mod commands

module commands

C-compatible wrappers for RADSex commands.

Functions

unsafe extern C fn rsx_depth(table_path: *const c_char, popmap_path: *const c_char, output_path: *const c_char, min_frequency: f32, streaming: bool) -> rsx_status_t

Run the depth command.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_distrib(table_path: *const c_char, popmap_path: *const c_char, output_path: *const c_char, min_depth: u32, signif_threshold: f32, group1: *const c_char, group2: *const c_char, correction: *const c_char, test: *const c_char, output_bayes: bool, prior_probability: f64, linked_probability: f64, null_prevalence: f64, group1_linked_weight: f64, bf_group1_alpha: f64, bf_group1_beta: f64, bf_group2_alpha: f64, bf_group2_beta: f64, bf_null_alpha: f64, bf_null_beta: f64, posterior_linked_family: *const c_char, posterior_linked_probability: f64, posterior_linked_alpha: f64, posterior_linked_beta: f64, posterior_null_family: *const c_char, posterior_null_probability: f64, posterior_null_alpha: f64, posterior_null_beta: f64) -> rsx_status_t

Run the distrib command.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_freq(table_path: *const c_char, output_path: *const c_char, min_depth: u32) -> rsx_status_t

Run the freq command.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_merge(input_files: *const *const c_char, n_files: usize, output_path: *const c_char, buffer_size: usize, output_parquet: bool) -> rsx_status_t

Run the merge command.

input_files is an array of n_files null-terminated C strings. buffer_size of 0 selects the default buffer.

Safety input_files must point to n_files valid C string pointers and the remaining pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_pca(table_path: *const c_char, output_dir: *const c_char, min_depth: u32, n_components: usize) -> rsx_status_t

Run the pca command.

n_components of 0 selects the default number of components.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_process(input_dir: *const c_char, output_path: *const c_char, n_threads: u32, min_depth: u32) -> rsx_status_t

Run the process command.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_signif(table_path: *const c_char, popmap_path: *const c_char, output_path: *const c_char, min_depth: u32, signif_threshold: f32, group1: *const c_char, group2: *const c_char, correction: *const c_char, test: *const c_char, output_fasta: bool, output_bayes: bool, prior_probability: f64, linked_probability: f64, null_prevalence: f64, group1_linked_weight: f64, bf_group1_alpha: f64, bf_group1_beta: f64, bf_group2_alpha: f64, bf_group2_beta: f64, bf_null_alpha: f64, bf_null_beta: f64, posterior_linked_family: *const c_char, posterior_linked_probability: f64, posterior_linked_alpha: f64, posterior_linked_beta: f64, posterior_null_family: *const c_char, posterior_null_probability: f64, posterior_null_alpha: f64, posterior_null_beta: f64) -> rsx_status_t

Run the signif command.

Safety All string pointers must be valid null-terminated C strings.

unsafe extern C fn rsx_triage(table_path: *const c_char, popmap_path: *const c_char, output_path: *const c_char, min_depth: u32, signif_threshold: f32, posterior_threshold: f64, bayes_factor_threshold: f64, prior_probability: f64, linked_probability: f64, null_prevalence: f64, group1_linked_weight: f64, bf_group1_alpha: f64, bf_group1_beta: f64, bf_group2_alpha: f64, bf_group2_beta: f64, bf_null_alpha: f64, bf_null_beta: f64, group1: *const c_char, group2: *const c_char, posterior_linked_family: *const c_char, posterior_linked_probability: f64, posterior_linked_alpha: f64, posterior_linked_beta: f64, posterior_null_family: *const c_char, posterior_null_probability: f64, posterior_null_alpha: f64, posterior_null_beta: f64) -> rsx_status_t

Run the triage command.

Safety All string pointers must be valid null-terminated C strings.