/usr/include/io_lib/cram_encode.h is in libstaden-read-dev 1.14.6-2.
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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
*/
/*! \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 encoding portion of CRAM I/O. Also see
* cram_codecs.[ch] for the actual encoding functions themselves.
*/
#ifndef _CRAM_WRITE_H_
#define _CRAM_WRITE_H_
#ifdef __cplusplus
extern "C" {
#endif
/* ----------------------------------------------------------------------
* CRAM sequence iterators.
*/
/*! Write iterator: put BAM format sequences into a CRAM file.
*
* We buffer up a containers worth of data at a time.
*
* FIXME: break this into smaller pieces.
*
* @return
* Returns 0 on success;
* -1 on failure
*/
int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b);
/* ----------------------------------------------------------------------
* Internal functions
*/
/*! INTERNAL:
* Encodes a compression header block into a generic cram_block structure.
*
* @return
* Returns cram_block ptr on success;
* NULL on failure
*/
cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
cram_block_compression_hdr *h);
/*! INTERNAL:
* Encodes a slice compression header.
*
* @return
* Returns cram_block on success;
* NULL on failure
*/
cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s);
/*! INTERNAL:
* Encodes all slices in a container into blocks.
*
* @return
* Returns 0 on success;
* -1 on failure
*
* FIXME: separate into encode_container and write_container. Ideally
* we should be able to do read_container / write_container or
* decode_container / encode_container.
*/
int cram_encode_container(cram_fd *fd, cram_container *c);
/*! INTERNAL:
*
* During cram_next_container or before the final flush at end of
* file, we update the current slice headers and increment the slice
* number to the next slice.
*
* See cram_next_container() and cram_close().
*/
void cram_update_curr_slice(cram_container *c);
#ifdef __cplusplus
}
#endif
#endif
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