/dports/biology/plink/plink-ng-79b2df8c/2.0/include/ |
H A D | pgenlib_read.cc | 3744 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 D | pgenlib_misc.h | 584 …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 D | pgenlib_read.h | 253 HEADER_INLINE uintptr_t GetAux1aAlleleEntryByteCt(uint32_t allele_ct, uint32_t rare01_ct) { in GetAux1aAlleleEntryByteCt()
|
H A D | pgenlib_write.cc | 1291 const uint32_t allele_ct = pwcp->allele_idx_offsets[vidx + 1] - pwcp->allele_idx_offsets[vidx]; in PwcAppendMultiallelicMain() local
|
H A D | pgenlib_misc.cc | 2657 …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 D | pvar.cpp | 62 uint32_t allele_ct = 2; in GetAlleleCode() local
|
H A D | pvar_ffi_support.cpp | 161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local
|
/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_fasta.cc | 90 uint32_t allele_ct = 2; variable 177 uint32_t allele_ct = 2; in VNormalizeContig() local
|
H A D | pvar_ffi_support.cc | 161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local
|
H A D | plink2_common.h | 455 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 D | plink2_misc.cc | 3717 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 D | plink2_filter.cc | 3724 …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 D | plink2_data.cc | 1765 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 D | plink2_common.cc | 2676 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 D | plink2_import.cc | 119 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 D | plink2_pvar.cc | 1547 uint32_t allele_ct = extra_alt_ct + 2; in LoadPvar() local
|
H A D | plink2_glm.cc | 3337 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 D | plink2_cmdline.cc | 2096 …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 D | plink2_export.cc | 3498 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 D | plink2.cc | 2440 …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 D | plink_assoc.c | 11084 uint32_t allele_ct; in cmh_assoc() local
|
H A D | plink_data.c | 14750 uint32_t allele_ct; in merge_bim_scan() local
|