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