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#ifndef __PLINK2_EXPORT_H__
#define __PLINK2_EXPORT_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_data.h"
#ifdef __cplusplus
namespace plink2 {
#endif
ENUM_U31_DEF_START()
kVcfExport0,
kVcfExportGp,
kVcfExportDs,
kVcfExportDsForce,
kVcfExportDsOnly,
kVcfExportHds,
kVcfExportHdsForce
ENUM_U31_DEF_END(VcfExportMode);
FLAGSET_DEF_START()
kfIdpaste0,
kfIdpasteMaybefid = (1 << 0),
kfIdpasteFid = (1 << 1),
kfIdpasteIid = (1 << 2),
kfIdpasteMaybesid = (1 << 3),
kfIdpasteSid = (1 << 4),
kfIdpasteDefault = (kfIdpasteMaybefid | kfIdpasteIid | kfIdpasteMaybesid)
FLAGSET_DEF_END(IdpasteFlags);
typedef struct ExportfStruct {
ExportfFlags flags;
IdpasteFlags idpaste_flags;
char id_delim;
uint32_t bgen_bits;
VcfExportMode vcf_mode;
char* export_allele_fname;
} ExportfInfo;
void InitExportf(ExportfInfo* exportf_info_ptr);
void CleanupExportf(ExportfInfo* exportf_info_ptr);
PglErr Exportf(const uintptr_t* sample_include, const PedigreeIdInfo* piip, const uintptr_t* sex_nm, const uintptr_t* sex_male, const PhenoCol* pheno_cols, const char* pheno_names, 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 AlleleCode* allele_permute, const uintptr_t* pvar_qual_present, const float* pvar_quals, const uintptr_t* pvar_filter_present, const uintptr_t* pvar_filter_npass, const char* const* pvar_filter_storage, const char* pvar_info_reload, const double* variant_cms, const ExportfInfo* eip, const char* legacy_output_missing_pheno, const uint32_t* contig_lens, uintptr_t xheader_blen, InfoFlags info_flags, uint32_t raw_sample_ct, uint32_t sample_ct, uint32_t pheno_ct, uintptr_t max_pheno_name_blen, uint32_t raw_variant_ct, uint32_t variant_ct, uint32_t max_variant_id_slen, uint32_t max_allele_slen, uint32_t max_filter_slen, uint32_t info_reload_slen, char input_missing_geno_char, char output_missing_geno_char, char legacy_output_missing_geno_char, uint32_t max_thread_ct, MakePlink2Flags make_plink2_flags, uintptr_t pgr_alloc_cacheline_ct, char* xheader, PgenFileInfo* pgfip, PgenReader* simple_pgrp, char* outname, char* outname_end);
#ifdef __cplusplus
} // namespace plink2
#endif
#endif // __PLINK2_EXPORT_H__
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