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

/dports/biology/plink/plink-ng-79b2df8c/2.0/include/
H A Dpgenlib_read.cc3723 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()
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H A Dpgenlib_misc.h582 …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 Dpgenlib_read.h253 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 Dpgenlib_write.cc1291 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 Dpgenlib_misc.cc2657 …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 Dpvar.cpp62 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 Dpvar_ffi_support.cpp161 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 Dplink2_fasta.cc90 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 Dpvar_ffi_support.cc161 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 Dplink2_misc.cc3717 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()
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H A Dplink2_data.cc1765 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()
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H A Dplink2_glm.cc3337 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
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H A Dplink2_common.h455 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 Dplink2_import.cc226 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 Dplink2_filter.cc3725 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 Dplink2_common.cc2676 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 Dplink2_export.cc3498 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) {
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H A Dplink2_pvar.cc1547 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 Dplink2_cmdline.cc2096 …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 Dplink2.cc2440 …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 Dplink_data.c14750 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()
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H A Dplink_assoc.c11084 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()