Class RAFReader: read a raf file. More...

#include "rafreader.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	RAFReader_cmp (const RAFReader lhs, const RAFReader rhs)
	Compare two RAFReader objects. More...

void	RAFReader_popen (RAFReader *self)

RAFReader *	RAFReader_new (const char *fname)
	RAFReader constructor.

void	RAFReader_clearChromosomes (int n, RAFReader *r[n])
	Clear all chromosome names.

void	RAFReader_free (RAFReader *self)
	RAFReader destructor.

int	RAFReader_next (RAFReader *self)
	Read the next site and set derived allele frequency (daf) within each reader. More...

int	RAFReader_rewind (RAFReader *self)
	Rewind raf file. More...

int	RAFReader_multiNext (int n, RAFReader *r[n])
	Advance an array of RAFReaders to the next shared position, and set derived allele frequency within each RAFReader. More...

int	RAFReader_findDaf (int n, RAFReader *r[n])
	Set derived allele frequency within each RAFReader. More...

int	RAFReader_alleleCheck (int n, RAFReader *r[n])
	Return 0 if ref and alt alleles of all readers match; return REF_MISMATCH if there is a mismatch in REF alleles; return MULTIPLE_ALT if there is a mismatch in ALT alleles.

void	RAFReader_printHdr (FILE *fp)
	Print header for raf file.

void	RAFReader_print (RAFReader r, FILE fp)
	Print current line of raf file.

void	RAFReader_printArray (int n, RAFReader r[n], FILE fp)

double	RAFReader_raf (RAFReader *r)
	Return reference allele frequency of current line of raf file.

double	RAFReader_daf (RAFReader *r)
	Return derived allele frequency of current line of raf file.

Detailed Description

Class RAFReader: read a raf 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

◆ RAFReader_cmp()

int RAFReader_cmp	(	const RAFReader *	lhs,
		const RAFReader *	rhs
	)

Compare two RAFReader 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.

◆ RAFReader_findDaf()

int RAFReader_findDaf	(	int	n,
		RAFReader *	r[n]
	)

Set derived allele frequency within each RAFReader.

Parameters

[in]	n	number of RAFReader objects in array
[in]	r	array of RAFReader objects. Last one should be outgroup.

Returns: 0 on success, or one of several error codes on failure.

◆ RAFReader_multiNext()

int RAFReader_multiNext	(	int	n,
		RAFReader *	r[n]
	)

Advance an array of RAFReaders to the next shared position, and set derived allele frequency within each RAFReader.

Parameters

[in]	n	number of RAFReader objects in array
[in]	r	array of RAFReader objects. Last one should be outgroup.

Returns: 0 on success, or one of several error codes on failure.

◆ RAFReader_next()

int RAFReader_next ( RAFReader * self )

Read the next site and set derived allele frequency (daf) within each reader.

Returns: 0 on success, or else EOF, NO_ANCESTRAL_ALLELE, BUFFER_OVERFLOW, BAD_RAF_INPUT, BAD_SORT, MONOMORPHIC_SITE, or an errno code for failure to parse a floating-point number.

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

◆ RAFReader_rewind()

int RAFReader_rewind ( RAFReader * self )

Rewind raf file.

Returns: 0 on success; -1 on failure

Macros