vg
tools for working with variation graphs
vg::HaplotypeIndexer Member List

This is the complete list of members for vg::HaplotypeIndexer, including all inherited members.

batch_file_prefixvg::HaplotypeIndexer
build_gbwt(const PathHandleGraph *graph, map< string, Path > &alt_paths, bool index_paths, const string &vcf_filename, const vector< string > &aln_filenames, const string &aln_format)vg::HaplotypeIndexer
create_progress(const string &message, long count)vg::Progressive
create_progress(long count)vg::Progressive
destroy_progress(void)vg::Progressive
discard_overlapsvg::HaplotypeIndexer
excluded_samplesvg::HaplotypeIndexer
force_phasingvg::HaplotypeIndexer
found_missing_variantsvg::HaplotypeIndexer
gbwt_buffer_sizevg::HaplotypeIndexer
generate_threads(const PathHandleGraph *graph, map< string, Path > &alt_paths, bool index_paths, const string &vcf_filename, const vector< string > &aln_filenames, const string &aln_format, const function< void(size_t)> &bit_width_ready, const function< void(const gbwt::vector_type &, const gbwt::size_type(&)[4])> &each_thread)vg::HaplotypeIndexer
HaplotypeIndexer()vg::HaplotypeIndexer
id_intervalvg::HaplotypeIndexer
increment_progress()vg::Progressive
index_pathsvg::HaplotypeIndexer
last_progressvg::Progressiveprivate
max_missing_variant_warningsvg::HaplotypeIndexer
parse_vcf(const PathHandleGraph *graph, map< string, Path > &alt_paths, const vector< path_handle_t > &contigs, vcflib::VariantCallFile &variant_file, std::vector< std::string > &sample_names, const function< void(size_t, const gbwt::VariantPaths &, gbwt::PhasingInformation &)> &handle_contig_haplotype_batch)vg::HaplotypeIndexer
path_to_vcfvg::HaplotypeIndexer
phase_homozygousvg::HaplotypeIndexer
preload_progress(const string &message)vg::Progressive
progressvg::Progressiveprivate
progress_countvg::Progressiveprivate
progress_messagevg::Progressiveprivate
progress_seenvg::Progressiveprivate
regionsvg::HaplotypeIndexer
rename_variantsvg::HaplotypeIndexer
sample_rangevg::HaplotypeIndexer
samples_in_batchvg::HaplotypeIndexer
show_progressvg::Progressive
update_progress(long i)vg::Progressive
warn_on_missing_variantsvg::HaplotypeIndexer