comparison ezBAMQC/src/htslib/cram/cram.h @ 0:dfa3745e5fd8

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/*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <[e-mail]>

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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*/

/*! \file
 * CRAM interface.
 *
 * Consider using the higher level hts_*() API for programs that wish to
 * be file format agnostic (see htslib/hts.h).
 *
 * This API should be used for CRAM specific code. The specifics of the
 * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
 * although these should not be included directly (use this file instead).
 */

#ifdef __cplusplus
extern "C" {
#endif

#ifndef _CRAM_H_
#define _CRAM_H_

#include "cram/cram_samtools.h"
#include "cram/sam_header.h"
#include "cram_structs.h"
#include "cram_io.h"
#include "cram_encode.h"
#include "cram_decode.h"
#include "cram_stats.h"
#include "cram_codecs.h"
#include "cram_index.h"

#endif

#ifdef __cplusplus
}
#endif