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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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29
Process_Read.h
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@@ -30,29 +30,13 @@ KSEQ_INIT(gzFile, gzread)
static 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
};
extern uint8_t seq_nt6_table[256];
extern char bit_t_seq_table[256][4];
extern char bit_t_seq_table_rc[256][4];
extern char s_H[5];
extern char rc_Table[5];
static char bit_t_seq_table[256][4] = {0};
static char bit_t_seq_table_rc[256][4] = {0};
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]]
@@ -204,7 +188,6 @@ void write_All_reads(All_reads* r, char* read_file_name);
int load_All_reads(All_reads* r, char* read_file_name);
void destory_All_reads(All_reads* r);
void Counting_block();
void destory_R_buffer_block(R_buffer_block* curr_sub_block);
void destory_R_buffer();
void clear_R_buffer();