dafreader.c File Reference

Class DAFReader: read a daf file. More...

#include "dafreader.h"
#include "tokenizer.h"
#include "misc.h"
#include "error.h"
#include <errno.h>
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <ctype.h>
#include <unistd.h>

Macros
#define	MAXFIELDS   5
#define	MAX(X, Y)   ((X) > (Y) ? (X) : (Y))
#define	MIN(X, Y)   ((X) > (Y) ? (Y) : (X))

Functions
int	iscomment (const char *s)
	Return 1 if first non-white character in string is '#'; 0 otherwise.
int	DAFReader_cmp (const DAFReader *lhs, const DAFReader *rhs)
	Compare two DAFReader objects. More...
DAFReader *	DAFReader_new (const char *fname)
	DAFReader constructor.
void	DAFReader_clearChromosomes (int n, DAFReader *r[n])
	Clear all chromosome names.
void	DAFReader_free (DAFReader *self)
	DAFReader destructor.
int	DAFReader_next (DAFReader *self)
	Read the next site. More...
int	DAFReader_rewind (DAFReader *self)
	Rewind daf file. More...
int	DAFReader_multiNext (int n, DAFReader *r[n])
int	DAFReader_allelesMatch (int n, DAFReader *r[n])
	Return 1 if ancestral and derived alleles of all readers match; 0 otherwise.
void	DAFReader_printHdr (FILE *fp)
	Print header for daf file.
void	DAFReader_print (DAFReader *r, FILE *fp)
	Print current line of daf file.
double	DAFReader_daf (DAFReader *r)
	Return derived allele frequency of current line of daf file.

Detailed Description

Class DAFReader: read a daf file.

Copyright

Copyright (c) 2016, Alan R. Rogers roger.nosp@m.s@an.nosp@m.thro..nosp@m.utah.nosp@m..edu. This file is released under the Internet Systems Consortium License, which can be found in file "LICENSE".

Function Documentation

DAFReader_cmp()

int DAFReader_cmp	(	const DAFReader *	lhs,
		const DAFReader *	rhs
	)

Compare two DAFReader objects.

If the "chr" fields differ, return positive if lhs->chr > rhs->chr; return negative if the reverse inequality holds. Otherwise return positive, 0, or negative to match the sign of lhs->nucpos - rhs->nucpos.

DAFReader_next()

int DAFReader_next

(

DAFReader *

self

)

Read the next site.

Returns

0 on success; EOF on end of file; abort on other errors.

References iscomment(), strlowercase(), Tokenizer_print(), Tokenizer_printSummary(), Tokenizer_split(), Tokenizer_strip(), and Tokenizer_token().

DAFReader_rewind()

int DAFReader_rewind

(

DAFReader *

self

)

Rewind daf file.

Returns

0 on success; -1 on failure