117 lines
3.6 KiB
C
117 lines
3.6 KiB
C
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/*
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Copyright (c) 2012-2013, 2018 Genome Research Ltd.
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Author: James Bonfield <jkb@sanger.ac.uk>
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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Institute nor the names of its contributors may be used to endorse or promote
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products derived from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
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ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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/*! \file
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* Include cram.h instead.
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*
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* This is an internal part of the CRAM system and is automatically included
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* when you #include cram.h.
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*
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* Implements the encoding portion of CRAM I/O. Also see
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* cram_codecs.[ch] for the actual encoding functions themselves.
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*/
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#ifndef CRAM_ENCODE_H
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#define CRAM_ENCODE_H
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#ifdef __cplusplus
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extern "C" {
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#endif
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/* ----------------------------------------------------------------------
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* CRAM sequence iterators.
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*/
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/*! Write iterator: put BAM format sequences into a CRAM file.
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*
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* We buffer up a containers worth of data at a time.
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*
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* FIXME: break this into smaller pieces.
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*
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* @return
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* Returns 0 on success;
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* -1 on failure
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*/
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int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b);
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/* ----------------------------------------------------------------------
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* Internal functions
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*/
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/*! INTERNAL:
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* Encodes a compression header block into a generic cram_block structure.
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*
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* @return
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* Returns cram_block ptr on success;
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* NULL on failure
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*/
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cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
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cram_block_compression_hdr *h,
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int embed_ref);
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/*! INTERNAL:
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* Encodes a slice compression header.
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*
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* @return
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* Returns cram_block on success;
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* NULL on failure
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*/
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cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s);
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/*! INTERNAL:
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* Encodes all slices in a container into blocks.
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*
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* @return
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* Returns 0 on success;
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* -1 on failure
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*
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* FIXME: separate into encode_container and write_container. Ideally
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* we should be able to do read_container / write_container or
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* decode_container / encode_container.
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*/
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int cram_encode_container(cram_fd *fd, cram_container *c);
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/*! INTERNAL:
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*
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* During cram_next_container or before the final flush at end of
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* file, we update the current slice headers and increment the slice
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* number to the next slice.
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*
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* See cram_next_container() and cram_close().
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*/
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void cram_update_curr_slice(cram_container *c, int version);
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#ifdef __cplusplus
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}
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#endif
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#endif
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