_i] = (uint64_t** )calloc(readlen_max / pair_ran_intvp, sizeof(uint64_t* ));
for(m = 0; m < readlen_max / pair_ran_intvp; m++)
if((seed_k_pos[r_i][m] = (uint64_t* )calloc(RANDOM_RANGE, 8)) == NULL)
exit(1);
}
seedposk = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedposk[r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 8);
#else
seedpos[0][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[0][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[0][1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[1][0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seedpos[1][1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos[1][1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_pos[0] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[0][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_pos[1] = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_pos[1][r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_k_pos = (uint32_t*** )calloc(thread_n, sizeof(uint32_t** ));
for(r_i = 0; r_i < thread_n; r_i++) //2000
{
seed_k_pos[r_i] = (uint32_t** )calloc(readlen_max / pair_ran_intvp, sizeof(uint32_t* ));
for(m = 0; m < readlen_max / pair_ran_intvp; m++)
if((seed_k_pos[r_i][m] = (uint32_t* )calloc(RANDOM_RANGE, 4)) == NULL)
exit(1);
}
seedposk = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedposk[r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
#endif
seed_posf[0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_posf[0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seed_posf[1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_posf[1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seed_single_ld[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_ld[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_ld[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_ld[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_rd[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_rd[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_rd[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_rd[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_dm[0] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_dm[0][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
seed_single_dm[1] = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
seed_single_dm[1][r_i] = (int* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 4);
if((seed_single_refs[0] = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ))) == NULL)
exit(1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if((seed_single_refs[0][r_i] = (uint64_t** )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, sizeof(uint64_t* ))) == NULL)
exit(1);
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
{
if((seed_single_refs[0][r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
}
if((seed_single_refs[1] = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ))) == NULL)
exit(1);
for(r_i = 0; r_i < thread_n; r_i++)
{
if((seed_single_refs[1][r_i] = (uint64_t** )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, sizeof(uint64_t* ))) == NULL)
exit(1);
for(m = 0; m < (readlen_max / pair_ran_intvp) * RANDOM_RANGE; m++)
{
if((seed_single_refs[1][r_i][m] = (uint64_t* )calloc((((readlen_max - 1) >> 5) + 3), 8)) == NULL)
exit(1);
}
}
#ifdef PR_SINGLE
seedpos_mis[0][0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[0][0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[0][1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[0][1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[1][0] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[1][0][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
seedpos_mis[1][1] = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
seedpos_mis[1][1][r_i] = (uint8_t* )calloc((readlen_max / pair_ran_intvp) * RANDOM_RANGE, 1);
pr_chr_res1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_chr_res1[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_sam_pos1 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_sam_pos1[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
pr_xa_d1 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_xa_d1[r_i] = (char* )calloc(pr_single_outputn, 1);
pr_lv_re1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_lv_re1[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_chr_res2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_chr_res2[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
pr_sam_pos2 = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_sam_pos2[r_i] = (uint32_t* )calloc(pr_single_outputn, 4);
pr_xa_d2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_xa_d2[r_i] = (char* )calloc(pr_single_outputn, 1);
pr_lv_re2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pr_lv_re2[r_i] = (uint8_t* )calloc(pr_single_outputn, 1);
#endif
fprintf(stderr, "Load pair random allocation\n");
#ifdef PAIR_RANDOM_SEED
seed_r_dup = (uint32_t* )calloc(RANDOM_RANGE, 4);
srand((unsigned)time(0));
pos_r_nr = RANDOM_RANGE;
r_dup_i = 0;
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_MAX; pos_r_ir++)
if((rand() % (RANDOM_RANGE_MAX - pos_r_ir)) < pos_r_nr)
{
seed_r_dup[r_dup_i++] = pos_r_ir;
pos_r_nr--;
}
random_buffer = (uint32_t* )malloc((RAN_CIR) << 2);
for(pos_r_ir = 0; pos_r_ir < RAN_CIR; pos_r_ir++)
random_buffer[pos_r_ir] = (uint32_t )rand();
#endif
#endif
#ifdef READN_RANDOM_SEED
random_buffer_readn = (uint32_t* )calloc(RANDOM_RANGE_READN, 4);
for(pos_r_ir = 0; pos_r_ir < RANDOM_RANGE_READN; pos_r_ir++)
random_buffer_readn[pos_r_ir] = (uint32_t )rand();
#endif
//thread gloabl value
rc_cov_f = (uint8_t* )calloc(thread_n, 1);
cov_a_n = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
cov_a_n[r_i] = (uint8_t* )calloc(2,1);
cov_a_n_s = (uint8_t* )calloc(thread_n, 1);
s_uid_f = (uint8_t* )calloc(thread_n, 1);
min_mis = (uint8_t* )calloc(thread_n, 1);
de_m_p = (uint8_t* )calloc(thread_n, 1);
de_m_p_o = (uint8_t* )calloc(thread_n, 1);
seed_l = (int16_t* )calloc(thread_n, 2);//cannot be 0
max_mismatch1 = (uint16_t* )calloc(thread_n, 2);
max_mismatch2 = (uint16_t* )calloc(thread_n, 2);
max_mismatch1_single = (uint16_t* )calloc(thread_n, 2);
max_mismatch2_single = (uint16_t* )calloc(thread_n, 2);
#ifdef PR_SINGLE
pr_o_f = (uint8_t* )calloc(thread_n, 1);
seed_re_r = (uint8_t* )calloc(thread_n, 1);
#endif
end_dis1 = (uint16_t* )calloc(thread_n, 2);
end_dis2 = (uint16_t* )calloc(thread_n, 2);
mat_posi = (uint32_t* )calloc(thread_n, 4);
#ifdef PAIR_SEED_LENGTH_FILT
max_lengtht = (uint32_t* )calloc(thread_n, 4);
#endif
#ifdef REDUCE_ANCHOR
orders1 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
orders1[r_i] = (uint16_t* )calloc(cus_max_output_ali << 1, 2);
orders2 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
orders2[r_i] = (uint16_t* )calloc(cus_max_output_ali << 1, 2);
dms1 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
dms1[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
dms2 = (int** )calloc(thread_n, sizeof(int* ));
for(r_i = 0; r_i < thread_n; r_i++)
dms2[r_i] = (int* )calloc(cus_max_output_ali << 1, 4);
#endif
dm_op = (int* )calloc(thread_n, 4);
dm_ops = (int* )calloc(thread_n, 4);
low_mask1 = (uint64_t* )calloc(thread_n, 8);
low_mask2 = (uint64_t* )calloc(thread_n, 8);
pos_add = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
pos_add[r_i] = (uint8_t* )calloc(pos_n_max, 1);
cigar_m1 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
cigar_m1[r_i] = (char* )calloc(CIGARMN, 1);
cigar_m2 = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
cigar_m2[r_i] = (char* )calloc(CIGARMN, 1);
ali_ref_seq = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
ali_ref_seq[r_i] = (char* )calloc(readlen_max + 64, 1);
read_char = (char** )calloc(thread_n, sizeof(char* ));
for(r_i = 0; r_i < thread_n; r_i++)
read_char[r_i] = (char* )calloc(readlen_max + 32, 1);
pos_ren[0][0] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[0][1] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[1][0] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
pos_ren[1][1] = (uint16_t* )calloc(thread_n, sizeof(uint16_t ));
sub_mask1 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
sub_mask1[r_i] = (uint16_t* )calloc(33, 2);
sub_mask2 = (uint16_t** )calloc(thread_n, sizeof(uint16_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
sub_mask2[r_i] = (uint16_t* )calloc(33, 2);
seedpos_misn[0][0] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[0][1] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[1][0] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
seedpos_misn[1][1] = (uint32_t* )calloc(thread_n, sizeof(uint32_t ));
ex_d_mask1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ex_d_mask1[r_i] = (uint64_t* )calloc(33, 8);
ex_d_mask2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ex_d_mask2[r_i] = (uint64_t* )calloc(33, 8);
#ifdef PAIR_RANDOM
#ifdef UNPIPATH_OFF_K20
b = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
b[r_i] = (uint64_t* )calloc((readlen_max / pair_ran_intvp) + 1, 8);
#else
b = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
b[r_i] = (uint32_t* )calloc((readlen_max / pair_ran_intvp) + 1, 4);
#endif
ls = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
ls[r_i] = (uint32_t* )calloc(readlen_max / pair_ran_intvp, 4);
read_bit_pr = (uint64_t*** )calloc(thread_n, sizeof(uint64_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
read_bit_pr[r_i] = (uint64_t** )calloc(4, sizeof(uint64_t* ));
read_val_pr = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
read_val_pr[r_i] = (uint8_t** )calloc(4, sizeof(uint8_t* ));
kcol = (uint32_t** )calloc(thread_n, sizeof(uint32_t* ));
for(r_i = 0; r_i < thread_n; r_i++)
kcol[r_i] = (uint32_t* )calloc(readlen_max / pair_ran_intvp, 4);
seed_posn[0] = (uint32_t* )calloc(thread_n, 4);
seed_posn[1] = (uint32_t* )calloc(thread_n, 4);
seedn = (uint16_t* )calloc(thread_n, 2);
#endif
read_bit_1 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
read_bit_2 = (uint64_t** )calloc(thread_n, sizeof(uint64_t* ));
read_val_1 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
read_val_2 = (uint8_t** )calloc(thread_n, sizeof(uint8_t* ));
read_val1 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
read_val1[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
read_val1[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
read_val1[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
read_val2 = (uint8_t*** )calloc(thread_n, sizeof(uint8_t** ));
for(r_i = 0; r_i < thread_n; r_i++)
{
read_val2[r_i] = (uint8_t** )calloc(2, sizeof(uint8_t* ));
read_val2[r_i][0] = (uint8_t* )calloc(readlen_max, 1);
read_val2[r_i][1] = (uint8_t* )calloc(readlen_max, 1);
}
#ifdef QUAL_FILT_LV