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Searched refs:patch_01_set (Results 1 – 15 of 15) sorted by relevance

/dports/biology/plink/plink-ng-79b2df8c/2.0/include/
H A Dpgenlib_write.h202 …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 Dpgenlib_write.cc1310 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()
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H A Dpgenlib_misc.h641 uintptr_t* patch_01_set; member
H A Dpgenlib_misc.cc2816 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 Dpgenlib_read.cc5732 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 Dplink2_export.cc4475 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()
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H A Dplink2_common.h1042 …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 Dplink2_import.cc227 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
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H A Dplink2_data.cc1566 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 Dplink2_misc.cc3574 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 Dplink2_glm.cc3756 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()
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H A Dplink2_matrix_calc.cc3466 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 Dplink2_common.cc54 bigstack_alloc_w(sample_ctl, &(pgvp->patch_01_set)) || in BigstackAllocPgv()
62 pgvp->patch_01_set = nullptr; in BigstackAllocPgv()
H A Dplink2_filter.cc1025 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 Dpgenlibr.cpp207 _pgv.patch_01_set = reinterpret_cast<uintptr_t*>(pgr_alloc_iter); in Load()
216 _pgv.patch_01_set = nullptr; in Load()