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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 bed.h
Reading and writing of features to/from .BED files.
Bed files are read or written as sets of features.
These sets of features are stored in GFF_Set objects
which contain all information pertinant to a each feature.
See http://genome.ucsc.edu/goldenPath/help/customTrack.html
@ingroup feature
*/
#ifndef BED_H
#define BED_H
#include <gff.h>
/** Create new feature set from file
@param[in] F File descriptor of BED file
@param[out] gff Feature set to populate with features from file
@note
@code
#include <stdio.h>
#include <gff.h> //To use GFF_Set object
#include <bed.h> //To read from BED file
int main(int argc, char *argv[]) {
char *filename = "file.bed";
GFF_Set *FeatureSet = gff_new_set();
gff_read_from_bed(FeatureSet, phast_fopen(filename, "r"));
}
@endcode
*/
void gff_read_from_bed(GFF_Set *gff, FILE *F);
/** Save feature set to a file
@param[in] OUTF File descriptor of output file
@param[in] gff Feature set to save to file
@param[in] use_groups If TRUE, all members of a group
are described by a single line in
the BED file (12-column format); if
FALSE, any groups are ignored and
each feature gets its own line.
@note Features must already be grouped if use_groups == TRUE.
@code
#include <stdio.h>
#include <gff.h> //To use GFF_Set object
#include <bed.h> //To read in from BED file
#include <misc.h> //To use TRUE/FALSE
int main(int argc, char *argv[]) {
char *filename = "file.bed";
GFF_Set *FeatureSet = gff_new_set();
gff_read_from_bed(FeatureSet, phast_fopen(filename, "r"));
gff_print_bed(stdout, FeatureSet, FALSE); //If we had groups we would have used TRUE
}
OUTPUT:
chr22 49300442 49300573 hpmrc.1 0 +
chr22 49301519 49302857 hpmrc.2 0 +
chr22 49302939 49303037 hpmrc.3 0 +
chr22 49303476 49304046 hpmrc.4 0 +
chr22 49309025 49309154 hpmrc.5 0 +
chr22 49310089 49310131 hpmrc.6 0 +
chr22 49310179 49310218 hpmrc.7 0 +
chr22 49314992 49315043 hpmrc.8 0 +
chr22 49315445 49315520 hpmrc.9 0 +
chr22 49315555 49315641 hpmrc.10 0 +
@endcode
*/
void gff_print_bed(FILE *OUTF, GFF_Set *gff, int use_groups);
#endif
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