bedidx.h

/*  bedidx.h -- BED file indexing header file.

    Copyright (C) 2017, 2026 Genome Research Ltd.

    Author: Valeriu Ohan <vo2@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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DEALINGS IN THE SOFTWARE.  */

#ifndef BEDIDX_H
#define BEDIDX_H

#include "htslib/hts.h"

#define LIDX_SHIFT 13
#define ALL 0
#define FILTERED 1

#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )

/*
 * Bed file reading.  The main functions are bed_read and bed_destroy.
 * The void* return value from bed_read is the same "void *reg_hash" used in
 * bed_overlap, bed_hash_regions, bed_unify and bed_reglist.
 *
 * Due to the data structures used, the order of chromosomes in the BED file
 * is not preserved and iterators will return chromosomes in hash key order.
 */
void *bed_read(const char *fn);
void bed_destroy(void *_h);

/*
 * bed_reglist will turn the bed file into a list of regions structured as
 * an hts_reglist_t: an array with one entry per chromosome, with each
 * element containing a further array of regions within that chromosome.
 *
 * Note however this function does not take a SAM or VCF header, so the
 * hts_reglist_t "tid" member will be invalid.  Users are expected to perform
 * this conversion themselves from the "chr" string member instead.  (See
 * hts_itr_regions for example code which does this.)
 *
 * Use filtered = ALL (0) unless you have previously applied bed_hash_regions
 * with reg_hash != NULL and *op == 0, in which case FILTERED may be used to
 * perform an intersection of bed file and an array of region strings.
 *
 * Free using hts_reglist_free()
 */
hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *count_regs);

int bed_overlap(const void *_h, const char *chr, hts_pos_t beg, hts_pos_t end);
void *bed_hash_regions(void *reg_hash, char **regs, int first, int last, int *op);
void bed_unify(void *_h);

#endif