- a -

• aux_first_marker_col : options.h
• aux_id_cols : options.h
• aux_input_fname : options.h
• aux_label_col : options.h
• aux_marker_cols : options.h
• aux_num_markers : options.h
• aux_sequential_markers : options.c

- b -

• bmm_conf_thresh_fname : options.h
• bmm_info_fname : options.h
• bmm_tree_fname : options.h

- c -

• cluster_type : haplo_cluster.c

- d -

• data_out_dirname : haplo_train.c

- e -

• exclude_one : options.h

- f -

• first_marker_col : options.h

- g -

• gmm_bmm_conf_thresh_fname : options.h
• gmm_bmm_info_fname : options.h
• gmm_bmm_tree_fname : options.h

- h -

• haplo_groups : haplo_groups.c
• haplo_groups_xml : haplo_groups.c
• header_in : options.h
• header_out : options.h

- i -

• id_cols : options.h
• input_dtd_fname : options.h
• input_format : options.h

- l -

• label_col : options.h
• labels_dtd_fname : options.h
• labels_fname : options.h

- m -

• marker_cols : options.h
• means_out_fname : haplo_cluster.c
• members_out_fname : haplo_cluster.c
• model_dirname : options.h
• mv_gmm_confusion_cnt_fname : haplo_test.c
• mv_gmm_confusion_pct_fname : haplo_test.c
• mv_gmm_details_cnt_fname : haplo_test.c
• mv_gmm_details_pct_fname : haplo_test.c
• mv_gmm_dtd_fname : options.h
• mv_gmm_fname : options.h
• mv_gmm_preds_fname : haplo_test.c
• mv_gmm_summary_fname : haplo_test.c
• mv_mmm_dtd_fname : options.h
• mv_mmm_fname : options.h

- n -

• nb_freq_confusion_cnt_fname : haplo_test.c
• nb_freq_confusion_pct_fname : haplo_test.c
• nb_freq_details_cnt_fname : haplo_test.c
• nb_freq_details_pct_fname : haplo_test.c
• nb_freq_dtd_fname : options.h
• nb_freq_fname : options.h
• nb_freq_preds_fname : haplo_test.c
• nb_freq_summary_fname : haplo_test.c
• nb_gauss_confusion_cnt_fname : haplo_test.c
• nb_gauss_confusion_pct_fname : haplo_test.c
• nb_gauss_details_cnt_fname : haplo_test.c
• nb_gauss_details_pct_fname : haplo_test.c
• nb_gauss_dtd_fname : options.h
• nb_gauss_fname : options.h
• nb_gauss_preds_fname : haplo_test.c
• nb_gauss_summary_fname : haplo_test.c
• nb_gmm_confusion_cnt_fname : haplo_test.c
• nb_gmm_confusion_pct_fname : haplo_test.c
• nb_gmm_details_cnt_fname : haplo_test.c
• nb_gmm_details_pct_fname : haplo_test.c
• nb_gmm_dtd_fname : options.h
• nb_gmm_fname : options.h
• nb_gmm_preds_fname : haplo_test.c
• nb_gmm_summary_fname : haplo_test.c
• nearest_confusion_cnt_fname : haplo_test.c
• nearest_confusion_pct_fname : haplo_test.c
• nearest_details_cnt_fname : haplo_test.c
• nearest_details_pct_fname : haplo_test.c
• nearest_dtd_fname : options.h
• nearest_fname : options.h
• nearest_max_d : options.h
• nearest_preds_fname : haplo_test.c
• nearest_summary_fname : haplo_test.c
• num_clusters : haplo_cluster.c
• num_cv_folds : haplo_test.c
• num_cv_iters : haplo_test.c
• num_gmm_markers : options.h
• num_haplo_groups : haplo_groups.c
• num_markers : options.h
• num_threads : options.h

- o -

• opts : options.h
• opts_no_arg : options.c , haplo_train.c , haplo_predict.c , haplo_cluster.c , haplo_test.c
• opts_with_arg : haplo_test.c , options.c , haplo_cluster.c , haplo_predict.c , haplo_train.c
• output_fname : haplo_predict.c
• output_format : options.h

- r -

• responses_out_fname : haplo_cluster.c

- s -

• seed : options.h
• sequential_markers : options.c
• svm_confusion_cnt_fname : haplo_test.c
• svm_confusion_pct_fname : haplo_test.c
• svm_details_cnt_fname : haplo_test.c
• svm_details_pct_fname : haplo_test.c
• svm_preds_fname : haplo_test.c
• svm_summary_fname : haplo_test.c

- t -

• tandem : haplo_test.c
• tandem_agree_details_cnt_fname : haplo_test.c
• tandem_agree_details_pct_fname : haplo_test.c
• tandem_agree_summary_fname : haplo_test.c
• tandem_confusion_cnt_fname : haplo_test.c
• tandem_confusion_pct_fname : haplo_test.c
• tandem_details_cnt_fname : haplo_test.c
• tandem_details_pct_fname : haplo_test.c
• tandem_preds_fname : haplo_test.c
• tandem_summary_fname : haplo_test.c
• test_type : haplo_test.c
• tmp_dirname : haplo_test.c

- w -

• weights_out_fname : haplo_cluster.c
• weka_j48_confusion_cnt_fname : haplo_test.c
• weka_j48_confusion_pct_fname : haplo_test.c
• weka_j48_details_cnt_fname : haplo_test.c
• weka_j48_details_pct_fname : haplo_test.c
• weka_j48_preds_fname : haplo_test.c
• weka_j48_summary_fname : haplo_test.c
• weka_part_confusion_cnt_fname : haplo_test.c
• weka_part_confusion_pct_fname : haplo_test.c
• weka_part_details_cnt_fname : haplo_test.c
• weka_part_details_pct_fname : haplo_test.c
• weka_part_preds_fname : haplo_test.c
• weka_part_summary_fname : haplo_test.c