/usr/include/io_lib/cram_decode.h is in libstaden-read-dev 1.14.6-2.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 | /*
* Copyright (c) 2013 Genome Research Ltd.
* Author(s): James Bonfield
*
* 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
* Include cram.h instead.
*
* This is an internal part of the CRAM system and is automatically included
* when you #include cram.h.
*
* Implements the decoding portion of CRAM I/O. Also see
* cram_codecs.[ch] for the actual encoding functions themselves.
*/
#ifndef _CRAM_READ_H_
#define _CRAM_READ_H_
#ifdef __cplusplus
extern "C" {
#endif
/* ----------------------------------------------------------------------
* CRAM sequence iterators.
*/
/*! Read the next cram record and return it as a cram_record.
*
* Note that to decode cram_record the caller will need to look up some data
* in the current slice, pointed to by fd->ctr->slice. This is valid until
* the next call to cram_get_seq (which may invalidate it).
*
* @return
* Returns record pointer on success (do not free);
* NULL on failure
*/
cram_record *cram_get_seq(cram_fd *fd);
/*! Read the next cram record and convert it to a bam_seq_t struct.
*
* @return
* Returns 0 on success;
* -1 on EOF or failure (check fd->err)
*/
int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
/* ----------------------------------------------------------------------
* Internal functions
*/
/*! INTERNAL:
* Decodes a CRAM block compression header.
*
* @return
* Returns header ptr on success;
* NULL on failure
*/
cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
cram_block *b);
/*! INTERNAL:
* Decodes a CRAM (un)mapped slice header block.
*
* @return
* Returns slice header ptr on success;
* NULL on failure
*/
cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
/*! INTERNAL:
* Decode an entire slice from container blocks. Fills out s->crecs[] array.
*
* @return
* Returns 0 on success;
* -1 on failure
*/
int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
SAM_hdr *hdr);
#ifdef __cplusplus
}
#endif
#endif
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