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- /*
- Copyright (c) 2012-2013 Genome Research Ltd.
- Author: James Bonfield <jkb@sanger.ac.uk>
- 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
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
- /*! \file
- * CRAM interface.
- *
- * Consider using the higher level scram_*() API for programs that wish to
- * be file format agnostic.
- *
- * 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
- #ifdef SAMTOOLS
- # include "cram/cram_samtools.h"
- #endif
- #ifndef _CRAM_H_
- #define _CRAM_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
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