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/***************************************************************************
* PHAST: PHylogenetic Analysis with Space/Time models
* Copyright (c) 2002-2005 University of California, 2006-2010 Cornell
* University. All rights reserved.
*
* This source code is distributed under a BSD-style license. See the
* file LICENSE.txt for details.
***************************************************************************/
/** @file gff.h
Reading and writing of sequence features in wig format.
Obeys file specification at
http://genome.ucsc.edu/goldenPath/help/wiggle.html
@ingroup feature
*/
#ifndef WIG_H
#define WIG_H
#include <gff.h>
/** Check if a string is a wig file header and parse the arguments.
@param line[in] A string which may be a wig header file (fixed or variable step)
@param fixed[out] If not NULL, will be set to 1 if line is a header for a fixedStep wig,
and 0 if line is header for a variableStep wig. Will not be set if line is not a wig
header. If not NULL, must be allocated large enough to hold the chrom value.
@param chrom[out] If not NULL, will be set to the chrom argument in a wig header. Will
not be set if line is not a wig header.
@param start[out] Will be set to the start argument if line is a fixedStep wig header.
@param step[out] Will be set to the step argument if line is a fixedStep wig header
@param span[out] Will be set to the span argument if line is a wig header. If line is a
wig header but span is not given, it will be set to the default value of 1. Will not
be set if line is not a wig header.
@return 1 if line is a wig header, 0 otherwise. None
*/
int wig_parse_header(String *line, int *fixed, char *chrom, int *start, int *step, int *span);
/** Read a wig file and store as a GFF. Can read either fixed or variable wig files.
@param F wig file to read
@return A newly allocated GFF set populated with the data from the wig file.
@note although not technically allowed in the specification, this function will accept a wig
file with a mix of fixed/variable sections.
*/
GFF_Set *gff_read_wig(FILE *F);
/** Write a GFF object as a fixedStep wig file.
@param F file stream to write to
@param set The GFF set to write.
@note all elements in set must have the same length and have a defined score.
*/
void wig_print(FILE *outfile, GFF_Set *set);
#endif
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