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Searched defs:allele_ct (Results 1 – 22 of 22) sorted by relevance

/dports/biology/plink/plink-ng-79b2df8c/2.0/include/
H A Dpgenlib_read.cc3744 uint32_t GetAux1aWidth(uint32_t allele_ct) { in GetAux1aWidth()
4026 uint32_t GetAux1bConsts(uint32_t allele_ct, uintptr_t* detect_hom_mask_lo_ptr) { in GetAux1bConsts()
4341 const uint32_t allele_ct = allele_idx_offsets[vidx + 1] - allele_idx_offsets[vidx]; variable
5124 const uint32_t allele_ct = allele_idx_offsets[vidx + 1] - allele_idx_offsets[vidx]; in Get1Multiallelic() local
5707 const uint32_t allele_ct = allele_idx_offsets[vidx + 1] - allele_idx_offsets[vidx]; in IMPLPgrGet2() local
6448 const uint32_t allele_ct = allele_idx_offsets[vidx + 1] - allele_idx_offsets[vidx]; in GetMultiallelicCodes() local
6729 …const uint32_t allele_ct = allele_idx_offsets? (allele_idx_offsets[vidx + 1] - allele_idx_offsets[… in ReadGenovecHphaseSubsetUnsafe() local
6944 const uint32_t allele_ct = allele_idx_offsets[vidx + 1] - allele_idx_offsets[vidx]; in PgrGet2P() local
7316 …const uint32_t allele_ct = allele_idx_offsets? (allele_idx_offsets[vidx + 1] - allele_idx_offsets[… in IMPLPgrGetD() local
7324 …const uint32_t allele_ct = allele_idx_offsets? (allele_idx_offsets[vidx + 1] - allele_idx_offsets[… in PgrGet1D() local
[all …]
H A Dpgenlib_misc.h584 …4_t* __restrict sums, const uint64_t* __restrict ssqs, uint32_t nm_sample_ct, uint32_t allele_ct) { in MultiallelicDiploidMachR2()
669 HEADER_INLINE uintptr_t GetAux1bAlleleEntryByteCt(uint32_t allele_ct, uint32_t rare10_ct) { in GetAux1bAlleleEntryByteCt()
H A Dpgenlib_read.h253 HEADER_INLINE uintptr_t GetAux1aAlleleEntryByteCt(uint32_t allele_ct, uint32_t rare01_ct) { in GetAux1aAlleleEntryByteCt()
H A Dpgenlib_write.cc1291 const uint32_t allele_ct = pwcp->allele_idx_offsets[vidx + 1] - pwcp->allele_idx_offsets[vidx]; in PwcAppendMultiallelicMain() local
H A Dpgenlib_misc.cc2657 …ms, const uint64_t* __restrict hap_ssqs_x2, uint32_t nm_sample_ct, uint32_t allele_ct, uint32_t ex… in MultiallelicDiploidMinimac3R2()
/dports/biology/plink/plink-ng-79b2df8c/2.0/pgenlibr/src/
H A Dpvar.cpp62 uint32_t allele_ct = 2; in GetAlleleCode() local
H A Dpvar_ffi_support.cpp161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local
/dports/biology/plink/plink-ng-79b2df8c/2.0/
H A Dplink2_fasta.cc90 uint32_t allele_ct = 2; variable
177 uint32_t allele_ct = 2; in VNormalizeContig() local
H A Dpvar_ffi_support.cc161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local
H A Dplink2_common.h455 HEADER_INLINE double GetNonmajFreq(const double* cur_allele_freqs, uint32_t allele_ct) { in GetNonmajFreq()
470 …INE double GetAlleleFreq(const double* cur_allele_freqs, uint32_t allele_idx, uint32_t allele_ct) { in GetAlleleFreq()
H A Dplink2_misc.cc3717 uint32_t allele_ct = 2; variable
4543 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; variable
4615 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; variable
4783 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; in ComputeHweXPvalsMain() local
5020 uint32_t allele_ct = 2; variable
5234 uint32_t allele_ct = 2; variable
7462 uint32_t allele_ct = 2; in SdiffCountsOnly() local
7867 …uint32_t sample_idx1, uint32_t sample_idx2, uint32_t variant_uidx, uint32_t allele_ct, CompressStr… in AppendSdiffPregenoFields()
8090 uint32_t allele_ct = 2; in SdiffMainBatch() local
H A Dplink2_filter.cc3724 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; variable
3838 double GetTypedFreq(const double* cur_allele_freqs, uint32_t allele_ct, FreqFilterMode mode) { in GetTypedFreq()
3877 uint64_t GetTypedDdosage(const uint64_t* cur_allele_ddosages, uint32_t allele_ct, FreqFilterMode mo… in GetTypedDdosage()
3928 uint32_t allele_ct = 2; variable
H A Dplink2_data.cc1765 uint32_t allele_ct = 2; in LoadAlleleAndGenoCountsThread() local
2905 JoinVtype JoinCount(const char* const* cur_alleles, uintptr_t allele_ct, JoinCounts* jcp) { in JoinCount()
3029 uint32_t allele_ct = 2; in PlanMultiallelicJoin() local
3161 const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offset_base; in PlanMultiallelicSplit() local
3221 uint32_t VaridSplitOk(const char* orig_variant_id, uint32_t allele_ct) { in VaridSplitOk()
5194 uint32_t allele_ct = 2; in MakePgenThread() local
H A Dplink2_common.cc2676 uintptr_t allele_ct = 0; in CountAlleles() local
3077 char* PrintMultiallelicHcAsDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start) { in PrintMultiallelicHcAsDs()
3107 char* PrintMultiallelicHcAsHaploidDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start) { in PrintMultiallelicHcAsHaploidDs()
H A Dplink2_import.cc119 uint64_t GparseWriteByteCt(uint32_t sample_ct, uint32_t allele_ct, GparseFlags flags) { in GparseWriteByteCt()
173 uintptr_t* GparseGetPointers(unsigned char* record_start, uint32_t sample_ct, uint32_t allele_ct, G… in GparseGetPointers()
226 uint32_t allele_ct = 2; in GparseFlush() local
1489 …cLine(const VcfImportBaseContext* vibcp, const char* linebuf_iter, uintptr_t allele_ct, uint32_t* … in VcfConvertUnphasedMultiallelicLine()
1982 …cLine(const VcfImportBaseContext* vibcp, const char* linebuf_iter, uintptr_t allele_ct, uint32_t* … in VcfConvertPhasedMultiallelicLine()
3520 uint32_t allele_ct = 0; in VcfToPgen() local
5357 …licHaploidInt8Gt(const unsigned char* gt_main, uint32_t sample_ct, uint32_t allele_ct, uintptr_t* … in BcfConvertMultiallelicHaploidInt8Gt()
5403 …icHaploidInt16Gt(const unsigned char* gt_main, uint32_t sample_ct, uint32_t allele_ct, uintptr_t* … in BcfConvertMultiallelicHaploidInt16Gt()
5445 …t GparseReadBcfMetadata* metap, const unsigned char* record_start, uint32_t allele_ct, uint32_t* _… in BcfConvertUnphasedMultiallelic()
6098 …, const GparseReadBcfMetadata* metap, unsigned char* record_start, uint32_t allele_ct, uint32_t* _… in BcfConvertPhasedMultiallelic()
H A Dplink2_pvar.cc1547 uint32_t allele_ct = extra_alt_ct + 2; in LoadPvar() local
H A Dplink2_glm.cc3337 uint32_t allele_ct = 2; in GlmLogisticThread() local
5774 uint32_t allele_ct = 2; in GlmLogistic() local
6474 uint32_t allele_ct = 2; in GlmLinearThread() local
7941 uint32_t allele_ct = 2; in GlmLinear() local
8537 uint32_t allele_ct = 2; in GlmLinearSubbatchThread() local
10151 uint32_t allele_ct = 2; in GlmLinearBatch() local
10977 uint32_t allele_ct = 2; in GlmMain() local
H A Dplink2_cmdline.cc2096 …const uintptr_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx… in CountExtraAlleles() local
2116 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; in MaxAlleleCtSubset() local
H A Dplink2_export.cc3498 uint32_t allele_ct = 2; variable
4621 uint32_t allele_ct = 2; variable
7909 uint32_t allele_ct = 2; variable
8222 uint32_t allele_ct = 2; variable
H A Dplink2.cc2440 …const uint32_t allele_ct = allele_idx_offsets? (allele_idx_offsets[variant_uidx + 1] - allele_idx_… in Plink2Core() local
/dports/biology/plink/plink-ng-79b2df8c/1.9/
H A Dplink_assoc.c11084 uint32_t allele_ct; in cmh_assoc() local
H A Dplink_data.c14750 uint32_t allele_ct; in merge_bim_scan() local