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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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275
Process_Read.cpp
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@@ -21,30 +21,44 @@ pthread_cond_t i_readinputstallCond;
pthread_mutex_t i_doneMutex;
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[5] = {'T', 'G', 'C', 'A', 'N'};
void init_All_reads(All_reads* r)
{
r->index_size = READ_INIT_NUMBER;
/**********should remove**********/
///r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
///r->index[0] = 0;
///r->read = NULL;
/**********should remove**********/
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
r->read_sperate = NULL;
r->N_site = NULL;
r->total_reads_bases = 0;
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;
r->name = NULL;
r->total_name_length = 0;
r->total_reads = 0;
}
void destory_All_reads(All_reads* r)
@@ -60,24 +74,19 @@ void destory_All_reads(All_reads* r)
}
free(r->N_site);
free(r->read_sperate);
///free(r->read);
free(r->name);
free(r->name_index);
free(r->read_length);
}
void write_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Writing reads to disk ...... \n");
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(&adapterLen, sizeof(adapterLen), 1, fp);
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);
@@ -90,12 +99,10 @@ void write_All_reads(All_reads* r, char* read_file_name)
{
if (r->N_site[i] != NULL)
{
///这个实际上是N的个数
///number of Ns
fwrite(&r->N_site[i][0], sizeof(r->N_site[i][0]), 1, fp);
if (r->N_site[i][0])
{
///r->N_site[i]这实际是个长为r->N_site[i][0]+1
///这里从r->N_site[i] + 1写入了r->N_site[i][0]个元素
fwrite(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
@@ -108,36 +115,25 @@ void write_All_reads(All_reads* r, char* read_file_name)
}
/**********should remove**********/
///fwrite(r->index, sizeof(uint64_t), r->index_size, fp);
/**********should remove**********/
fwrite(r->read_length, sizeof(uint64_t), r->total_reads, fp);
/**********should remove**********/
///fwrite(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), fp);
/**********should remove**********/
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);
free(index_name);
fflush(fp);
fclose(fp);
fprintf(stdout, "Reads has been written.\n");
fprintf(stderr, "Reads has been written.\n");
}
int load_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Loading reads to disk ...... \n");
fprintf(stderr, "Loading reads from 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, "r");
@@ -145,20 +141,20 @@ int load_All_reads(All_reads* r, char* read_file_name)
{
return 0;
}
int local_adapterLen;
fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != adapterLen)
int f_flag;
f_flag = fread(&local_adapterLen, sizeof(local_adapterLen), 1, fp);
if(local_adapterLen != asm_opt.adapterLen)
{
fprintf(stdout, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, 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);
}
fread(&r->index_size, sizeof(r->index_size), 1, fp);
fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
fread(&r->total_reads_bases, sizeof(r->total_reads_bases), 1, fp);
fread(&r->total_name_length, sizeof(r->total_name_length), 1, fp);
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;
@@ -166,7 +162,7 @@ int load_All_reads(All_reads* r, char* read_file_name)
for (i = 0; i < r->total_reads; i++)
{
fread(&zero, sizeof(zero), 1, fp);
f_flag += fread(&zero, sizeof(zero), 1, fp);
if (zero)
{
@@ -175,9 +171,7 @@ int load_All_reads(All_reads* r, char* read_file_name)
r->N_site[i][0] = zero;
if (r->N_site[i][0])
{
///r->N_site[i]这实际是个长为r->N_site[i][0]+1
///这里从r->N_site[i] + 1写入了r->N_site[i][0]个元素
fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
f_flag += fread(r->N_site[i]+1, sizeof(r->N_site[i][0]), r->N_site[i][0], fp);
}
}
else
@@ -187,34 +181,25 @@ int load_All_reads(All_reads* r, char* read_file_name)
}
/**********should remove**********/
///r->index = (uint64_t*)malloc(sizeof(uint64_t)*r->index_size);
///fread(r->index, sizeof(uint64_t), r->index_size, fp);
/**********should remove**********/
r->read_length = (uint64_t*)malloc(sizeof(uint64_t)*r->total_reads);
fread(r->read_length, sizeof(uint64_t), r->total_reads, fp);
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);
/**********should remove**********/
///r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
///fread(r->read, sizeof(uint8_t), (r->total_reads_bases/4 + r->total_reads + 5), fp);
/**********should remove**********/
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));
fread(r->read_sperate[i], sizeof(uint8_t), r->read_length[i]/4+1, fp);
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);
fread(r->name, sizeof(char), r->total_name_length, fp);
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);
fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
f_flag += fread(r->name_index, sizeof(uint64_t), r->name_index_size, fp);
r->cigars = (Compressed_Cigar_record*)malloc(sizeof(Compressed_Cigar_record)*r->total_reads);
@@ -234,13 +219,9 @@ int load_All_reads(All_reads* r, char* read_file_name)
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
}
free(index_name);
fclose(fp);
fprintf(stdout, "Reads has been loaded.\n");
fprintf(stderr, "Reads has been loaded.\n");
return 1;
}
@@ -253,27 +234,17 @@ inline void insert_read(All_reads* r, kstring_t* read, kstring_t* name)
r->total_reads_bases = r->total_reads_bases + read->l;
r->total_name_length = r->total_name_length + name->l;
///必须要+1
///must +1
if (r->index_size < r->total_reads + 2)
{
r->index_size = r->index_size * 2 + 2;
/**********should remove**********/
///r->index = (uint64_t*)realloc(r->index,sizeof(uint64_t)*(r->index_size));
/**********should remove**********/
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));
}
/**********should remove**********/
///r->index[r->total_reads] = r->index[r->total_reads-1] + read->l;
/**********should remove**********/
r->read_length[r->total_reads - 1] = read->l;
//r->index[r->total_reads] = r->index[r->total_reads-1] + read->l/4 + 1;
r->name_index[r->total_reads] = r->name_index[r->total_reads-1] + name->l;
}
void malloc_All_reads(All_reads* r)
@@ -282,13 +253,9 @@ 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);
///必须加r->total_reads
/**********should remove**********/
///r->read = (uint8_t*)malloc(sizeof(uint8_t)*(r->total_reads_bases/4 + r->total_reads + 5));
/**********should remove**********/
r->read_sperate = (uint8_t**)malloc(sizeof(uint8_t*)*r->total_reads);
long long i = 0;
for (i = 0; i < r->total_reads; i++)
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));
}
@@ -297,7 +264,7 @@ void malloc_All_reads(All_reads* r)
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);
for (i = 0; i < r->total_reads; i++)
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;
@@ -310,15 +277,6 @@ void malloc_All_reads(All_reads* r)
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
@@ -422,13 +380,13 @@ void recover_UC_Read_sub_region_begin_end
if (R_INF->N_site[ID])
{
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= start_pos && R_INF->N_site[ID][i] <= end_pos)
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(R_INF->N_site[ID][i] > end_pos)
else if((long long)R_INF->N_site[ID][i] > end_pos)
{
break;
}
@@ -468,14 +426,14 @@ void recover_UC_Read_sub_region_begin_end
{
long long offset = readLen - start_pos - 1;
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= end_pos && R_INF->N_site[ID][i] <= start_pos)
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(R_INF->N_site[ID][i] > start_pos)
else if((long long)R_INF->N_site[ID][i] > start_pos)
{
break;
}
@@ -529,13 +487,13 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
if (R_INF->N_site[ID])
{
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= start_pos && R_INF->N_site[ID][i] <= end_pos)
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(R_INF->N_site[ID][i] > end_pos)
else if((long long)R_INF->N_site[ID][i] > end_pos)
{
break;
}
@@ -575,14 +533,14 @@ void recover_UC_Read_sub_region(char* r, long long start_pos, long long length,
{
long long offset = readLen - start_pos - 1;
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
for (i = 1; i <= (long long)R_INF->N_site[ID][0]; i++)
{
if (R_INF->N_site[ID][i] >= end_pos && R_INF->N_site[ID][i] <= start_pos)
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(R_INF->N_site[ID][i] > start_pos)
else if((long long)R_INF->N_site[ID][i] > start_pos)
{
break;
}
@@ -609,7 +567,7 @@ void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID)
uint64_t i = 0;
while (i < r->length)
while ((long long)i < r->length)
{
memcpy(r->seq+i, bit_t_seq_table[src[i>>2]], 4);
i = i + 4;
@@ -660,7 +618,7 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
if (R_INF->N_site[ID])
{
for (i = 1; i <= R_INF->N_site[ID][0]; i++)
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';
}
@@ -670,7 +628,7 @@ void recover_UC_Read_RC(UC_Read* r, All_reads* R_INF, uint64_t ID)
#define COMPRESS_BASE {c = seq_nt6_table[src[i]];\
#define COMPRESS_BASE {c = seq_nt6_table[(uint8_t)src[i]];\
if (c >= 4)\
{\
c = 0;\
@@ -699,59 +657,31 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
uint64_t dest_i = 0;
uint8_t tmp = 0;
uint8_t c = 0;
/**
fprintf(stderr, "src_l: %lld\n", src_l);
fflush(stderr);
**/
while (i + 4 <= src_l)
{
// fprintf(stderr, "0 i: %d, dest_i: %d, src_l: %d\n",
// i, dest_i, src_l);
// fflush(stderr);
tmp = 0;
COMPRESS_BASE;
tmp = tmp | (c<<6);
// fprintf(stderr, "*******1******1 i: %d, tmp: %d, c: %d\n",
// i, tmp, c);
// fflush(stderr);
COMPRESS_BASE;
tmp = tmp | (c<<4);
// fprintf(stderr, "*******2******1 i: %d, tmp: %d, c: %d\n",
// i, tmp, c);
// fflush(stderr);
COMPRESS_BASE;
tmp = tmp | (c<<2);
// fprintf(stderr, "*******3******1 i: %d, tmp: %d, c: %d\n",
// i, tmp, c);
// fflush(stderr);
COMPRESS_BASE;
tmp = tmp | c;
// fprintf(stderr, "*******4******1 i: %d, tmp: %d, c: %d\n",
// i, tmp, c);
// fflush(stderr);
dest[dest_i] = tmp;
// fprintf(stderr, "2 i: %d, dest_i: %d, src_l: %d\n",
// i, dest_i, src_l);
// fflush(stderr);
dest_i++;
}
//最多还剩3个字符
//at most 3 bases here
uint64_t shift = 6;
if (i < src_l)
{
@@ -773,6 +703,11 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
void init_kseq(char* file)
{
fp = gzopen(file, "r");
if (fp == 0)
{
fprintf(stderr, "[ERROR] Cannot find the input file: %s\n", file);
exit(0);
}
seq = kseq_init(fp);
}
@@ -805,14 +740,14 @@ int get_read(kseq_t *s, int adapterLen)
if(adapterLen > 0)
{
if(s->seq.l <= adapterLen*2)
if((int)s->seq.l <= adapterLen*2)
{
s->seq.l = 0;
}
else
{
long long i;
for (i = 0; i < (s->seq.l - adapterLen*2); i++)
for (i = 0; i < ((int)s->seq.l - adapterLen*2); i++)
{
s->seq.s[i] = s->seq.s[i + adapterLen];
}
@@ -864,7 +799,6 @@ void init_R_buffer(int thread_num)
void destory_R_buffer_block(R_buffer_block* curr_sub_block)
{
kseq_destroy(curr_sub_block->read);
///free(curr_sub_block->read);
}
@@ -975,7 +909,6 @@ void* input_reads_muti_threads(void* arg)
total_reads = 0;
int i = 0;
int file_flag = 1;
R_buffer_block tmp_buf;
@@ -986,10 +919,7 @@ void* input_reads_muti_threads(void* arg)
while (1)
{
load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert, adapterLen);
load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert, asm_opt.adapterLen);
if (file_flag == 0)
{
@@ -1020,13 +950,11 @@ void* input_reads_muti_threads(void* arg)
destory_R_buffer_block(&tmp_buf);
fprintf(stdout, "total_reads: %llu\n",total_reads);
///fprintf(stdout, "R_INF.total_reads: %llu\n",R_INF.total_reads);
///fprintf(stdout, "R_INF.index[R_INF.total_reads]: %llu\n",R_INF.index[R_INF.total_reads]);
fprintf(stdout, "R_INF.total_reads_bases: %llu\n",R_INF.total_reads_bases);
///fprintf(stdout, "R_INF.name_index[R_INF.total_reads]: %llu\n",R_INF.name_index[R_INF.total_reads]);
fprintf(stdout, "R_INF.total_name_length: %llu\n",R_INF.total_name_length);
fprintf(stderr, "Reads #: %lu\n",total_reads);
fprintf(stderr, "Bases #: %lu\n",R_INF.total_reads_bases);
return NULL;
}
@@ -1078,7 +1006,7 @@ int get_reads_mul_thread(R_buffer_block* curr_sub_block)
void reverse_complement(char* pattern, uint64_t length)
{
int i = 0;
uint64_t i = 0;
uint64_t end = length / 2;
char k;
uint64_t index;
@@ -1099,44 +1027,3 @@ void reverse_complement(char* pattern, uint64_t length)
}
void Counting_block()
{
long long read_number = 0;
int i = 0;
int file_flag = 1;
R_buffer_block tmp_buf;
init_R_buffer_block(&tmp_buf);
while (1)
{
load_read_block(&tmp_buf, RDB.block_inner_size,
&file_flag, 0, adapterLen);
if (file_flag == 0)
{
break;
}
for (i = 0; i < tmp_buf.num; i++)
{
fprintf(stderr,"@%s\n", tmp_buf.read[i].name.s);
fprintf(stderr,"%s\n",tmp_buf.read[i].seq.s);
fprintf(stderr,"+\n");
fprintf(stderr,"%s\n",tmp_buf.read[i].qual.s);
read_number++;
}
}
fprintf(stdout, "read_number: %lld\n",read_number);
}