48 lines
1.3 KiB
C
48 lines
1.3 KiB
C
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/*
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* Copyright 2018, Chanhee Park <parkchanhee@gmail.com> and Daehwan Kim <infphilo@gmail.com>
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*
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* This file is part of HISAT 2.
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*
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* HISAT 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef __HT2_HANDLE_H__
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#define __HT2_HANDLE_H__
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#if 1
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#define EXPORT __attribute__((visibility("default")))
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#else
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#define EXPORT
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#endif
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typedef TIndexOffU index_t;
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typedef uint16_t local_index_t;
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struct ht2_handle {
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ALTDB<TIndexOffU>* altdb;
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ALTDB<TIndexOffU>* raltdb;
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RepeatDB<TIndexOffU>* repeatdb;
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HGFM<TIndexOffU, local_index_t>* gfm;
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RFM<TIndexOffU> *rgfm;
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string tmp_str;
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string ht2_idx_name;
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struct ht2_options options;
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};
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#endif /* __HT2_HANDLE_H__ */
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