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#ifndef __PLINK2_MERGE_H__
#define __PLINK2_MERGE_H__
// This file is part of PLINK 2.0, copyright (C) 2005-2025 Shaun Purcell,
// Christopher Chang.
//
// This program is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// This program is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
// more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.
#include "plink2_common.h"
#ifdef __cplusplus
namespace plink2 {
#endif
ENUM_U31_DEF_START()
kPmergeListModeBfile,
kPmergeListModeBpfile,
kPmergeListModePfile,
kPmergeListModePfileVzs
ENUM_U31_DEF_END(PmergeListMode);
FLAGSET_DEF_START()
kfPmerge0,
kfPmergeSampleInnerJoin = (1 << 0),
kfPmergeVariantInnerJoin = (1 << 1),
kfPmergePhenoInnerJoin = (1 << 2),
kfPmergeMultiallelicsAlreadyJoined = (1 << 3),
kfPmergeOutputVzs = (1 << 4)
FLAGSET_DEF_END(PmergeFlags);
ENUM_U31_DEF_START()
kMergeModeNmMatch,
kMergeModeNmFirst,
kMergeModeFirst
ENUM_U31_DEF_END(MergeMode);
ENUM_U31_DEF_START()
kMergePhenoModeNmMatch,
kMergePhenoModeNmFirst,
kMergePhenoModeFirst
ENUM_U31_DEF_END(MergePhenoMode);
ENUM_U31_DEF_START()
kMergeXheaderModeErase,
kMergeXheaderModeMatch,
kMergeXheaderModeFirst
ENUM_U31_DEF_END(MergeXheaderMode);
ENUM_U31_DEF_START()
kMergeQualModeErase,
kMergeQualModeNmMatch,
kMergeQualModeNmFirst,
kMergeQualModeFirst,
kMergeQualModeMin
ENUM_U31_DEF_END(MergeQualMode);
ENUM_U31_DEF_START()
kMergeFilterModeErase,
kMergeFilterModeNmMatch,
kMergeFilterModeNmFirst,
kMergeFilterModeFirst,
kMergeFilterModeNonpassUnion
ENUM_U31_DEF_END(MergeFilterMode);
ENUM_U31_DEF_START()
kMergeInfoCmModeErase,
kMergeInfoCmModeNmMatch,
kMergeInfoCmModeNmFirst,
kMergeInfoCmModeFirst
ENUM_U31_DEF_END(MergeInfoCmMode);
ENUM_U31_DEF_START()
kSort0,
kSortNone,
kSortNatural,
kSortAscii,
kSortFile
ENUM_U31_DEF_END(SortMode);
// --pgen-diff based here due to --merge-mode 6/7 history
FLAGSET_DEF_START()
kfPgenDiff0,
kfPgenDiffIncludeMissing = (1 << 0),
kfPgenDiffZs = (1 << 1),
kfPgenDiffColChrom = (1 << 2),
kfPgenDiffColPos = (1 << 3),
kfPgenDiffColId = (1 << 4),
kfPgenDiffColRef = (1 << 5),
kfPgenDiffColAlt = (1 << 6),
kfPgenDiffColMaybeprovref = (1 << 7),
kfPgenDiffColProvref = (1 << 8),
kfPgenDiffColMaybefid = (1 << 9),
kfPgenDiffColFid = (1 << 10),
kfPgenDiffColMaybesid = (1 << 11),
kfPgenDiffColSid = (1 << 12),
kfPgenDiffColGeno = (1 << 13),
kfPgenDiffColDefault = (kfPgenDiffColId | kfPgenDiffColMaybeprovref | kfPgenDiffColMaybefid | kfPgenDiffColMaybesid | kfPgenDiffColGeno),
kfPgenDiffColAll = ((kfPgenDiffColGeno * 2) - kfPgenDiffColPos)
FLAGSET_DEF_END(PgenDiffFlags);
typedef struct PmergeStruct {
NONCOPYABLE(PmergeStruct);
PmergeFlags flags;
PmergeListMode list_mode;
MergeMode merge_mode;
MergePhenoMode merge_parents_mode;
MergePhenoMode merge_sex_mode;
MergePhenoMode merge_pheno_mode;
MergeXheaderMode merge_xheader_mode;
MergeQualMode merge_qual_mode;
MergeFilterMode merge_filter_mode;
MergeInfoCmMode merge_info_mode;
MergeInfoCmMode merge_cm_mode;
SortMode merge_pheno_sort;
SortMode merge_info_sort;
uint32_t max_allele_ct;
char* pgen_fname;
char* pvar_fname;
char* psam_fname;
char* list_fname;
char* list_base_dir;
} PmergeInfo;
typedef struct PgenDiffStruct {
NONCOPYABLE(PgenDiffStruct);
PgenDiffFlags flags;
Dosage dosage_hap_tol; // missing value when 'dosage' not specified
char* pgen_fname;
char* pvar_fname;
char* psam_fname;
} PgenDiffInfo;
void InitPmerge(PmergeInfo* pmerge_info_ptr);
void CleanupPmerge(PmergeInfo* pmerge_info_ptr);
void InitPgenDiff(PgenDiffInfo* pgen_diff_info_ptr);
void CleanupPgenDiff(PgenDiffInfo* pgen_diff_info_ptr);
PglErr Pmerge(const PmergeInfo* pmip, const char* sample_sort_fname, const char* missing_catname, const char* varid_template_str, const char* varid_multi_template_str, const char* varid_multi_nonsnp_template_str, const char* missing_varid_match, MiscFlags misc_flags, SortMode sample_sort_mode, FamCol fam_cols, int32_t missing_pheno, uint32_t new_variant_id_max_allele_slen, char input_missing_geno_char, uint32_t max_thread_ct, SortMode sort_vars_mode, char* pgenname, char* psamname, char* pvarname, char* outname, char* outname_end, ChrInfo* cip);
PglErr PgenDiff(const uintptr_t* orig_sample_include, const SampleIdInfo* siip, const uintptr_t* sex_nm, const uintptr_t* sex_male, const uintptr_t* variant_include, const ChrInfo* cip, const uint32_t* variant_bps, const char* const* variant_ids, const uintptr_t* allele_idx_offsets, const char* const* allele_storage, const PgenDiffInfo* pdip, uint32_t raw_sample_ct, uint32_t orig_sample_ct, uint32_t raw_variant_ct, uint32_t max_allele_ct1, uint32_t max_allele_slen, char input_missing_geno_char, uint32_t max_thread_ct, PgenFileInfo* pgfip, PgenReader* simple_pgrp, char* outname, char* outname_end);
#ifdef __cplusplus
} // namespace plink2
#endif
#endif // __PLINK2_MERGE_H__
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