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final DP-based assembly

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This commit is contained in:
Haoyu Cheng
2019-11-13 20:18:11 -05:00
parent d6c6a1fa11
commit ada03ea388
22 changed files with 19432 additions and 1178 deletions
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96
Process_Read.cpp
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@@ -74,9 +74,10 @@ void destory_All_reads(All_reads* r)
void write_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Writing reads to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
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(&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);
@@ -127,6 +128,7 @@ void write_All_reads(All_reads* r, char* read_file_name)
free(index_name);
fflush(fp);
fclose(fp);
fprintf(stdout, "Reads has been written.\n");
}
@@ -136,7 +138,7 @@ void write_All_reads(All_reads* r, char* read_file_name)
int load_All_reads(All_reads* r, char* read_file_name)
{
fprintf(stdout, "Loading reads to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
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)
@@ -144,7 +146,14 @@ 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)
{
fprintf(stdout, "the adapterLen of index is: %d, but the adapterLen set by user is: %d\n",
local_adapterLen, 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);
@@ -210,6 +219,8 @@ int load_All_reads(All_reads* r, char* read_file_name)
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);
for (i = 0; i < r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
@@ -219,9 +230,14 @@ int load_All_reads(All_reads* r, char* read_file_name)
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]));
}
free(index_name);
fclose(fp);
fprintf(stdout, "Reads has been loaded.\n");
@@ -279,6 +295,8 @@ void malloc_All_reads(All_reads* r)
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);
for (i = 0; i < r->total_reads; i++)
{
r->second_round_cigar[i].size = r->cigars[i].size = 0;
@@ -288,9 +306,19 @@ void malloc_All_reads(All_reads* r)
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]));
}
r->name = (char*)malloc(sizeof(char)*r->total_name_length);
r->N_site = (uint64_t**)calloc(r->total_reads, sizeof(uint64_t*));
@@ -658,21 +686,47 @@ void compress_base(uint8_t* dest, char* src, uint64_t src_l, uint64_t** N_site_l
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++;
}
@@ -716,7 +770,7 @@ inline void exchage_kstring_t(kstring_t* a, kstring_t* b)
*b = tmp;
}
int get_read(kseq_t *s)
int get_read(kseq_t *s, int adapterLen)
{
int l;
@@ -727,6 +781,24 @@ int get_read(kseq_t *s)
exchage_kstring_t(&seq->name, &s->name);
exchage_kstring_t(&seq->qual, &s->qual);
exchage_kstring_t(&seq->seq, &s->seq);
if(adapterLen > 0)
{
if(s->seq.l <= adapterLen*2)
{
s->seq.l = 0;
}
else
{
long long i;
for (i = 0; i < (s->seq.l - adapterLen*2); i++)
{
s->seq.s[i] = s->seq.s[i + adapterLen];
}
s->seq.l -= adapterLen*2;
}
}
return 1;
}
@@ -770,8 +842,8 @@ void init_R_buffer(int thread_num)
void destory_R_buffer_block(R_buffer_block* curr_sub_block)
{
free(curr_sub_block->read);
kseq_destroy(curr_sub_block->read);
///free(curr_sub_block->read);
}
@@ -790,7 +862,7 @@ void destory_R_buffer()
inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
int* return_file_flag, int is_insert)
int* return_file_flag, int is_insert, int adapterLen)
{
int inner_i = 0;
int file_flag = 1;
@@ -801,18 +873,18 @@ inline void load_read_block(R_buffer_block* read_batch, int batch_read_size,
while (inner_i<batch_read_size)
{
file_flag = get_read(&read_batch->read[inner_i]);
file_flag = get_read(&read_batch->read[inner_i], adapterLen);
if (file_flag == 1)
{
read_batch->read[inner_i].ID = total_reads;
total_reads++;
///fprintf(stderr, "is_insert: %d\n", is_insert);
if (is_insert)
{
insert_read(&R_INF, &read_batch->read[inner_i].seq, &read_batch->read[inner_i].name);
insert_read(&R_INF, &read_batch->read[inner_i].seq,
&read_batch->read[inner_i].name);
}
inner_i++;
@@ -896,7 +968,7 @@ void* input_reads_muti_threads(void* arg)
load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert);
load_read_block(&tmp_buf, RDB.block_inner_size, &file_flag, is_insert, adapterLen);
if (file_flag == 0)
{
@@ -1022,7 +1094,7 @@ void Counting_block()
load_read_block(&tmp_buf, RDB.block_inner_size,
&file_flag, 0);
&file_flag, 0, adapterLen);
if (file_flag == 0)