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 |
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