1 /* 2 This file is part of the BOLT-LMM linear mixed model software package 3 developed by Po-Ru Loh. Copyright (C) 2014-2019 Harvard University. 4 5 This program is free software: you can redistribute it and/or modify 6 it under the terms of the GNU General Public License as published by 7 the Free Software Foundation, either version 3 of the License, or 8 (at your option) any later version. 9 10 This program is distributed in the hope that it will be useful, 11 but WITHOUT ANY WARRANTY; without even the implied warranty of 12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 GNU General Public License for more details. 14 15 You should have received a copy of the GNU General Public License 16 along with this program. If not, see <http://www.gnu.org/licenses/>. 17 */ 18 19 #include <vector> 20 #include <string> 21 #include <cstdio> 22 23 #include "RestrictSnpSet.hpp" 24 #include "SnpData.hpp" 25 26 namespace LMM { 27 28 using std::vector; 29 using std::string; 30 RestrictSnpSet(const string & restrictPartnerFile,bool _matchID,int Nautosomes)31 RestrictSnpSet::RestrictSnpSet(const string &restrictPartnerFile, bool _matchID, int Nautosomes) { 32 matchID = _matchID; 33 vector <SnpInfo> restrictSnps; 34 if (!restrictPartnerFile.empty()) { 35 restrictSnps = SnpData::readBimFile(restrictPartnerFile, Nautosomes); 36 for (uint64 m = 0; m < restrictSnps.size(); m++) 37 keys.insert(makeKey(restrictSnps[m])); 38 } 39 } 40 makeKey(const SnpInfo & snp) const41 string RestrictSnpSet::makeKey(const SnpInfo &snp) const { 42 if (matchID) return snp.ID; 43 else { 44 char buf[20]; 45 sprintf(buf, "%d,%d", snp.chrom, snp.physpos); 46 return string(buf); 47 } 48 } 49 isAllowed(const SnpInfo & snp) const50 bool RestrictSnpSet::isAllowed(const SnpInfo &snp) const { 51 return keys.empty() || keys.find(makeKey(snp)) != keys.end(); 52 } 53 54 } 55