# Generated by roxygen2: do not edit by hand

export(R_determine_where_to_stop)
export(Rcpp_get_hap_info_from_vcf)
export(Rcpp_ref_run_backward_haploid)
export(Rcpp_ref_run_forward_haploid)
export(Rcpp_rhb_reader_chunk_process)
export(Rcpp_run_backward_haploid)
export(Rcpp_run_forward_haploid)
export(STITCH)
export(assign_positions_to_grid)
export(buildAlleleCount)
export(calc_dist_between_rhb_t_and_hap)
export(calculate_pse)
export(check_program_dependency)
export(check_vcf_info_scores)
export(collapse_diploid_gamma)
export(convertScaledBQtoProbs)
export(cpp_cigar_split_many)
export(cpp_deal_with_soft_clipped_bases)
export(cpp_read_reassign)
export(downsampleToFraction)
export(extract_hd_to_cube)
export(file_date)
export(file_sampleReads)
export(file_sampleReadsInfo)
export(forwardBackwardDiploid)
export(forwardBackwardHaploid)
export(generate_hwe_on_counts)
export(generate_or_refactor_input)
export(getSampleRange)
export(get_and_validate_genetic_map)
export(get_and_validate_pos_gen_and_phase)
export(get_bundling_position_information)
export(get_haplotypes_from_reference)
export(get_haplotypes_from_vcf)
export(get_header_using_SeqLib)
export(get_max_gen_rapid)
export(get_min_from_position)
export(get_output_filename)
export(get_random_values)
export(get_read_span)
export(get_rhb_from_vcf)
export(get_sampleReadsRaw_from_SeqLib)
export(get_sample_data_from_SeqLib)
export(get_sample_names)
export(get_sample_names_from_bam_or_cram_files)
export(get_transMatRate_m)
export(increment2N)
export(inflate_fhb)
export(inflate_fhb_t)
export(inflate_fhb_t_in_place)
export(initialize_chrStart_and_chrEnd)
export(initialize_directories)
export(int_determine_rspo)
export(int_expand)
export(loadBamAndConvert)
export(load_all_sampleReads_into_memory)
export(load_validate_and_match_genetic_map)
export(make_STITCH_cli)
export(make_acceptance_test_data_package)
export(make_fb_test_package)
export(make_gammaEK_t_from_gammaK_t)
export(make_genetic_map_file)
export(make_haploid_gammaUpdate_t)
export(make_reference_package)
export(make_rhb_t_equality)
export(make_rhb_t_from_rhi_t)
export(make_simple_bam)
export(make_unique_tempdir)
export(match_gen_and_phase_to_samples)
export(match_genetic_map_to_L)
export(pseudoHaploid_update_model_9)
export(ram_test)
export(rcpp_calculate_fbd_dosage)
export(rcpp_calculate_hapDosage)
export(rcpp_calculate_hwe_p)
export(rcpp_determine_where_to_stop)
export(rcpp_evaluate_bxtag)
export(rcpp_finalize_alphaMatSum_tc)
export(rcpp_int_contract)
export(rcpp_int_expand)
export(rcpp_make_alphaMatSumX_tc)
export(rcpp_make_and_bound_eMatGrid_diploid_t)
export(rcpp_make_column_of_vcf)
export(rcpp_make_diploid_jUpdate)
export(rcpp_make_eMatGrid_t)
export(rcpp_make_eMatRead_t)
export(rcpp_make_fb_snp_offsets)
export(rcpp_make_sampleReads_from_hap)
export(rcpp_make_smoothed_rate)
export(rcpp_ref_bound_eMatGrid_t)
export(rcpp_ref_make_eMatGrid_t)
export(rcpp_sample_path)
export(ref_make_ehh)
export(ref_make_haploid_gammaUpdate_t)
export(reference_fbh)
export(removeTmpSamplesFile)
export(remove_buffer_from_variables)
export(sample_diploid_path)
export(shrinkReads)
export(shrink_region)
export(snap_sampleReads_to_grid)
export(test_eHaps_options)
export(validate_bamlist_and_cramlist_for_input_generation)
export(validate_chr)
export(validate_downsampleFraction)
export(validate_nCores)
export(validate_nGen)
export(validate_output_filename)
export(validate_outputdir)
export(validate_posfile)
export(validate_reference_files)
export(validate_regionStart_regionEnd_and_buffer)
export(validate_region_to_impute_when_using_regionStart)
export(validate_tempdir)
export(validate_vcf_output_name)
importFrom(Rcpp,sourceCpp)
useDynLib(STITCH)
