FastqPuri
struct_trimFilter.h
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20 
30 #ifndef STRUCT_TRIMFILTER_H_
31 #define STRUCT_TRIMFILTER_H_
32 
33 #include "defines.h"
34 #include "bloom.h"
35 
39 typedef struct _adapter {
40  char *ad_fa;
41  char *ad2_fa;
42  int mismatches;
43  double threshold;
44  int Nad;
45 } Adapter;
46 
51 typedef struct _iparam_trimFilter {
52  char *Ifq;
53  char *Ifq2;
54  char *Ifa;
55  char *Iidx;
56  char *Iinfo;
57  char *Oprefix;
58  bool uncompress;
61  int trimQ;
62  int trimN;
63  int method;
64  bool is_fa;
65  bool is_idx;
66  bool is_adapter;
67  double score;
68  int minQ;
69  int L;
70  int minL;
71  int nlowQ;
72  int kmersize;
73  int globleft;
74  int globright;
75  int percent;
77 
78 void free_parTF(Iparam_trimFilter *ptr_parTF);
79 
80 #endif // endif _STRUCT_TRIMFILTER_H_
int globright
Definition: struct_trimFilter.h:74
Adapter ad
Definition: struct_trimFilter.h:59
void free_parTF(Iparam_trimFilter *ptr_parTF)
frees the allocated memory in Iparam_trimFilter
Definition: struct_trimFilter.c:36
trimFilter input parameters
Definition: struct_trimFilter.h:51
char * Oprefix
Definition: struct_trimFilter.h:57
int minQ
Definition: struct_trimFilter.h:68
int method
Definition: struct_trimFilter.h:63
struct _adapter Adapter
functions that implement the bloom filter
int mismatches
Definition: struct_trimFilter.h:42
char * Iidx
Definition: struct_trimFilter.h:55
char * Ifa
Definition: struct_trimFilter.h:54
char * ad2_fa
Definition: struct_trimFilter.h:41
double threshold
Definition: struct_trimFilter.h:43
char * Ifq2
Definition: struct_trimFilter.h:53
double score
Definition: struct_trimFilter.h:67
int trimQ
Definition: struct_trimFilter.h:61
bool is_adapter
Definition: struct_trimFilter.h:66
Macro definitions.
int globleft
Definition: struct_trimFilter.h:73
struct _iparam_trimFilter Iparam_trimFilter
trimFilter input parameters
int trimN
Definition: struct_trimFilter.h:62
Definition: struct_trimFilter.h:39
int nlowQ
Definition: struct_trimFilter.h:71
int kmersize
Definition: struct_trimFilter.h:72
char * Ifq
Definition: struct_trimFilter.h:52
int L
Definition: struct_trimFilter.h:69
stores a processed kmer (2 bits pro nucleotide)
Definition: bloom.h:57
bool is_idx
Definition: struct_trimFilter.h:65
int minL
Definition: struct_trimFilter.h:70
char * Iinfo
Definition: struct_trimFilter.h:56
bool is_fa
Definition: struct_trimFilter.h:64
Bfkmer * ptr_bfkmer
Definition: struct_trimFilter.h:60
bool uncompress
Definition: struct_trimFilter.h:58
int Nad
Definition: struct_trimFilter.h:44
char * ad_fa
Definition: struct_trimFilter.h:40
int percent
Definition: struct_trimFilter.h:75