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

Global functions
add_deletion Source code
add_hap_set_haps Source code
add_insertion Source code
add_ref_genome_chroms Source code
add_ssites_cpp Source code
add_substitution Source code
builtin_illumina_profiles Source code
check_file_existence Source code
check_illumina_args Source code
check_pacbio_args Source code
clean_ref_genome_chrom_names Source code
coal_file_sites Source code
comparable Source code
create_genome Man page Source code
create_genome_cpp Source code
create_haplotypes Man page Source code
dup_hap_set_haps Source code
err_msg Source code
evo_rates Man page
evolve_across_trees Source code
examine_mutations Source code
fill_coal_mat_pos Source code
filter_chromosomes_cpp Source code
find_profile_file Source code
format_profile Source code
gtrees_to_info_list Source code
haplotypes Man page
haps_functions Man page
haps_gtrees Man page Source code
haps_phylo Man page Source code
haps_ssites Man page Source code
haps_theta Man page Source code
haps_vcf Man page Source code
illumina Man page Source code
illumina_hap_cpp Source code
illumina_ref_cpp Source code
indels Man page Source code
is_type Source code
jackalope Man page
jackalope-package Man page
make_hap_set Source code
make_ref_genome Source code
merge_all_chromosomes_cpp Source code
merge_chromosomes_cpp Source code
pacbio Man page Source code
pacbio_hap_cpp Source code
pacbio_ref_cpp Source code
phylo_to_info_list Source code
positive_vector Source code
print_hap_set Source code
print_ref_genome Source code
process_coal_obj_sites Source code
process_coal_tree_string Source code
process_phy Source code
rando_chroms 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_vcf_cpp Source code
ref_genome Man page
remove_hap_set_haps Source code
remove_ref_genome_chroms Source code
replace_Ns_cpp Source code
seq_sys_by_read_length Source code
set_hap_set_hap_names Source code
set_ref_genome_chrom_names Source code
single_integer Source code
single_number Source code
sub_F81 Man page Source code
sub_F84 Man page Source code
sub_GTR Man page Source code
sub_GTR_cpp 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_TN93__ Source code
sub_TN93_cpp Source code
sub_UNREST Man page Source code
sub_UNREST_cpp Source code
sub_arg_checks Source code
sub_models Man page
to_hap_set Source code
to_hap_set__haps_gtrees_info Source code
to_hap_set__haps_phylo_info Source code
to_hap_set__haps_ssites_info Source code
to_hap_set__haps_theta_info Source code
to_hap_set__haps_vcf_info Source code
trees_to_hap_set Source code
using_openmp Source code
view_hap_genome Source code
view_hap_genome_chrom Source code
view_hap_genome_chrom_sizes Source code
view_hap_set_gc_content Source code
view_hap_set_hap_names Source code
view_hap_set_nchroms Source code
view_hap_set_nhaps Source code
view_hap_set_nt_content Source code
view_mutations Source code
view_ref_genome Source code
view_ref_genome_chrom Source code
view_ref_genome_chrom_names Source code
view_ref_genome_chrom_sizes Source code
view_ref_genome_gc_content Source code
view_ref_genome_nchroms Source code
view_ref_genome_nt_content Source code
write_fasta Man page Source code
write_gtrees Man page Source code
write_haps_fasta Source code
write_ref_fasta Source code
write_vcf Man page Source code
write_vcf_cpp Source code
jackalope documentation built on Oct. 15, 2023, 9:06 a.m.