40 char seq[READ_MAXLEN];
43 unsigned char pack[(READ_MAXLEN+1)/2];
49 int process_seq(
unsigned char *packed,
unsigned char *read,
int L,
bool shift,
56 #endif // endif INIT_ALIGNER_H_ int L
Definition: adapters.h:39
unsigned char pack_sh[(READ_MAXLEN+1)/2]
Definition: adapters.h:44
stores a fastq entry
Definition: fq_read.h:37
stores sequences of a fasta file
Definition: fa_read.h:46
struct _ad_seq Ad_seq
stores an adapter entry
Ad_seq * pack_adapter(Fa_data *ptr_fa)
reads a Fa_data with adapters and stores them in an array of Ad_seq structs.
Definition: adapters.c:129
reads in and stores fasta files
int Lpack
Definition: adapters.h:41
int Lpack_sh
Definition: adapters.h:42
stores an adapter entry
Definition: adapters.h:38
int process_seq(unsigned char *packed, unsigned char *read, int L, bool shift, bool isreverse)
Packs a sequence using alfw0, alfw1, albw0, albw1.
Definition: adapters.c:92
fastq entries manipulations (read/write)
double obtain_score(Fq_read *seq, int pos_seq, Ad_seq *ptr_adap, int pos_ad)
computes score of a possible alignment, after having found a seed.
Definition: adapters.c:155
unsigned char pack[(READ_MAXLEN+1)/2]
Definition: adapters.h:43
char seq[READ_MAXLEN]
Definition: adapters.h:40
void init_alLUTs()
look up table initialization for alignment (used for adapters)
Definition: adapters.c:59