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/*
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* divsufsort.h for libdivsufsort-lite
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* Copyright (c) 2003-2008 Yuta Mori All Rights Reserved.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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#ifndef _DIVSUFSORT_H
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#define _DIVSUFSORT_H 1
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#ifdef __cplusplus
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extern "C" {
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#endif /* __cplusplus */
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/*- Prototypes -*/
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/**
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* Constructs the suffix array of a given string.
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* @param T [0..n-1] The input string.
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* @param SA [0..n-1] The output array of suffixes.
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* @param n The length of the given string.
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* @param openMP enables OpenMP optimization.
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* @return 0 if no error occurred, -1 or -2 otherwise.
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*/
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int
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divsufsort(const unsigned char *T, int *SA, int n, int openMP);
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/**
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* Constructs the burrows-wheeler transformed string of a given string.
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* @param T [0..n-1] The input string.
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* @param U [0..n-1] The output string. (can be T)
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* @param A [0..n-1] The temporary array. (can be NULL)
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* @param n The length of the given string.
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* @param num_indexes The length of secondary indexes array. (can be NULL)
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* @param indexes The secondary indexes array. (can be NULL)
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* @param openMP enables OpenMP optimization.
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* @return The primary index if no error occurred, -1 or -2 otherwise.
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*/
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int
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divbwt(const unsigned char *T, unsigned char *U, int *A, int n, unsigned char * num_indexes, int * indexes, int openMP);
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#ifdef __cplusplus
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} /* extern "C" */
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#endif /* __cplusplus */
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#endif /* _DIVSUFSORT_H */
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