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Searched refs:ChrInfo (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/plink/plink-ng-79b2df8c/2.0/
H A Dplink2_common.h682 } 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);
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H A Dplink2_import.h95 …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);
H A Dplink2_filter.h42 …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…
H A Dplink2_matrix_calc.h177 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…
H A Dplink2_data.h63 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…
H A Dplink2_misc.h299 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…
H A Dplink2_ld.h55 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…
H A Dplink2_pvar.h61 …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…
H A Dplink2_set.h27 PglErr ExtractExcludeRange(const char* fnames, const ChrInfo* cip, const uint32_t* variant_bps, uin…
H A Dplink2_fasta.h35 …nst char* const* variant_ids, const uintptr_t* allele_idx_offsets, const ChrInfo* cip, const char*…
H A Dplink2_common.cc1168 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()
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H A Dplink2_adjust.h78 PglErr Multcomp(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* chr_ids, c…
H A Dplink2_export.h59 …o_cols, const char* pheno_names, const uintptr_t* variant_include, const ChrInfo* cip, const uint3…
H A Dplink2_glm.h122 …s, const char* covar_names, const uintptr_t* orig_variant_include, const ChrInfo* cip, const uint3…
H A Dplink2_set.cc32 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()
H A Dplink2_fasta.cc24 … 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*…
H A Dplink2_data.cc29 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()
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H A Dplink2_filter.cc41 …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()
H A Dplink2_pvar.cc39 …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()
H A Dplink2_misc.cc51 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()
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H A Dplink2_matrix_calc.cc1322 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()
H A Dplink2_adjust.cc83 PglErr Multcomp(const uintptr_t* variant_include, const ChrInfo* cip, const char* const* chr_ids, c… in Multcomp()
H A Dplink2_export.cc206 …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…
H A Dplink2_ld.cc885 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()
H A Dplink2_glm.cc134 …_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()
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