/usr/include/io_lib/cram_stats.h is in libstaden-read-dev 1.14.9-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* 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.
*/
/*
* Author: James Bonfield, Wellcome Trust Sanger Institute. 2013
*/
#ifndef _CRAM_STATS_H_
#define _CRAM_STATS_H_
#ifdef __cplusplus
extern "C" {
#endif
#include "io_lib/hash_table.h"
cram_stats *cram_stats_create(void);
void cram_stats_add(cram_stats *st, int32_t val);
void cram_stats_del(cram_stats *st, int32_t val);
void cram_stats_dump(cram_stats *st);
void cram_stats_free(cram_stats *st);
/*
* Computes entropy from integer frequencies for various encoding methods and
* picks the best encoding.
*
* FIXME: we could reuse some of the code here for the actual encoding
* parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
*
* Returns the best codec to use.
*/
enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st);
#ifdef __cplusplus
}
#endif
#endif
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