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prepare for integration with hifiasm

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This commit is contained in:
Heng Li
2020-03-26 11:33:52 -04:00
parent 60d94790a2
commit c3bbaa8a39
3 changed files with 38 additions and 157 deletions
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Process_Read.h
+3 -14
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@@ -25,11 +25,9 @@
#define Get_NAME(R_INF, ID) R_INF.name + R_INF.name_index[(ID)]
KSEQ_INIT(gzFile, gzread)
extern uint8_t seq_nt6_table[256];
extern char bit_t_seq_table[256][4];
extern char bit_t_seq_table_rc[256][4];
@@ -43,7 +41,6 @@ extern char rc_Table[5];
void init_aux_table();
int get_read(kseq_t *s, int adapterLen);
typedef struct
{
uint64_t x_id;
@@ -76,7 +73,6 @@ inline void init_PAF_alloc(PAF_alloc* list)
list->list = (PAF*)malloc(sizeof(PAF)*list->size);
}
inline void append_PAF_alloc(PAF_alloc* list, PAF* e)
{
if(list->length+1 > list->size)
@@ -89,9 +85,6 @@ inline void append_PAF_alloc(PAF_alloc* list, PAF* e)
list->length++;
}
typedef struct
{
/**[0-1] bits are type:**/
@@ -104,7 +97,7 @@ typedef struct
uint32_t lost_base_length;
uint32_t lost_base_size;
uint32_t new_length;
}Compressed_Cigar_record;
} Compressed_Cigar_record;
#define AMBIGU 0
#define FATHER 1
@@ -112,13 +105,13 @@ typedef struct
#define MIX_TRIO 3
#define NON_TRIO 4
#define DROP 5
typedef struct
{
uint64_t** N_site;
///uint8_t* read;
char* name;
uint8_t** read_sperate;
uint64_t* read_length;
uint64_t* read_size;
@@ -129,7 +122,6 @@ typedef struct
///uint64_t* index;
uint64_t index_size;
///name start pos in char* name
uint64_t* name_index;
uint64_t name_index_size;
@@ -143,7 +135,6 @@ typedef struct
ma_hit_t_alloc* paf;
ma_hit_t_alloc* reverse_paf;
ma_sub_t* coverage_cut;
} All_reads;
extern All_reads R_INF;
@@ -154,10 +145,8 @@ typedef struct
{
kseq_t* read;
long long num;
} R_buffer_block;
typedef struct
{
R_buffer_block* sub_block;
@@ -167,7 +156,6 @@ typedef struct
int all_read_end;
} R_buffer;
typedef struct
{
char* seq;
@@ -208,5 +196,6 @@ void clear_R_buffer();
void init_gz_files(hifiasm_opt_t* asm_opt);
void destory_gz_files();
void ha_insert_read_len(All_reads *r, int read_len, int name_len);
#endif