/dports/biology/plink/plink-ng-79b2df8c/2.0/include/ |
H A D | pgenlib_read.cc | 3723 if (allele_ct < 5) { in CountAux1aDense() 3735 if (allele_ct < 19) { in CountAux1aDense() 3745 if (allele_ct < 7) { in GetAux1aWidth() 3751 if (allele_ct < 19) { in GetAux1aWidth() 3760 if (allele_ct < 7) { in GetAux1aConsts() 3772 if (allele_ct < 19) { in GetAux1aConsts() 3989 if (allele_ct < 6) { in CountAux1bDense() 4027 if (allele_ct < 6) { in GetAux1bConsts() 6006 if (allele_ct < 7) { in GetAux1aCodes() 6211 if (allele_ct < 6) { in GetAux1bCodes() [all …]
|
H A D | pgenlib_misc.h | 582 …const uint64_t* __restrict hap_ssqs_x2, uint32_t nm_sample_ct, uint32_t allele_ct, uint32_t extra_… 584 …4_t* __restrict sums, const uint64_t* __restrict ssqs, uint32_t nm_sample_ct, uint32_t allele_ct) { in MultiallelicDiploidMachR2() argument 585 return 2 * MultiallelicDiploidMinimac3R2(sums, ssqs, nm_sample_ct, allele_ct, 0); in MultiallelicDiploidMachR2() 669 HEADER_INLINE uintptr_t GetAux1bAlleleEntryByteCt(uint32_t allele_ct, uint32_t rare10_ct) { in GetAux1bAlleleEntryByteCt() argument 670 assert(allele_ct >= 3); in GetAux1bAlleleEntryByteCt() 671 if (allele_ct == 3) { in GetAux1bAlleleEntryByteCt() 674 if (allele_ct < 6) { in GetAux1bAlleleEntryByteCt() 678 return ((allele_ct >= 18) + 1) * 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() argument 254 assert(allele_ct >= 3); in GetAux1aAlleleEntryByteCt() 255 if (allele_ct == 3) { in GetAux1aAlleleEntryByteCt() 258 if (allele_ct == 4) { in GetAux1aAlleleEntryByteCt() 261 if (allele_ct <= 6) { in GetAux1aAlleleEntryByteCt() 264 if (allele_ct <= 18) { 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 1292 assert(allele_ct > 2); in PwcAppendMultiallelicMain() 1321 if (allele_ct > 3) { in PwcAppendMultiallelicMain() 1322 if (allele_ct <= 18) { in PwcAppendMultiallelicMain() 1330 if (allele_ct == 4) { in PwcAppendMultiallelicMain() 1392 } else if (allele_ct <= 6) { in PwcAppendMultiallelicMain() 1493 if (allele_ct <= 17) { in PwcAppendMultiallelicMain() 1497 if (allele_ct == 3) { in PwcAppendMultiallelicMain() 1572 } else if (allele_ct <= 5) { in PwcAppendMultiallelicMain()
|
H A D | pgenlib_misc.cc | 2657 …const uint64_t* __restrict hap_ssqs_x2, uint32_t nm_sample_ct, uint32_t allele_ct, uint32_t extra_… in MultiallelicDiploidMinimac3R2() argument 2689 for (uint32_t allele_idx = 0; allele_idx != allele_ct; ++allele_idx) { in MultiallelicDiploidMinimac3R2() 2728 for (uint32_t allele_idx = 0; allele_idx != allele_ct; ++allele_idx) { 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 66 allele_ct = allele_idx_offsets[variant_idx + 1] - allele_idx_offset_base; in GetAlleleCode() 68 if (allele_idx >= allele_ct) { in GetAlleleCode() 70 sprintf(errbuf, "allele_num out of range (%d; must be 1..%d)", allele_idx + 1, allele_ct); in GetAlleleCode()
|
H A D | pvar_ffi_support.cpp | 161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local 187 allele_ct += extra_alt_ct; in LoadMinimalPvar() 227 allele_ct += 2 * variant_ct; in LoadMinimalPvar() 229 …const char** variant_ids = S_CAST(const char**, malloc((variant_ct + allele_ct) * sizeof(intptr_t)… in LoadMinimalPvar()
|
/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_fasta.cc | 90 uint32_t allele_ct = 2; variable 101 for (uint32_t allele_idx = 0; allele_idx != allele_ct; ++allele_idx) { 177 uint32_t allele_ct = 2; in VNormalizeContig() local 205 for (; aidx != allele_ct; ++aidx) { in VNormalizeContig() 210 if (aidx == allele_ct) { in VNormalizeContig() 220 for (uint32_t aidx = 0; aidx != allele_ct; ++aidx) { in VNormalizeContig() 279 if (++aidx == allele_ct) { in VNormalizeContig() 320 for (uint32_t aidx = first_aidx + 1; aidx != allele_ct; ++aidx) { in VNormalizeContig() 331 for (uint32_t aidx = first_aidx; aidx != allele_ct; ++aidx) { in VNormalizeContig() 371 for (uint32_t aidx = first_aidx + 1; aidx != allele_ct; ++aidx) { in VNormalizeContig() [all …]
|
H A D | pvar_ffi_support.cc | 161 uintptr_t allele_ct = 0; in LoadMinimalPvar() local 187 allele_ct += extra_alt_ct; in LoadMinimalPvar() 227 allele_ct += 2 * variant_ct; in LoadMinimalPvar() 229 …const char** variant_ids = S_CAST(const char**, malloc((variant_ct + allele_ct) * sizeof(intptr_t)… in LoadMinimalPvar()
|
H A D | plink2_misc.cc | 3717 uint32_t allele_ct = 2; variable 3885 ZeroU32Arr(allele_ct * allele_ct, diploid_pair_cts); 4784 if (allele_ct != 2) { in ComputeHweXPvalsMain() 7462 uint32_t allele_ct = 2; in SdiffCountsOnly() local 7482 if (allele_ct == 2) { in SdiffCountsOnly() 7496 allele_ct = 2; in SdiffCountsOnly() 7511 if (allele_ct == 2) { in SdiffCountsOnly() 8090 uint32_t allele_ct = 2; in SdiffMainBatch() local 8115 if (allele_ct == 2) { in SdiffMainBatch() 8129 allele_ct = 2; in SdiffMainBatch() [all …]
|
H A D | plink2_data.cc | 1765 uint32_t allele_ct = 2; in LoadAlleleAndGenoCountsThread() local 2918 if (allele_ct == 2) { in JoinCount() 2943 if (allele_ct == 2) { in JoinCount() 2951 jcp->nonsnp_ct = allele_ct - 1; in JoinCount() 3029 uint32_t allele_ct = 2; in PlanMultiallelicJoin() local 3162 if (allele_ct == 2) { in PlanMultiallelicSplit() 3185 cur_offset += allele_ct; in PlanMultiallelicSplit() 5194 uint32_t allele_ct = 2; in MakePgenThread() local 5234 assert(allele_ct > 2); in MakePgenThread() 5284 assert(allele_ct == 2); in MakePgenThread() [all …]
|
H A D | plink2_glm.cc | 3337 uint32_t allele_ct = 2; in GlmLogisticThread() local 3566 extra_regression_ct = allele_ct - 2; in GlmLogisticThread() 3882 ZeroU32Arr(allele_ct, case_one_cts); in GlmLogisticThread() 3883 ZeroU32Arr(allele_ct, case_two_cts); in GlmLogisticThread() 5774 uint32_t allele_ct = 2; in GlmLogistic() local 6474 uint32_t allele_ct = 2; in GlmLinearThread() local 6679 extra_regression_ct = allele_ct - 2; in GlmLinearThread() 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 [all …]
|
H A D | plink2_common.h | 455 HEADER_INLINE double GetNonmajFreq(const double* cur_allele_freqs, uint32_t allele_ct) { in GetNonmajFreq() argument 458 const uint32_t allele_ct_m1 = allele_ct - 1; in GetNonmajFreq() 470 …INE double GetAlleleFreq(const double* cur_allele_freqs, uint32_t allele_idx, uint32_t allele_ct) { in GetAlleleFreq() argument 471 const uint32_t allele_ct_m1 = allele_ct - 1; in GetAlleleFreq() 1109 char* PrintMultiallelicHcAsDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start); 1111 char* PrintMultiallelicHcAsHaploidDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start);
|
H A D | plink2_import.cc | 226 uint32_t allele_ct = 2; in GparseFlush() local 247 if (allele_ct == 2) { in GparseFlush() 262 if (allele_ct == 2) { in GparseFlush() 1518 if (allele_ct <= 10) { in VcfConvertUnphasedMultiallelicLine() 2018 if (allele_ct <= 10) { in VcfConvertPhasedMultiallelicLine() 3520 uint32_t allele_ct = 0; in VcfToPgen() local 3711 allele_ct = alt_ct + 1; in VcfToPgen() 5469 if (allele_ct >= 64) { in BcfConvertUnphasedMultiallelic() 5471 allele_ct = 63; in BcfConvertUnphasedMultiallelic() 6126 if (allele_ct >= 64) { in BcfConvertPhasedMultiallelic() [all …]
|
H A D | plink2_filter.cc | 3725 xallele_ct = (allele_ct == 2)? 0 : (allele_ct - 1); 3838 double GetTypedFreq(const double* cur_allele_freqs, uint32_t allele_ct, FreqFilterMode mode) { in GetTypedFreq() argument 3839 if ((allele_ct == 2) || (mode == kFreqFilterNref)) { in GetTypedFreq() 3851 const uint32_t allele_ct_m1 = allele_ct - 1; in GetTypedFreq() 3883 for (uint32_t allele_idx = 2; allele_idx != allele_ct; ++allele_idx) { in GetTypedDdosage() 3888 if (allele_ct == 2) { in GetTypedDdosage() 3894 for (uint32_t allele_idx = 1; allele_idx != allele_ct; ++allele_idx) { in GetTypedDdosage() 3905 for (uint32_t allele_idx = 1; allele_idx != allele_ct; ++allele_idx) { in GetTypedDdosage() 3928 uint32_t allele_ct = 2; variable 3936 allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offset_base; [all …]
|
H A D | plink2_common.cc | 2676 uintptr_t allele_ct = 0; in CountAlleles() local 2681 allele_ct += allele_idx_offsets[variant_uidx] - allele_idx_offsets[variant_uidx_start]; in CountAlleles() 2684 return allele_ct; in CountAlleles() 3077 char* PrintMultiallelicHcAsDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start) { in PrintMultiallelicHcAsDs() argument 3089 for (uint32_t uii = hc1 + 1; uii != allele_ct; ++uii) { in PrintMultiallelicHcAsDs() 3101 for (uint32_t uii = hc2 + 1; uii != allele_ct; ++uii) { in PrintMultiallelicHcAsDs() 3107 char* PrintMultiallelicHcAsHaploidDs(uint32_t hc1, uint32_t hc2, uint32_t allele_ct, char* start) { in PrintMultiallelicHcAsHaploidDs() argument 3119 for (uint32_t uii = hc1 + 1; uii != allele_ct; ++uii) { in PrintMultiallelicHcAsHaploidDs() 3131 for (uint32_t uii = hc2 + 1; uii != allele_ct; ++uii) { in PrintMultiallelicHcAsHaploidDs()
|
H A D | plink2_export.cc | 3498 uint32_t allele_ct = 2; variable 3578 if (allele_ct > 2) { 4621 uint32_t allele_ct = 2; variable 4700 if (allele_ct > 2) { 4760 if (allele_ct == 2) { 7909 uint32_t allele_ct = 2; variable 8222 uint32_t allele_ct = 2; variable 8307 if (allele_ct > 2) { 8619 if (allele_ct == 2) { 8979 if (allele_ct <= 63) { [all …]
|
H A D | plink2_pvar.cc | 1547 uint32_t allele_ct = extra_alt_ct + 2; in LoadPvar() local 1552 allele_ct = 1; in LoadPvar() 1555 if ((allele_ct < filter_min_allele_ct) || (allele_ct > filter_max_allele_ct)) { in LoadPvar()
|
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 2097 if (allele_ct != 2) { in CountExtraAlleles() 2098 result += allele_ct - const_subtract; in CountExtraAlleles() 2116 …const uint32_t allele_ct = allele_idx_offsets[variant_uidx + 1] - allele_idx_offsets[variant_uidx]; in MaxAlleleCtSubset() local 2117 if (allele_ct > subset_max_allele_ct) { in MaxAlleleCtSubset() 2118 if (allele_ct == max_allele_ct) { in MaxAlleleCtSubset() 2121 subset_max_allele_ct = allele_ct; in MaxAlleleCtSubset()
|
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 2441 if (allele_ct == 2) { in Plink2Core() 2454 for (uint32_t alt_idx = 2; alt_idx != allele_ct; ++alt_idx) { in Plink2Core()
|
/dports/biology/plink/plink-ng-79b2df8c/1.9/ |
H A D | plink_data.c | 14750 uint32_t allele_ct; in merge_bim_scan() local 14865 allele_ct = 0; in merge_bim_scan() 14868 allele_ct = 1; in merge_bim_scan() 14872 cur_alleles[allele_ct++] = bufptr3; in merge_bim_scan() 14875 for (ukk = 0; ukk < allele_ct; ukk++) { in merge_bim_scan() 14880 if (ukk == allele_ct) { in merge_bim_scan() 14881 if (allele_ct == 2) { in merge_bim_scan() 14897 cur_alleles[allele_ct++] = new_aptr; in merge_bim_scan() 14902 for (ukk = 0; ukk < allele_ct; ukk++) { in merge_bim_scan() 14907 if (ukk == allele_ct) { in merge_bim_scan() [all …]
|
H A D | plink_assoc.c | 11084 uint32_t allele_ct; in cmh_assoc() local 11159 allele_ct = ctrl_ct + case_ct; in cmh_assoc() 11160 allele_ct_recip = 1.0 / ((double)((int32_t)allele_ct)); in cmh_assoc() 11161 allele_ctm1_recip = 1.0 / ((double)((int32_t)(allele_ct - 1))); in cmh_assoc()
|