/dports/biology/plink/plink-ng-79b2df8c/2.0/include/ |
H A D | pgenlib_write.h | 202 …arse(const uintptr_t* __restrict genovec, const uintptr_t* __restrict patch_01_set, const AlleleCo… 204 …arse(const uintptr_t* __restrict genovec, const uintptr_t* __restrict patch_01_set, const AlleleCo… in SpgwAppendMultiallelicSparse() argument 209 …if (unlikely(PwcAppendMultiallelicSparse(genovec, patch_01_set, patch_01_vals, patch_10_set, patch… in SpgwAppendMultiallelicSparse() 216 …t32_t sample_ct, uintptr_t* __restrict genoarr, uintptr_t* __restrict patch_01_set, AlleleCode* __… 225 …ense(const uintptr_t* __restrict genovec, const uintptr_t* __restrict patch_01_set, const AlleleCo… 246 …hase(const uintptr_t* __restrict genovec, const uintptr_t* __restrict patch_01_set, const AlleleCo… 248 …hase(const uintptr_t* __restrict genovec, const uintptr_t* __restrict patch_01_set, const AlleleCo… in SpgwAppendMultiallelicGenovecHphase() argument 253 …if (unlikely(PwcAppendMultiallelicGenovecHphase(genovec, patch_01_set, patch_01_vals, patch_10_set… in SpgwAppendMultiallelicGenovecHphase()
|
H A D | pgenlib_write.cc | 1310 PwcAppendDeltalist(patch_01_set, patch_01_ct, pwcp, &vrec_len); in PwcAppendMultiallelicMain() 1317 …CopyGenomatchSubset(patch_01_set, genovec, kMask5555, 0, genovec_het_ct, R_CAST(uintptr_t*, pwcp->… in PwcAppendMultiallelicMain() 1698 …if (unlikely(PwcAppendMultiallelicMain(genovec, patch_01_set, patch_01_vals, patch_10_set, patch_1… in PwcAppendMultiallelicSparse() 1715 Halfword* patch_01_set_alias = R_CAST(Halfword*, patch_01_set); in PglMultiallelicDenseToSparse() 1783 uintptr_t cur_bits = patch_01_set[0]; in PglMultiallelicSparseToDense() 1786 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in PglMultiallelicSparseToDense() 1863 uintptr_t cur_bits = patch_01_set[0]; in PglMultiallelicSparseToDense() 1871 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in PglMultiallelicSparseToDense() 1876 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in PglMultiallelicSparseToDense() 1887 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in PglMultiallelicSparseToDense() [all …]
|
H A D | pgenlib_misc.h | 641 uintptr_t* patch_01_set; member
|
H A D | pgenlib_misc.cc | 2816 const uintptr_t* patch_01_set = pgvp->patch_01_set; in PglMultiallelicSparseToDenseMiss() local 2818 uintptr_t cur_bits = patch_01_set[0]; in PglMultiallelicSparseToDenseMiss() 2822 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in PglMultiallelicSparseToDenseMiss()
|
H A D | pgenlib_read.cc | 5732 pgvp->patch_01_set = nullptr; in PreinitPgv() 6033 …32_t raw_01_ct, const unsigned char** fread_pp, uintptr_t* __restrict patch_01_set, AlleleCode* __… in ExportAux1a() argument 6042 …r(patch_01_fset, raw_genoarr, kMask5555, NypCtToWordCt(raw_sample_ct), raw_01_ct, 0, patch_01_set); in ExportAux1a() 6044 …if (unlikely(ParseAndSaveDeltalistAsBitarr(fread_end, raw_sample_ct, fread_pp, patch_01_set, &rare… in ExportAux1a() 6452 …c, aux1a_mode, raw_sample_ct, allele_ct, raw_01_ct, &fread_ptr, pgvp->patch_01_set, pgvp->patch_01… in GetMultiallelicCodes() 6454 …de, raw_sample_ct, sample_ct, allele_ct, raw_01_ct, &fread_ptr, pgvp->patch_01_set, pgvp->patch_01… in GetMultiallelicCodes() 9019 uintptr_t* patch_01_set = loadbuf_iter; in PgrGetRaw() local 9023 …d, genovec, aux1a_mode, raw_sample_ct, allele_ct, het_ct, &fread_ptr, patch_01_set, patch_01_vals,… in PgrGetRaw()
|
/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_export.cc | 4475 pgv.patch_01_set = nullptr; 5521 ZeroWArr(sample_ctl, pgv.patch_01_set); 6641 const uintptr_t* patch_01_set = pgvp->patch_01_set; in FillBcf3allelicGtPloidy2() local 6645 uintptr_t patch_01_bits = patch_01_set[0]; in FillBcf3allelicGtPloidy2() 6721 const uintptr_t* patch_01_set = pgvp->patch_01_set; in FillBcf64allelicGtPloidy2() local 6725 uintptr_t patch_01_bits = patch_01_set[0]; in FillBcf64allelicGtPloidy2() 6808 const uintptr_t* patch_01_set = pgvp->patch_01_set; in FillBcfMultiallelicDsForce() local 6831 uintptr_t patch_01_word = patch_01_set[widx]; in FillBcfMultiallelicDsForce() 7117 const uintptr_t* patch_01_set = pgvp->patch_01_set; in FillBcfMultiallelicHdsForce() local 7310 uintptr_t patch_01_word = patch_01_set[widx]; in FillBcfMultiallelicHdsForce() [all …]
|
H A D | plink2_common.h | 1042 …ExpandMhc(sample_ct, mhc, &(pgvp->patch_01_set), &(pgvp->patch_01_vals), &(pgvp->patch_10_set), &(… in SetPgvMhc() 1047 pgvp->patch_01_set = nullptr; in SetPgvThreadMhcNull() 1052 …ExpandMhc(sample_ct, thread_mhc[tidx], &(pgvp->patch_01_set), &(pgvp->patch_01_vals), &(pgvp->patc… in SetPgvThreadMhcNull()
|
H A D | plink2_import.cc | 227 uintptr_t* patch_01_set = nullptr; in GparseFlush() local 1497 Halfword* patch_01_set_alias = R_CAST(Halfword*, patch_01_set); in VcfConvertUnphasedMultiallelicLine() 1990 Halfword* patch_01_set_alias = R_CAST(Halfword*, patch_01_set); in VcfConvertPhasedMultiallelicLine() 2510 uintptr_t* patch_01_set = nullptr; in VcfGenoToPgenThread() local 5455 patch_01_set[sample_ctl - 1] = 0; in BcfConvertUnphasedMultiallelic() 5474 ZeroWArr(sample_ctl, patch_01_set); in BcfConvertUnphasedMultiallelic() 6109 patch_01_set[sample_ctl - 1] = 0; in BcfConvertPhasedMultiallelic() 6131 ZeroWArr(sample_ctl, patch_01_set); in BcfConvertPhasedMultiallelic() 6365 ZeroWArr(sample_ctl, patch_01_set); in BcfConvertPhasedMultiallelic() 6842 uintptr_t* patch_01_set = nullptr; in BcfGenoToPgenThread() local [all …]
|
H A D | plink2_data.cc | 1566 const uintptr_t* patch_01_set = pgvp->patch_01_set; variable 1568 uintptr_t patch_01_bits = patch_01_set[0]; 1571 const uintptr_t lowbit = BitIter1y(patch_01_set, &sample_widx, &patch_01_bits); 1633 const uintptr_t* patch_01_set = pgvp->patch_01_set; variable 1635 uintptr_t patch_01_bits = patch_01_set[0]; 1638 const uintptr_t lowbit = BitIter1y(patch_01_set, &sample_widx, &patch_01_bits); 2218 uintptr_t patch_01_bits = pgv.patch_01_set[0]; in LoadAlleleAndGenoCountsThread() 2221 … const uintptr_t lowbit = BitIter1y(pgv.patch_01_set, &sample_widx, &patch_01_bits); in LoadAlleleAndGenoCountsThread() 6061 bigstack_alloc_w(raw_sample_ctl, &pgv.patch_01_set) || 6299 Halfword* patch_01_set_alias = R_CAST(Halfword*, pgv.patch_01_set);
|
H A D | plink2_misc.cc | 3574 pgv.patch_01_set = nullptr; 3587 bigstack_alloc_w(sample_ctl, &pgv.patch_01_set) || 3916 uintptr_t cur_patch_bits = pgv.patch_01_set[0]; 3919 const uintptr_t lowbit = BitIter1y(pgv.patch_01_set, &sample_widx, &cur_patch_bits); 4515 bigstack_alloc_w(founder_ctl, &(pgv.patch_01_set)) || 4661 uintptr_t cur_patch_bits = pgv.patch_01_set[0]; 4664 const uintptr_t lowbit = BitIter1y(pgv.patch_01_set, &sample_widx, &cur_patch_bits); 6158 const uintptr_t* patch_01_set = pgv.patch_01_set; in SampleCountsThread() local 6161 uintptr_t sample_idx_bits = patch_01_set[0]; in SampleCountsThread() 6163 … const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &sample_idx_bits); in SampleCountsThread()
|
H A D | plink2_glm.cc | 3756 const uintptr_t* patch_set_nm = pgv.patch_01_set; in GlmLogisticThread() 3758 CopyBitarrSubset(pgv.patch_01_set, sample_nm, nm_sample_ct, tmp_nm); in GlmLogisticThread() 3889 uintptr_t cur_bits = pgv.patch_01_set[0]; in GlmLogisticThread() 6457 pgv.patch_01_set = nullptr; in GlmLinearThread() 6463 pgv.patch_01_set = common->thread_mhc[tidx]; in GlmLinearThread() 6464 pgv.patch_01_vals = R_CAST(AlleleCode*, &(pgv.patch_01_set[max_sample_ctl])); in GlmLinearThread() 6878 const uintptr_t* patch_set_nm = pgv.patch_01_set; in GlmLinearThread() 8520 pgv.patch_01_set = nullptr; in GlmLinearSubbatchThread() 8526 pgv.patch_01_set = common->thread_mhc[tidx]; in GlmLinearSubbatchThread() 8527 pgv.patch_01_vals = R_CAST(AlleleCode*, &(pgv.patch_01_set[max_sample_ctl])); in GlmLinearSubbatchThread() [all …]
|
H A D | plink2_matrix_calc.cc | 3466 const uintptr_t* patch_01_set = pgvp->patch_01_set; in LoadMultiallelicCenteredVarmaj() local 3475 uintptr_t cur_bits = patch_01_set[0]; in LoadMultiallelicCenteredVarmaj() 3478 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in LoadMultiallelicCenteredVarmaj() 3485 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in LoadMultiallelicCenteredVarmaj() 3535 uintptr_t cur_bits = patch_01_set[0]; in LoadMultiallelicCenteredVarmaj() 3537 const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits); in LoadMultiallelicCenteredVarmaj()
|
H A D | plink2_common.cc | 54 bigstack_alloc_w(sample_ctl, &(pgvp->patch_01_set)) || in BigstackAllocPgv() 62 pgvp->patch_01_set = nullptr; in BigstackAllocPgv()
|
H A D | plink2_filter.cc | 1025 if ((!memequal(first_pgv.patch_01_set, cur_pgv.patch_01_set, sample_ctb)) || in RmDup()
|
/dports/biology/plink/plink-ng-79b2df8c/2.0/pgenlibr/src/ |
H A D | pgenlibr.cpp | 207 _pgv.patch_01_set = reinterpret_cast<uintptr_t*>(pgr_alloc_iter); in Load() 216 _pgv.patch_01_set = nullptr; in Load()
|