API for jackalope
A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

Global functions
add_deletion Source code
add_insertion Source code
add_ref_genome_seqs Source code
add_ssites_cpp Source code
add_substitution Source code
add_var_set_vars Source code
builtin_illumina_profiles Source code
check_file_existence Source code
check_gamma_mats Source code
check_illumina_args Source code
check_pacbio_args Source code
clean_ref_genome_seq_names Source code
coal_file_sites Source code
create_genome Man page Source code
create_genome_cpp Source code
create_mevo Source code
create_variants Man page Source code
dup_var_set_vars Source code
err_msg Source code
evo_rates Man page
evolve_seqs Source code
examine_mutations Source code
fill_coal_mat_pos Source code
filter_sequences_cpp Source code
find_profile_file Source code
format_profile Source code
gtrees_to_ptr Source code
illumina Man page Source code
illumina_ref_cpp Source code
illumina_var_cpp Source code
indels Man page Source code
is_type Source code
jackalope Man page
jackalope-package Man page
make_gamma_mats Source code
make_mutation_sampler_base Source code
make_ref_genome Source code
make_var_set Source code
merge_sequences_cpp Source code
mevo_obj_to_ptr Source code
pacbio Man page Source code
pacbio_ref_cpp Source code
pacbio_var_cpp Source code
phylo_info_to_trees Source code
phylo_to_ptr Source code
positive_vector Source code
print.indel_rates Source code
print.site_var_mats Source code
print.sub_model_info Source code
print.vars_gtrees_info Source code
print.vars_phylo_info Source code
print.vars_ssites_info Source code
print.vars_theta_info Source code
print.vars_vcf_info Source code
print_ref_genome Source code
print_var_set Source code
process_coal_obj_sites Source code
process_coal_tree_string Source code
rando_seqs Source code
read_fasta Man page Source code
read_fasta_ind Source code
read_fasta_noind Source code
read_ms_trees_ Source code
read_profile Source code
read_vcfr Source code
ref_genome Man page
remove_ref_genome_seqs Source code
remove_var_set_vars Source code
replace_Ns_cpp Source code
seq_sys_by_read_length Source code
set_ref_genome_seq_names Source code
set_var_set_var_names Source code
single_integer Source code
single_number Source code
site_var Man page Source code
sub_F81 Man page Source code
sub_F84 Man page Source code
sub_GTR Man page Source code
sub_HKY85 Man page Source code
sub_JC69 Man page Source code
sub_K80 Man page Source code
sub_TN93 Man page Source code
sub_UNREST Man page Source code
sub_models Man page
table_gammas Source code
test_rate Source code
to_var_set.vars_gtrees_info Source code
to_var_set.vars_phylo_info Source code
to_var_set.vars_ssites_info Source code
to_var_set.vars_theta_info Source code
to_var_set.vars_vcf_info Source code
trees_to_var_set Source code
using_openmp Source code
variants Man page
vars_functions Man page
vars_gtrees Man page Source code
vars_phylo Man page Source code
vars_ssites Man page Source code
vars_theta Man page Source code
vars_vcf Man page Source code
view_mutations Source code
view_ref_genome Source code
view_ref_genome_gc_content Source code
view_ref_genome_nseqs Source code
view_ref_genome_nt_content Source code
view_ref_genome_seq Source code
view_ref_genome_seq_names Source code
view_ref_genome_seq_sizes Source code
view_var_genome Source code
view_var_genome_seq Source code
view_var_genome_seq_sizes Source code
view_var_set_gc_content Source code
view_var_set_nseqs Source code
view_var_set_nt_content Source code
view_var_set_nvars Source code
view_var_set_var_names Source code
write_bed Source code
write_fasta Man page Source code
write_ref_fasta Source code
write_vars_fasta Source code
write_vcf Man page Source code
write_vcf_cpp Source code
jackalope documentation built on Oct. 30, 2019, 11:47 a.m.