1 /* 2 Copyright (c) 2012-2013 Genome Research Ltd. 3 Author: James Bonfield <jkb@sanger.ac.uk> 4 5 Redistribution and use in source and binary forms, with or without 6 modification, are permitted provided that the following conditions are met: 7 8 1. Redistributions of source code must retain the above copyright notice, 9 this list of conditions and the following disclaimer. 10 11 2. Redistributions in binary form must reproduce the above copyright notice, 12 this list of conditions and the following disclaimer in the documentation 13 and/or other materials provided with the distribution. 14 15 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger 16 Institute nor the names of its contributors may be used to endorse or promote 17 products derived from this software without specific prior written permission. 18 19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE 23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 29 */ 30 31 /*! \file 32 * CRAM interface. 33 * 34 * Consider using the higher level hts_*() API for programs that wish to 35 * be file format agnostic (see htslib/hts.h). 36 * 37 * This API should be used for CRAM specific code. The specifics of the 38 * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h 39 * although these should not be included directly (use this file instead). 40 */ 41 42 #ifndef _CRAM_H_ 43 #define _CRAM_H_ 44 45 #include "cram/cram_samtools.h" 46 #include "cram/sam_header.h" 47 #include "cram_structs.h" 48 #include "cram_io.h" 49 #include "cram_encode.h" 50 #include "cram_decode.h" 51 #include "cram_stats.h" 52 #include "cram_codecs.h" 53 #include "cram_index.h" 54 55 // Validate against the external cram.h, 56 // 57 // This contains duplicated portions from cram_io.h and cram_structs.h, 58 // so we want to ensure that the prototypes match. 59 #include "htslib/cram.h" 60 61 #endif 62