| alignment_end_matches(const Alignment &aln) const | vg::ReadFilter< Read > | private |
| alignment_overhang(const Alignment &aln) const | vg::ReadFilter< Read > | private |
| aln_emitter | vg::ReadFilter< Read > | private |
| annotation_to_match | vg::ReadFilter< Read > | |
| batch_size | vg::ReadFilter< Read > | |
| buffer_size | vg::ReadFilter< Read > | |
| complement_filter | vg::ReadFilter< Read > | |
| contains_subsequence(const Read &read) const | vg::ReadFilter< Read > | private |
| create_progress(const string &message, long count) | vg::Progressive | |
| create_progress(long count) | vg::Progressive | |
| defray_count | vg::ReadFilter< Read > | |
| defray_length | vg::ReadFilter< Read > | |
| destroy_progress(void) | vg::Progressive | |
| downsample_probability | vg::ReadFilter< Read > | |
| downsample_seed_mask | vg::ReadFilter< Read > | |
| drop_split | vg::ReadFilter< Read > | |
| emit(Read &read) | vg::ReadFilter< Read > | private |
| emit(Read &read1, Read &read2) | vg::ReadFilter< Read > | private |
| emit(Alignment &aln) | vg::ReadFilter< Read > | inlineprivate |
| emit(Alignment &aln1, Alignment &aln2) | vg::ReadFilter< Read > | inlineprivate |
| emit(MultipathAlignment &mp_aln) | vg::ReadFilter< Read > | inlineprivate |
| emit(MultipathAlignment &mp_aln1, MultipathAlignment &mp_aln2) | vg::ReadFilter< Read > | inlineprivate |
| emit_tsv(Read &read, std::ostream &out) | vg::ReadFilter< Read > | private |
| emit_tsv(MultipathAlignment &read, std::ostream &out) | vg::ReadFilter< Read > | inlineprivate |
| emit_tsv(Alignment &read, std::ostream &out) | vg::ReadFilter< Read > | inlineprivate |
| ensure_progress(long count) | vg::Progressive | |
| exact_name | vg::ReadFilter< Read > | |
| excluded_features | vg::ReadFilter< Read > | |
| excluded_refpos_contigs | vg::ReadFilter< Read > | |
| filter(istream *alignment_stream) | vg::ReadFilter< Read > | |
| filter(istream *alignment_stream) | vg::ReadFilter< Read > | inline |
| filter(istream *alignment_stream) | vg::ReadFilter< Read > | inline |
| filter_alignment(Read &aln) | vg::ReadFilter< Read > | |
| filter_internal(istream *in) | vg::ReadFilter< Read > | private |
| filter_on_all | vg::ReadFilter< Read > | |
| frac_score | vg::ReadFilter< Read > | |
| get_end_matches(const Read &read) const | vg::ReadFilter< Read > | private |
| get_end_matches(const MultipathAlignment &read) const | vg::ReadFilter< Read > | inlineprivate |
| get_end_matches(const Alignment &read) const | vg::ReadFilter< Read > | inlineprivate |
| get_is_paired(const Read &read) const | vg::ReadFilter< Read > | private |
| get_is_paired(const Alignment &aln) const | vg::ReadFilter< Read > | inlineprivate |
| get_is_paired(const MultipathAlignment &mp_aln) const | vg::ReadFilter< Read > | inlineprivate |
| get_length(const Read &read) const | vg::ReadFilter< Read > | inlineprivate |
| get_mapq(const Read &read) const | vg::ReadFilter< Read > | private |
| get_min_base_qual_fraction(const Read &read) const | vg::ReadFilter< Read > | private |
| get_overhang(const Read &read) const | vg::ReadFilter< Read > | private |
| get_overhang(const Alignment &aln) const | vg::ReadFilter< Read > | inlineprivate |
| get_overhang(const MultipathAlignment &mp_aln) const | vg::ReadFilter< Read > | inlineprivate |
| get_score(const Read &read) const | vg::ReadFilter< Read > | private |
| get_score(const Alignment &aln) const | vg::ReadFilter< Read > | inlineprivate |
| get_score(const MultipathAlignment &read) const | vg::ReadFilter< Read > | inlineprivate |
| graph | vg::ReadFilter< Read > | |
| has_excluded_refpos(const Read &read) const | vg::ReadFilter< Read > | private |
| has_excluded_refpos(const MultipathAlignment &read) const | vg::ReadFilter< Read > | inlineprivate |
| has_excluded_refpos(const Alignment &aln) const | vg::ReadFilter< Read > | inlineprivate |
| has_excuded_feature(const Read &read) const | vg::ReadFilter< Read > | private |
| has_repeat(const Read &read, int k) const | vg::ReadFilter< Read > | private |
| increment_progress() | vg::Progressive | |
| interleaved | vg::ReadFilter< Read > | |
| is_correctly_mapped(const Read &read) const | vg::ReadFilter< Read > | private |
| is_correctly_mapped(const Alignment &alignment) const | vg::ReadFilter< Read > | inlineprivate |
| is_correctly_mapped(const MultipathAlignment &alignment) const | vg::ReadFilter< Read > | inlineprivate |
| is_mapped(const Read &read) const | vg::ReadFilter< Read > | private |
| is_mapped(const Alignment &alignment) const | vg::ReadFilter< Read > | private |
| is_mapped(const MultipathAlignment &mp_alignment) const | vg::ReadFilter< Read > | private |
| is_proper_pair(const Read &read) const | vg::ReadFilter< Read > | private |
| is_secondary(const Read &read) const | vg::ReadFilter< Read > | private |
| is_secondary(const MultipathAlignment &mp_aln) const | vg::ReadFilter< Read > | inlineprivate |
| is_secondary(const Alignment &aln) const | vg::ReadFilter< Read > | inlineprivate |
| is_split(const Read &read) const | vg::ReadFilter< Read > | private |
| is_split(const Alignment &alignment) const | vg::ReadFilter< Read > | inlineprivate |
| is_split(const MultipathAlignment &mp_aln) const | vg::ReadFilter< Read > | inlineprivate |
| last_progress | vg::Progressive | private |
| matches_annotation(const Read &read) const | vg::ReadFilter< Read > | private |
| matches_name(const Read &read) const | vg::ReadFilter< Read > | private |
| max_length | vg::ReadFilter< Read > | |
| max_overhang | vg::ReadFilter< Read > | |
| max_reads | vg::ReadFilter< Read > | |
| max_reads_used | vg::ReadFilter< Read > | private |
| min_base_quality | vg::ReadFilter< Read > | |
| min_base_quality_fraction | vg::ReadFilter< Read > | |
| min_end_matches | vg::ReadFilter< Read > | |
| min_mapq | vg::ReadFilter< Read > | |
| min_primary | vg::ReadFilter< Read > | |
| min_secondary | vg::ReadFilter< Read > | |
| mp_aln_emitter | vg::ReadFilter< Read > | private |
| name_prefixes | vg::ReadFilter< Read > | |
| only_correctly_mapped | vg::ReadFilter< Read > | |
| only_first_alignment | vg::ReadFilter< Read > | |
| only_mapped | vg::ReadFilter< Read > | |
| only_proper_pairs | vg::ReadFilter< Read > | |
| output_fields | vg::ReadFilter< Read > | |
| overwrite_score | vg::ReadFilter< Read > | |
| preload_progress(const string &message) | vg::Progressive | |
| progress | vg::Progressive | private |
| progress_count | vg::Progressive | private |
| progress_message | vg::Progressive | private |
| progress_seen | vg::Progressive | private |
| repeat_size | vg::ReadFilter< Read > | |
| rescore | vg::ReadFilter< Read > | |
| sample_read(const Read &read) const | vg::ReadFilter< Read > | private |
| seen_read_names | vg::ReadFilter< Read > | |
| set_score(Read &read, double score) const | vg::ReadFilter< Read > | private |
| set_score(Alignment &aln, double score) const | vg::ReadFilter< Read > | inlineprivate |
| set_score(MultipathAlignment &aln, double score) const | vg::ReadFilter< Read > | inlineprivate |
| show_progress | vg::Progressive | |
| sub_score | vg::ReadFilter< Read > | |
| subsequences | vg::ReadFilter< Read > | |
| threads | vg::ReadFilter< Read > | |
| to_alignment(const MultipathAlignment &multipath_aln) const | vg::ReadFilter< Read > | private |
| trim_ambiguous_end(Alignment &alignment, int k) const | vg::ReadFilter< Read > | private |
| trim_ambiguous_ends(Read &read, int k) const | vg::ReadFilter< Read > | |
| trim_ambiguous_ends(Alignment &alignment, int k) const | vg::ReadFilter< Read > | inline |
| trim_ambiguous_ends(MultipathAlignment &aln, int k) const | vg::ReadFilter< Read > | inline |
| update_progress(long i) | vg::Progressive | |
| verbose | vg::ReadFilter< Read > | |
| with_progress(bool show_progress, const std::string &task, const std::function< void(const std::function< void(size_t, size_t)> &progress)> &callback) | vg::Progressive | static |
| write_output | vg::ReadFilter< Read > | |
| write_tsv | vg::ReadFilter< Read > | |
