116 lines
3.8 KiB
C
116 lines
3.8 KiB
C
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/*
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Copyright (c) 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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#ifndef CRAM_INDEX_H
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#define CRAM_INDEX_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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* Loads a CRAM .crai index into memory.
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* Returns 0 for success
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* -1 for failure
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*/
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int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx);
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void cram_index_free(cram_fd *fd);
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/*
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* Searches the index for the first slice overlapping a reference ID
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* and position.
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*
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* Returns the cram_index pointer on success
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* NULL on failure
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*/
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cram_index *cram_index_query(cram_fd *fd, int refid, hts_pos_t pos, cram_index *frm);
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cram_index *cram_index_last(cram_fd *fd, int refid, cram_index *from);
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cram_index *cram_index_query_last(cram_fd *fd, int refid, hts_pos_t end);
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/*
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* Skips to a container overlapping the start coordinate listed in
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* cram_range.
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*
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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_seek_to_refpos(cram_fd *fd, cram_range *r);
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void cram_index_free(cram_fd *fd);
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/*
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* Skips to a container overlapping the start coordinate listed in
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* cram_range.
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*
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* In theory we call cram_index_query multiple times, once per slice
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* overlapping the range. However slices may be absent from the index
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* which makes this problematic. Instead we find the left-most slice
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* and then read from then on, skipping decoding of slices and/or
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* whole containers when they don't overlap the specified cram_range.
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*
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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_seek_to_refpos(cram_fd *fd, cram_range *r);
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/*
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* Builds an index file.
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*
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* fd is a newly opened cram file that we wish to index.
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* fn_base is the filename of the associated CRAM file.
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* fn_idx is the filename of the index file to be written;
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* if NULL, we add ".crai" to fn_base to get the index filename.
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*
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* Returns 0 on success,
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* negative on failure (-1 for read failure, -4 for write failure)
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*/
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int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx);
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/*
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* Adds a single slice to the index.
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*
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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_index_slice(cram_fd *fd,
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cram_container *c,
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cram_slice *s,
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BGZF *fp,
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off_t cpos,
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off_t spos, // relative to cpos
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off_t sz);
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#ifdef __cplusplus
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}
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#endif
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#endif
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