| AL.engine |
Man page
Source code
|
| BAM_file_position_pair_frequencies.error |
Man page
|
| BAM_pileup |
Man page
Source code
|
| Haplo |
Man page
Source code
|
| RegressHaploSolutions |
Man page
Source code
|
| adjacency_matrix.read_table |
Man page
|
| all_pos.read_table |
Man page
|
| bam_to_variant_calls.pipeline |
Man page
Source code
|
| best_K.RegressHaploSolutions |
Man page
Source code
|
| calculate_position_pair_error.error |
Man page
|
| clean.read_table |
Man page
|
| compare.Haplo |
Man page
Source code
|
| compute_solution.RegressHaplo |
Man page
Source code
|
| consensus |
Man page
|
| consensus.read_table |
Man page
Source code
|
| consistent_haplotypes.read_table |
Man page
|
| consistent_haplotypes_across_loci.read_table |
Man page
|
| constraint_value.engine |
Source code
|
| coverage.read_table |
Man page
Source code
|
| create_position_pair_comparison_read_table.error |
Man page
Source code
|
| create_refspace_seq |
Man page
|
| debug_optimize.engine |
Source code
|
| divergence_variant_calls |
Man page
|
| end_pos.read_table |
Man page
|
| error_filter.read_table |
Man page
|
| filter_and_optimize.RegressHaplo |
Man page
Source code
|
| filter_true_variants.read_table |
Man page
|
| fix_out_dir |
Man page
|
| full_pipeline |
Man page
|
| get_K.RegressHaploSolutions |
Source code
|
| get_count.Haplo |
Source code
|
| get_df.RegressHaplo |
Source code
|
| get_error_rate |
Man page
|
| get_fit.RegressHaplo |
Source code
|
| get_freq.Haplo |
Source code
|
| get_h.RegressHaplo |
Source code
|
| get_h.RegressHaploSolutions |
Source code
|
| get_hap.Haplo |
Source code
|
| get_hap_seq.Haplo |
Source code
|
| get_loci.RegressHaplo |
Source code
|
| get_nhap.Haplo |
Source code
Source code
|
| get_nonzero_solution.RegressHaplo |
Source code
|
| get_pi.RegressHaplo |
Source code
|
| get_position_pair_comparison_read_table.error |
Man page
Source code
|
| get_solutions.RegressHaploSolutions |
Source code
|
| get_solutions_haplotype_reconstruction.pipeline |
Man page
|
| get_solutions_summary.pipeline |
Man page
|
| get_stats_df.RegressHaploSolutions |
Source code
|
| get_variant_call_pos |
Man page
|
| grad_AL.engine |
Man page
Source code
|
| gradient_norm.engine |
Source code
|
| haplotype_match.readFit |
Man page
Source code
|
| haplotype_permute.RegressHaplo |
Source code
|
| haplotypes_to_fasta.pipeline |
Man page
|
| haplotypes_to_parameters.pipeline |
Man page
Source code
|
| hello |
Man page
|
| loci_to_haplotypes.pipeline |
Man page
Source code
|
| max_Hessian_eigenvalue.engine |
Man page
Source code
|
| merge_haplotypes.read_table |
Man page
|
| nofilter_and_optimize.RegressHaplo |
Man page
Source code
|
| nucs_at_pos.read_table |
Man page
Source code
|
| number_global_haplotypes.RegressHaplo |
Source code
|
| optimize.engine |
Source code
|
| optimize_fast.engine |
Source code
|
| paired_end_read_table |
Man page
Source code
|
| parameters.RegressHaplo |
Man page
Source code
|
| parameters_to_solutions.pipeline |
Man page
Source code
|
| parse_solutions.RegressHaploSolutions |
Man page
Source code
|
| paths_exceed_limit.read_table |
Man page
|
| paths_to_haplotypes.read_table |
Man page
|
| penalized_regression.RegressHaplo |
Man page
Source code
|
| penalized_regression_parameters.RegressHaplo |
Man page
Source code
|
| plot.readFit |
Man page
Source code
|
| plot_pair_position_error.error |
Man page
|
| plot_single_position.error |
Man page
Source code
|
| pos_names.read_table |
Man page
Source code
|
| position_fit.readFit |
Man page
Source code
|
| position_pairs.error |
Man page
Source code
|
| read.Haplo |
Source code
|
| readFit |
Man page
Source code
|
| read_BAM_pileup |
Man page
Source code
|
| read_fit.readFit |
Man page
Source code
|
| read_table |
Man page
Source code
|
| read_table_to_loci.pipeline |
Man page
Source code
|
| reads_covering_haplotypes.read_table |
Man page
Source code
|
| reads_covering_positions.read_table |
Man page
Source code
|
| reconstructed_position_pair_frequencies.error |
Man page
|
| regroup.read_table |
Man page
|
| seq.read_table |
Man page
|
| set_pos_names.Haplo |
Man page
Source code
|
| single_end_read_table |
Man page
Source code
|
| single_position.error |
Man page
Source code
|
| solution_accuracy.pipeline |
Man page
|
| solutions.RegressHaplo |
Man page
Source code
|
| solutions_to_haplotypes.pipeline |
Man page
|
| split.read_table |
Man page
|
| split_allele.readFit |
Man page
Source code
|
| split_paired_ends.read_table |
Man page
|
| split_unlinked_loci.read_table |
Man page
|
| start_pos.read_table |
Man page
|
| subset.read_table |
Man page
|
| template_alleles.read_table |
Man page
Source code
|
| template_fit.readFit |
Man page
Source code
|
| template_indices.read_table |
Man page
Source code
|
| templates.read_table |
Man page
Source code
|
| unique.Haplo |
Man page
Source code
|
| unlinked_pos.read_table |
Man page
|
| variant_calls |
Man page
|
| variant_calls_cutoff |
Man page
|
| variant_calls_sig |
Man page
|
| variant_calls_to_read_table.pipeline |
Man page
Source code
|
| write.Haplo |
Source code
|
