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Searched refs:SnpInfo (Results 1 – 12 of 12) sorted by relevance

/dports/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/
H A DSnpInfo.cpp25 const int SnpInfo::MAX_VC_NUM = 1000;
27 bool SnpInfo::isProximal(const SnpInfo &snp2, double genWindow) const { in isProximal()
30 bool SnpInfo::isProximal(const SnpInfo &snp2, int physWindow) const { in isProximal()
H A DSnpInfo.hpp25 class SnpInfo { // note: non-POD b/c of string class
37 bool isProximal(const SnpInfo &snp2, double genWindow) const;
38 bool isProximal(const SnpInfo &snp2, int physWindow) const;
H A DRestrictSnpSet.cpp33 vector <SnpInfo> restrictSnps; in RestrictSnpSet()
41 string RestrictSnpSet::makeKey(const SnpInfo &snp) const { in makeKey()
50 bool RestrictSnpSet::isAllowed(const SnpInfo &snp) const { in isAllowed()
H A DSnpData.hpp57 std::vector <SnpInfo> snps; // [VECTOR]: M
89 std::vector <SnpInfo> processSnps(std::vector <uint64> &Mfiles,
95 void processMap(std::vector <SnpInfo> &bedSnps, const std::string &geneticMapFile,
119 static std::vector <SnpInfo> readBimFile(const std::string &bimFile, int Nauto);
148 const std::vector <SnpInfo> &getSnpInfo(void) const;
H A DLDscoreCalibration.hpp38 (const std::vector <LMM::SnpInfo> &snps, const std::vector <double> &stats,
52 (const std::vector <LMM::SnpInfo> &snps, const std::vector <double> &statsRef,
68 (const std::vector <LMM::SnpInfo> &snps, const std::vector <double> &stats,
H A DRestrictSnpSet.hpp37 std::string makeKey(const SnpInfo &snp) const;
38 bool isAllowed(const SnpInfo &snp) const;
H A DSnpData.cpp290 vector <SnpInfo> SnpData::processSnps(vector <uint64> &Mfiles, const vector <string> &bimFiles, in processSnps()
297 vector <SnpInfo> bedSnps; in processSnps()
301 vector <SnpInfo> snps_i = readBimFile(bimFiles[i], Nautosomes); in processSnps()
416 if (vcNum > SnpInfo::MAX_VC_NUM) { in processSnps()
418 << SnpInfo::MAX_VC_NUM << endl; in processSnps()
477 void SnpData::processMap(vector <SnpInfo> &bedSnps, const string &geneticMapFile, in processMap()
638 vector <SnpInfo> bedSnps = processSnps(Mfiles, bimFiles, excludeFiles, modelSnpsFiles, in SnpData()
767 vector <SnpInfo> SnpData::readBimFile(const string &bimFile, int Nauto) { in readBimFile()
768 vector <SnpInfo> ret; in readBimFile()
774 SnpInfo snp; string chrom_str; in readBimFile()
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H A DLDscoreCalibration.cpp63 (const vector <LMM::SnpInfo> &snps, const vector <double> &stats, vector <bool> maskSnps, in removeOutlierWindows()
191 (const vector <LMM::SnpInfo> &snps, const vector <double> &statsRef, in calibrateStatPair()
242 (const vector <LMM::SnpInfo> &snps, const vector <double> &stats, in calibrateStat()
H A DPhenoBuilder.cpp112 const vector <SnpInfo> &snps = bolt.getSnpData().getSnpInfo(); in genPhenoCausal()
215 const vector <SnpInfo> &snps = bolt.getSnpData().getSnpInfo(); in genPhenoCausalRegions()
H A DMakefile126 …inearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o…
H A DBolt.cpp205 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in makeChunkAssignments()
279 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in findChunkAssignment()
1217 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in init()
1668 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in computeWritePredBetas()
1677 const SnpInfo &snp = snps[m]; in computeWritePredBetas()
H A DBoltMain.cpp136 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in main()