73 lines
2.3 KiB
C++
73 lines
2.3 KiB
C++
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/*
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* Copyright 2015, 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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#include <string>
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#include "gfm.h"
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using namespace std;
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#ifdef BOWTIE_64BIT_INDEX
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const std::string gfm_ext("ht2l");
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#else
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const std::string gfm_ext("ht2");
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#endif // BOWTIE_64BIT_INDEX
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string gLastIOErrMsg;
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/**
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* Try to find the Bowtie index specified by the user. First try the
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* exact path given by the user. Then try the user-provided string
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* appended onto the path of the "indexes" subdirectory below this
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* executable, then try the provided string appended onto
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* "$HISAT2_INDEXES/".
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*/
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string adjustEbwtBase(const string& cmdline,
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const string& gfmFileBase,
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bool verbose)
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{
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string str = gfmFileBase;
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ifstream in;
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if(verbose) cout << "Trying " << str.c_str() << endl;
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in.open((str + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
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if(!in.is_open()) {
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if(verbose) cout << " didn't work" << endl;
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in.close();
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if(getenv("HISAT2_INDEXES") != NULL) {
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str = string(getenv("HISAT2_INDEXES")) + "/" + gfmFileBase;
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if(verbose) cout << "Trying " << str.c_str() << endl;
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in.open((str + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
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if(!in.is_open()) {
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if(verbose) cout << " didn't work" << endl;
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in.close();
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} else {
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if(verbose) cout << " worked" << endl;
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}
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}
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}
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if(!in.is_open()) {
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cerr << "Could not locate a HISAT2 index corresponding to basename \"" << gfmFileBase.c_str() << "\"" << endl;
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throw 1;
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}
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return str;
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}
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