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Auxiliary.h
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Auxiliary.h
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/*
Authors:
Haoyu Cheng
chhy@mail.ustc.edu.cn
*/
#ifndef __COMMON__
#define __COMMON__
#include "bwt.h"
#define READS_QUENUE_MAX_LENGTH 10000
#define SEQ_MAX_LENGTH 1000 // Seq Max Length
#define NAME_LENGTH 1000 // Filename Max Length
#define MAX_Thread 1024
extern unsigned char WINDOW_SIZE; // WINDOW SIZE for indexing/searching
extern unsigned char default_ws;
extern unsigned char MERGE_STEP;
extern unsigned short SEQ_LENGTH; // Sequence(read) length
extern char *versionN;
extern unsigned int THREAD_COUNT;
extern int is_index;
extern int is_search;
extern int is_pairedEnd;
extern int cropSize;
extern char *Read_File1;
extern char *Read_File2;
extern char *seqUnmapped;
extern char *Mapped_File;
extern char *Mapped_FilePath;
extern char *folder_path;
extern char *Un_Mapped_File;
extern unsigned char thread_e;
extern double thread_e_f;
extern unsigned char maxHits;
extern int minDistance_pair;
extern int maxDistance_pair;
extern char fileName[2][NAME_LENGTH];
extern int fileCnt;
extern int each_length;
extern double bs_score_threshold;
extern double bs_edit_distance_threshold;
extern int is_local;
extern int bs_available_seed_length;
extern int pbat;
extern char rc_table[128];
extern int sub_block_inner_size;
extern int sub_block_number;
extern int ouput_buffer_size;
extern int over_all_seed_length;
extern int methylation_size;
extern int output_methy;
extern bitmapper_bs_iter genome_cuts;
extern bitmapper_bs_iter cut_length;
extern double methylation_buffer_times;
extern int is_methy;
extern int bam_output;
extern double maxVariantFrac;
extern int minVariantDepth;
extern int CpG;
extern int CHG;
extern int CHH;
extern int unmapped_out;
extern int ambiguous_out;
extern int mapstats;
extern int GapOpenPenalty;
extern int GapExtensionPenalty;
extern int MistMatchPenaltyMax;
extern int MistMatchPenaltyMin;
extern int N_Penalty;
extern int Q_base;
extern char *Mapstats_File;
extern char *Mapstats_File_Path;
double Get_T(void);
void reverseComplement (char *seq, char *rcSeq , int length);
///void reverse_pattern(char* pattern, char* rev_pattern, int length);
void reverse (char *seq, char *rcSeq , int length);
void stripPath(char *full, char **path, char **fileName);
inline void reverse_pattern(char* pattern, char* rev_pattern, int length)
{
int i = 0;
for (i = 0; i < length; i++)
{
rev_pattern[i] = pattern[length - i - 1];
}
rev_pattern[i] = '\0';
}
#endif