| adjacency_matrix.read_table | Create edge matrix for read graph |
| AL.engine | Compute the augmented lagrangian |
| all_pos.read_table | Return the positions covered by each read group in a read... |
| BAM_file_position_pair_frequencies.error | Extract the position pair frequencies from read table... |
| BAM_pileup | Calculate pileup for each position of reference from BAM file |
| bam_to_variant_calls.pipeline | Given a bam file, create variant call file |
| best_K.RegressHaploSolutions | Determines the best fit solution |
| calculate_position_pair_error.error | Calculate error for each position pair |
| clean.read_table | Clean read table |
| compare.Haplo | Compare frequencies and haplotypes of H1 using the... |
| compute_solution.RegressHaplo | Fit regression for a given rho |
| consensus | Returns a consensus sequence given a VSeqTools_pileup object |
| consensus.read_table | Return the consensus sequence at each position of the read... |
| consistent_haplotypes_across_loci.read_table | Split read table into loci with no spanning reads, create... |
| consistent_haplotypes.read_table | Split read table into loci with no spanning single end reads,... |
| coverage.read_table | Return coverage at each position in read table |
| create_position_pair_comparison_read_table.error | Create a read table for analyzing frequencies of positions... |
| create_refspace_seq | Converts reads to a sequence in the reference space |
| divergence_variant_calls | Calls nt positions at which a BAM file differs from a base... |
| end_pos.read_table | Return the end position of each read group in a read table |
| error_filter.read_table | Remove reads that are below error noise. |
| filter_and_optimize.RegressHaplo | Generate consistent haplotypes for a read table and, if... |
| filter_true_variants.read_table | Filter read table for variant calls |
| fix_out_dir | Add a / to out_dir if it is not there |
| full_pipeline | Execute full RegressHaplo pipeline |
| get_error_rate | Estimate error rate of pileup |
| get_position_pair_comparison_read_table.error | Get 'position_pair_read_table.csv' from directory |
| get_solutions_haplotype_reconstruction.pipeline | Haplotype reconstruction of given solution |
| get_solutions_summary.pipeline | Summary of regression fits over all starting points |
| get_variant_call_pos | Get variant call positions from a VSeqTools_variant_call... |
| grad_AL.engine | Compute gradient of augmented lagrangian |
| Haplo | Haplo object construct |
| haplotype_match.readFit | Determine haplotypes that match a nucleotide pattern |
| haplotypes_to_fasta.pipeline | Given RegressHaplo haplotypes file, produce fasta file... |
| haplotypes_to_parameters.pipeline | Given a read table and loci, create parameter files for... |
| hello | Hello, World! |
| loci_to_haplotypes.pipeline | Given loci, create global haplotypes |
| max_Hessian_eigenvalue.engine | Compute maximum eigenvalue of Hessian to scale gradient |
| merge_haplotypes.read_table | A helper function that create haplotype permutations from a... |
| nofilter_and_optimize.RegressHaplo | Generate consistent haplotypes for a read table and applies a... |
| nucs_at_pos.read_table | Return nucleotide counts at each position |
| paired_end_read_table | A helper function that creates read tables from paired end... |
| parameters.RegressHaplo | Generate the y vector and P matrix of the RegressHaplo... |
| parameters_to_solutions.pipeline | Given a parameter files, run RegressHaplo to produce multiple... |
| parse_solutions.RegressHaploSolutions | Parse solutions matrix |
| paths_exceed_limit.read_table | Quickly determine if the number of paths in an adjacency... |
| paths_to_haplotypes.read_table | A helper function that converts read graph paths to haplotype... |
| penalized_regression_parameters.RegressHaplo | Returns the matrices and vectors associated with the... |
| penalized_regression.RegressHaplo | Solves min_pi |y - P*pi|^2 + rho*pi^T*M*pi |
| plot_pair_position_error.error | Plot the position errors |
| plot.readFit | Visualize a readfit object |
| plot_single_position.error | Plot the position errors |
| position_fit.readFit | Return a readFit object base on nucleotide positions |
| position_pairs.error | Get position pairs with threshold coverage |
| pos_names.read_table | Returns positions of read table as character vector |
| read_BAM_pileup | Read a VSeqTools_pileup object |
| readFit | readFit constructor |
| read_fit.readFit | Build a readFit object base on reads |
| reads_covering_haplotypes.read_table | For each haplotype, return reads that match haplotype at... |
| reads_covering_positions.read_table | For each position, return reads that cover the position |
| read_table | Read table constructor |
| read_table_to_loci.pipeline | Given a read table, split variable positions into loci |
| reconstructed_position_pair_frequencies.error | Extract the position pair frequencies from haplotypes |
| RegressHaploSolutions | Loads a set of solutions created by solutions.RegressHaplo |
| regroup.read_table | Merges identical read over an edited read table |
| seq.read_table | Return the nucleotides in each read group of a read table |
| set_pos_names.Haplo | Set the position names for the characters (nucleotides)... |
| single_end_read_table | A helper function that creates read tables from single end... |
| single_position.error | Determine the frequency error at variable positions |
| solution_accuracy.pipeline | At each position, plot the pileup frequency for a given... |
| solutions.RegressHaplo | Solve the RegressHaplo optimization repeatedly |
| solutions_to_haplotypes.pipeline | Given a RegressHaplo solutions file, determine optimal... |
| split_allele.readFit | Split alleles while accounting for insertions |
| split_paired_ends.read_table | Split reads which have a gap between the paired ends |
| split.read_table | Split a read table into two read tables. |
| split_unlinked_loci.read_table | Split a read_table into multiple read_tables representing... |
| start_pos.read_table | Return the start position of each read group in a read table |
| subset.read_table | Limit read table to a subset of positions |
| template_alleles.read_table | Return all alleles matching a read template |
| template_fit.readFit | Build a readFit object base on templates. This is a generic... |
| template_indices.read_table | Return read indices corresponding to the template |
| templates.read_table | Retrieve all templates matching at least one read in the read... |
| unique.Haplo | Returns Haplo object with identical haplotype frequencies... |
| unlinked_pos.read_table | Determines loci in read table that have no overlapping reads |
| variant_calls | Returns variant calls given a VSeqTools_pileup object |
| variant_calls_cutoff | Returns variant calls given a VSeqTools_pileup object |
| variant_calls_sig | Returns variant calls given a VSeqTools_pileup object |
| variant_calls_to_read_table.pipeline | Given variant calls and a bam file, create a read table |
