| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_data.h | 23 … uint32_t new_id_max_allele_slen, const char* missing_marker_id_match, Chrom_info* chrom_info_ptr,…
29 …, char* cluster_ids, uintptr_t max_cluster_id_len, uint32_t hh_exists, Chrom_info* chrom_info_ptr,…
33 …ng_code, int32_t missing_pheno, uint64_t misc_flags, uint32_t is_bgen, Chrom_info* chrom_info_ptr);
35 …me_end, uint32_t fam_cols, uint64_t misc_flags, int32_t missing_pheno, Chrom_info* chrom_info_ptr);
39 …nt64_t misc_flags, uint32_t lgen_modifier, char* lgen_reference_fname, Chrom_info* chrom_info_ptr);
41 …char* tfamname, char* outname, char* outname_end, uint64_t misc_flags, Chrom_info* chrom_info_ptr);
43 …attened, double vcf_min_gq, double vcf_min_gp, uint32_t vcf_half_call, Chrom_info* chrom_info_ptr);
45 …dspace_to, double vcf_min_qual, char* vcf_filter_exceptions_flattened, Chrom_info* chrom_info_ptr);
47 …o_23, uint64_t misc_flags, char* paternal_id_23, char* maternal_id_23, Chrom_info* chrom_info_ptr);
53 …no, uint32_t map_is_unsorted, uint64_t misc_flags, uint32_t hh_exists, Chrom_info* chrom_info_ptr);
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| H A D | plink_misc.h | 62 …, uintptr_t* marker_exclude, uint32_t* marker_pos, double* marker_cms, Chrom_info* chrom_info_ptr);
66 …r_exclude_ct_ptr, uint32_t* marker_pos, uint32_t* map_is_unsorted_ptr, Chrom_info* chrom_info_ptr);
84 …tr_t marker_exclude_ct, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,…
90 …ink_maxsnp, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, Chrom_info* chrom_info_ptr,…
92 …ltered_marker_ct, uintptr_t* marker_exclude, double* set_allele_freqs, Chrom_info* chrom_info_ptr,…
94 …h, double check_sex_mthresh, uint32_t max_f_yobs, uint32_t min_m_yobs, Chrom_info* chrom_info_ptr,…
100 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,…
102 …_t plink_maxiid, uintptr_t max_sample_id_len, uintptr_t* founder_info, Chrom_info* chrom_info_ptr,…
104 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,…
106 …no_c, double* pheno_d, char* output_missing_pheno, uint32_t hh_exists, Chrom_info* chrom_info_ptr,…
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| H A D | plink_assoc.h | 30 … char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,…
32 …lele_ptrs, uintptr_t max_marker_allele_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
34 …2_t* marker_pos, char** marker_allele_ptrs, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
36 …t max_marker_id_len, uint32_t plink_maxsnp, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
38 … char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,…
40 …2_t* marker_pos, char** marker_allele_ptrs, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
42 …r* marker_ids, uintptr_t max_marker_id_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
44 …lele_ptrs, uintptr_t max_marker_allele_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
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| H A D | plink_ld.h | 132 …tptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,…
134 …nk_maxsnp, char** marker_allele_ptrs, uintptr_t max_marker_allele_len, Chrom_info* chrom_info_ptr,…
136 …llele_ptrs, uintptr_t max_marker_allele_len, double* set_allele_freqs, Chrom_info* chrom_info_ptr,…
138 …tptr_t max_marker_id_len, uint32_t plink_maxsnp, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,…
140 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,…
142 …t max_marker_id_len, uint32_t plink_maxsnp, char** marker_allele_ptrs, Chrom_info* chrom_info_ptr,…
144 …tptr_t max_marker_id_len, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,…
146 …tptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,…
150 …len, uint32_t plink_maxsnp, char** marker_allele_ptrs, double min_maf, Chrom_info* chrom_info_ptr,…
154 …_id_len, uintptr_t* marker_reverse, double* orig_chisq, Set_info* sip, Chrom_info* chrom_info_ptr,…
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| H A D | plink_set.h | 114 …arker_exclude_ct_ptr, uint32_t is_exclude, uint32_t allow_no_variants, Chrom_info* chrom_info_ptr);
120 … marker_exclude_ct_ptr, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,…
122 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr);
134 …ptr_t subset_ct, char* sorted_subset_ids, uintptr_t max_subset_id_len, Chrom_info* chrom_info_ptr,…
136 … allow_extra_chroms, char* outname, char* outname_end, double pfilter, Chrom_info* chrom_info_ptr);
138 …nst char* snp_field, char* outname, char* outname_end, double pfilter, Chrom_info* chrom_info_ptr);
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| H A D | plink_filter.h | 57 …t* sample_id_map, uintptr_t unfiltered_sample_ct, uintptr_t* sex_male, Chrom_info* chrom_info_ptr,…
63 …r, char* sample_ids, uintptr_t max_sample_id_len, uintptr_t* sex_male, Chrom_info* chrom_info_ptr,…
65 …ale_ct_ptr, uint32_t* sample_f_ct_ptr, uint32_t* sample_f_male_ct_ptr, Chrom_info* chrom_info_ptr,…
67 … unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t marker_ct, Chrom_info* chrom_info_ptr,…
69 …llfs, int32_t* hwe_hh_allfs, uint32_t pheno_nm_ct, uintptr_t* pheno_c, Chrom_info* chrom_info_ptr);
71 …, int32_t* hwe_ll_allfs, int32_t* hwe_lh_allfs, int32_t* hwe_hh_allfs, Chrom_info* chrom_info_ptr);
75 …arker_exclude, uint32_t* marker_pos, uintptr_t* marker_exclude_ct_ptr, Chrom_info* chrom_info_ptr);
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| H A D | plink_calc.h | 58 … marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, Chrom_info* chrom_info_ptr,…
62 …r_t max_sample_id_len, double* set_allele_freqs, double** rel_ibc_ptr, Chrom_info* chrom_info_ptr);
65 …ar* sample_ids, uintptr_t max_sample_id_len, double* set_allele_freqs, Chrom_info* chrom_info_ptr,…
68 …e, uintptr_t sample_ct, char* sample_ids, uintptr_t max_sample_id_len, Chrom_info* chrom_info_ptr);
70 … marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, Chrom_info* chrom_info_ptr,…
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| H A D | plink_family.h | 74 …char* maternal_ids, uintptr_t max_maternal_id_len, uint32_t hh_exists, Chrom_info* chrom_info_ptr,…
103 …ax_paternal_id_len, char* maternal_ids, uintptr_t max_maternal_id_len, Chrom_info* chrom_info_ptr,…
105 …ax_paternal_id_len, char* maternal_ids, uintptr_t max_maternal_id_len, Chrom_info* chrom_info_ptr,…
107 …ax_paternal_id_len, char* maternal_ids, uintptr_t max_maternal_id_len, Chrom_info* chrom_info_ptr,…
109 …_paternal_id_blen, char* maternal_ids, uintptr_t max_maternal_id_blen, Chrom_info* chrom_info_ptr,…
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| H A D | plink_glm.h | 31 …ntptr_t* marker_reverse, char* condition_mname, char* condition_fname, Chrom_info* chrom_info_ptr,…
34 …ntptr_t* marker_reverse, char* condition_mname, char* condition_fname, Chrom_info* chrom_info_ptr,…
37 …ntptr_t* marker_reverse, char* condition_mname, char* condition_fname, Chrom_info* chrom_info_ptr,…
40 …ntptr_t* marker_reverse, char* condition_mname, char* condition_fname, Chrom_info* chrom_info_ptr,…
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| H A D | plink_lasso.h | 21 int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t* marker_reverse, Chrom_info* …
23 …x_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
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| H A D | plink_common.h | 2209 } Chrom_info; typedef
2214 int32_t init_chrom_info(Chrom_info* chrom_info_ptr);
2216 void init_species(uint32_t species_code, Chrom_info* chrom_info_ptr);
2218 void init_default_chrom_mask(Chrom_info* chrom_info_ptr);
2220 HEADER_INLINE int32_t init_chrom_info_human(Chrom_info* chrom_info_ptr) { in init_chrom_info_human()
2230 void forget_extra_chrom_names(uint32_t reinitialize, Chrom_info* chrom_info_ptr);
2235 int32_t finalize_chrom_info(Chrom_info* chrom_info_ptr);
2237 void cleanup_chrom_info(Chrom_info* chrom_info_ptr);
2257 char* chrom_name_write(const Chrom_info* chrom_info_ptr, uint32_t chrom_idx, char* buf);
2261 uint32_t get_max_chrom_slen(const Chrom_info* chrom_info_ptr);
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| H A D | plink_rserve.h | 21 …har** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,…
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| H A D | plink_cnv.h | 21 …ichment_test_mperms, int32_t marker_pos_start, int32_t marker_pos_end, Chrom_info* chrom_info_ptr);
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| H A D | plink_homozyg.h | 44 …lele_ptrs, uintptr_t max_marker_allele_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,…
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| H A D | plink_dosage.h | 52 …r* output_missing_pheno, uint32_t mpheno_col, uint32_t pheno_modifier, Chrom_info* chrom_info_ptr,…
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| H A D | plink_cnv.c | 73 …marker_pos_start, int32_t marker_pos_end, uint32_t allow_extra_chroms, Chrom_info* chrom_info_ptr)… in cnv_intersect_load()
458 int32_t cnv_make_map_write(FILE* new_mapfile, Chrom_info* chrom_info_ptr, uint32_t chrom_idx, uint3… in cnv_make_map_write()
477 …rker_pos_end, uint32_t allow_extra_chroms, uint32_t zero_extra_chroms, Chrom_info* chrom_info_ptr,… in cnv_make_map()
709 …s_start_ptr, int32_t* marker_pos_end_ptr, uint32_t allow_extra_chroms, Chrom_info* chrom_info_ptr,… in validate_cnv_map()
863 int32_t load_cnv_map(FILE* mapfile, int32_t marker_pos_start, int32_t marker_pos_end, Chrom_info* c… in load_cnv_map()
925 …ichment_test_mperms, int32_t marker_pos_start, int32_t marker_pos_end, Chrom_info* chrom_info_ptr)… in plink_cnv()
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| H A D | plink_lasso.c | 59 …ptr_t* marker_exclude, uintptr_t marker_ct, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,… in lasso_bigmem()
432 int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t* marker_reverse, Chrom_info* … in lasso_lambda()
635 …ptr_t* marker_exclude, uintptr_t marker_ct, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,… in lasso_smallmem()
994 …x_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,… in lasso()
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| H A D | plink_set.c | 272 … sorted_subset_ids, uintptr_t max_subset_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,… in load_range_list()
588 …arker_exclude_ct_ptr, uint32_t is_exclude, uint32_t allow_no_variants, Chrom_info* chrom_info_ptr)… in extract_exclude_range()
992 … marker_exclude_ct_ptr, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,… in define_sets()
1690 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr)… in write_set()
2204 …ptr_t subset_ct, char* sorted_subset_ids, uintptr_t max_subset_id_len, Chrom_info* chrom_info_ptr,… in load_range_list_sortpos()
2351 int32_t scrape_extra_chroms(const char* fname, const char* file_descrip, Chrom_info* chrom_info_ptr… in scrape_extra_chroms()
2402 … allow_extra_chroms, char* outname, char* outname_end, double pfilter, Chrom_info* chrom_info_ptr)… in annotate()
3240 …nst char* snp_field, char* outname, char* outname_end, double pfilter, Chrom_info* chrom_info_ptr)… in gene_report()
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| H A D | plink_common.c | 4349 int32_t init_chrom_info(Chrom_info* chrom_info_ptr) { in init_chrom_info()
4390 void init_species(uint32_t species_code, Chrom_info* chrom_info_ptr) { in init_species()
4458 void init_default_chrom_mask(Chrom_info* chrom_info_ptr) { in init_default_chrom_mask()
4473 void forget_extra_chrom_names(uint32_t reinitialize, Chrom_info* chrom_info_ptr) { in forget_extra_chrom_names()
4490 int32_t finalize_chrom_info(Chrom_info* chrom_info_ptr) { in finalize_chrom_info()
4546 void cleanup_chrom_info(Chrom_info* chrom_info_ptr) { in cleanup_chrom_info()
4563 char* chrom_name_std(const Chrom_info* chrom_info_ptr, uint32_t chrom_idx, char* buf) { in chrom_name_std()
4602 char* chrom_name_write(const Chrom_info* chrom_info_ptr, uint32_t chrom_idx, char* buf) { in chrom_name_write()
4642 uint32_t get_max_chrom_slen(const Chrom_info* chrom_info_ptr) { in get_max_chrom_slen()
4668 uint32_t haploid_chrom_present(const Chrom_info* chrom_info_ptr) { in haploid_chrom_present()
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| H A D | plink_filter.c | 1159 …t* sample_id_map, uintptr_t unfiltered_sample_ct, uintptr_t* sex_male, Chrom_info* chrom_info_ptr,… in load_oblig_missing()
1587 …r, char* sample_ids, uintptr_t max_sample_id_len, uintptr_t* sex_male, Chrom_info* chrom_info_ptr,… in mind_filter()
1941 …ale_ct_ptr, uint32_t* sample_f_ct_ptr, uint32_t* sample_f_male_ct_ptr, Chrom_info* chrom_info_ptr,… in calc_freqs_and_hwe()
2490 … unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t marker_ct, Chrom_info* chrom_info_ptr,… in write_missingness_reports()
2876 …llfs, int32_t* hwe_hh_allfs, uint32_t pheno_nm_ct, uintptr_t* pheno_c, Chrom_info* chrom_info_ptr)… in hardy_report()
3065 …, int32_t* hwe_ll_allfs, int32_t* hwe_lh_allfs, int32_t* hwe_hh_allfs, Chrom_info* chrom_info_ptr)… in enforce_hwe_threshold()
3178 …arker_exclude, uint32_t* marker_pos, uintptr_t* marker_exclude_ct_ptr, Chrom_info* chrom_info_ptr)… in enforce_min_bp_space()
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| H A D | plink_misc.c | 476 …, uintptr_t* marker_exclude, uint32_t* marker_pos, double* marker_cms, Chrom_info* chrom_info_ptr)… in apply_cm_map()
773 …r_exclude_ct_ptr, uint32_t* marker_pos, uint32_t* map_is_unsorted_ptr, Chrom_info* chrom_info_ptr)… in update_marker_pos()
1863 …tr_t marker_exclude_ct, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,… in read_external_freqs()
2663 …ink_maxsnp, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, Chrom_info* chrom_info_ptr,… in write_cc_freqs()
2847 …ltered_marker_ct, uintptr_t* marker_exclude, double* set_allele_freqs, Chrom_info* chrom_info_ptr,… in write_freqs()
3003 …h, double check_sex_mthresh, uint32_t max_f_yobs, uint32_t min_m_yobs, Chrom_info* chrom_info_ptr,… in sexcheck()
3427 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,… in list_duplicate_vars()
3711 …_t plink_maxiid, uintptr_t max_sample_id_len, uintptr_t* founder_info, Chrom_info* chrom_info_ptr,… in het_report()
3934 …, char* marker_ids, uintptr_t max_marker_id_len, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,… in fst_report()
4209 …no_c, double* pheno_d, char* output_missing_pheno, uint32_t hh_exists, Chrom_info* chrom_info_ptr,… in score_report()
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| H A D | plink_rserve.c | 33 …har** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,… in rserve_call()
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| H A D | plink_data.c | 2351 …rker_cms, uint32_t* marker_pos, char** marker_allele_ptrs, char delim, Chrom_info* chrom_info_ptr)… in write_map_or_bim()
2418 …t_chrom(char* bimname, uintptr_t* marker_exclude, uintptr_t marker_ct, Chrom_info* chrom_info_ptr,… in load_bim_split_chrom()
2470 void fill_ll_buf(uintptr_t* marker_exclude, uintptr_t marker_ct, Chrom_info* chrom_info_ptr, int64_… in fill_ll_buf()
2488 … marker_ids, uintptr_t max_marker_id_len, uint32_t allow_extra_chroms, Chrom_info* chrom_info_ptr,… in update_marker_chroms()
3027 …, uintptr_t* marker_exclude, uint32_t marker_ct, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,… in merge_or_split_x()
3945 …ng_code, int32_t missing_pheno, uint64_t misc_flags, uint32_t is_bgen, Chrom_info* chrom_info_ptr)… in oxford_to_bed()
5730 …me_end, uint32_t fam_cols, uint64_t misc_flags, int32_t missing_pheno, Chrom_info* chrom_info_ptr)… in ped_to_bed()
6399 …nt64_t misc_flags, uint32_t lgen_modifier, char* lgen_reference_fname, Chrom_info* chrom_info_ptr)… in lgen_to_bed()
7037 …char* tfamname, char* outname, char* outname_end, uint64_t misc_flags, Chrom_info* chrom_info_ptr)… in transposed_to_bed()
9099 …dspace_to, double vcf_min_qual, char* vcf_filter_exceptions_flattened, Chrom_info* chrom_info_ptr)… in bcf_to_bed()
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| H A D | plink_ld.c | 638 uint32_t ld_prune_next_valid_chrom_start(uintptr_t* marker_exclude, uint32_t cur_uidx, Chrom_info* … in ld_prune_next_valid_chrom_start()
652 …w_size_ptr, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, Chrom_info* chrom_info_ptr,… in ld_prune_start_chrom()
691 … uintptr_t* pruned_arr, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,… in ld_prune_write()
752 …tptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, Chrom_info* chrom_info_ptr,… in ld_prune()
1976 static Chrom_info* g_ld_chrom_info_ptr;
2206 Chrom_info* chrom_info_ptr = g_ld_chrom_info_ptr; in ld_report_matrix()
2601 Chrom_info* chrom_info_ptr = g_ld_chrom_info_ptr; in ld_regular_emitn()
5238 Chrom_info* chrom_info_ptr = g_ld_chrom_info_ptr; in ld_report_dprime()
5690 Chrom_info* chrom_info_ptr = g_ld_chrom_info_ptr; in ld_report_regular()
6315 …tptr_t max_marker_id_len, uint32_t plink_maxsnp, uint32_t* marker_pos, Chrom_info* chrom_info_ptr,… in show_tags()
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| H A D | plink_homozyg.c | 412 … char* marker_ids, uintptr_t max_marker_id_len, uint32_t plink_maxsnp, Chrom_info* chrom_info_ptr,… in write_main_roh_reports()
1333 …lele_ptrs, uintptr_t max_marker_allele_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,… in roh_pool()
2426 …lele_ptrs, uintptr_t max_marker_allele_len, uintptr_t* marker_reverse, Chrom_info* chrom_info_ptr,… in calc_homozyg()
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