84 lines
2.0 KiB
C
84 lines
2.0 KiB
C
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/*
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* Copyright 2016, 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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/*
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* gp.h
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*
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*/
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#ifndef GP_H_
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#define GP_H_
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#include <iostream>
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#include <stdint.h>
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/**
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* Encapsulates alignment policy for graph
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*/
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class GraphPolicy {
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public:
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GraphPolicy() { reset(); }
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GraphPolicy(size_t maxAltsTried,
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bool useHaplotype,
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bool haplotypeOnly,
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bool enableCODIS)
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{
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init(maxAltsTried,
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useHaplotype,
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haplotypeOnly,
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enableCODIS);
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}
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/**
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*/
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void reset() {
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init(0);
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}
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/**
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*/
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void init(size_t maxAltsTried,
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bool useHaplotype = false,
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bool haplotypeOnly = false,
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bool enableCODIS = false)
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{
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maxAltsTried_ = maxAltsTried;
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useHaplotype_ = useHaplotype;
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haplotypeOnly_ = haplotypeOnly;
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enableCODIS_ = enableCODIS;
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}
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size_t maxAltsTried() const { return maxAltsTried_; }
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bool useHaplotype() const { return useHaplotype_; }
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bool haplotypeOnly() const { return haplotypeOnly_; }
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bool enableCODIS() const { return enableCODIS_; }
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private:
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size_t maxAltsTried_;
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bool useHaplotype_;
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bool haplotypeOnly_;
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bool enableCODIS_;
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};
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#endif /*ndef GP_H_*/
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