/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_common.h | 682 } ChrInfo; typedef 686 PglErr InitChrInfo(ChrInfo* cip); 688 void FinalizeChrset(MiscFlags misc_flags, ChrInfo* cip); 690 HEADER_INLINE PglErr InitChrInfoHuman(ChrInfo* cip) { in InitChrInfoHuman() 699 void ForgetExtraChrNames(uint32_t reinitialize, ChrInfo* cip); 704 PglErr FinalizeChrInfo(ChrInfo* cip); 706 void CleanupChrInfo(ChrInfo* cip); 710 char* chrtoa(const ChrInfo* cip, uint32_t chr_idx, char* buf); 712 uint32_t GetMaxChrSlen(const ChrInfo* cip); 714 uint32_t IsHaploidChrPresent(const ChrInfo* cip); [all …]
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H A D | plink2_import.h | 95 …mCol fam_cols, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip, uint32_t* p… 97 …mCol fam_cols, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip, uint32_t* p… 99 …e import_dosage_certainty, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip); 101 …id_delim, char idspace_to, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip); 103 …Flags oxford_import_flags, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip); 105 …e import_dosage_certainty, uint32_t max_thread_ct, char* outname, char* outname_end, ChrInfo* cip); 107 …ase_thresh, uint32_t max_thread_ct, sfmt_t* sfmtp, char* outname, char* outname_end, ChrInfo* cip);
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H A D | plink2_filter.h | 42 …t_id_slen, uintptr_t variant_id_htable_size, uintptr_t* variant_include, ChrInfo* cip, uint32_t* v… 44 …ize, uint32_t do_exclude, int32_t window_bp, uintptr_t* variant_include, ChrInfo* cip, uint32_t* v… 61 PglErr RmDup(const uintptr_t* sample_include, const ChrInfo* cip, const uint32_t* variant_bps, cons… 89 …ngCts(const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, uint32_t ra… 93 void EnforceGenoThresh(const ChrInfo* cip, const uint32_t* variant_missing_cts, const uint32_t* var… 95 void EnforceHweThresh(const ChrInfo* cip, const uintptr_t* allele_idx_offsets, const STD_ARRAY_PTR_… 107 void EnforceImpR2Thresh(const ChrInfo* cip, const double* imp_r2_vals, double imp_r2_min, double im… 109 void EnforceMinBpSpace(const ChrInfo* cip, const uint32_t* variant_bps, uint32_t min_bp_space, uint…
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H A D | plink2_matrix_calc.h | 177 PglErr CalcKing(const SampleIdInfo* siip, const uintptr_t* variant_include_orig, const ChrInfo* cip… 179 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const char*… 181 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… 184 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 187 …o_cols, const char* pheno_names, const uintptr_t* variant_include, const ChrInfo* cip, const char*… 189 PglErr Vscore(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bps, co…
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H A D | plink2_data.h | 63 PglErr WriteMapOrBim(const char* outname, const uintptr_t* variant_include, const ChrInfo* cip, con… 71 void AppendChrsetLine(const ChrInfo* cip, char** write_iter_ptr); 73 uint32_t ChrLenLbound(const ChrInfo* cip, const uint32_t* variant_bps, const uintptr_t* allele_idx_… 89 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… 95 …uint32_t* new_sample_idx_to_old, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 97 …uint32_t* new_sample_idx_to_old, const uintptr_t* variant_include, const ChrInfo* cip, const uint3…
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H A D | plink2_misc.h | 299 PglErr UpdateVarBps(const ChrInfo* cip, const char* const* variant_ids, const uint32_t* variant_id_… 305 PglErr RecoverVarIds(const char* fname, const uintptr_t* variant_include, const ChrInfo* cip, const… 327 PglErr WriteAlleleFreqs(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* varia… 329 …lude, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 331 …nst uint32_t* sample_hethap_cts, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 333 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… 337 PglErr HardyReport(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bp… 339 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… 341 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3…
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H A D | plink2_ld.h | 55 PglErr LdPrune(const uintptr_t* orig_variant_include, const ChrInfo* cip, const uint32_t* variant_b… 57 PglErr LdConsole(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* variant_i…
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H A D | plink2_pvar.h | 61 …ar* chrset_iter, const char* file_descrip, MiscFlags misc_flags, uintptr_t line_idx, ChrInfo* cip); 91 …er_min_allele_ct, uint32_t filter_max_allele_ct, uint32_t max_thread_ct, ChrInfo* cip, uint32_t* m…
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H A D | plink2_set.h | 27 PglErr ExtractExcludeRange(const char* fnames, const ChrInfo* cip, const uint32_t* variant_bps, uin…
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H A D | plink2_fasta.h | 35 …nst char* const* variant_ids, const uintptr_t* allele_idx_offsets, const ChrInfo* cip, const char*…
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H A D | plink2_common.cc | 1168 PglErr InitChrInfo(ChrInfo* cip) { in InitChrInfo() 1232 void FinalizeChrset(MiscFlags misc_flags, ChrInfo* cip) { in FinalizeChrset() 1312 void ForgetExtraChrNames(uint32_t reinitialize, ChrInfo* cip) { in ForgetExtraChrNames() 1329 PglErr FinalizeChrInfo(ChrInfo* cip) { in FinalizeChrInfo() 1385 void CleanupChrInfo(ChrInfo* cip) { in CleanupChrInfo() 1400 char* ChrNameStd(const ChrInfo* cip, uint32_t chr_idx, char* buf) { in ChrNameStd() 1451 char* chrtoa(const ChrInfo* cip, uint32_t chr_idx, char* buf) { in chrtoa() 1469 uint32_t GetMaxChrSlen(const ChrInfo* cip) { in GetMaxChrSlen() 1495 uint32_t IsHaploidChrPresent(const ChrInfo* cip) { in IsHaploidChrPresent() 1508 uint32_t IsAutosomalDiploidChrPresent(const ChrInfo* cip) { in IsAutosomalDiploidChrPresent() [all …]
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H A D | plink2_adjust.h | 78 PglErr Multcomp(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* chr_ids, c…
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H A D | plink2_export.h | 59 …o_cols, const char* pheno_names, const uintptr_t* variant_include, const ChrInfo* cip, const uint3…
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H A D | plink2_glm.h | 122 …s, const char* covar_names, const uintptr_t* orig_variant_include, const ChrInfo* cip, const uint3…
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H A D | plink2_set.cc | 32 PglErr LoadIntervalBed(const ChrInfo* cip, const uint32_t* variant_bps, const char* sorted_subset_i… in LoadIntervalBed() 345 PglErr ExtractExcludeRange(const char* fnames, const ChrInfo* cip, const uint32_t* variant_bps, uin… in ExtractExcludeRange()
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H A D | plink2_fasta.cc | 24 … uintptr_t* allele_idx_offsets, const char* const* allele_storage, const ChrInfo* cip, const char*… 157 …nst char* const* variant_ids, const uintptr_t* allele_idx_offsets, const ChrInfo* cip, const char*… in VNormalizeContig() 461 …nst char* const* variant_ids, const uintptr_t* allele_idx_offsets, const ChrInfo* cip, const char*…
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H A D | plink2_data.cc | 29 PglErr WriteMapOrBim(const char* outname, const uintptr_t* variant_include, const ChrInfo* cip, con… 239 void AppendChrsetLine(const ChrInfo* cip, char** write_iter_ptr) { in AppendChrsetLine() 294 uint32_t ChrLenLbound(const ChrInfo* cip, const uint32_t* variant_bps, const uintptr_t* allele_idx_… in ChrLenLbound() 1672 const ChrInfo* cip; 1734 const ChrInfo* cip = ctx->cip; in LoadAlleleAndGenoCountsThread() 3009 PglErr PlanMultiallelicJoin(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* v… in PlanMultiallelicJoin() 4658 const ChrInfo* cip; 4707 const ChrInfo* cip = mcp->cip; in MakeBedlikeThread() 5110 const ChrInfo* cip = mcp->cip; in MakePgenThread() 7313 BoolErr SortChr(const ChrInfo* cip, const uint32_t* chr_idx_to_size, uint32_t use_nsort, ChrInfo* w… in SortChr() [all …]
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H A D | plink2_filter.cc | 41 …t_id_slen, uintptr_t variant_id_htable_size, uintptr_t* variant_include, ChrInfo* cip, uint32_t* v… in FromToFlag() 120 …ize, uint32_t do_exclude, int32_t window_bp, uintptr_t* variant_include, ChrInfo* cip, uint32_t* v… in SnpFlag() 653 PglErr RmDup(const uintptr_t* sample_include, const ChrInfo* cip, const uint32_t* variant_bps, cons… in RmDup() 3249 const ChrInfo* cip; 3271 const ChrInfo* cip = ctx->cip; in LoadSampleMissingCtsThread() 3406 …ngCts(const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, uint32_t ra… in LoadSampleMissingCts() 3628 void EnforceGenoThresh(const ChrInfo* cip, const uint32_t* variant_missing_cts, const uint32_t* var… in EnforceGenoThresh() 3669 void EnforceHweThresh(const ChrInfo* cip, const uintptr_t* allele_idx_offsets, const STD_ARRAY_PTR_… 3978 void EnforceImpR2Thresh(const ChrInfo* cip, const double* imp_r2_vals, double imp_r2_min, double im… in EnforceImpR2Thresh() 4027 void EnforceMinBpSpace(const ChrInfo* cip, const uint32_t* variant_bps, uint32_t min_bp_space, uint… in EnforceMinBpSpace()
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H A D | plink2_pvar.cc | 39 …r* chrset_iter, const char* file_descrip, MiscFlags misc_flags, uintptr_t line_idx, ChrInfo* cip) { in ReadChrsetHeaderLine() 422 void BackfillChrIdxs(const ChrInfo* cip, uint32_t chrs_encountered_m1, uint32_t offset, uint32_t en… in BackfillChrIdxs() 697 …splitpar_bound2, uintptr_t* variant_include, uintptr_t* loaded_chr_mask, ChrInfo* cip, uint32_t* c… in SplitPar() 776 …er_min_allele_ct, uint32_t filter_max_allele_ct, uint32_t max_thread_ct, ChrInfo* cip, uint32_t* m… in LoadPvar()
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H A D | plink2_misc.cc | 51 PglErr UpdateVarBps(const ChrInfo* cip, const char* const* variant_ids, const uint32_t* variant_id_… in UpdateVarBps() 625 PglErr RecoverVarIds(const char* fname, const uintptr_t* variant_include, const ChrInfo* cip, const… in RecoverVarIds() 3137 PglErr WriteAlleleFreqs(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* varia… in WriteAlleleFreqs() 3554 …sed)) const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 4496 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… 5757 const ChrInfo* cip; 5822 const ChrInfo* cip = ctx->cip; in SampleCountsThread() 6378 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… in SampleCounts() 7417 …strict pair_sex_male, const uintptr_t* __restrict variant_include, const ChrInfo* cip, const uintp… in SdiffCountsOnly() 7908 …strict pair_sex_male, const uintptr_t* __restrict variant_include, const ChrInfo* cip, const uint3… in SdiffMainBatch() [all …]
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H A D | plink2_matrix_calc.cc | 1322 PglErr CalcKing(const SampleIdInfo* siip, const uintptr_t* variant_include_orig, const ChrInfo* cip… in CalcKing() 2635 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const char*… in CalcKingTableSubset() 3929 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const uintp… in CalcGrm() 4711 PglErr FlushBiallelicVarWts(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* v… in FlushBiallelicVarWts() 4808 PglErr FlushAlleleWts(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant… in FlushAlleleWts() 4946 …clude, const SampleIdInfo* siip, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… in CalcPca() 5711 …o_cols, const char* pheno_names, const uintptr_t* variant_include, const ChrInfo* cip, const char*… in ScoreReport() 6902 const ChrInfo* cip; 6947 const ChrInfo* cip = ctx->cip; in VscoreThread() 7259 PglErr Vscore(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bps, co… in Vscore()
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H A D | plink2_adjust.cc | 83 PglErr Multcomp(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* chr_ids, c… in Multcomp()
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H A D | plink2_export.cc | 206 …pcounts, const char* sample_ids, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 928 …unts, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 1213 …t uintptr_t* sex_male_collapsed, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 1718 …unts, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 2294 const ChrInfo* cip; 2362 const ChrInfo* cip = ctx->cip; in ExportBgen13Thread() 3243 …x_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 4175 …t uintptr_t* sex_male_collapsed, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 7395 …uintptr_t* sex_female_collapsed, const uintptr_t* variant_include, const ChrInfo* cip, const uint3… 9822 …o_cols, const char* pheno_names, const uintptr_t* variant_include, const ChrInfo* cip, const uint3…
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H A D | plink2_ld.cc | 885 PglErr IndepPairwise(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_… in IndepPairwise() 1204 PglErr LdPruneSubcontigSplitAll(const uintptr_t* variant_include, const ChrInfo* cip, const uint32_… in LdPruneSubcontigSplitAll() 1569 PglErr LdPrune(const uintptr_t* orig_variant_include, const ChrInfo* cip, const uint32_t* variant_b… in LdPrune() 2797 PglErr LdConsole(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* variant_i… in LdConsole()
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H A D | plink2_glm.cc | 134 …_pvar_fname, const char* local_psam_fname, const char* sample_ids, const ChrInfo* cip, const uint3… in GlmLocalOpen() 3204 const ChrInfo* cip; 3302 const ChrInfo* cip = common->cip; in GlmLogisticThread() 4881 const ChrInfo* cip = common->cip; in ReadLocalCovarBlock() 5043 const ChrInfo* cip = common->cip; in ReadRfmix2Block() 5400 const ChrInfo* cip = common->cip; in GlmLogistic() 6430 const ChrInfo* cip = common->cip; in GlmLinearThread() 7603 const ChrInfo* cip = common->cip; in GlmLinear() 8492 const ChrInfo* cip = common->cip; in GlmLinearSubbatchThread() 9718 const ChrInfo* cip = common->cip; in GlmLinearBatch() [all …]
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