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- /* bedidx.h -- BED file indexing header file.
-
- Copyright (C) 2017 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
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
- THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- 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) )
-
- void *bed_read(const char *fn);
- void bed_destroy(void *_h);
- 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);
- const char* bed_get(void *reg_hash, int index, int filter);
- hts_reglist_t *bed_reglist(void *reg_hash, int filter, int *count_regs);
- void bed_unify(void *_h);
-
- #endif
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