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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(as.data.frame,hash)
export(absmin)
export(add_annotation_blocks)
export(add_file_highlight)
export(add_slope_intercept_info)
export(align_all_vs_all_using_minimap2_shred_merge)
export(annotate_pairs_with_hash)
export(annotate_res_out_with_positions_lens)
export(areColors)
export(bresenham)
export(bressiwrap)
export(calc_coarse_grained_aln_score)
export(calc_symm)
export(calculate_estimated_aln_score)
export(carry_out_compressed_sv)
export(clean_after_yourself)
export(colMax)
export(compress_paf_fnct)
export(concat_triplet)
export(confirm_loaded_nw)
export(correct_paf)
export(create_mmi_if_doesnt_exists)
export(create_vcf_line)
export(customChromosomeOrder)
export(decide_loop_continue_symmetry)
export(define_output_files)
export(determine_chunklen)
export(determine_compression)
export(determine_plot_minlen)
export(determine_xpad)
export(dfs)
export(dfsutil)
export(diagonalize)
export(dotplotly_dotplot_return_aln)
export(enforce_slope_one)
export(enlarge_interval_by_factor)
export(extract_sequence_wrapper)
export(extract_subseq_bedtools)
export(extract_test_list_from_paf)
export(find_coords_extrapolated)
export(find_coords_mad)
export(find_minlen_compression_params_wiggle)
export(find_punctual_liftover)
export(find_sv_opportunities)
export(find_threshold)
export(flip_bitl_y_if_needed)
export(format_julia_output)
export(generate_gt_strings)
export(generate_header)
export(get_fasta_info)
export(gridlist_to_gridmatrix)
export(highlight_region)
export(inform_about_tests)
export(init_log_with_def_values)
export(is_cluttered)
export(is_cluttered_paf)
export(liftover_coarse)
export(load_and_prep_paf_for_gridplot_transform)
export(mad_mask_outliers)
export(make_chunked_minimap_alnment)
export(make_genome_file)
export(make_karyogram)
export(make_modified_grid_plot)
export(make_output_folder_structure)
export(make_params_conversionpaf)
export(make_segmented_pairwise_plot)
export(make_xy_grid_fast)
export(manufacture_output_res_name)
export(matrix_remove_zero_pads)
export(merge_paf_entries_intraloop)
export(merge_rows)
export(modify_gridmatrix)
export(nahrwhals)
export(nahrwhals_singlerun)
export(paf_to_bed)
export(paf_to_sd_paf)
export(paf_write_bed)
export(pafdotplot_make)
export(plot_alignments)
export(plot_matrix_ggplot)
export(plot_matrix_ggplot_named)
export(plot_paf)
export(pmsqrt)
export(pmsqrt_rev)
export(preprocess_data)
export(produce_pairwise_alignments_minimap2)
export(read_and_prep_paf)
export(reduce_depth_if_needed)
export(remove_duplicates_triple)
export(repeat_col_in_matrix)
export(repeat_row_in_matrix)
export(return_diag_values_new)
export(run_minimap2)
export(run_n_tests)
export(run_silent)
export(run_solver_julia)
export(run_steepest_descent_one_layer_down)
export(save_plot_custom)
export(save_to_logfile)
export(scan_for_windows)
export(shred_seq_bedtools)
export(solve_mutation)
export(solve_mutation_julia_wrapper)
export(sort_new_by_penalised)
export(transform_res_new_to_old)
export(translate_t2t_chr_to_readable)
export(tsv_to_bed_regional_dominance)
export(turn_mut_max_into_svdf)
export(update_params)
export(version_nw)
export(wga_write_interval_list)
export(wrapper_aln_and_analyse)
export(wrapper_condense_paf)
export(wrapper_paf_to_bitlocus)
export(writeFasta)
export(write_results)
export(write_vcf)
export(write_x_y_sequences)