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phasing

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This commit is contained in:
Haoyu Cheng
2019-09-02 10:30:14 -04:00
parent 3c0c201cdf
commit d5327fe9ee
15 changed files with 3396 additions and 656 deletions
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Process_Read.h
+18 -2
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@@ -48,8 +48,8 @@ static uint8_t seq_nt6_table[256] = {
static char bit_t_seq_table[256][4] = {0};
static char bit_t_seq_table_rc[256][4] = {0};
static char s_H[4] = {'A', 'C', 'G', 'T'};
static char rc_Table[4] = {'T', 'G', 'C', 'A'};
static char s_H[5] = {'A', 'C', 'G', 'T', 'N'};
static char rc_Table[5] = {'T', 'G', 'C', 'A', 'N'};
#define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
@@ -58,6 +58,19 @@ void init_kseq(char* file);
void destory_kseq();
int get_read(kseq_t *s);
typedef struct
{
/**[0-1] bits are type:**/
/**[2-31] bits are length**/
uint32_t* record;
uint32_t length;
uint32_t size;
char* lost_base;
uint32_t lost_base_length;
uint32_t lost_base_size;
uint32_t new_length;
}Compressed_Cigar_record;
typedef struct
@@ -69,6 +82,7 @@ typedef struct
uint8_t** read_sperate;
uint64_t* read_length;
uint64_t* read_size;
///seq start pos in uint8_t* read
///do not need it
@@ -83,6 +97,8 @@ typedef struct
uint64_t total_reads_bases;
uint64_t total_name_length;
Compressed_Cigar_record* cigars;
} All_reads;
extern All_reads R_INF;