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Haplo Prediction
predict haplogroups
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Options used for all haplo programs. More...
#include <config.h>#include <stdlib.h>#include <stdio.h>#include <string.h>#include <inttypes.h>#include <assert.h>#include <jwsc/base/error.h>#include <jwsc/base/option.h>#include <jwsc/vector/vector.h>#include "haplo_groups.h"#include "options.h"Go to the source code of this file.
Defines | |
| #define | HEADER_IN 0 |
| #define | HEADER_OUT 0 |
| #define | EXCLUDE_ONE 0 |
| #define | NUM_THREADS 1 |
| #define | INPUT_FORMAT HAPLO_INPUT_TXT |
| #define | INPUT_DTD_FNAME 0 |
| #define | OUTPUT_FORMAT HAPLO_OUTPUT_TXT |
| #define | LABELS_FNAME 0 |
| #define | LABELS_DTD_FNAME 0 |
| #define | FIRST_MARKER_COL 2 |
| #define | NUM_MARKERS 9 |
| #define | AUX_INPUT_FNAME 0 |
| #define | AUX_LABEL_COL 0 |
| #define | AUX_FIRST_MARKER_COL 2 |
| #define | AUX_NUM_MARKERS 9 |
| #define | NB_FREQ_FNAME 0 |
| #define | NB_FREQ_DTD_FNAME 0 |
| #define | NB_GAUSS_FNAME 0 |
| #define | NB_GAUSS_DTD_FNAME 0 |
| #define | NB_GMM_FNAME 0 |
| #define | NB_GMM_DTD_FNAME 0 |
| #define | MV_GMM_FNAME 0 |
| #define | MV_GMM_DTD_FNAME 0 |
| #define | MV_MMM_FNAME 0 |
| #define | MV_MMM_DTD_FNAME 0 |
| #define | SVM_FNAME 0 |
| #define | SVM_DTD_FNAME 0 |
| #define | WEKA_J48_FNAME 0 |
| #define | WEKA_PART_FNAME 0 |
| #define | WEKA_JAR_FNAME 0 |
| #define | WEKA_DTD_FNAME 0 |
| #define | NEAREST_FNAME 0 |
| #define | NEAREST_DTD_FNAME 0 |
| #define | NEAREST_MAX_D 1 |
| #define | BMM_TREE_FNAME 0 |
| #define | BMM_INFO_FNAME 0 |
| #define | BMM_CONF_THRESH_FNAME 0 |
| #define | GMM_BMM_TREE_FNAME 0 |
| #define | GMM_BMM_INFO_FNAME 0 |
| #define | GMM_BMM_CONF_THRESH_FNAME 0 |
| #define | MODEL_DIRNAME "." |
Functions | |
| uint32_t | get_num_opts_no_arg () |
| Returns the number of options not taking an argument. | |
| uint32_t | get_num_opts_with_arg () |
| Returns the number of options taking an argument. | |
| void | print_usage () |
| Prints the program usage to stderr. | |
| Error * | process_help_opt () |
| Process the 'help' program option. | |
| Error * | process_version_opt () |
| Process the 'version' program option. | |
| Error * | process_header_in_opt () |
| Process the 'header-in' program option. | |
| Error * | process_header_out_opt () |
| Process the 'no-header-out' program option. | |
| Error * | process_exclude_one_opt () |
| Process the 'exclude-one' program option. | |
| Error * | process_options_opt (Option_arg arg) |
| Process the 'options' program option. | |
| Error * | process_num_threads_opt (Option_arg arg) |
| Process the 'num-threads' program option. | |
| Error * | process_seed_opt (Option_arg arg) |
| Process the 'seed' program option. | |
| static Error * | process_input_format_opt (Option_arg arg) |
| Process the 'input-format' program option. | |
| Error * | process_input_dtd_opt (Option_arg arg) |
| Process the 'input-dtd' program option. | |
| static Error * | process_output_format_opt (Option_arg arg) |
| Process the 'output-format' program option. | |
| Error * | process_labels_opt (Option_arg arg) |
| Process the 'labels' program option. | |
| Error * | process_labels_dtd_opt (Option_arg arg) |
| Process the 'labels-dtd' program option. | |
| Error * | process_id_cols_opt (Option_arg arg) |
| Process the 'id-cols' program option. | |
| Error * | process_label_col_opt (Option_arg arg) |
| Process the 'label-col' program option. | |
| Error * | process_first_marker_col_opt (Option_arg arg) |
| Process the '1st-marker-col' program option. | |
| Error * | process_num_markers_opt (Option_arg arg) |
| Process the 'num-markers' program option. | |
| Error * | process_marker_cols_opt (Option_arg arg) |
| Process the 'marker-cols' program option. | |
| Error * | process_aux_input_opt (Option_arg arg) |
| Process the 'aux-input' program option. | |
| Error * | process_aux_id_cols_opt (Option_arg arg) |
| Process the 'aux-id-cols' program option. | |
| Error * | process_aux_label_col_opt (Option_arg arg) |
| Process the 'aux-label-col' program option. | |
| Error * | process_aux_first_marker_col_opt (Option_arg arg) |
| Process the 'aux-1st-marker-col' program option. | |
| Error * | process_aux_num_markers_opt (Option_arg arg) |
| Process the 'aux-num-markers' program option. | |
| Error * | process_aux_marker_cols_opt (Option_arg arg) |
| Process the 'aux-marker-cols' program option. | |
| Error * | process_num_gmm_bmm_markers_opt (Option_arg arg) |
| Process the 'num-gmm-bmm-markers' program option. | |
| Error * | process_model_dir_opt (Option_arg arg) |
| Process the 'model-dir' program option. | |
| Error * | process_nb_freq_opt (Option_arg arg) |
| Process the 'nb-freq' program option. | |
| Error * | process_nb_freq_dtd_opt (Option_arg arg) |
| Process the 'nb-freq-dtd' program option. | |
| Error * | process_nb_gauss_opt (Option_arg arg) |
| Process the 'nb-gauss' program option. | |
| Error * | process_nb_gauss_dtd_opt (Option_arg arg) |
| Process the 'nb-gauss-dtd' program option. | |
| Error * | process_nb_gmm_opt (Option_arg arg) |
| Process the 'nb-gmm' program option. | |
| Error * | process_nb_gmm_dtd_opt (Option_arg arg) |
| Process the 'nb-gmm-dtd' program option. | |
| Error * | process_mv_gmm_opt (Option_arg arg) |
| Process the 'mv-gmm' program option. | |
| Error * | process_mv_gmm_dtd_opt (Option_arg arg) |
| Process the 'mv-gmm-dtd' program option. | |
| Error * | process_mv_mmm_opt (Option_arg arg) |
| Process the 'mv-mmm' program option. | |
| Error * | process_mv_mmm_dtd_opt (Option_arg arg) |
| Process the 'mv-mmm-dtd' program option. | |
| Error * | process_nearest_max_d_opt (Option_arg arg) |
| Process the 'nearest-max-d' program option. | |
| Error * | process_nearest_opt (Option_arg arg) |
| Process the 'nearest' program option. | |
| Error * | process_nearest_dtd_opt (Option_arg arg) |
| Process the 'nearest-dtd' program option. | |
| Error * | process_bmm_tree_opt (Option_arg arg) |
| Process the 'bmm-tree' program option. | |
| Error * | process_bmm_info_opt (Option_arg arg) |
| Process the 'bmm-info' program option. | |
| Error * | process_bmm_conf_thresh_opt (Option_arg arg) |
| Process the 'bmm-conf-thresh' program option. | |
| Error * | process_gmm_bmm_tree_opt (Option_arg arg) |
| Process the 'gmm-bmm-tree' program option. | |
| Error * | process_gmm_bmm_info_opt (Option_arg arg) |
| Process the 'gmm-bmm-info' program option. | |
| Error * | process_gmm_bmm_conf_thresh_opt (Option_arg arg) |
| Process the 'gmm-bmm-conf-thresh' program option. | |
| void | init_options (Option_no_arg *opts_no_arg, Option_with_arg *opts_with_arg) |
| Initializes the shared program options. | |
Variables | |
| Option_no_arg | opts_no_arg [] |
| Program options not taking an argument. | |
| Option_with_arg | opts_with_arg [] |
| Program options taking an argument. | |
| uint8_t | sequential_markers = 0 |
| Boolean indicating whether sequential markers are used through the first_marker_col and num_markers variables; otherwise marker_cols is used. | |
| uint8_t | aux_sequential_markers = 0 |
| Boolean indicating whether sequential markers are used through the first_marker_col and num_markers variables; otherwise marker_cols is used. | |
Options used for all haplo programs.
Definition in file options.c.
| uint32_t get_num_opts_no_arg | ( | ) |
Returns the number of options not taking an argument.
Definition at line 131 of file haplo_cluster.c.
| uint32_t get_num_opts_with_arg | ( | ) |
Returns the number of options taking an argument.
Definition at line 137 of file haplo_cluster.c.
| void print_usage | ( | ) |
Prints the program usage to stderr.
Definition at line 143 of file haplo_cluster.c.
| Error* process_help_opt | ( | void | ) |
| Error* process_version_opt | ( | void | ) |
| Error* process_header_in_opt | ( | ) |
| Error* process_header_out_opt | ( | ) |
| Error* process_exclude_one_opt | ( | ) |
| Error* process_options_opt | ( | Option_arg | arg | ) |
| Error* process_num_threads_opt | ( | Option_arg | arg | ) |
| Error* process_seed_opt | ( | Option_arg | arg | ) |
| static Error* process_input_format_opt | ( | Option_arg | arg | ) | [static] |
| Error* process_input_dtd_opt | ( | Option_arg | arg | ) |
| static Error* process_output_format_opt | ( | Option_arg | arg | ) | [static] |
| Error* process_labels_opt | ( | Option_arg | arg | ) |
| Error* process_labels_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_id_cols_opt | ( | Option_arg | arg | ) |
| Error* process_label_col_opt | ( | Option_arg | arg | ) |
| Error* process_first_marker_col_opt | ( | Option_arg | arg | ) |
| Error* process_num_markers_opt | ( | Option_arg | arg | ) |
| Error* process_marker_cols_opt | ( | Option_arg | arg | ) |
| Error* process_aux_input_opt | ( | Option_arg | arg | ) |
| Error* process_aux_id_cols_opt | ( | Option_arg | arg | ) |
| Error* process_aux_label_col_opt | ( | Option_arg | arg | ) |
| Error* process_aux_first_marker_col_opt | ( | Option_arg | arg | ) |
| Error* process_aux_num_markers_opt | ( | Option_arg | arg | ) |
| Error* process_aux_marker_cols_opt | ( | Option_arg | arg | ) |
| Error* process_num_gmm_bmm_markers_opt | ( | Option_arg | arg | ) |
| Error* process_model_dir_opt | ( | Option_arg | arg | ) |
| Error* process_nb_freq_opt | ( | Option_arg | arg | ) |
| Error* process_nb_freq_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_nb_gauss_opt | ( | Option_arg | arg | ) |
| Error* process_nb_gauss_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_nb_gmm_opt | ( | Option_arg | arg | ) |
| Error* process_nb_gmm_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_mv_gmm_opt | ( | Option_arg | arg | ) |
| Error* process_mv_gmm_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_mv_mmm_opt | ( | Option_arg | arg | ) |
| Error* process_mv_mmm_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_nearest_max_d_opt | ( | Option_arg | arg | ) |
| Error* process_nearest_opt | ( | Option_arg | arg | ) |
| Error* process_nearest_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_bmm_tree_opt | ( | Option_arg | arg | ) |
| Error* process_bmm_info_opt | ( | Option_arg | arg | ) |
| Error* process_bmm_conf_thresh_opt | ( | Option_arg | arg | ) |
| Error* process_gmm_bmm_tree_opt | ( | Option_arg | arg | ) |
| Error* process_gmm_bmm_info_opt | ( | Option_arg | arg | ) |
| Error* process_gmm_bmm_conf_thresh_opt | ( | Option_arg | arg | ) |
| void init_options | ( | Option_no_arg * | opts_no_arg, |
| Option_with_arg * | opts_with_arg | ||
| ) |
Program options not taking an argument.
Definition at line 106 of file haplo_cluster.c.
Program options taking an argument.
Definition at line 109 of file haplo_cluster.c.
| uint8_t sequential_markers = 0 |
| uint8_t aux_sequential_markers = 0 |
1.7.4