87 lines
3.2 KiB
C
87 lines
3.2 KiB
C
/*
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* Copyright (c) 2019 Genome Research Ltd.
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* Author(s): James Bonfield
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*
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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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*
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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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*
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* 2. Redistributions in binary form must reproduce the above
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* copyright notice, this list of conditions and the following
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* disclaimer in the documentation and/or other materials provided
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* with the distribution.
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*
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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
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* or promote products derived from this software without specific
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* prior written permission.
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*
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* THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
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* IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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* TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
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* LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (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 HTS_PACK_H
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#define HTS_PACK_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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* Packs multiple symbols into a single byte if the total alphabet of symbols
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* used is <= 16. Each new symbol takes up 1, 2, 4 or 8 bits, or 0 if the
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* alphabet used is 1 (constant).
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*
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* If successful, out_meta/out_meta_len are set to hold the mapping table
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* to be used during decompression.
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*
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* Returns the packed buffer on success with new length in out_len,
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* NULL of failure
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*/
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uint8_t *hts_pack(uint8_t *data, int64_t len,
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uint8_t *out_meta, int *out_meta_len, uint64_t *out_len);
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/*
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* Unpacks the meta-data portions of the hts_pack algorithm.
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* This consists of the count of symbols and their values.
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*
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* The "map" array is filled out with the used symbols.
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* "nsym" is set to contain the number of symbols per byte;
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* 0, 1, 2, 4 or 8.
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*
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* Returns number of bytes of data[] consumed on success,
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* zero on failure.
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*/
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uint8_t hts_unpack_meta(uint8_t *data, uint32_t data_len,
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uint64_t udata_len, uint8_t *map, int *nsym);
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/*
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* Unpacks a packed data steam (given the unpacked meta-data).
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*
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* "map" is the pack map, mapping 0->n to the expanded symbols.
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* The "out" buffer must be preallocated by the caller to be the correct
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* size. For error checking purposes, out_len is set to the size of
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* this buffer.
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*
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* Returns uncompressed data (out) on success,
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* NULL on failure.
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*/
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uint8_t *hts_unpack(uint8_t *data, int64_t len, uint8_t *out, uint64_t out_len, int nsym, uint8_t *map);
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#ifdef __cplusplus
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}
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#endif
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#endif /* HTS_PACK_H */
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