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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 <inttypes.h>#include <jwsc/base/error.h>#include <jwsc/base/option.h>#include <jwsc/vector/vector.h>#include "output.h"#include "input.h"Go to the source code of this file.
Defines | |
| #define | NUM_THREAD_OPTS 0 |
| #define | NUM_SHARED_OPTS_NO_ARG 4 |
| #define | NUM_SHARED_OPTS_WITH_ARG 12 + NUM_THREAD_OPTS |
Functions | |
| Error * | process_exclude_one_opt () |
| Process the 'exclude-one' 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_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_nearest_max_d_opt (Option_arg arg) |
| Process the 'nearest-max-d' 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 | |
| struct { | |
| uint8_t header_in | |
| Boolean indicating whether the input data has a header (descriptive) line. | |
| uint8_t header_out | |
| Boolean indicating whether to write a header (descriptive) line to the output file. | |
| uint8_t exclude_one | |
| Boolean indicating whether to exclude at most one prediction when deciding on an agreed label from the set of classification algorithms. | |
| uint32_t seed | |
| Random seed. | |
| uint32_t num_threads | |
| Number of pthreads to use at any given time. | |
| Haplo_input_format input_format | |
| Input file format. | |
| const char * input_dtd_fname | |
| XML input file DTD. | |
| Haplo_output_format output_format | |
| Output file format. | |
| const char * labels_fname | |
| XML file containin the haplo group labels. | |
| const char * labels_dtd_fname | |
| XML labels file DTD. | |
| Vector_u32 * id_cols | |
| Columns in input CSV file containing sample IDs. | |
| uint32_t label_col | |
| Column in input CSV file containing the haplo labels. | |
| uint32_t first_marker_col | |
| Column in input CSV file containing the first marker. | |
| uint32_t num_markers | |
| Number of marker columns in the input CSV file. | |
| Vector_u32 * marker_cols | |
| Marker columns to use. | |
| const char * aux_input_fname | |
| Auxiliary input file. | |
| Vector_u32 * aux_id_cols | |
| Columns in input CSV file containing sample IDs. | |
| uint32_t aux_label_col | |
| Column in input CSV file containing the haplo labels. | |
| uint32_t aux_first_marker_col | |
| Column in input CSV file containing the first marker. | |
| uint32_t aux_num_markers | |
| Number of marker columns in the input CSV file. | |
| Vector_u32 * aux_marker_cols | |
| Marker columns to use. | |
| uint32_t num_gmm_markers | |
| Number of marker columns in the input CSV file. | |
| const char * nb_freq_fname | |
| Naive Bayes non-parametric frequency model tree information. | |
| const char * nb_freq_dtd_fname | |
| XML DTD for nb_freq_fname. | |
| const char * nb_gauss_fname | |
| Naive Bayes Gaussian model tree information. | |
| const char * nb_gauss_dtd_fname | |
| XML DTD for nb_gauss_fname. | |
| const char * nb_gmm_fname | |
| Naive Bayes Gaussian mixture model tree information. | |
| const char * nb_gmm_dtd_fname | |
| XML DTD for nb_gmm_fname. | |
| const char * mv_gmm_fname | |
| Multivariate Gaussian mixture model tree information. | |
| const char * mv_gmm_dtd_fname | |
| XML DTD for mv_gmm_fname. | |
| const char * mv_mmm_fname | |
| Multivariate multinomial mixture model tree information. | |
| const char * mv_mmm_dtd_fname | |
| XML DTD for mv_mmm_fname. | |
| const char * nearest_fname | |
| Nearest neighbor model information. | |
| const char * nearest_dtd_fname | |
| XML DTD for the nearest neighbor model. | |
| uint32_t nearest_max_d | |
| Maximum allowed nearest neighbor distance for a prediction. | |
| const char * bmm_tree_fname | |
| Name of the Bernoulli mixture model tree file. | |
| const char * bmm_info_fname | |
| Name of the Bernoulli mixture model info file. | |
| const char * bmm_conf_thresh_fname | |
| Name of the Bernoulli mixture model confidence threshold file. | |
| const char * gmm_bmm_tree_fname | |
| Name of the Gaussian and Bernoulli mixture model tree file. | |
| const char * gmm_bmm_info_fname | |
| Name of the Gaussian and Bernoulli mixture model info file. | |
| const char * gmm_bmm_conf_thresh_fname | |
| Name of the Gaussian and Bernoulli mixture model confidence threshold file. | |
| const char * model_dirname | |
| Director to find the models in. | |
| } | opts |
Options used for all haplo programs.
Definition in file options.h.
| Error* process_exclude_one_opt | ( | ) |
| 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_opt | ( | Option_arg | arg | ) |
| Error* process_nearest_dtd_opt | ( | Option_arg | arg | ) |
| Error* process_nearest_max_d_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 | ||
| ) |
| uint8_t header_in |
| uint8_t header_out |
| uint8_t exclude_one |
| uint32_t seed |
| uint32_t num_threads |
| const char* input_dtd_fname |
| const char* labels_fname |
| const char* labels_dtd_fname |
| uint32_t label_col |
| uint32_t first_marker_col |
| uint32_t num_markers |
| const char* aux_input_fname |
| uint32_t aux_label_col |
| uint32_t aux_first_marker_col |
| uint32_t aux_num_markers |
| uint32_t num_gmm_markers |
| const char* nb_freq_fname |
| const char* nb_freq_dtd_fname |
| const char* nb_gauss_fname |
| const char* nb_gauss_dtd_fname |
| const char* nb_gmm_fname |
| const char* nb_gmm_dtd_fname |
| const char* mv_gmm_fname |
| const char* mv_gmm_dtd_fname |
| const char* mv_mmm_fname |
| const char* mv_mmm_dtd_fname |
| const char* nearest_fname |
| const char* nearest_dtd_fname |
| uint32_t nearest_max_d |
| const char* bmm_tree_fname |
| const char* bmm_info_fname |
| const char* bmm_conf_thresh_fname |
| const char* gmm_bmm_tree_fname |
| const char* gmm_bmm_info_fname |
| const char* gmm_bmm_conf_thresh_fname |
| const char* model_dirname |
| struct { ... } opts |
1.7.4