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Searched refs:snpInfo (Results 1 – 21 of 21) sorted by relevance

/dports/biology/gemma/GEMMA-0.98.3/src/
H A Dvarcov.cpp64 snpInfo = cPar.snpInfo; in CopyFromParam()
259 CalcNB(snpInfo); in AnalyzeBimbam()
290 n_nb = snpInfo[t].n_nb + 1; in AnalyzeBimbam()
292 n_nb = snpInfo[t].n_nb - n_nb + 1; in AnalyzeBimbam()
318 n_nb = snpInfo[t].n_nb; in AnalyzeBimbam()
322 snpInfo_sub.push_back(snpInfo[t]); in AnalyzeBimbam()
359 CalcNB(snpInfo); in AnalyzePlink()
390 n_nb = snpInfo[t].n_nb + 1; in AnalyzePlink()
392 n_nb = snpInfo[t].n_nb - n_nb + 1; in AnalyzePlink()
418 n_nb = snpInfo[t].n_nb; in AnalyzePlink()
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H A Dlm.cpp72 snpInfo = cPar.snpInfo; in CopyFromParam()
126 outfile << snpInfo[t].rs_number << "\t"; in WriteFiles()
190 for (size_t i = 0; i < snpInfo.size(); ++i) { in WriteFiles()
195 outfile << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteFiles()
196 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss << "\t" in WriteFiles()
197 << ni_test - snpInfo[i].n_miss << "\t" << snpInfo[i].a_minor in WriteFiles()
198 << "\t" << snpInfo[i].a_major << "\t" << fixed << setprecision(3) in WriteFiles()
199 << snpInfo[i].maf << "\t"; in WriteFiles()
548 for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) { in AnalyzePlink()
549 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlink()
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H A Dgemma_io.h45 bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo);
68 map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
72 vector<int> &indicator_snp, vector<SNPINFO> &snpInfo,
119 vector<SNPINFO> &snpInfo, size_t &ng_total);
138 const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
145 const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
H A Dparam.cpp251 snpInfo.clear(); in ReadFiles()
376 msnpInfo.push_back(snpInfo); in ReadFiles()
429 msnpInfo.push_back(snpInfo); in ReadFiles()
1874 rs = snpInfo[i].rs_number; in WriteVar()
2230 rs = snpInfo[i].rs_number; in ObtainWeight()
2250 snpInfo = msnpInfo[t]; in ObtainWeight()
2367 rs = snpInfo[i].rs_number; in UpdateSNPnZ()
2368 a1 = snpInfo[i].a_minor; in UpdateSNPnZ()
2386 snpInfo = msnpInfo[t]; in UpdateSNPnZ()
2394 a1 = snpInfo[i].a_minor; in UpdateSNPnZ()
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H A Dldr.cpp66 snpInfo = cPar.snpInfo; in CopyFromParam()
H A Dprdt.cpp55 snpInfo = cPar.snpInfo; in CopyFromParam()
343 for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) { in AnalyzePlink()
344 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlink()
345 ProgressBar("Reading SNPs ", t, snpInfo.size() - 1); in AnalyzePlink()
348 rs = snpInfo[t].rs_number; in AnalyzePlink()
H A Dlmm.cpp83 snpInfo = cPar.snpInfo; in CopyFromParam()
182 outfile << snpInfo[t].rs_number << "\t"; in WriteFiles()
199 for (size_t i = 0; i < snpInfo.size(); ++i) { in WriteFiles()
202 auto snp = snpInfo[i].rs_number; in WriteFiles()
206 outfile << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteFiles()
207 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss << "\t" in WriteFiles()
208 << snpInfo[i].a_minor << "\t" << snpInfo[i].a_major << "\t" in WriteFiles()
1750 for (size_t t = 0; t < snpInfo.size(); ++t) { in AnalyzePlink()
1756 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlink()
2430 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlinkGXE()
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H A Dgemma_io.cpp512 snpInfo.clear(); in ReadFile_bim()
546 snpInfo.push_back(sInfo); in ReadFile_bim()
645 snpInfo.clear(); in ReadFile_geno()
708 snpInfo.push_back(sInfo); in ReadFile_geno()
790 snpInfo.push_back(sInfo); in ReadFile_geno()
926 snpInfo[t].n_miss = -9; in ReadFile_bed()
928 snpInfo[t].maf = -9; in ReadFile_bed()
983 snpInfo[t].n_miss = n_miss; in ReadFile_bed()
985 snpInfo[t].maf = maf; in ReadFile_bed()
987 snpInfo[t].n_nb = 0; in ReadFile_bed()
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H A Dldr.h56 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dvarcov.h42 vector<SNPINFO> snpInfo; variable
H A Dbslmmdap.cpp88 snpInfo = cPar.snpInfo; in CopyFromParam()
391 outfile_bf << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteResult()
392 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss; in WriteResult()
H A Dprdt.h46 vector<SNPINFO> snpInfo; variable
H A Dlm.h59 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dbslmm.cpp99 snpInfo = cPar.snpInfo; in CopyFromParam()
174 outfile << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteParam()
175 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss << "\t"; in WriteParam()
224 outfile << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteParam()
225 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss << "\t"; in WriteParam()
H A Dmvlmm.h73 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dbslmmdap.h74 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dlmm.h86 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dbslmm.h89 vector<SNPINFO> snpInfo; variable
H A Dparam.h323 vector<SNPINFO> snpInfo; // Record SNP information. variable
H A Dmvlmm.cpp88 snpInfo = cPar.snpInfo; in CopyFromParam()
168 for (size_t i = 0; i < snpInfo.size(); ++i) { in WriteFiles()
173 outfile << snpInfo[i].chr << "\t" << snpInfo[i].rs_number << "\t" in WriteFiles()
174 << snpInfo[i].base_position << "\t" << snpInfo[i].n_miss << "\t" in WriteFiles()
175 << snpInfo[i].a_minor << "\t" << snpInfo[i].a_major << "\t" << fixed in WriteFiles()
176 << setprecision(3) << snpInfo[i].maf << "\t"; in WriteFiles()
3668 for (vector<SNPINFO>::size_type t = 0; t < snpInfo.size(); ++t) { in AnalyzePlink()
3669 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlink()
3670 ProgressBar("Reading SNPs", t, snpInfo.size() - 1); in AnalyzePlink()
4654 if (t % d_pace == 0 || t == snpInfo.size() - 1) { in AnalyzePlinkGXE()
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/dports/biology/hisat2/hisat2-2.2.1/li_hla/
H A Dmain.cpp45 std::vector<struct _snpInfo> snpInfo ; // When using this, we already convert the snp name into snp… variable
140 snpInfo.push_back( info ) ; in main()
238 if ( snpInfo[ snpId ].type == 'd' ) in main()
240 alleleLength[ alleleId ] -= snpInfo[ snpId ].length ; in main()
242 else if ( snpInfo[ snpId ].type == 'i' ) in main()
244 alleleLength[ alleleId ] += snpInfo[ snpId ].length ; in main()
329 if ( snpInfo[ snpId ].type == 'd' && snpInfo[ snpId ].position < k in main()