API for SLeviyang/RegressHaplo
Haplotype Reconstruction Using Penalized Regression

Global functions
AL.engine Man page Source code
BAM_file_position_pair_frequencies.error Man page Source code
BAM_pileup Man page Source code
Haplo Man page Source code
RegressHaploSolutions Man page Source code
adjacency_matrix.read_table Man page Source code
all_pos.read_table Man page Source code
bam_to_variant_calls.pipeline Man page Source code
best_K.RegressHaploSolutions Man page Source code
best_fit.RegressHaploSolutions Source code
calculate_position_pair_error.error Man page Source code
clean.read_table Man page Source code
compare.Haplo Man page Source code
compute_solution.RegressHaplo Man page Source code
consensus Man page Source code
consensus.read_table Man page Source code
consistent_haplotypes.read_table Man page Source code
consistent_haplotypes_across_loci.read_table Man page Source code
consistent_haplotypes_single_end.read_table Source code
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 Source code
debug_optimize.engine Source code
divergence_variant_calls Man page Source code
end_pos.read_table Man page Source code
error_filter.read_table Man page Source code
filter_and_optimize.RegressHaplo Man page Source code
filter_haplotypes_with_paired_ends.read_table Source code
filter_true_variants.read_table Man page Source code
fix_out_dir Man page Source code
full_pipeline Man page Source code
get_K.RegressHaploSolutions Source code
get_P.pipeline Source code
get_count.Haplo Source code
get_df.RegressHaplo Source code
get_error_rate Man page Source code
get_fasta.pipeline Source code
get_fit.RegressHaplo Source code
get_freq.Haplo Source code
get_h.RegressHaplo Source code
get_h.RegressHaploSolutions Source code
get_h.pipeline Source code
get_hap.Haplo Source code
get_hap_seq.Haplo Source code
get_haplo.pipeline Source code
get_loci.RegressHaplo Source code
get_loci.pipeline Source code
get_nhap.Haplo Source code Source code
get_nonzero_solution.RegressHaplo Source code
get_pi.RegressHaplo Source code
get_pileup_nt_names Source code
get_position_pair_comparison_read_table.error Man page Source code
get_read_table.pipeline Source code
get_solutions.RegressHaploSolutions Source code
get_solutions.pipeline Source code
get_solutions_haplotype_reconstruction.pipeline Man page Source code
get_solutions_summary.pipeline Man page Source code
get_stats_df.RegressHaploSolutions Source code
get_variable_positions.pipeline Source code
get_variant_call_pos Man page Source code
get_variant_calls.pipeline Source code
get_y.pipeline Source code
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 Source code
haplotypes_to_parameters.pipeline Man page Source code
hello Man page
join_unlinked_loci.read_table Source code
join_unlinked_loci_pair.read_table Source code
loci_to_haplotypes.pipeline Man page Source code
max_Hessian_eigenvalue.engine Man page Source code
merge_haplotypes.read_table Man page Source code
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 Source code
paths_to_haplotypes.read_table Man page Source code
penalized_regression.RegressHaplo Man page Source code
penalized_regression_parameters.RegressHaplo Man page Source code
plot.readFit Man page Source code
plot_cover.read_table Source code
plot_graph.read_table Source code
plot_pair_position_error.error Man page Source code
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_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 Source code
regroup.read_table Man page Source code
save_loci.pipeline Source code
seq.read_table Man page Source code
set_pos_names.Haplo Man page Source code
single_end_read_table Man page Source code
single_position.error Man page Source code
solutions.RegressHaplo Man page Source code
solutions_to_haplotypes.pipeline Man page Source code
split.read_table Man page Source code
split_allele.readFit Man page Source code
split_paired_ends.read_table Man page Source code
split_unlinked_loci.read_table Man page Source code
start_pos.read_table Man page Source code
subset.read_table Man page Source code
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 Source code
variant_calls Man page Source code
variant_calls_cutoff Man page Source code
variant_calls_sig Man page Source code
variant_calls_to_read_table.pipeline Man page Source code
write.Haplo Source code
SLeviyang/RegressHaplo documentation built on Aug. 26, 2017, 10:22 p.m.