/* $Id: seq.h,v 1.9 2002/06/19 06:12:57 schwartz Exp $ */#ifndef PIPLIB_SEQ#define PIPLIB_SEQ#include "util.h"#include "nib.h"typedef unsigned char uchar;#define ZFREE(p) /*CONSTCOND*/do{ckfree(p);(p)=0;}while(0)extern const signed char fasta_encoding[256];extern const signed char nfasta_encoding[256];enum /* powerset */{ SEQ_IS_SUBRANGE = (1<<0) /* seq is a subrange of a file */, SEQ_IS_REVCOMP  = (1<<1) /* seq is reverse compliment of a file */, SEQ_IS_SUBSEQ   = (1<<2) /* seq is a reference to another seq */, SEQ_HAS_MASK    = (1<<3) /* seq has a mask applied */, SEQ_HAS_PIPE    = (1<<4) /* input fd is a pipe */, SEQ_DO_REVCOMP  = (1<<5) /* make it so after open */, SEQ_DO_SUBRANGE = (1<<6) /* make it so after open */, SEQ_DO_MASK     = (1<<7) /* make it so after open */, SEQ_ALLOW_AMB   = (1<<8) /* checked while reading */, SEQ_DISALLOW_AMB  = (1<<9) /* checked while reading */};enum { SEQ_TYPE_GUESS = 0, SEQ_TYPE_FASTA, SEQ_TYPE_NIB};typedef struct seq_file {	uchar *seq;	int slen; /* bytes in seq, not including '\0' */	int from; /* 1 based */	FILE *fp;	int type; // guess, fasta, nib, ...	int flags;	int count;  /* how many contigs we have already read */	long offset; /* the starting offset of the contig we just read */	char *maskname;	char *fname;	char *header;	int hlen; /* bytes in header, not including '\0' */} SEQ;#define SEQ_NAME(s) ((s)->fname)#define SEQ_LEN(s) ((s)->slen)#define SEQ_TO(s)  ((s)->slen + (s)->from - 1)#define SEQ_FROM(s) ((s)->from)#define SEQ_AT(s,i) ((s)->seq[i])#define SEQ_HEAD(s) ((s)->header)#define SEQ_HLEN(s) ((s)->hlen)#define SEQ_CHARS(s) ((s)->seq)#define SEQ_SAME(a,b) ((a)==(b))SEQ* seq_open(const char *fname);SEQ* seq_open_type(const char *fname, int type);SEQ* seq_close(SEQ *s);int seq_read(SEQ *seq);int seq_read_nib(SEQ *seq);int seq_read_fasta(SEQ *seq);SEQ *seq_copy(const SEQ *s);SEQ *seq_revcomp_inplace(SEQ *seq);SEQ *seq_get(const char *fname);	/* seq_open + seq_read */void do_revcomp(uchar *s, int len);uchar dna_cmpl(unsigned char);#endif