/usr/include/io_lib/cram_index.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 | /*
* 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.
*/
#ifndef _CRAM_INDEX_H_
#define _CRAM_INDEX_H_
#ifdef __cplusplus
extern "C" {
#endif
/*
* Loads a CRAM .crai index into memory.
* Returns 0 for success
* -1 for failure
*/
int cram_index_load(cram_fd *fd, char const * fn);
#if defined(CRAM_IO_CUSTOM_BUFFERING)
/*
* Loads a CRAM .crai index into memory using callbacks. fn denotes the name of the cram file.
* The suffix .crai will be appended to obtain the name of the index.
*
* Returns 0 for success
* -1 for failure
*/
extern int cram_index_load_via_callbacks(
cram_fd *fd, char const * fn,
cram_io_allocate_read_input_t callback_allocate_function,
cram_io_deallocate_read_input_t callback_deallocate_function
);
#endif
void cram_index_free(cram_fd *fd);
/*
* Searches the index for the first slice overlapping a reference ID
* and position.
*
* Returns the cram_index pointer on sucess
* NULL on failure
*/
cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm);
/*
* Skips to a container overlapping the start coordinate listed in
* cram_range.
*
* Returns 0 on success
* -1 on failure
*/
int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
/*
* Seek within a cram file.
*
* Returns 0 on success
* -1 on failure
*/
int cram_seek(cram_fd *fd, off_t offset, int whence);
/*
* Builds an index file.
*
* fd is a newly opened cram file that we wish to index.
* fn_base is the filename of the associated CRAM file. Internally we
* add ".crai" to this to get the index filename.
*
* Returns 0 on success
* -1 on failure
*/
int cram_index_build(cram_fd *fd, const char *fn_base);
#ifdef __cplusplus
}
#endif
#endif
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